(updated: Wed Dec 6 17:05:44 2017)

In these diagrams sets of entries from the database are clustered to show their interface (left) and overall structural (right) similarity. Mouse over complex names to check their SCOP superfamilies and click on the L links to see their structure-based sequence logos. Please check the help page for more details.


> 1a0a_B:PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX

  
  RG--HGKT----EA----RCRC------   L                 +----1a0a_B    
                                             +-----4 
  ----HG------ET----RTRG------   L     +-----5     +----5v0l_A    
                                       !     ! 
  ----HG----ITEC----RCRG------   L   +-6     +----------5nj8_D    
                                     ! ! 
  --QG------VTEC----RCRG----QG   L   ! !           +----1an4_A    
                                     ! +-----------3 
  --------HGST--ITET----RCRG--   L --7             +----4h10_A    
                                     ! 
  ----HGNT----EC----RCRG------   L   !                  +1nkp_E    
                                     !                +-1 
  ----HGNT--LGEC----RCRC------   L   +----------------2 +5i50_B    
                                                      ! 
  ----HGNT--MTEA----RCRG------   L                    +-1nlw_D    
                                   


> 1a66_A:SOLUTION NMR STRUCTURE OF THE CORE NFATC1/DNA COMPLEX, 18 STRUCTURES

  
  --RGRGYTCTEC--------   L                              +--1gji_A    
                             +--------------------------2 
  --RGRGYTCCEC----KG--   L   !                          ! +1a3q_A    
                           --3                          +-1 
  --RGRGYTCCECKT----KT   L   !                            +1nfk_A    
                             ! 
  TG------------AG----   L   +-----------------------------4ibu_A    
                           


> 1a6y_A:REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX

  
  --HAEC--KG--RGRG----FT   L              +1a6y_A    
                               +----------7 
  ----EC--KA--RGRG------   L   !          +4nqa_I    
                               !  
  ----EA--KG--RTRG------   L   !               +1kb2_B    
                               !             +-3 
  ----EC--KG--RGRG------   L   !           +-8 +2nll_B    
                               !           ! ! 
  ----EA--KG--RTRTRT----       !           ! +2han_B    
                               !        +-11  
  ----DG--KG--RTRG------   L   !        !  !   +3cbb_A    
                               !        !  ! +-2 
  CA--EC--KG--KGRG------   L -16        !  +-9 +1cit_A    
                               !        !    ! 
  --HGECAGKGAAKGRT------   L   !        !    +1lo1_A    
                               !     +-14  
  --HC----KGVT--RG--RT--       !     !  !     +-3g9m_B    
                               !     !  !  +-12  
  ----EC--KG--KGRG------   L   !     !  !  !  +-1dsz_B    
                               !     !  !  !  
  --------KAVA--RA------   L   !     !  +-13      +5e69_A    
                               !     !     !    +-4 
  --------KGVT--RG------   L   !     !     !  +-5 +5cbz_E    
                               +----15     !  ! ! 
  --------KGVT--RG--RC--   L         !     +-10 +2c7a_B    
                                     !        !  
  ----ET--KGAT--RG------   L         !        ! +1lat_A    
                                     !        +-6 
  --------KGVT--RG------             !          +5emc_A    
                                     !  
  ----EC--KG--KGRA------   L         !     +5l0m_A    
                                     +-----1 
  ----EC--KG--KGRG------   L               +2ff0_A    
                             


> 1am9_A:HUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER

  
  ------HGNT--IAEC----YCRG------   L                +1am9_A    
                                                +---2 
  KT----HGNT----EC----RCRG------   L            !   ! +1nkp_A    
                                                !   +-1 
  ------------HGNT--LGEC----RCRC   L          +-6     +5i50_B    
                                              ! ! 
  --HGNT--MTEA----RCRG----------   L          ! !   +1nlw_D    
                                       +------7 +---3 
  NT----------------------------   L   !      !     +1nkp_E    
                                       !      ! 
  --RT------NT--RGEC----RCQT----       !      !   +--2ypa_A    
                                     --8      +---5 
  ----NT----EC----RCRT----------   L   !          +--4ati_B    
                                       ! 
  ------HGST--ITET----RCRG------   L   !           +-4h10_A    
                                       +-----------4 
  ------HG------ET----RTRG------   L               +-5v0l_A    
                                     


> 1an4_A:STRUCTURE AND FUNCTION OF THE B/HLH/Z DOMAIN OF USF

  
  --QG----VTECRCRGQG   L             +-----1an4_A    
                                     ! 
  ----HGSTITETRCRG--   L             !       +4h10_A    
                                +----4    +--1 
  RT----NTRGECRCQT--            !    !  +-2  +2ypa_A    
                                !    !  ! ! 
  ----HGNTIAECRCRT--   L   +----5    +--3 +--4ati_B    
                           !    !       ! 
  ----HGNTMTEARCRG--   L   !    !       +--1nlw_D    
                         --6    ! 
  ----HG--ITECRCRG--   L   !    +----------5nj8_D    
                           ! 
  RG--HGKT--EARCRC--   L   +---------------1a0a_B    
                         


> 1au7_A:PIT-1 MUTANT/DNA COMPLEX

  
  --STQATT--CARGLTNT----RA--------RCVTCTNAQTRC--   L                   +--------------1au7_A    
                                                                    +-18  
  --SGQATT--STRG--------------------------------   L                !  +--------------1gt0_C    
                                                                    !  
  ------------------KG--RC----------IAQCNAYA----   L                !                           +1nk3_P    
                                                                    !                         +-6 
  ----------------------RA----------IAQTNAMC----   L                !                       +-7 +1puf_A    
                                                                    !                       ! ! 
  ----------------------RT----------VAQTNA------   L                !                    +-10 +5hod_A    
                                                                    !                    !  !  
  ----------------------RT----------IAQTNA----KT   L                !                    !  ! +4rdu_A    
                                                                    !                 +-11  +-5 
  ----------------------RT----------IAQCNAMG----   L                !                 !  !    +1b72_A    
                                                                    !                 !  !  
  ----------------------RT------------KGNA------   L                !                 !  ! +2hos_A    
                                                                    !                 !  +-1 
  --------------------YARA----------IAQTNA------   L   +-----------19                 !    +5lux_L    
                                                       !            !                 !  
  ----------------------RT----------IAKGNA------   L   !            !              +-14        +2hdd_A    
                                                       !            !              !  !      +-3 
  ------------------------HTRT------NCSTNARG----   L   !            !              !  !    +-4 +1k61_B    
                                                       !            !              !  !    ! ! 
  ----------------------RT----------NT--NAIARG--   L   !            !              !  !  +-9 +1puf_B    
                                                       !            !           +-15  !  ! ! 
  ----------------------RA----RCET--SAQAKG------   L   !            !           !  !  +-13 +5lxu_A    
                                                       !            !           !  !     !  
  ------------------------RT--------NT--NAIARG--   L   !            !           !  !     +-4cyc_B    
                                                       !            !           !  !  
  ----------------------RT----------VAQTNA------   L -20            !        +-16  !   +1fjl_B    
                                                       !            !        !  !  +---8 
  ------------------------------VTKTIAQTNA----RT   L   !            !        !  !      +2me6_A    
                                                       !            !        !  !  
  --------------------------------RTVAIANAMCRG--   L   !            +-------17  !     +1le8_A    
                                                       !                     !  +----12  
  ----------------------RT----STVCKGDCRG--------   L   !                     !        +1w0t_A    
                                                       !                     !  
  ----------------------RT----------VASGNA------   L   !                     !      +3cmy_A    
                                                       !                     +------2 
  QASTQAST--SART--------------------------QT----   L   !                            +3d1n_M    
                                                       !  
  --NTQASAHT------------RT--------YCNAATNAKG----   L   +----------------------------1ic8_B    
                                                     


> 1awc_A:MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA

  
  --------KT--RGAT--RGYT------------   L                  +------1awc_A    
                                                          ! 
  ------DCKT--RG----RGYA------------   L             +----5      +1dux_F    
                                                     !    !    +-1 
  --------KT--RGAT--RGYA------------   L             !    +----3 +1bc8_C    
                                               +-----6         ! 
  --------KT--RGSA--RGQA------RA----   L       !     !         +-1yo5_C    
                                               !     ! 
  --------ST--------RTQT--MT--------   L   +---7     !          +5d8k_B    
                                           !   !     +----------2 
  --KTHG----------------------------       !   !                +5hdn_C    
                                         --8   ! 
  TT----KATTQTTG----LTRT----KA--FTYT   L   !   +-----------------2p7c_B    
                                           ! 
  ------------NT--RGCT--NGST--------   L   !                   +-1if1_B    
                                           +-------------------4 
  ------------------------RG--------                           +-4hly_B    
                                         


> 1b3t_A:EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX

  
  WCFT----KG--------KGTAYCNG--RT----------------------------------------   L                         +5t7x_B    
                                                                                    +----------------1 
  WGFTRTNTKGFT------KTTGYCNG--RT----------------------------------------   L   +----2                +1b3t_A    
                                                                               !    ! 
  ------------TAFCSG--------------LATGSG--VGFA------------RAECACKCSCTAKC   L --3    +-----------------5tkz_B    
                                                                               ! 
  --------------------------VC--RC------RC----PANAFAKCKCDC--------------   L   +----------------------3vke_A    
                                                                             


> 1b72_A:PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX

  
  ------RT----------IAQCNAMG------   L                +-1b72_A    
                                                  +--13  
  ------RA----------IAQTNAMC------   L            !   +-1puf_A    
                                                  !  
  RA----RT----------IAQTNA------KT   L            !                +4rdu_A    
                                                  !              +-1 
  --KG--RC----------IAQCNAYA------   L            !           +-10 +1nk3_P    
                                                  !           !  !  
  ----YARA----------IAQTNA--------   L            !           !  +5lux_L    
                                                  !        +-11  
  RA----RT----------VASGNA--------   L            !        !  !   +3cmy_A    
                                                  !        !  ! +-2 
  ------RT----------VAQTNA--------   L            !        !  ! ! +5hod_A    
                                               +-18     +-15  +-8 
  RT----RT----------VAQTNA--------   L         !  !     !  !    ! +1fjl_B    
                                               !  !     !  !    +-5 
  ------RT----------NT--NAIARG----   L         !  !     !  !      +1puf_B    
                                               !  !     !  !  
  ------RT----------VASCNAQA------   L         !  !     !  +-1gt0_C    
                                               !  !  +-16  
  ------RT----------IAKGNA--------   L         !  !  !  !      +2hdd_A    
                                               !  !  !  !    +-3 
  --------HTRT------NCSTNARG------   L         !  !  !  !  +-9 +1k61_B    
                                            +-19  !  !  !  ! ! 
  --------RT--------NT--NAIARG----   L      !  !  !  !  +-14 +4cyc_B    
                                            !  !  +-17     !  
  ----------------RTVAIANAMCRG----   L      !  !     !     ! +1le8_A    
                                            !  !     !     +-6 
  ------RT----------VA--NAQT------   L      !  !     !       +3d1n_M    
                                            !  !     !  
  ------RT------------KGNA--------   L   +-20  !     !   +2hos_A    
                                         !  !  !     +---4 
  ------RA--------RCVTCTNAQTRC----   L   !  !  !         +1au7_A    
                                         !  !  !  
  --------------VTKTIAQTNA------RT   L   !  !  +------2me6_A    
                                         !  !  
  ------RA----RCET--SAQAKG--------   L -21  !       +5lxu_A    
                                         !  +------12  
  ------RT----STVCKGDCRG----------   L   !          ! +1w0t_A    
                                         !          +-7 
  ------------YTVCKGDCKC----------   L   !            +2qhb_A    
                                         !  
  --------------------KG--NA--EC--   L   +----------1xpx_A    
                                       


> 1bc8_C:STRUCTURES OF SAP-1 BOUND TO DNA SEQUENCES FROM THE E74 AND C-FOS PROMOTERS PROVIDE INSIGHTS INTO HOW ETS PROTEINS DISCRIMINATE BETWEEN RELATED DNA TARGETS

  
  --------KT--RGAT--RGYA------------   L                      +-1bc8_C    
                                                              ! 
  ------DCKT--RG----RGYA------------   L            +---------6   +1dux_F    
                                                    !         ! +-1 
  --------KT--RGAT--RGYT------------   L            !         +-4 +1awc_A    
                                             +------8           ! 
  --------KT--RGSA--RGQA------RA----   L     !      !           +1yo5_C    
                                             !      ! 
  --------ST--------RTQT--MT--------   L     !      !           +5d8k_B    
                                           +-9      +-----------3 
  --KTHG----------------------------       ! !                  +5hdn_C    
                                           ! ! 
  ----------NA----RAHT--STLT--------   L   ! !             +----2a07_K    
                                         -10 +-------------7 
  TT----KATTQTTG----LTRT----KA--FTYT   L   !               +----2p7c_B    
                                           !  
  --------------NT--CT--NGST--------   L   !                    +1if1_B    
                                           !                  +-2 
  ------KG----ATNT--CT----SC--------   L   +------------------5 +2irf_L    
                                                              ! 
  ------------------------RG--------                          +-4hly_B    
                                         


> 1bf5_A:TYROSINE PHOSPHORYLATED STAT-1/DNA COMPLEX

  
  --------KC--EC--STNTVGSTQT--   L                               +1bf5_A    
                                                        +--------1 
  ----------------STNT----QT--         +----------------2        +1bg1_A    
                                       !                ! 
  --------------KAVTHG--NTQT--   L   +-3                +---------4y5w_B    
                                     ! ! 
  NCTTATRG--------------------   L --4 +--------------------------2dgc_A    
                                     ! 
  ----------KG----AGCC----RGRT   L   +----------------------------4ibu_A    
                                   


> 1bg1_A:TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX

  
  ------------STNT----QT                                 +-1bg1_A    
                                                 +-------1 
  --------KC--STNTVGSTQT   L   +-----------------2       +-1bf5_A    
                               !                 ! 
  ----------KAVTHG--NTQT   L --3                 +--------4y5w_B    
                               ! 
  NCTTATRG--------------   L   +---------------------------2dgc_A    
                             


> 1cf7_A:STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP

  
  RC--------------------------RGRG--YC--------------------------   L                                            +1cf7_A    
                                                                                                  +-------------1 
  ----------TTQT------------------------------------------------   L                           +-13             +3gpl_A    
                                                                                               !  !  
  ------------------------ST--PTTC----QG------RG----------------   L                           !  +-------------1f5t_A    
                                                                                               !  
  ------------------------------------------YGRG----------------                               !               +4wcg_B    
                                                                                               !  +------------5 
  --------------ST--------STQAQGST--SART------------------KT----   L                        +-16  !            +5trd_B    
                                                                                            !  !  !  
  ------------------------------------------YG------------------                            !  !  !              +2heo_D    
                                                                                            !  !  !          +---3 
  ------------------------------------------YG------------------                            !  !  !          !   ! +4ka4_B    
                                                                                            !  !  !        +-8   +-2 
  ----------------------------KGTA----TA------RG----------------   L                        !  +-14        ! !     +1xsd_A    
                                                                                            !     !      +-9 ! 
  --------------TT------------KATT--QTTG----LTRT----KA------FTYT   L                        !     !      ! ! +---2p7c_B    
                                                                                            !     !      ! ! 
  ----------------------------------NA----RAHT--STLT------------   L                     +-17     !      ! +-----2a07_K    
                                                                                         !  !     !   +-10  
  ----------------SGQG------YCNC--------------------------------                         !  !     !   !  !       +2ve9_C    
                                                                                         !  !     !   !  !   +---4 
  --------------------------RGSTRT--STHG------------------RA----   L                     !  !     +--11  +---7   +3zpl_B    
                                                                                         !  !         !      ! 
  ------------------------TT--PTTC--STNT------------------RT----   L                  +-18  !         !      +---4lln_I    
                                                                                      !  !  !         !  
  ------------------------STKTPTTT--FT------------------RA------   L                  !  !  !         +---------4aso_F    
                                                                                      !  !  !  
  --SGITMTPT----------RT----------------------------------------   L               +-19  !  +-----------------5fmf_V    
                                                                                   !  !  !  
  ----------------------------------NAST--RTHT--ST--------------   L               !  !  +-------------------3l2c_A    
                                                                                +-20  !  
  ----------------------------NTVC--ECSTYT--STYC------RA--------   L            !  !  +---------------------5ed4_A    
                                                                                !  !  
  ----------------------------HT----RTITYT----------------------   L            !  !        +-------------4kfc_B    
                                                                                !  +-------15  
  --------------------------RG----DTVT----STRG--------RC--------   L         +-21           +-------------4nhj_A    
                                                                             !  !  
  ------------------------TTLTECTA--STRG------------------------   L         !  !                  +---4i2o_B    
                                                                             !  !           +------6 
  ------------------------ITRGECSC--SGKG------------------------   L      +-22  +----------12      +---5i2d_R    
                                                                          !  !              !  
  ----------------RG------STRGMCTT--RT--------------------------   L      !  !              +----------4u0y_B    
                                                                       +-23  !  
  --------KC----------------MGSGTT--TTYC------------------------   L   !  !  +------------------------5f7q_C    
                                                                     -24  !  
  ----------------------------DCKT----RG----RGYA----------------   L   !  +-------------------------1dux_F    
                                                                       !  
  ----------------------NG----RGRG--YC--------------------------   L   +-------------------------1cf7_B    
                                                                     


> 1cf7_B:STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP

  
  ------------NGRGRGYC--------------------   L                       +-------1cf7_B    
                                                         +-----------4 
  --------------QA------------------------   L           !           +-------2vla_A    
                                                         ! 
  ------------------NA--RAHT--STLT--------   L           !             +-----2a07_K    
                                                 +-------7           +-3 
  ----TT--------KATTQTTG--LTRT----KA--FTYT   L   !       !   +-------5 +-----2p7c_B    
                                                 !       !   !       ! 
  KAFA------------------------------MC----       !       !   !       +-------3aaf_B    
                                                 !       +---6 
  --------------RGRGYC--------------------   L --8           !           +---1cf7_A    
                                                 !           +-----------2 
  ------------------------YGRG------------       !                       ! +-4wcg_B    
                                                 !                       +-1 
  ------------------------YG--------------       !                         +-2heo_D    
                                                 ! 
  ------QGVCRC----------------------------   L   +---------------------------5dwa_A    
                                               


> 1cit_A:DNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B

  
  CA--EC--KG--KGRG------RT--RT--   L                         +-1cit_A    
                                                          +-12  
  ----EA--KG--RTRG--------------   L                      !  ! +1kb2_B    
                                                          !  +-1 
  ----EC--KG--RGRG------KA------   L                   +-14    +2nll_B    
                                                       !  !  
  ----EA--KG--RTRTRT------------                       !  !  +--2han_B    
                                                       !  +-13  
  ----DG--KG--RTRG--------------   L                   !     !  +3cbb_A    
                                                    +-15     +--2 
  ----EC--KG--KGRG--------------   L                !  !        +1dsz_B    
                                                    !  !  
  --HGECAGKGAAKGRT--------RT--RC   L                !  !     +1lo1_A    
                                                    !  !   +-7 
  ----EC--KG--KGRA----RT--------   L                !  +---9 +5l0m_A    
                                                    !      ! 
  ----EC--KG--KGRG----RC--------   L                !      +2ff0_A    
                                                    !  
  --------KGVG--RG--RA----------   L   +-----------16         +3g6t_A    
                                       !            !       +-4 
  --HAEC--KG--RGRG--------------   L   !            !       ! +1a6y_A    
                                       !            !       !  
  --------KGVT--RG--------------   L   !            !    +-10   +5cbz_E    
                                       !            !    !  ! +-5 
  --------KGVT--RG--------------   L   !            !    !  ! ! +2c7a_B    
                                       !            !    !  +-8 
  --------KAVA--RA--------------   L -17            !    !    ! +5e69_A    
                                       !            +---11    +-6 
  ----ET--KGAT--RG--------------   L   !                 !      ! +1lat_A    
                                       !                 !      +-3 
  --HC----KGVT--RG--------------       !                 !        +3g9m_B    
                                       !                 !  
  --------KGVT--RG--------------       !                 +-5emc_A    
                                       !  
  ----EC--KA--RGRG--------------   L   +-------------------4nqa_I    
                                     


> 1dh3_C:CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR CREB FAIMLY SELECTIVE DIMERIZATION AND DNA BINDING

  
  ----------RG------NC----YGAT----RC   L     +------4eot_A    
                                             ! 
  ----------------NTRT--ATAT--CTRA--   L     !       +5vpe_D    
                                           +-5     +-1 
  --RG------NC----YGAT----CTRG------   L   ! !  +--3 +2wt7_B    
                                           ! !  !  ! 
  --RC------NC----AAAT----CTRC------   L   ! +--4  +2wt7_A    
                                         --6    ! 
  RA--NA----AAVT----STRG------------   L   !    !   +1nwq_C    
                                           !    +---2 
  RG--QGNART--AGQT----FTRG----------   L   !        +1gd2_G    
                                           ! 
  ----------NCTT----AT------RG------   L   +--------2dgc_A    
                                         


> 1dsz_A:STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1

  
  ----EC--KG--KGRG----   L                 +-1dsz_B    
                                         +-8 
  ----EA--KG--RTRTRT--                +-10 +-2han_B    
                                      !  !  
  ----EC--KG--RGRG----   L         +-13  +-2nll_B    
                                   !  !  
  CA--EC--KG--KGRG----   L      +-14  +--1cit_A    
                                !  !  
  ----EA--KG--RTRG----   L      !  !  +-1kb2_B    
                                !  +-11  
  ----DG--KG--RTRG----   L      !     ! +3cbb_A    
                             +-15     +-1 
  ----EC--KA--RGRG----   L   !  !       +4nqa_I    
                             !  !  
  --HGECAGKGAAKGRT----   L   !  !     +1lo1_A    
                             !  !   +-6 
  ----EC--KG--KGRA----   L   !  +---7 +5l0m_A    
                             !      ! 
  ----EC--KG--KGRG----   L -17      +-2ff0_A    
                             !  
  --HAEC--KG--RGRG----   L   !  +-----1a6y_A    
                             !  !  
  --------KGVG------RA   L   !  !       +3g6t_A    
                             !  !     +-2 
  --HC----KGVT--RG--RT       +-16     ! +3g9m_B    
                                !   +-9 
  --------KGVT--RG----   L      !   ! !   +5cbz_E    
                                !   ! ! +-3 
  --------KGVT--RG----   L      !   ! +-5 +2c7a_B    
                                +--12   ! 
  --------KAVA--RA----   L          !   +5e69_A    
                                    !  
  ----ET--KGAT--RG----   L          ! +1lat_A    
                                    +-4 
  --------KGVT--RG----                +5emc_A    
                           


> 1dsz_B:STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1

  
  ----EC--KG--KGRG----   L               +1dsz_B    
                             +-----------8 
  ----EC--KA--RGRG----   L   !           +4nqa_I    
                             !  
  ----EA--KG--RTRTRT--       !            +-2han_B    
                             !        +--10  
  ----EC--KG--RGRG----   L   !        !   +-2nll_B    
                             !        !  
  ----DG--KG--RTRG----   L   !        !      +3cbb_A    
                             !        !    +-2 
  ----EA--KG--RTRG----   L   !     +-14  +-4 +1kb2_B    
                             !     !  !  ! ! 
  CA--EC--KG--KGRG----   L   !     !  !  ! +1cit_A    
                           -17     !  !  !  
  --------KGVT--RG----   L   !     !  !  !      +5cbz_E    
                             !     !  +-13    +-5 
  --------KGVT--RG----   L   !     !     !    ! +2c7a_B    
                             !     !     !  +-9 
  --------KAVA--RA----   L   !     !     !  ! ! +5e69_A    
                             !  +-15     !  ! +-7 
  ----ET--KGAT--RG----   L   !  !  !     +-11   ! +1lat_A    
                             !  !  !        !   +-3 
  --HC----KGVT--RG----       !  !  !        !     +3g9m_B    
                             !  !  !        !  
  --------KGVT--RG----       !  !  !        +-5emc_A    
                             !  !  !  
  ----EC--KG--KGRA----   L   +-16  !      +5l0m_A    
                                !  !    +-1 
  ----EC--KG--KGRG----   L      !  +---12 +2ff0_A    
                                !       !  
  --HGECAGKGAAKGRT----   L      !       +-1lo1_A    
                                !  
  --------KGVG--RG--RA   L      !        +3g6t_A    
                                +--------6 
  --HAEC--KG--RGRG----   L               +1a6y_A    
                           


> 1dux_F:ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA- BINDING SURFACE AFFECT DNA-RECOGNITION

  
  ----------DCKT--RG----RGYA----------------   L                              +1dux_F    
                                                                           +--1 
  ------------KT--RGAT--RGYT----------------   L                           !  +1awc_A    
                                                                   +-------6 
  ------------KT--RGAT--RGYA----------------   L                   !       ! +--1bc8_C    
                                                                   !       +-5 
  ------------KT--RGSA--RGQA----------RA----   L              +----8         +--1yo5_C    
                                                              !    ! 
  ------------ST--------RTQT--MT------------   L              !    !          +5d8k_B    
                                                      +-------9    +----------2 
  --KTHG------------------------------------          !       !               +5hdn_C    
                                                      !       ! 
  ----------KG----ATNT--CT----SC------------   L      !       !              +-2irf_L    
                                                      !       +--------------3 
  ------------------NT--CT--NGST------------   L      !                      +-1if1_B    
                                                   +-12  
  TT--------KATTQTTG----LTRT----KA------FTYT   L   !  !                       +-2p7c_B    
                                                   !  !                  +----4 
  ----------KGTA--TA------RG----------------   L   !  !      +-----------7    +-1xsd_A    
                                                   !  !      !           ! 
  --------------------RAHT--STLT------------   L -13  !  +--10           +------2a07_K    
                                                   !  !  !   !  
  ----------RGRGYC--------------------------   L   !  +-11   +------------------1cf7_A    
                                                   !     !  
  --------------------------------KGKG------   L   !     +----------------------5xfr_B    
                                                   !  
  ------ITRGECSCSGKG------------------------   L   +---------------------------5i2d_R    
                                                 


> 1e3o_C:CRYSTAL STRUCTURE OF OCT-1 POU DIMER BOUND TO MORE

  
  ----STQATTCARGLTNT--------------------------   L                 +---------------1au7_A    
                                                                   !  
  --------------------RT------------KGNA------   L                 !                               +2hos_A    
                                                                   !                             +-1 
  --------------------RT----------IAQTNA----KT   L                 !                           +-2 +4rdu_A    
                                                                   !                           ! ! 
  --------------------RC----------IAQCNAYA----   L                 !                         +-8 +1nk3_P    
                                                                   !                         ! ! 
  --------------------RA----------IAQTNAMC----   L                 !                       +-9 +1puf_A    
                                                                   !                       ! ! 
  --------------------RT----------VAQTNA------   L                 !                    +-11 +5hod_A    
                                                                   !                    !  !  
  ------------------YARA----------IAQTNA------   L                 !                    !  +5lux_L    
                                                                   !                 +-13  
  --------------------RT----------IAKGNA------   L                 !                 !  !   +2hdd_A    
                                                                   !                 !  ! +-3 
  --------------------RT----------VASGNA------   L   +------------19                 !  +-4 +3cmy_A    
                                                     !             !                 !    ! 
  --------------------RT----------IAQCNAMG----   L   !             !              +-15    +1b72_A    
                                                     !             !              !  !  
  ----------------------HTRT------NCSTNARG----   L   !             !              !  !       +1k61_B    
                                                     !             !              !  !     +-6 
  --------------------RT----------NT--NAIARG--   L   !             !              !  !  +-10 +1puf_B    
                                                     !             !           +-16  !  !  !  
  ----------------------RT--------NT--NAIARG--   L   !             !           !  !  +-14  +4cyc_B    
                                                     !             !           !  !     !  
  --------------------RA----RCET--SAQAKG------   L   !             !           !  !     +-5lxu_A    
                                                     !             !           !  !  
  --------------------RT----------VAQTNA------   L -20             !           !  !   +1fjl_B    
                                                     !             !        +-17  +---5 
  ----SGQATTSTRG------------------------------   L   !             !        !  !      +1gt0_C    
                                                     !             !        !  !  
  ------------------------------RTVAIANAMCRG--   L   !             !        !  !      +1le8_A    
                                                     !             +-------18  !    +-7 
  QA--STQASTSART------------------------------   L   !                      !  +---12 +3d1n_M    
                                                     !                      !       !  
  --------------------RT----STVCKGDCRG--------   L   !                      !       +1w0t_A    
                                                     !                      !  
  ----------------------------VTKTIAQTNA----RT   L   !                      +------2me6_A    
                                                     !  
  --AT--QAATSA--------------------------------       +-----------------------------4z5h_A    
                                                   


> 1efa_B:CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF

  
  LTYCSGYGQC--STRG--HT--AGLGAC   L     +1efa_B    
                                     +-2 
  ITYTSGMTAA--STRG--NT--AGLCAT   L   ! ! +3oqm_C    
                                   --3 +-1 
  IT--ST--ATTTSTRG----VTAGLCAC   L   !   +1rzr_C    
                                     ! 
  ----SG--TC------RG------LCKA   L   +1qpz_A    
                                   


> 1emh_A:CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO UNCLEAVED SUBSTRATE-CONTAINING DNA

  
  --------PTLA----------                         +1emh_A    
                                             +---1 
  --------PALA----------       +-------------2   +4uqm_A    
                               !             ! 
  KT----TT------RA------     --4             +---4yig_E    
                               ! 
  ----RA--RCQTNT--QGTCRC   L   !   +-------------2dp6_A    
                               +---3 
  VGRG----------PG------           +-------------1oe4_B    
                             


> 1ewq_A:CRYSTAL STRUCTURE TAQ MUTS COMPLEXED WITH A HETERODUPLEX DNA AT 2.2 A RESOLUTION

  
  ----FGET----------                                  +--1ewq_A    
                                                    +-1 
  MGDAFGTTRCMC--PT--   L                          +-2 +--1wb9_A    
                                                  ! ! 
  --YGKA------SAPA--                           +--3 +----3thx_B    
                                               !  ! 
  VCKCFGET------PG--       +-------------------4  +-----2o8b_B    
                           !                   ! 
  --DGFG------VGSG--     --5                   +--------3thx_A    
                           ! 
  ----------------RT       +----------------------------1jfi_B    
                         


> 1eyg_D:CRYSTAL STRUCTURE OF CHYMOTRYPTIC FRAGMENT OF E. COLI SSB BOUND TO TWO 35-MER SINGLE STRAND DNAS

  
  --RCVC----NC------RC----------VCNCTCACSCECWC--TCECWCRC----FC--KCECVCECYC--------QC------RC--------------NCVC--TCQC   L                           +1eyg_D    
                                                                                                                                            +------1 
  ET--------RTCT----KT--LTNT----VTTTSTATNTETWTKTTTDTWTRT--YT------------YT----RT------HT--RTKT--WTQTITETITST--------   L   +----------------2      +3ulp_D    
                                                                                                                           !                ! 
  ------NT----------RT------MT--VTET------------------RTST--LT--------------------TT--ETYTRTQT----------------------   L   !                +------3udg_C    
                                                                                                                         --5 
  --------YT------------------------------------------------YGDG----------------ST--HT----------------------YTRT----   L   !     +-----------------3kjp_A    
                                                                                                                           ! +---3 
  ------------DGTGFGYGKT------YT----KG------------------------------FG----IGHG--------------------------------------   L   +-4   +-----------------2i0q_A    
                                                                                                                             ! 
  ----------------RTWT--------------------------------------FTNT--------------------RT--------KT--------------------   L     +---------------------4gnx_Z    
                                                                                                                         


> 1f2i_J:COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA

  
  ----HCHGRG--TA--ACNA--KGRG   L   +----------------1tf6_A    
                                   ! 
  LT--ETYC----NTYGQG--------   L   !       +--------4f6m_A    
                                   !     +-3 
  QA--TTNA--STQAQTATSTNTAT--   L --6     ! !       +1g2f_F    
                                   !     ! +-------1 
  RGSTDAHARG--RGSTDCHG--TT--   L   !  +--4         +5kl3_A    
                                   !  !  ! 
  --TCYCKARG--QA----TC------   L   !  !  !   +------5yeg_A    
                                   +--5  +---2 
  QA--ATHG----RG--DCNA--TT--   L      !      +------2i13_A    
                                      ! 
  RG--DGECRG--RGSGDCHA------   L      +-------------2wbs_A    
                                 


> 1f4k_B:CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B- SITE DNA COMPLEX

  
  ----------TT--RGRT----------------SG----RT----KT----   L                            +--2v1u_A    
                                                             +------------------------2 
  ----------ST--RG--------------------NGRA------VG----   L   !                        +--2qby_B    
                                                             ! 
  ----TT--------KATTQTTG--LTRT----KA--------------FTYT   L   !                       +----2p7c_B    
                                                             !                     +-3 
  ------------------NA--RAHT--STLT--------------------   L   !              +------4 +----2a07_K    
                                                             !              !      ! 
  KAFA------------------------------------------------     --9              !      +------3aaf_B    
                                                             !    +---------6 
  ------------------NASTRTHT--ST----------------------   L   !    !         !   +---------3l2c_A    
                                                             !    !         +---5 
  --------SG--YCNC------------------------------------       ! +--7             !       +-2ve9_C    
                                                             ! !  !             +-------1 
  ------------------------YG--------------------------       ! !  !                     +-4lb5_B    
                                                             +-8  ! 
  ------YC--KTHGSTQTYTPT------------------LG----------   L     !  +-----------------------5x11_A    
                                                               ! 
  ----------DCKGRG----NARTKT----------------KGRA------   L     +--------------------------5ddg_A    
                                                           


> 1f5t_A:DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE

  
  --------------ST--PTTC--QG------RG--------------   L                    +------------1f5t_A    
                                                                          !  
  ----------------RGSTRTSTHG----------------------   L                    !      +-----3zpl_B    
                                                                    +----14      ! 
  --------------TT--PTTCSTNT----------------------   L              !     !    +-9      +4lln_I    
                                                                    !     !    ! !    +-4 
  --------------DCSA--TATT--------RT--------------   L              !     !    ! +----6 +1z9c_A    
                                                                    !     +---12      ! 
  ----------------RGTCTA--RGNT--------------------   L              !          !      +4fx4_B    
                                                                    !          !  
  ------------------QC----------------------------                  !          +-------5hso_A    
                                                                    !  
  ------------------RGRGYC------------------------   L              !                  +1cf7_A    
                                                                 +-16      +-----------3 
  TTQT--------------------------------------------   L           !  !      !           +3gpl_A    
                                                                 !  !      !  
  ------------------------------YG----------------               !  !      !            +2heo_D    
                                                                 !  !      !          +-1 
  ------------------------------YGRG--------------               !  !   +-13        +-5 +4wcg_B    
                                                                 !  !   !  !        ! ! 
  ----------SGQG--YCNC----------------------------               !  !   !  !    +---7 +2ve9_C    
                                                                 !  !   !  !    !   ! 
  ------------------------------YG----------------               !  !   !  !    !   !  +4ka4_B    
                                                             +--17  !   !  +---10   +--2 
  ------------------KGTA--TA------RG--------------   L       !   !  +--15       !      +1xsd_A    
                                                             !   !      !       !  
  ----------RG--STRGMCTTRT------------------------   L       !   !      !       +------4u0y_B    
                                                             !   !      !  
  --------TT--------KATTQTTG----LTRT--KA------FTYT   L       !   !      !          +---2p7c_B    
                                                         +--18   !      !       +--8 
  --------------STQASGATSTQT----------------QA----   L   !   !   !      +------11  +---4on0_B    
                                                         !   !   !              !  
  --------------STKTPTTTFT--------------RA--------   L   !   !   !              +------4aso_F    
                                                       -19   !   !  
  --------ST----STQAQGSTSART----------------------   L   !   !   +--------------------5trd_B    
                                                         !   !  
  ----KAFA------------------------------FGMC------       !   +------------------------3aaf_B    
                                                         !  
  ------------------SAQT------RGQT--NG------QT----   L   +----------------------------3wgi_D    
                                                       


> 1fiu_C:TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA

  
  DCSC------QC--------RGSGDCRGRG   L           +-------------------1fiu_C    
                                       +-------2 
  ----NGACKG------RCSGRGSADCRG--   L   !       !           +-------3dvo_D    
                                     --3       +-----------1 
  ------------SCNG--SGRG----RG--   L   !                   +-------3v1z_B    
                                       ! 
  ------------VCRC----AAEARG----   L   +---------------------------5dwa_A    
                                     


> 1fjl_B:HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE

  
  ------RT----------------VAQTNA------   L                              +5hod_A    
                                                                   +----1 
  RA----RA----------------IAQTNAMC----   L                      +-16    +1puf_A    
                                                                !  !  
  ------RT----------------NT--NAIARG--   L                      !  +----1puf_B    
                                                                !  
  --KG--RC----------------IAQCNAYA----   L                      !     +-1nk3_P    
                                                             +-17  +-11  
  RA----RT----------------VASGNA------   L                   !  !  !  ! +3cmy_A    
                                                             !  !  !  +-2 
  ------RT----------------IAQCNAMG----   L                   !  !  !    +1b72_A    
                                                             !  +-15  
  RT----RT----------------VAQTNA------   L                   !     !      +1fjl_B    
                                                             !     !    +-6 
  RA----RT----------------IAQTNA------   L                   !     !  +-7 +4rdu_A    
                                                             !     !  ! ! 
  ----YARA----------------IAQTNA------   L                +-18     +-13 +5lux_L    
                                                          !  !        !  
  ----------------YTVC--KGDCKC--------   L                !  !        +-2qhb_A    
                                                          !  !  
  ------RA--------RCET----SAQAKG------   L                !  !     +-5lxu_A    
                                                          !  !  +-12  
  --------HTRT------------NCSTNARG----   L                !  !  !  +-1k61_B    
                                                          !  !  !  
  ------RT----------------IAKGNA------   L                !  +-14      +2hdd_A    
                                                       +-20     !    +-3 
  ------RT------------------KGNA------   L             !  !     !  +-8 +2hos_A    
                                                       !  !     !  ! ! 
  --------RT--------------NT--NAIARG--   L             !  !     +-10 +4cyc_B    
                                                       !  !        !  
  ----------------------RTVAIANAMCRG--   L             !  !        ! +1le8_A    
                                                +-----21  !        +-5 
  --------------------------KG--NA--EC   L      !      !  !          +1xpx_A    
                                                !      !  !  
  ------RT--------STVC--KGDCRG--------   L      !      !  +--------1w0t_A    
                                                !      !  
  RT----------------VT--KTIAQTNA------   L   +-23      !  +-------2me6_A    
                                             !  !      +-19  
  ------RA--------------RCVTCTNAQTRC--   L   !  !         +-------1au7_A    
                                             !  !  
  RA----RT----------------VA--NAQT----   L   !  !  +-----------------3d1n_M    
                                           -24  +-22  
  ------RT----------------VASCNAQA----   L   !     +-----------------1gt0_C    
                                             !  
  --------NGRGTGLC--LCRG--------------       !                    +4ofa_A    
                                             !                  +-4 
  --------NGRGTGLG--LCRG--------------       +------------------9 +4ew0_A    
                                                                ! 
  --------NGRGTGLG--LCRG--------------                          +4e9f_A    
                                           


> 1fok_A:STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA

  
  QANARGQGDTNTWC----NGNCECSA--KG--RGMG----------------------------------------   L          +-------------------------1fok_A    
                                                                                            !  
  --------------------------------------------SG--QG--YCNC--------------------              !                         +2ve9_C    
                                                                                            !                       +-9 
  ------------------------------------------TT----------KATTQTTGLTRT--KA------   L          !                       ! +2p7c_B    
                                                                                            !                   +--13  
  --------------------------------------------------------------YG------------              !                   !   !    +4ka4_B    
                                                                                        +--19                   !   !  +-8 
  --------------------------------------------------------------YGRG----------          !   !                   !   +-12 +4wcg_B    
                                                                                        !   !            +-----16      !  
  --------------------------------------------------------------YG------------          !   !            !      !      +4lb5_B    
                                                                                        !   !            !      !  
  --------------------------------------------------------------YG------------          !   !       +---17      !   +-2heo_D    
                                                                                     +-20   !       !    !      +--14  
  ----------------------------------------------RG--STRGMCTTRT----------------   L   !  !   !       !    !          +-4u0y_B    
                                                                                     !  !   +------18    !  
  --------------------------KTPTTTFT------------------------------------------   L   !  !           !    +------------4aso_F    
                                                                                     !  !           !  
  --------------KAFA----------------------------------------------------------       !  !           +-----------------3aaf_B    
                                                                                     !  !  
  ------------------------------------------------------------------------RTEG       !  +-----------------------------5gke_A    
                                                                                   -21  
  ------------------------------------------------------------IAKGNA----------   L   !                              +2hdd_A    
                                                                                     !                            +-1 
  ------------------------------------HTRT--------------------NCSTNARG--------   L   !                         +-11 +1k61_B    
                                                                                     !                         !  !  
  ------------------------------------------------------------NT--NAIARG------   L   !                         !  +4cyc_B    
                                                                                     !                         !  
  --------------------------------------------------------------KGNA----------   L   !                         !      +2hos_A    
                                                                                     +------------------------15    +-4 
  ------------------------------------------------------------VAQTNA----------   L                             !  +-5 +5hod_A    
                                                                                                               !  ! ! 
  ------------------------------------------------------------IAQCNAYA--------   L                             !  ! +1nk3_P    
                                                                                                               !  !  
  ----------------------------------------RT----------STVC--KGDCRG------------   L                             +-10   +1w0t_A    
                                                                                                                  ! +-2 
  ------------------------------------------------------------VASGNA----------   L                                ! ! +3cmy_A    
                                                                                                                  +-7 
  ----------------------------------------------------------RTVAIANAMCRG------   L                                  !   +1le8_A    
                                                                                                                    ! +-3 
  ------------------------------------------------------------VAQTNA----------   L                                  +-6 +1fjl_B    
                                                                                                                      ! 
  ------------------------------------------------------------IAQTNA----KT----   L                                    +4rdu_A    
                                                                                   


> 1g2d_F:STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (CLONE #2)

  
  QA--TTNA--STQAQTATSTNTATTTLAHGTCRG--   L                    +1g2f_F    
                                                      +-------1 
  KG--WTKA--------HCHG--RGTA--ACNAKGRG   L            !       +1tf6_A    
                                                   +--4 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG--   L         !  !      +-5kl3_A    
                                                   !  ! +----2 
  EC--SCKGRG----TCYCKA--RGQA----TC----   L   +-----5  +-3    +-5yeg_A    
                                             !     !    ! 
  ----TTSGRG--LT--ETYC----NTYGQG------   L   !     !    +------4f6m_A    
                                           --6     ! 
  QARGATNA----QA--ATHG----RG--DCNATT--   L   !     +----------2i13_A    
                                             ! 
  ------------RG--DGEC--RGRGSGDCHA----   L   +----------------2wbs_A    
                                           


> 1g2f_F:STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (TATAZF;CLONE #6)

  
  KG--WTKA--------HCHG--RGTA--ACNAKGRG   L     +---------------1tf6_A    
                                               ! 
  QARGATNA----QA--ATHG----RG--DCNATT--   L   +-5    +----------2i13_A    
                                             ! !    ! 
  QA--TTNA--STQAQTATSTNTATTTLAHGTCRG--   L   ! !    !          +1g2f_F    
                                             ! +----4        +-1 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG--   L   !      !     +--2 +5kl3_A    
                                           --6      !     !  ! 
  EC--SCKGRG----TCYCKA--RGQA----TC----   L   !      +-----3  +-5yeg_A    
                                             !            ! 
  ----TTSGRG--LT--ETYC----NTYGQG------   L   !            +----4f6m_A    
                                             ! 
  ------------RG--DGEC--RGRGSGDCHA----   L   +----------------2wbs_A    
                                           


> 1gcc_A:SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE

  
  RGRG--WA--EC--RG------RGWC--   L                         +1gcc_A    
                                         +-----------------1 
  RGRG------EC--RG------RGWC--   L   +---2                 +5wx9_A    
                                     !   ! 
  ----RT--------------------QG   L --3   +-----------------5d3g_A    
                                     ! 
  --KA----YT--KG--RGECSARG----   L   +---------------------3rmp_A    
                                   


> 1gd2_G:CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA

  
  --------------RG------NC----YGAT--CTRG   L     +------2wt7_B    
                                                 ! 
  RGQGNART--AGQT----FTRG----------------   L   +-5     +1gd2_G    
                                               ! !     ! 
  RC--NC----AAAT----CTRC----------------   L   ! !     !     +2wt7_A    
                                               ! +-----4   +-1 
  ----NTRT--ATAT----CTRA----------------   L   !       ! +-2 +5vpe_D    
                                             --6       ! ! ! 
  --------RG------NC----YGAT------RC----   L   !       +-3 +4eot_A    
                                               !         ! 
  ------RA----NA----AAVT----STRG--------   L   !         +1nwq_C    
                                               ! 
  ----NCTT----AT------RG----------------   L   +--------2dgc_A    
                                             


> 1gji_A:CRYSTAL STRUCTURE OF C-REL BOUND TO DNA

  
  RGRGYTCTEC--------RT------   L                               +1gji_A    
                                                             +-1 
  RGRGYTCTEC--SG----RT------   L                         +---2 +2i9t_A    
                                                         !   ! 
  RGRGYTCTECRG------KT------   L   +---------------------4   +3do7_A    
                                   !                     ! 
  RGRGYTCCEC------KTKTPTKTRG   L   !                     ! +--1nfk_A    
                                 --5                     +-3 
  RGRGYTCCEC----HG--KG------   L   !                       +--1a3q_A    
                                   ! 
  RGRG----EGRG--------------   L   +-------------------------1bvo_A    
                                 


> 1gm5_A:STRUCTURE OF RECG BOUND TO THREE-WAY DNA JUNCTION

  
  KAFAMGIA--KA--FGNCQCYG----------EA--NG--------             +-----------------------1gm5_A    
                                                           +-1 
  ------------------------------------------NALA   L     +-2 +-----------------------3v4r_B    
                                                         ! ! 
  ----------------------------------------RT----   L   +-3 +-------------------------5vvr_M    
                                                       ! ! 
  --------------------------------------VC------     --4 +---------------------------2wwy_B    
                                                       ! 
  --------RT--IG--WGDG--KGDTHTLTYAEGIG----------   L   +----------------------------4hja_A    
                                                     


> 1gt0_C:CRYSTAL STRUCTURE OF A POU/HMG/DNA TERNARY COMPLEX

  
  --SGQATTSTRG----------RT----------VASCNAQA--   L   +----------------1gt0_C    
                                                     !  
  ----------------RA----RT----------VASGNA----   L   !                    +3cmy_A    
                                                     !                  +-1 
  ----------------------RT----------VAQTNA----   L   !                +-2 +5hod_A    
                                                     !                ! ! 
  ------------------KG--RC----------IAQCNAYA--   L   !              +-3 +1nk3_P    
                                                     !              ! ! 
  ----------------RA----RA----------IAQTNAMC--   L   !          +--11 +1puf_A    
                                                     !          !   !  
  ----------------RT----RT----------VAQTNA----   L   !          !   ! +1fjl_B    
                                                     !          !   +-4 
  QASTQASTSART--------------------------------   L   !          !     +3d1n_M    
                                                     !          !  
  ----------------RA----RT----------IAQTNA----   L   !          !          +4rdu_A    
                                                   -18          !        +-7 
  ----------------------RT----------IAQCNAMG--   L   !     +---15     +-12 +1b72_A    
                                                     !     !    !     !  !  
  --------------------YARA----------IAQTNA----   L   !     !    !  +-13  +-5lux_L    
                                                     !     !    !  !  !  
  ------------------------HTRT------NCSTNARG--   L   !     !    !  !  !  +1k61_B    
                                                     !     !    !  !  +--5 
  ----------------------RT----------NT--NAIARG   L   !     !    !  !     +1puf_B    
                                                     !     !    +-14  
  ----------------------RT----------IAKGNA----   L   !     !       !      +2hdd_A    
                                                     !  +-16       !    +-6 
  ----------------------RT------------KGNA----   L   !  !  !       !  +-8 +2hos_A    
                                                     !  !  !       !  ! ! 
  ----------------RT------------VTKTIAQTNA----   L   !  !  !       +-10 +2me6_A    
                                                     !  !  !          !  
  --------------------------------RTVAIANAMCRG   L   +-17  !          ! +1le8_A    
                                                        !  !          +-9 
  ------------------------RT--------NT--NAIARG   L      !  !            +4cyc_B    
                                                        !  !  
  ----------------------RT----STVCKGDCRG------   L      !  +----------1w0t_A    
                                                        !  
  --STQATTCARGLTNT----------------------------   L      +-------------1au7_A    
                                                   


> 1gt0_D:CRYSTAL STRUCTURE OF A POU/HMG/DNA TERNARY COMPLEX

  
  KCNT--MAMA--EGSAACNT--YT   L      +----2lef_A    
                                    ! 
  RTNTFTMA--RT--NG--SAYA--   L   +--3   +4y60_C    
                                 !  ! +-1 
  RCNTFTMA--RAHGNT--SAYA--   L   !  +-2 +3f27_D    
                               --4    ! 
  --STYGLASGLA--TGTCIT----   L   !    +--3tq6_B    
                                 ! 
  ----FTIA--RT--QTLAMT----   L   +-------5jh0_D    
                               


> 1gxp_A:PHOB EFFECTOR DOMAIN IN COMPLEX WITH PHO BOX DNA.

  
  ------------NTVC--ECSTYT--STYC------RA----   L                   +---------------------5ed4_A    
                                                               +--10  
  ----------RCET------SA----QAKG------------   L               !   +---------------------5lxu_A    
                                                               !  
  --------------HT----RTITYT----------------   L               !           +-------------4kfc_B    
                                                            +-11     +-----8 
  ------------RG----DTVT----ST--RG----RC----   L            !  !     !     +-------------4nhj_A    
                                                            !  !     ! 
  --------------------------------YG--------                !  !     !                  +4lb5_B    
                                                            !  +-----9       +----------2 
  TT----------KATT--QTTG----------LTRT--FTYT   L            !        !       !          +2p7c_B    
                                                            !        !       ! 
  ------------RGRG--YC----------------------   L            !        !       !        +---1cf7_A    
                                                            !        +-------7        ! 
  --------------------------------YG--------             +-12                !      +-5    +4ka4_B    
                                                         !  !                !      ! !  +-3 
  ----SGQG--YCNC----------------------------             !  !                !      ! !  ! +2ve9_C    
                                                         !  !                !      ! +--4 
  --------------------------------YG--------             !  !                +------6    ! +2heo_D    
                                                         !  !                       !    +-1 
  ----------------------------------RG------          +-13  !                       !      +4wcg_B    
                                                      !  !  !                       ! 
  --RG----STRGMCTT--RT----------------------   L      !  !  !                       +----4u0y_B    
                                                      !  !  !  
  ------------KGTC--KGTCHT------------------   L   +-14  !  +--------------------------4wuh_B    
                                                   !  !  !  
  LTET----TTRAECRC--RCQC--------------------   L   !  !  +----------------------------3n97_A    
                                                 -15  !  
  --------------RGAC----LG------------------       !  +-----------------------------4wx9_A    
                                                   !  
  YG------------TG--RGSG----FTRG------------   L   +-----------------------------2h27_A    
                                                 


> 1h89_C:CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2

  
  ------KG--RTEC----NAKGNANTST   L                    +---1h89_C    
                                     +----------------2 
  --NA--RTQT--EC----NG--NA----   L   !                !  +2kdz_A    
                                   --3                +--1 
  ------KG--RAEA--DCNAKGNANTST   L   !                   +3zqc_A    
                                     ! 
  RT--STVC--KGDCRG------------   L   +--------------------1w0t_A    
                                   


> 1h8a_C:CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3

  
  ------KG--RTEC----NAKGNANTST   L                    +---1h89_C    
                                     +----------------2 
  ------KG--RAEA--DCNAKGNANTST   L   !                ! +--3zqc_A    
                                   --3                +-1 
  --NA--RTQT--EC----NG--NA----   L   !                  +--2kdz_A    
                                     ! 
  RT--STVC--KGDCRG------------   L   +--------------------1w0t_A    
                                   


> 1h9t_B:FADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN COMPLEX WITH FADB OPERATOR

  
  RG--TGRGTG--RTET------HA------   L                      +--1h9t_B    
                                       +------------------6 
  RG--TTRGTTTTRTET------HA------   L   !                  +--4p9u_B    
                                       !  
  RG--STRGMCTTRT----------------   L   !       +-------------4u0y_B    
                                     -10       ! 
  SGQG--YCNC--------------------       !       !               +2ve9_C    
                                       !       !             +-2 
  --------KATTQTTGLTRTKA----FTYT   L   !       !           +-4 +2p7c_B    
                                       +-------9           ! ! 
  ----------------YG------------               !           ! +4lb5_B    
                                               !    +------5 
  ----------------YGRG----------               !    !      ! +4wcg_B    
                                               !    !      +-3 
  ----------------YG------------               !    !        ! +2heo_D    
                                               +----8        +-1 
  ----------------YG------------                    !          +4ka4_B    
                                                    ! 
  --------RGRGYC----------------   L                !  +-----1cf7_A    
                                                    +--7 
  ----STKTPTTTFT----------RA----   L                   +-----4aso_F    
                                     


> 1hcq_E:THE CRYSTAL STRUCTURE OF THE ESTROGEN RECEPTOR DNA-BINDING DOMAIN BOUND TO DNA: HOW RECEPTORS DISCRIMINATE BETWEEN THEIR RESPONSE ELEMENTS

  
  ----EA--KG--RTRTRT                   +2han_B    
                                    +-10  
  ----EA--KG--RTRG--   L            !  +1kb2_B    
                                 +-13  
  ----EC--KG--KGRG--   L         !  !  +-1dsz_B    
                                 !  +-12  
  --HGECAGKGAAKGRT--   L      +-14     +-1lo1_A    
                              !  !  
  ----ET--KGAT--RG--   L      !  !  +1lat_A    
                              !  +--3 
  ----EC--KG--RGRG--   L   +-16     +2nll_B    
                           !  !  
  --------KAVA--RA--   L   !  !     +5e69_A    
                           !  !   +-1 
  --------KGVT--RG--   L   !  +---2 +2c7a_B    
                           !      ! 
  ----EC--KA--RGRG--   L   !      +4nqa_I    
                           !  
  --------KGVT--RG--   L   !         +5cbz_E    
                         -17       +-8 
  --------KGVG--RG--   L   !       ! ! +3g6t_A    
                           !     +-9 +-7 
  --HAEC--KG--RGRG--   L   !     ! !   +1a6y_A    
                           !     ! ! 
  --HC----KGVT--RG--       !  +-11 +3g9m_B    
                           !  !  !  
  ----DG--KG--RTRG--   L   !  !  ! +3cbb_A    
                           !  !  +-6 
  CA--EC--KG--KGRG--   L   +-15    +1cit_A    
                              !  
  --------KGVT--RG--          !    +5emc_A    
                              !  +-4 
  ----EC--KG--KGRA--   L      +--5 +5l0m_A    
                                 ! 
  ----EC--KG--KGRG--   L         +2ff0_A    
                         


> 1hlo_B:THE CRYSTAL STRUCTURE OF AN INTACT HUMAN MAX-DNA COMPLEX: NEW INSIGHTS INTO MECHANISMS OF TRANSCRIPTIONAL CONTROL

  
  KT----HGNT----EC--RCRG   L                      +1nkp_A    
                                              +---1 
  ------HGNT--LGEC--RCRC   L                  !   +5i50_B    
                                            +-7 
  ------HGNT--LCEC--RCRG   L                ! !  +1hlo_B    
                                            ! +--3 
  ------HGNT--IAEC--YCRG   L   +------------9    +1am9_A    
                               !            ! 
  ----HGNT--IAEC--RCRT--   L   !            ! +--4ati_B    
                               !            +-6 
  ------HGNT--MTEA--RCRG   L   !              ! +1nlw_D    
                               !              +-5 
  ------HGNT----EC--RCRG   L   !                +1nkp_E    
                               !  
  ------RTNT----EC--RCRG   L -13                   +4h10_B    
                               !           +-------2 
  --RT----NT--RGEC--RCQT       !     +----10       +2ypa_A    
                               !     !     !  
  ----QG------VTEC--RCRG   L   !     !     +-------1an4_A    
                               !  +-11  
  --RG----TT--RAEC--RC--       !  !  !         +---1mdy_C    
                               !  !  +---------8 
  ------HGST--ITET--RCRG   L   +-12            !  +4h10_A    
                                  !            +--4 
  ------HG----ITEC--RCRG   L      !               +5nj8_D    
                                  !  
  ------HG------ET--RTRG   L      +--------------5v0l_A    
                             


> 1ic8_B:HEPATOCYTE NUCLEAR FACTOR 1A BOUND TO DNA : MODY3 GENE PRODUCT

  
  NTQASAHT--STQT----TTPGRTYCNAATNAKG--   L                             +-1ic8_B    
                                                     +-----------------1 
  NTQASTHT--STQT----TT--RAYT----NAKG--   L       +---2                 +-2h8r_B    
                                                 !   ! 
  STQATT----------RG----RARCVTCTNAQTRC   L   +---3   +-------------------1au7_A    
                                             !   ! 
  TTQA--LT--SAET----------------------   L --4   +-----------------------2o4a_A    
                                             ! 
  ST--SCATRT--NCQT--HT----------------   L   +---------------------------4jcy_A    
                                           


> 1if1_B:INTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA

  
  HC------NT--RGCT--NGST   L                         +1if1_B    
                                                   +-1 
  --KG--ATNT--RTCT----SC   L         +-------------3 +2irf_L    
                                     !             ! 
  --------------------RG             !             +-4hly_B    
                                     ! 
  ----KTRGAT----RGYA----   L   +-----7             +-1bc8_C    
                               !     !          +--4 
  ----KTRGSA----RGQA----   L   !     !          !  ! +1yo5_C    
                               !     +----------5  +-2 
  --DCKTRG------RGYA----   L --8                !    +1dux_F    
                               !                ! 
  ----KT--RGAT--RGYT----   L   !                +----1awc_A    
                               ! 
  ------NA----RAHT--STLT   L   !               +-----2a07_K    
                               +---------------6 
  ------NAST--RTHT--ST--   L                   +-----3l2c_A    
                             


> 1ig7_A:MSX-1 HOMEODOMAIN/DNA COMPLEX STRUCTURE

  
  ----RT------------------IAQTNA------KT   L                                        +4rdu_A    
                                                                                  +-1 
  ----RA------------------IAQTNAMC------   L                                   +-15 +1puf_A    
                                                                               !  !  
  ----RT------------------IAQCNAMG------   L                                   !  +-1b72_A    
                                                                               !  
  ----RT------------------VASGNA--------   L                                   !        +3cmy_A    
                                                                            +-17      +-2 
  KG--RC------------------IAQCNAYA------   L                                !  !    +-7 +1nk3_P    
                                                                            !  !    ! ! 
  ----RT------------------VAQTNA--------   L                                !  !  +-9 +5hod_A    
                                                                            !  !  ! ! 
  ----RT------------------NT--NAIARG----   L                             +-18  +-12 +1puf_B    
                                                                         !  !     !  
  --YARA------------------IAQTNA--------   L                             !  !     +5lux_L    
                                                                         !  !  
  ----RT------------------VAQTNA--------   L                          +-19  !   +1fjl_B    
                                                                      !  !  +---3 
  ----RT------------------VASCNAQA------   L                          !  !      +1gt0_C    
                                                                      !  !  
  ----RA----------------RCVTCTNAQTRC----   L                       +-20  +-----1au7_A    
                                                                   !  !  
  ----RA----------RCET----SAQAKG--------   L                       !  !     +--5lxu_A    
                                                                   !  !     !  
  ----------------------RTVAIANAMCRG----   L                       !  +----16    +1le8_A    
                                                                +-21        !  +-5 
  --------------------------KG--NA--EC--   L                    !  !        +-14 +1xpx_A    
                                                                !  !           !  
  ----RT----------STVC--KGDCRG----------   L                    !  !           +-1w0t_A    
                                                                !  !  
  ------------------VT--KTIAQTNA------RT   L                    !  +---------2me6_A    
                                                                !  
  ----RT------------------IAKGNA--------   L                 +-22                 +2hdd_A    
                                                             !  !               +-4 
  ------HTRT--------------NCSTNARG------   L                 !  !             +-8 +1k61_B    
                                                             !  !             ! ! 
  ------RT----------------NT--NAIARG----   L                 !  !          +-11 +4cyc_B    
                                                             !  !          !  !  
  ----RT--------------------KGNA--------   L                 !  !          !  +2hos_A    
                                                         +--23  +---------13  
  ------NGRGTG--LG--LCRG----------------                 !   !             !    +4ew0_A    
                                                         !   !             !  +-6 
  ------NGRGTG--LC--LCRG----------------                 !   !             +-10 +4ofa_A    
                                                  +-----24   !                !  
  ------NGRGTG--LG--LCRG----------------          !      !   !                +4e9f_A    
                                                  !      !   !  
  ----------------YTVC--KGDCKC----------   L   +-25      !   +---------------2qhb_A    
                                               !  !      !  
  ----RT------------------VA--NAQT------   L   !  !      +-------------------3d1n_M    
                                             -26  !  
  --------QGCGTALC----------------------       !  +--------------------------1orn_A    
                                               !  
  ------------------RGRGYC--------------   L   +--------------------------1cf7_A    
                                             


> 1ign_A:DNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE

  
  ----HG--NCSCRGHCRG--YC----KANA--RGDC--RGKT----TCTCPTNC   L   +-------------------1ign_A    
                                                               ! 
  --------------------------RT--NT----NA----IARG--------   L   !             +-----1puf_B    
                                                               !             ! 
  ------------RTVAIANA--MCRG----------------------------   L   !             !         +1le8_A    
                                                             --8             !       +-1 
  HTRT----------NCSTNA--RG------------------------------   L   !     +-------6     +-2 +1k61_B    
                                                               !     !       !     ! ! 
  RT------------NT--NA--IARG----------------------------   L   !     !       !   +-4 +4cyc_B    
                                                               !     !       !   ! ! 
  ----------------KGNA----------------------------------   L   !     !       !   ! ! +2hos_A    
                                                               +-----7       +---5 +-3 
  --------------IAKGNA----------------------------------   L         !           !   +2hdd_A    
                                                                     !           ! 
  ------RCET----SAQAKG----------------------------------   L         !           +-5lxu_A    
                                                                     ! 
  ------STVC--KGDCRG------------------------------------   L         +-------------1w0t_A    
                                                             


> 1imh_C:TONEBP/DNA COMPLEX

  
  RG--YTTTECRG--QA--   L   +---------------1imh_C    
                           ! 
  RGRGYTCC--HTKT--RG   L --3             +--1nfk_A    
                           !           +-1 
  RGRGYTEC--HG------   L   +-----------2 +--1a3q_A    
                                       ! 
  RGRGYTEC----------   L               +---1gji_A    
                         


> 1j1v_A:CRYSTAL STRUCTURE OF DNAA DOMAINIV COMPLEXED WITH DNAABOX DNA

  
  RALTPTDCHGTCTCLTHT----------   L               +-------------1j1v_A    
                                     +-----------3 
  ----------------NT----NAIARG   L   !           !       +-----1puf_B    
                                     !           +-------2 
  --------RCET----SA--QAKG----   L --4                   !   +-5lxu_A    
                                     !                   +---1 
  ----------------NT----NAIARG   L   !                       +-4cyc_B    
                                     ! 
  ----------KGTCKGTCHT--------   L   +-------------------------4wuh_B    
                                   


> 1j47_A:3D SOLUTION NMR STRUCTURE OF THE M9I MUTANT OF THE HMG-BOX DOMAIN OF THE HUMAN MALE SEX DETERMINING FACTOR SRY COMPLEXED TO DNA

  
  --RC--NAFTIA--RG--NC----SALT------YAKTEAKA   L   +----------------------2gzk_A    
                                                   !  
  --RC--NTFTMA--RA--NGSC--ST--------YA--RG--   L   !                      +1gt0_D    
                                                   !              +-------2 
  --KC--NT--MAMA--EGSAAC--NT------------YT--   L   !              !       +2lef_A    
                                                 -10              ! 
  --RC--NTFTMA--RAHTNTAT--SA--------YA------   L   !       +------7          +3u2b_C    
                                                   !       !      !        +-1 
  --RT--NTFTMA--RA--NGAC--ST--------YA------   L   !       !      !      +-4 +4s2q_D    
                                                   !       !      !      ! ! 
  --RT--NTFTMA--RT--NG----SA--------YA------   L   !       !      +------6 +4y60_C    
                                                   +-------9             ! 
  --RC--NTFTMA--RAHGNT----SA--------YA------   L           !             +3f27_D    
                                                           ! 
  ------------VT----FG--FCSA----------------               !              +4qr9_A    
                                                           !  +-----------3 
  ------STYGLASGLA--TGTC--IT----------------   L           !  !           +3tq6_B    
                                                           +--8 
  KCRC----YTMALTRA--VCTG--AA----VCEC--------   L              !           +1qrv_A    
                                                              +-----------5 
  --RTTASTYAFALT----PTAT--ST--RA------------   L                          +5jh0_D    
                                                 


> 1j5n_A:SOLUTION STRUCTURE OF THE NON-SEQUENCE-SPECIFIC HMGB PROTEIN NHP6A IN COMPLEX WITH SRY DNA

  
  VGTTRTTGRTRT--SAYCMT------FT------   L           +-----1j5n_A    
                                              +----3 
  ----------RTTASTYAFALT----PTATSTRA   L   +--4    +-----5jh0_D    
                                           !  ! 
  --------------STYGLASGLA--TGTCIT--   L   !  +----------3tq6_B    
                                         --5 
  ----------RT--NTFTMA--RT--NG--SA--   L   !            +4y60_C    
                                           +------------2 
  ----------RC--NTFTMA--RAHGNT--SA--   L                ! +3f27_D    
                                                        +-1 
  ----------KC--NT--MAMA--EGSAACNT--   L                  +2lef_A    
                                         


> 1je8_F:TWO-COMPONENT RESPONSE REGULATOR NARL/DNA COMPLEX: DNA BENDING FOUND IN A HIGH AFFINITY SITE

  
  ------KGTC--KGTCHT--------   L          +-----------------4wuh_B    
                                   +------4 
  TT----KATT----QTTG--LTRTYT   L   !      !            +----2p7c_B    
                                   !      +------------2 
  --ST--RG------------------   L --5                   +----2qby_B    
                                   ! 
  --DCSA----TA--TT------RT--   L   !       +----------------1z9c_A    
                                   +-------3 
  ------------------YG------               !               +2heo_D    
                                           +---------------1 
  --------------------YG----                               +4ka4_B    
                                 


> 1jfi_A:CRYSTAL STRUCTURE OF THE NC2-TBP-DNA TERNARY COMPLEX

  
  ----------RG                    +4jjn_G    
                        +---------2 
  ----------RT          !         +5gt0_C    
                        ! 
  ----------RG          !         +5t5k_E    
                        !      +--1 
  ----------RC       +--9    +-5  +1kx5_B    
                     !  !    ! ! 
  ------RT----       !  !  +-7 +--4jjn_F    
                     !  !  ! ! 
  ----AT------       !  !  ! ! +--4awl_B    
                     !  !  ! +-6 
  ----IT------       !  +--8   +--3wkj_D    
                   -10     ! 
  RA--ET--RT--       !     !      +4ne1_p    
                     !     +------4 
  ----LT----RC       !            ! +5av9_A    
                     !            +-3 
  ----LC----RG       !              +4jjn_A    
                     !  
  --RAAANA----       +------------1jfi_B    
                   


> 1jfi_B:CRYSTAL STRUCTURE OF THE NC2-TBP-DNA TERNARY COMPLEX

  
  ----RAAANA----RT                       +---------1jfi_B    
                                      +-10  
  ------IT--------                    !  !         +3wkj_D    
                                      !  +---------1 
  RG--------------   L                !            +1kx5_D    
                                      !  
  ------AT--------          +--------11       +----4awl_B    
                            !         !   +---7 
  ------------RC--          !         !   !   +----1kx5_B    
                            !         !   ! 
  ------------RG--          !         !   !         +5t5k_E    
                            !         !   !     +---2 
  ----------RT----          !         +---9     !   +4jjn_F    
                            !             ! +---6 
  --RA--ET--RT----          !             ! !   ! +-4ne1_p    
                         +-12             ! !   +-5 
  ------------RT--       !  !             ! !     ! +5gt0_C    
                         !  !             +-8     +-4 
  ------------RG--       !  !               !       +4jjn_G    
                         !  !               ! 
  ------LT----RC--     -13  !               !      +5av9_A    
                         !  !               +------3 
  ------LC----RG--       !  !                      +4jjn_A    
                         !  !  
  ------IT--------       !  +----------------------5b1m_D    
                         !  
  ------IT--------       +-----------------------5b0z_D    
                       


> 1jgg_B:EVEN-SKIPPED HOMEODOMAIN COMPLEXED TO AT-RICH DNA

  
  YARA------------------IAQTNA--------   L                                +5lux_L    
                                                                       +-10  
  --RC------------------IAQCNAYA------   L                             !  ! +1nk3_P    
                                                                    +-14  +-1 
  --RA------------------IAQTNAMC------   L                          !  !    +1puf_A    
                                                                    !  !  
  --RT------------------IAQCNAMG------   L                          !  +-1b72_A    
                                                                 +-15  
  --RT------------------VAQTNA--------   L                       !  !   +5hod_A    
                                                                 !  ! +-5 
  --RT------------------VASGNA--------   L                       !  +-7 +3cmy_A    
                                                             +--17    ! 
  --RT------------------VASCNAQA------   L                   !   !    +1gt0_C    
                                                             !   !  
  --RT------------------IAQTNA------KT   L                   !   !  +4rdu_A    
                                                             !   +-12  
  --RT------------------VAQTNA--------   L                +-20      ! +1fjl_B    
                                                          !  !      +-6 
  ----------------VT--KTIAQTNA------RT   L                !  !        +2me6_A    
                                                          !  !  
  --RT------------------NT--NAIARG----   L                !  !  +------1puf_B    
                                                          !  +-19  
  --RT------------------IAKGNA--------   L                !     !      +2hdd_A    
                                                     +---22     +------2 
  --------------YTVC--KGDCKC----------   L           !    !            +2qhb_A    
                                                     !    !  
  --RA------------------IAQCNAMG------   L           !    !  +-----2r5z_A    
                                                     !    !  !  
  ----HTRT--------------NCSTNARG------   L           !    !  !          +1k61_B    
                                                     !    !  !        +-8 
  ----RT----------------NT--NAIARG----   L           !    +-18     +-11 +4cyc_B    
                                                +---23       !     !  !  
  --RT--------------------KGNA--------   L      !    !       !  +-13  +2hos_A    
                                                !    !       !  !  !  
  --RA----------RCET----SAQAKG--------   L      !    !       +-16  +-5lxu_A    
                                                !    !          !  
  --------------------RTVAIANAMCRG----   L   +-24    !          !   +1le8_A    
                                             !  !    !          +---4 
  ------------------------KG--NA--EC--   L   !  !    !              +1xpx_A    
                                             !  !    !  
  --RA----------------RCVTCTNAQTRC----   L   !  !    +-------------1au7_A    
                                             !  !  
  --RT------------------VA--NAQT------   L -25  +------------------3d1n_M    
                                             !  
  ----NGRGTGLC----LCRG----------------       !                     +4ofa_A    
                                             !                   +-3 
  ----NGRGTGLG----LCRG----------------       !            +------9 +4ew0_A    
                                             !            !      ! 
  ----NGRGTGLG----LCRG----------------       +-----------21      +4e9f_A    
                                                          !  
  ------------YG----------------------   L                +-------5kn8_A    
                                           


> 1jj4_B:HUMAN PAPILLOMAVIRUS TYPE 18 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET



> 1jt0_C:CRYSTAL STRUCTURE OF A COOPERATIVE QACR-DNA COMPLEX

  
  TG--SAKG--NTYTYT   L            +----1jt0_C    
                                  ! 
  TA--STECAGATYTRG   L            !        +4gck_A    
                                  !      +-1 
  VT--AGDT--TTYTLA   L      +-----5   +--2 +5gpc_B    
                            !     !   !  ! 
  TA----ECAC--YCRA          !     ! +-3  +5haw_A    
                            !     ! ! ! 
  TA--AT----LCFGHA       +--6     +-4 +---4i6z_B    
                         !  !       ! 
  --EC--KGQCTGYGRC   L   !  !       +---4jl3_B    
                       --7  ! 
  ----SCKGSG--IGYC   L   !  +----------2yvh_A    
                         ! 
  ----TGKG----YCFA   L   +-------------4pxi_B    
                       


> 1k3x_A:CRYSTAL STRUCTURE OF A TRAPPED REACTION INTERMEDIATE OF THE DNA REPAIR ENZYME ENDONUCLEASE VIII WITH BROMINATED-DNA

  
  QALGYA------------------RG                       +-1k3x_A    
                                                 +-3 
  RA--------FT------------RA   L                 ! ! +3gpu_A    
                                          +------4 +-1 
  RGMG------FC------------RG   L          !      !   +3u6p_A    
                                      +---5      ! 
  --MG------RC--FCKGDGACQTRG   L      !   !      +-1k82_A    
                                      !   ! 
  --MG--ITRC--FG------HG--RG   L   +--6   +--------5itu_A    
                                   !  ! 
  RTMTET--RC--------------RT       !  !          +-4pd2_A    
                                 --7  +----------2 
  --LG----RC--FC------NG--RT   L   !             +-3vk8_B    
                                   ! 
  --MG------RG--FG--------RG       +---------------3twm_A    
                                 


> 1k4t_A:HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX

  
  --ECRA--YAMCKT--NT--KT----------NT                             +------1k4t_A    
                                                    +------------1 
  NT--RGMGYAMCKT--NC--KTDA----TT----   L      +-----2            +------2b9s_A    
                                              !     ! 
  --------------RG--------RG--------   L   +--3     +-------------------3m4a_A    
                                           !  ! 
  ------------------KA------RA------   L --4  +-------------------------5u91_B    
                                           ! 
  ------------------------------NT--       +----------------------------2b9s_B    
                                         


> 1k61_B:MATALPHA2 HOMEODOMAIN BOUND TO DNA

  
  --HTRT--------------NCSTNA--RG------   L                                    +1k61_B    
                                                                         +----1 
  RT------------------NT--NA--IARG----   L                            +-17    +1puf_B    
                                                                      !  !  
  RA----------------RCVTCTNA--QTRC----   L                            !  +----1au7_A    
                                                                      !  
  --RT----------------NT--NA--IARG----   L                            !            +-4cyc_B    
                                                                      !         +-13  
  RT------------------IAKGNA----------   L                            !         !  ! +2hdd_A    
                                                                      !         !  +-2 
  RA------------------IAQTNA--MC------   L                            !         !    +1puf_A    
                                                                      !         !  
  RA------------------IAQTNA----------   L                            !      +-15     +-5lux_L    
                                                                   +-19      !  !     !  
  RT------------------VAQTNA----------   L                         !  !      !  !  +-11   +5hod_A    
                                                                   !  !      !  !  !  ! +-4 
  RC------------------IAQCNA--YA------   L                         !  !      !  !  !  +-9 +1nk3_P    
                                                                   !  !      !  +-12    ! 
  RT------------------VASGNA----------   L                         !  !      !     !    +3cmy_A    
                                                                   !  !  +--16     !  
  RT------------------IAQTNA--------KT   L                         !  !  !   !     ! +4rdu_A    
                                                                   !  !  !   !     +-3 
  RT------------------IAQCNA--MG------   L                      +-20  !  !   !       +1b72_A    
                                                                !  !  !  !   !  
  RT--------------------KGNA----------   L                      !  !  +-18   !    +2hos_A    
                                                                !  !     !   !  +-6 
  --------------VT--KTIAQTNA----------   L                      !  !     !   +-10 +2me6_A    
                                                                !  !     !      !  
  RT------------------VAQTNA----------   L                      !  !     !      +1fjl_B    
                                                             +-21  !     !  
  ----------------------KG----NA--EC--   L                   !  !  !     +------1xpx_A    
                                                             !  !  !  
  RT------------------VASCNA--QA------   L                   !  !  +--------1gt0_C    
                                                             !  !  
  RA----------RCET----SAQAKG----------   L            +-----22  !        +-5lxu_A    
                                                      !      !  +-------14  
  ------------------RTVAIANA--MCRG----   L            !      !           ! +1le8_A    
                                                      !      !           +-5 
  --------HG----NCSCRGHCRG--YC--------   L            !      !             +1ign_A    
                                                +----23      !  
  RT------------------VA--NA--QT------   L      !     !      +-------------3d1n_M    
                                                !     !  
  --NGRGTG--LG--LCRG------------------          !     !                     +4ew0_A    
                                             +-24     !                   +-7 
  --NGRGTG--LC--LCRG------------------       !  !     +-------------------8 +4ofa_A    
                                             !  !                         ! 
  --NGRGTG--LG--LCRG------------------     -25  !                         +4e9f_A    
                                             !  !  
  --------------RGRGYC----------------   L   !  +--------------------------1cf7_A    
                                             !  
  ------------RGKG--SGSAQAVC--RT------   L   +----------------------------5gzb_A    
                                           


> 1k82_A:CRYSTAL STRUCTURE OF E.COLI FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (FPG) COVALENTLY TRAPPED WITH DNA

  
  RA--MG----RCFCKGDGACQTRG   L                  +--1k82_A    
                                              +-3 
  --RTMTET--RCFA--------RT                    ! !  +4pd2_A    
                                         +----4 +--2 
  --QALGYA--------------RG               !    !    +1k3x_A    
                                       +-5    ! 
  ----LG--MTRCFC----NG--RT   L         ! !    +---3vk8_B    
                                       ! ! 
  ----MG--ITRCFG----HG--RG   L   +-----6 +--------5itu_A    
                                 !     ! 
  --RGMG----RCFC--------RG   L   !     !         +3u6p_A    
                               --7     +---------1 
  --RA------RGFT--------RA   L   !               +3gpu_A    
                                 ! 
  ----MG----RGFG--------RG       +---------------3twm_A    
                               


> 1kb2_B:CRYSTAL STRUCTURE OF VDR DNA-BINDING DOMAIN BOUND TO MOUSE OSTEOPONTIN (SPP) RESPONSE ELEMENT

  
  ------EC--KG--RGRG--------KA   L                                   +-----2nll_B    
                                                                     !  
  ------EA--KG--RTRG----------   L                                +-17     +1kb2_B    
                                                                  !  !   +-9 
  ------EA--KG--RTRT--RT------                                    !  +--12 +2han_B    
                                                             +---19      !  
  ------EC--KA--RGRG----------   L                           !    !      +-4nqa_I    
                                                             !    !  
  CA----EC--KG--KGRG--------RT   L                           !    !    +--1cit_A    
                                                             !    +---14  
  --HG--ECAGKGAAKGRT------RT--   L                           !         +--1lo1_A    
                                                             !  
  ------EC--KG----RA------PA--   L                           !              +5krb_G    
                                                             !         +----3 
  ------EC--KG--KGRG----RC----   L                           !         !    +2ff0_A    
                                                             !         !  
  ------EA--KG--KTRG----------   L                           !         !       +4cn3_D    
                                                 +----------20         !     +-1 
  ------EC--KG--KGRG----------   L               !           !      +-16  +--6 +1dsz_B    
                                                 !           !      !  !  !  ! 
  ------DG--KG--RTRG----------   L               !           !      !  !  !  +3cbb_A    
                                                 !           !      !  !  !  
  ------EA--KG--KTRG----------   L               !           !      !  !  !       +2han_A    
                                                 !           !      !  +-15     +-4 
  ------EC--KG--KGRA----RT----   L               !           !      !     !     ! +5l0m_A    
                                                 !           !      !     !  +-11  
  ----------KGVT--RG----------   L               !           !      !     !  !  ! +5cbz_E    
                                                 !           !      !     !  !  +-8 
  ----------KAVA--RA----------   L               !           +-----18     !  !    ! +5e69_A    
                                              +-21                  !     +-13    +-2 
  ----------KGVT--RG----------   L            !  !                  !        !      +2c7a_B    
                                              !  !                  !        !  
  ------ET--KGAT--RG----------   L            !  !                  !        ! +1lat_A    
                                              !  !                  !        +-7 
  ----------KGVT--RG----------                !  !                  !          +5emc_A    
                                              !  !                  !  
  ------EC--KG--RGRG----------   L         +-22  !                  !      +1dsz_A    
                                           !  !  !                  !    +-5 
  --HA--EC--KG--RGRG----------   L         !  !  !                  +---10 +1a6y_A    
                                           !  !  !                       !  
  --HC------KGVT--RG------RT--             !  !  !                       +3g9m_B    
                                        +-23  !  !  
  ------EC--KGAG--RG----------   L      !  !  !  +------------------------4ond_A    
                                        !  !  !  
  ----------KGVG--RG----------   L   +-24  !  +------------------------4tnt_B    
                                     !  !  !  
  ------EC--KGAGKGRG----------   L   !  !  +---------------------------1hcq_E    
                                   -25  !  
  ----YGEC--KGAGKGRG----------   L   !  +---------------------------4oln_B    
                                     !  
  ------EC--KG--RGRGRT--------   L   +----------------------------3e00_D    
                                   


> 1kln_A:DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX



> 1kx5_B:X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION

  
  RC----------RC--                               +-----1kx5_B    
                                               +-9 
  ----------RT----                             ! +-----4jjn_F    
                                            +-10  
  --------AT------                          !  !    +-4awl_B    
                                            !  +----6 
  ------RAAANA----                          !       +-1jfi_B    
                                            !  
  ----RA--ET------                    +----11        +4ne1_p    
                                      !     !   +----5 
  --LT--------RC--                    !     !   !    ! +5av9_A    
                                      !     !   !    +-4 
  --------LC--RG--                    !     !   !      +4jjn_A    
                                      !     +---8 
  ------------RG--                    !         !     +5t5k_E    
                                 +---12         ! +---1 
  ------------RG--               !    !         +-7   +4jjn_G    
                                 !    !           ! 
  ------IT--------               !    !           +---3wkj_D    
                                 !    !  
  ------------RART            +-13    !                 +3x1t_G    
                              !  !    !               +-2 
  ------------RT--            !  !    +---------------3 +5gt0_C    
                              !  !                    ! 
  ------------RT--       +---14  !                    +5b0z_C    
                         !    !  !  
  --LT------------       !    !  +--------------------3wtp_A    
                       -15    !  
  --------------RT       !    +---------------------5b31_G    
                         !  
  ------------RT--       +--------------------------4x23_O    
                       


> 1kx5_D:X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION

  
  KAKTRGRG--RG----------------   L         +-------1kx5_D    
                                           !  
  --------RC------------------             !       +2nqb_D    
                                        +-11    +--4 
  ----------RG----------------          !  !    !  ! +4xzq_D    
                                        !  !  +-7  +-1 
  ------------------IT--------          !  !  ! !    +3wkj_D    
                                        !  +--9 ! 
  ----------------AT----------          !     ! +---4awl_B    
                                        !     ! 
  ----------------RAAA--NA----       +-13     +----1jfi_B    
                                     !  !  
  --------------------------RT       !  !         +5gt0_C    
                                     !  !  +------5 
  --------------------------RG       !  !  !      +4jjn_G    
                                     !  !  !  
  --------------------------RG       !  +-12        +5t5k_E    
                                     !     !      +-2 
  --------------------RT------     -14     !  +---6 +4jjn_F    
                                     !     !  !   ! 
  --------------------------RC       !     +-10   +-1kx5_B    
                                     !        !  
  --------------RA--ET----RT--       !        +-----4ne1_p    
                                     !  
  ------------LC------------RG       !           +4jjn_A    
                                     !       +---3 
  ------------LT------------RC       +-------8   +5av9_A    
                                             ! 
  ------------LT--------------               +---3wtp_A    
                                   


> 1kx5_E:X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION

  
  --RAYT----LT----RC                +5av9_A    
                           +--------2 
  HGRG------LC----RG       !        +4jjn_A    
                           !  
  HGRA------LT----RA       !        +-5ay8_E    
                         -11  +-----5 
  ------KT--LT------       !  !     +-3wtp_A    
                           !  !  
  --------RAET--RT--       !  !      +4ne1_p    
                           !  !    +-4 
  ----------------RG       +-10    ! ! +4jjn_G    
                              !    ! +-3 
  ----------------RT          ! +--6   +5gt0_C    
                              ! !  ! 
  ----------------RG          ! !  !  +5t5k_E    
                              ! !  +--1 
  --------------IT--          +-9     +3wkj_D    
                                ! 
  ------------RT----            !   +--4jjn_F    
                                ! +-7 
  ----------------RC            +-8 +--1kx5_B    
                                  ! 
  ----------AT------              +----4awl_B    
                         


> 1kx5_G:X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION

  
  ------------RT                 +5gt0_C    
                       +---------3 
  ------------RG       !         +4jjn_G    
                       !  
  ----IT--------       !         +3wkj_D    
                       !       +-5 
  RAAA--NA------       !   +---6 +1jfi_B    
                       !   !   ! 
  ----AT--------     -10   !   +--4awl_B    
                       !   ! 
  RA--ET----RT--       ! +-8     +4ne1_p    
                       ! ! !  +--4 
  LC----------RG       ! ! !  !  ! +4jjn_A    
                       ! ! !  !  +-2 
  ----LT------RC       ! ! +--7    +5av9_A    
                       +-9    ! 
  ------------RG         !    !   +5t5k_E    
                         !    +---1 
  --------RT----         !        +4jjn_F    
                         ! 
  ------------RC         +--------1kx5_B    
                     


> 1lat_A:GLUCOCORTICOID RECEPTOR MUTANT/DNA COMPLEX

  
  ----DG--KG--RTRG--   L                      +3cbb_A    
                                            +-1 
  ----EA--KG--RTRG--   L                  +-4 +1kb2_B    
                                          ! ! 
  ----EC--KG--RGRG--   L               +-10 +2nll_B    
                                       !  !  
  CA--EC--KG--KGRG--   L            +-13  +-1cit_A    
                                    !  !  
  --HAEC--KG--RGRG--   L            !  +--1a6y_A    
                                 +-14  
  --HC----KGVT--RG--             !  !  +-3g9m_B    
                                 !  !  !  
  --------KAVA--RA--   L         !  +-12    +5e69_A    
                                 !     !  +-3 
  ----EA--KG--RTRTRT             !     !  ! +2han_B    
                                 !     +-11  
  --------KGVT--RG--   L         !        !   +5cbz_E    
                              +-15        ! +-5 
  --HGECAGKGAAKGRT--   L      !  !        +-8 +1lo1_A    
                              !  !          ! 
  --------KGVT--RG--   L      !  !          +2c7a_B    
                              !  !  
  ----ET--KGAT--RG--   L   +-16  !     +1lat_A    
                           !  !  !   +-2 
  ----EC--KG--KGRA--   L   !  !  +---6 +5l0m_A    
                           !  !      ! 
  ----EC--KG--KGRG--   L   !  !      +2ff0_A    
                         -17  !  
  --------KGVT--RG--       !  +----5emc_A    
                           !  
  --------KGVG--RG--   L   !        +3g6t_A    
                           !      +-7 
  ----EC--KA--RGRG--   L   +------9 +4nqa_I    
                                  ! 
  ----EC--KG--KGRG--   L          +1dsz_B    
                         


> 1le8_A:CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2-3A HETERODIMER BOUND TO DNA COMPLEX

  
  ------------------VA--NA--QT--   L        +-------------------3d1n_M    
                                            !  
  --------------------KGNA------   L        !                               +2hos_A    
                                            !                             +-1 
  ------------------IAQTNA------   L        !                             ! +5lux_L    
                                            !                             !  
  ------------------IAKGNA------   L        !                             !           +2hdd_A    
                                            !                             !         +-2 
  ------------------VAQTNA------   L        !                             !       +-5 +5hod_A    
                                            !                          +-15       ! ! 
  ------------------IAQCNA--YA--   L        !                          !  !     +-7 +1nk3_P    
                                            !                          !  !     ! ! 
  ------------------IAQTNA--MC--   L        !                          !  !  +-10 +1puf_A    
                                            !                          !  !  !  !  
  ------------------IAQTNA------   L        !                          !  !  !  +4rdu_A    
                                            !                          !  +-13  
  ------------------VAQTNA------   L        !                       +-16     !   +1fjl_B    
                                            !                       !  !     ! +-3 
  ------------------VASGNA------   L        !                       !  !     +-4 +3cmy_A    
                                            !                       !  !       ! 
  ------------------IAQCNA--MG--   L        !                       !  !       +1b72_A    
                                       +---24                       !  !  
  HTRT--------------NCSTNA--RG--   L   !    !                    +-17  !    +1k61_B    
                                       !    !                    !  !  !  +-8 
  ------------------NT--NA--IARG   L   !    !                    !  !  +-11 +1puf_B    
                                       !    !                    !  !     !  
  RT----------------NT--NA--IARG   L   !    !                    !  !     +4cyc_B    
                                       !    !                 +-18  !  
  ----------------RTVAIANA--MCRG   L   !    !                 !  !  !   +1le8_A    
                                       !    !                 !  !  +---6 
  ------------------VASCNA--QA--   L   !    !                 !  !      +1gt0_C    
                                       !    !              +-19  !  
  ----------RCET----SAQAKG------   L   !    !              !  !  !     +5lxu_A    
                                       !    !              !  !  +----12  
  ----------YTVC--KGDCKC--------   L   !    !           +-20  !        +2qhb_A    
                                     -25    !           !  !  !  
  ------------VT--KTIAQTNA------   L   !    !           !  !  +------2me6_A    
                                       !    !        +-21  !  
  ----------STVC--KGDCRG--------   L   !    !        !  !  +---------1w0t_A    
                                       !    !  +----22  !  
  ----------------RCVTCTNA--QTRC   L   !    !  !     !  +----------1au7_A    
                                       !    !  !     !  
  --------------------KG----NA--   L   !    !  !     +------------1xpx_A    
                                       !    +-23  
  --RGTG--LC--LCRG--------------       !       !                   +4ofa_A    
                                       !       !                 +-9 
  --RGTG--LG--LCRG--------------       !       +----------------14 +4ew0_A    
                                       !                         !  
  --RGTG--LG--LCRG--------------       !                         +4e9f_A    
                                       !  
  ------HG----NCSCRGHCRG--YC----   L   +------------------------1ign_A    
                                     


> 1le8_B:CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2-3A HETERODIMER BOUND TO DNA COMPLEX

  
  RT----------------------NT----NA----IARG----   L                  +-----1puf_B    
                                                                    !  
  --HTRT------------------NC--STNA----RG------   L                  !              +1k61_B    
                                                                    !           +-11  
  --RT--------------------NT----NA----IARG----   L                  !           !  +4cyc_B    
                                                                    !           !  
  RT----------------------IA--QTNA----------KT   L                  !        +-15      +4rdu_A    
                                                                    !        !  !    +-1 
  RC----------------------IA--QCNA----YA------   L                  !        !  !  +-7 +1nk3_P    
                                                                    !        !  !  ! ! 
  RA----------------------IA--QTNA----MC------   L                  !        !  +-13 +1puf_A    
                                                                    !        !     !  
  RA----------------------IA--QTNA------------   L                  !        !     +5lux_L    
                                                                 +-19     +-16  
  RT--------------------------KGNA------------   L               !  !     !  !      +2hos_A    
                                                                 !  !     !  !    +-2 
  RT----------------------VA--QTNA------------   L               !  !     !  !  +-9 +5hod_A    
                                                                 !  !     !  !  ! ! 
  RA--------------------RCVT--CTNA----QTRC----   L               !  !     !  !  ! +1au7_A    
                                                                 !  !     !  +-14  
  RT----------------------IA--KGNA------------   L               !  !  +-17     !   +2hdd_A    
                                                                 !  !  !  !     ! +-3 
  RT----------------------VA--SGNA------------   L               !  !  !  !     +-4 +3cmy_A    
                                                                 !  !  !  !       ! 
  RT----------------------IA--QCNA----MG------   L      +-------20  !  !  !       +1b72_A    
                                                        !        !  !  !  !  
  RT----------------------VA--QTNA------------   L      !        !  +-18  !  +1fjl_B    
                                                        !        !     !  +--6 
  RT----------------------VA----NA----QT------   L      !        !     !     +3d1n_M    
                                                        !        !     !  
  ----------------------RTVA--IANA----MCRG----   L      !        !     !      +1le8_A    
                                                        !        !     !    +-5 
  RA------------RCET------SA--QAKG------------   L   +-21        !     +---10 +5lxu_A    
                                                     !  !        !          !  
  --------------YTVC----KGDC--KC--------------   L   !  !        !          +2qhb_A    
                                                     !  !        !  
  --------------------------KG------NA----EC--   L   !  !        +--------1xpx_A    
                                                     !  !  
  --NGRGTG--LG----LCRG------------------------     -22  !                  +4ew0_A    
                                                     !  !                +-8 
  --NGRGTG--LC----LCRG------------------------       !  +---------------12 +4ofa_A    
                                                     !                   !  
  --NGRGTG----LG----LCRG----------------------       !                   +4e9f_A    
                                                     !  
  KA------HG------NCSC--RGHC--RG--YC----------   L   +--------------------1ign_A    
                                                   


> 1llm_D:CRYSTAL STRUCTURE OF A ZIF23-GCN4 CHIMERA BOUND TO DNA

  
  ----QA--TTNA--STQAQTATSTNTAT   L                                 +1g2f_F    
                                                                 +-1 
  ----RGSTDAHARG--RGSTDCHG--TT   L                          +----2 +5kl3_A    
                                                            !    ! 
  ------TCYCKARG--QA----TC----   L                 +--------3    +-5yeg_A    
                                                   !        ! 
  --------TTSGRG--LT--ETYC----   L   +-------------4        +------4f6m_A    
                                     !             ! 
  ----RG--DGECRG--RGSGDCHA----   L --5             +---------------2wbs_A    
                                     ! 
  NTEC--RCRG------------------   L   +-----------------------------1nkp_A    
                                   


> 1lmb_4:REFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OPERATOR COMPLEX

  
  KGKG--ET--QASG----------NG   L                  +1lmb_4    
                                      +-----------1 
  KGKG------QASG----------NG   L      !           +1rio_A    
                                   +--4 
  ----QT--STNTVTATSTQTRTETTT   L   !  !          +2r1j_L    
                                   !  !   +------2 
  ----------SCATRTNCQT----HT   L --5  +---3      +4jcy_A    
                                   !      ! 
  ------AT--QAAT--SA--------       !      +-------4z5h_A    
                                   ! 
  --------TT----ATYTQTQT----   L   +--------------3qws_B    
                                 


> 1lo1_A:ESTROGEN RELATED RECEPTOR 2 DNA BINDING DOMAIN IN COMPLEX WITH DNA

  
  --HGECAGKGAAKGRT------RT--RC   L             +1lo1_A    
                                          +----9 
  ----EC--KG--KGRA------RT--RC   L        !    ! +5l0m_A    
                                     +---16    +-1 
  ----EC--KG--KGRG------RC--RC   L   !    !      +2ff0_A    
                                     !    !  
  ----EC--KA--RGRG------------   L   !    +-----4nqa_I    
                                     !  
  CA--EC--KG--KGRG----RT--RT--   L   !        +--1cit_A    
                                     !        !  
  ----EA--KG--RTRTRT----------     -17     +-13     +2han_B    
                                     !     !  !  +-10  
  ----EA--KG--RTRG------------   L   !     !  !  !  ! +1kb2_B    
                                     !     !  +-12  +-2 
  ----EC--KG--RGRG------------   L   !     !     !    +2nll_B    
                                     !     !     !  
  ----EC--KG--KGRG------------   L   !     !     +-1dsz_B    
                                     +----15  
  ----DG--KG--RTRG------------   L         !     +3cbb_A    
                                           !  +--3 
  --HC----KGVT--RG--RT--------             !  !  +3g9m_B    
                                           !  !  
  --------KGVT--RG------------   L         !  !        +5cbz_E    
                                           !  !      +-4 
  --------KGVT--RG------------   L         +-14    +-7 +2c7a_B    
                                              !    ! ! 
  --------KAVA--RA------------   L            !  +-8 +5e69_A    
                                              !  ! ! 
  --------KGVG------RA--------   L            !  ! ! +3g6t_A    
                                              +-11 +-5 
  --HAEC--KG--RGRG------------   L               !   +1a6y_A    
                                                 !  
  ----ET--KGAT--RG------------   L               ! +1lat_A    
                                                 +-6 
  --------KGVT--RG------------                     +5emc_A    
                                   


> 1m5x_B:CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE I-MSOI BOUND TO ITS DNA SUBSTRATE

  
  SAYCLCITRGDCYA----QG--------IGNARG----RG--DTIC--RG--   L                         +--2fld_B    
                                                                             +-----8 
  STITQAKGRG--STNT--QTST----ATTC------YT--SC--VCDTRGST   L                   !     ! +-3mxb_B    
                                                                             !     +-6 
  SANCSCKGLT----------DAEC--NATG--RCKGST------------DA   L                   !       +-2ex5_A    
                                                                             ! 
  ST--NAVTHG--TCNA--ATLCYC--ECAT--YG--NA--SADCTCKTKGSA   L                   !           +4lq0_A    
                                                                             !         +-1 
  SGMGRGRG----KTYA--LTVT------TT----KT--SC--------RGEC   L                 +-9       +-4 +4lox_A    
                                                                           ! !       ! ! 
  STMG--------KGYC--RT--RG--VTSA----FC--MC----STQTRGEC   L                 ! !       ! +5esp_A    
                                                                           ! !     +-5 
  STIGRGRG------MC--LTEC----STKG----TT--NA------MGRTSC   L                 ! !     ! !   +5t2n_A    
                                                                           ! !     ! ! +-2 
  ------RARG------RTRGSTRT--QGTA--------SC----ATMCRGTC   L   +------------10 +-----7 +-3 +5t2h_A    
                                                             !             !       !   ! 
  SCMCRGRG----------YTST----ECTT--------RG----TTRG----   L   !             !       !   +5thg_A    
                                                             !             !       ! 
  CGRGST----------KARGQTFA--QGNG----HC--SC----LAQGRGQA   L -11             !       +--4yit_A    
                                                             !             !  
  YCST--------------YCTGET----EC------RG--RG------RGRG   L   !             +----------3uvf_B    
                                                             !  
  --YTLT------------------VT------QG--VG------RTEARGSC   L   +------------------------2vs7_A    
                                                           


> 1mdy_C:CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION

  
  KT----HGNT----EC----RCRG--   L                       +1nkp_A    
                                                   +---1 
  --------HGNT--LGEC----RCRC   L                   !   +5i50_B    
                                                 +-5 
  ------HGNT--IAEC----YCRG--   L                 ! !  +1am9_A    
                                                 ! +--2 
  ------HGNT--MTEA----RCRG--   L              +--6    +1nlw_D    
                                              !  ! 
  --RT----NT--RGEC----RCQT--                  !  ! +---2ypa_A    
                                              !  +-4 
  ----HGNT--IAEC----RCRT----   L   +----------7    ! +-4ati_B    
                                   !          !    +-3 
  ------HGNT----EC----RCRG--   L   !          !      +-1nkp_E    
                                 --8          ! 
  ----HGST--ITET----RCRG----   L   !          +-------4h10_A    
                                   ! 
  --------HG----ITEC----RCRG   L   +------------------5nj8_D    
                                 


> 1mey_C:CRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA

  
  ----TTSGRG--LT--ETYC----NTYGQG------   L            +---------4f6m_A    
                                                      ! 
  QA--TTNA--STQAQTATSTNTATTTLAHGTCRG--   L          +-4         +1g2f_F    
                                                    ! ! +-------1 
  KG--WTKA--------HCHG--RGTA--ACNAKGRG   L          ! ! !       +1tf6_A    
                                                    ! +-3 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG--   L   +------5   !     +-5kl3_A    
                                             !      !   +-----2 
  EC--SCKGRG----TCYCKA--RGQA----TC----   L   !      !         +-5yeg_A    
                                           --6      ! 
  QARGATNA----QA--ATHG----RG--DCNATT--   L   !      +---------2i13_A    
                                             ! 
  ------------RG--DGEC--RGRGSGDCHA----   L   +----------------2wbs_A    
                                           


> 1mow_A:E-DREI

  
  --YTLT--YC----RGSGECRG----TG--QG--VG----DCTARTEARGSCSAIAQA--KG--NT--SCYA--QA----QA--TG--YC--RG--RG----VA----------------TC--   L                  +-------1mow_A    
                                                                                                                                                    ! 
  ST------------AT--LCYC--EC--ATYG--NA--SADC--TCKTKGSACTFTST--YA--ST--KTST--ATQA--KT--TG--RA--RG--------AT--DT----TA----------   L                  !        +4lq0_A    
                                                                                                                                                  +-9      +-1 
  SGMGRG--------LT--VT------TT----KT--SC----------RGECSAKGIG--KT------SGIT--QAIA--QA--TC------DT--RG----WT--YC----TC----------   L                ! !      ! +4lox_A    
                                                                                                                                                  ! !      ! 
  CGRG--ST--TTKARG--QTFA--QG--NG--HC--SC------LAQGRGQACCMT----AC--ST--AT----QAYA--IC--TA--RT------KGRT--VA--EC--QT------------   L                ! +------6   +4yit_A    
                                                                                                                                                  !        ! +-2 
  STMG----------RT----RGVT--SA--FC----MC------STQTRGECCTSTVA--FT--ST--TCSC--ATKA--IT--TC------STDA--RG--TC----KT--TG----------   L                !        ! ! +5esp_A    
                                                                                                                                            +----11        +-5 
  STIGRG--------LT--EC--ST--KG----TT--NA--------MGRTSCHT--NC--WC--RG----------QG------ST--LA--KG--RG----WC----RG--TG----------   L          !     !          !   +5t2n_A    
                                                                                                                                            !     !          ! +-3 
  ------RA----------------------------SC------ATMCRGTCHC--NA--KT------------YA--RG----SA--RT--KG--KG----WT--ECET--TT----------   L          !     !          +-4 +5t2h_A    
                                                                                                                                            !     !            ! 
  SCMC--------------------------------RG------TTRG----TTYTHG----------------YCRGRGIT----------QC--------MC--HT----TGKT--------   L          !     !            +5thg_A    
                                                                                                                                     +-----12     !  
  YCSTTC----KG--YC--TGET----EC------RG--RG--------RGRGCCST--YG--LTNT------YTITST----DT--AT----YA----TT--CC--RTKT--TA----------   L   !      !     +---------3uvf_B    
                                                                                                                                     !      !  
  ----------------------------------------------------STITQA--KG--RG--STNT--QTST--AT--TC------YT--SC----VC--DTRG--ST----KGTG--   L   !      !               +3mxb_B    
                                                                                                                                     !      !             +-7 
  ----------------------------------------------------SAYCLC--IT--RGDCYA----QG--------IG----NA--RG--DT--IC----RG--------------   L -13      +-------------8 +2fld_B    
                                                                                                                                     !                    ! 
  ----------------------------------------------------SANCSC--KG--LT----------DAECNA--TG------RC------------------DA--QA----QC   L   !                    +-2ex5_A    
                                                                                                                                     !  
  --YTLT--YC----RGSGECRGVT--TG--QG--VG------TARTEARGSC------------------------------WC--------DCDC--RGHA--VC------------------   L   !            +---------2vs7_A    
                                                                                                                                     +-----------10  
  YGRGRG----------------QG--EC------------------------------WADT----------------------------------NCKT------------------------   L                +---------3c0w_A    
                                                                                                                                   


> 1msw_D:STRUCTURAL BASIS FOR THE TRANSITION FROM INITIATION TO ELONGATION TRANSCRIPTION IN T7 RNA POLYMERASE

  
  RTKTNTQTKARAYTRGATYTDG--KG------RCRCYC--TC----TTYT--FARTQT--QGIGDG--------------HT--   L               +-------------1msw_D    
                                                                                             +-----------3 
  --------------------------SC--EG----------QG--TGYGVGYT----QG------WGEGRG------------   L   !           +-------------4boc_A    
                                                                                           --4 
  ----------------------------KT----RG--EG----YGACYCAC--------------------RTNG--QG--HC   L   !                  +------4xvk_A    
                                                                                             +------------------2 
  ----------------------------KC--------------FG--YGMG----------------------NG--QG--HG   L                      ! +----4bwj_A    
                                                                                                                +-1 
  ----------------------NA--KA------RG------QC----YCMC------------------------QC------                            +----4x0q_B    
                                                                                           


> 1nfk_A:STRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER

  
  RGRGYTCCEC----HTKTKTPTKTRG   L                +--1nfk_A    
                                              +-3 
  RGRGYTCCEC----HG--KG------   L   +----------4 +--1a3q_A    
                                   !          ! 
  RGRGYTCTEC--------RT------   L   !          +---1gji_A    
                                 --5 
  RGRG----EC--------RGPTKT--   L   !                +2ram_A    
                                   !              +-1 
  RGRGYTCTEC--SG----RT------   L   +--------------2 +2i9t_A    
                                                  ! 
  RGRGYTCTECRG------KT------   L                  +3do7_A    
                                 


> 1nk3_P:VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE

  
  --KG--RC------------------IAQCNAYA------   L                                       +1nk3_P    
                                                                                 +---1 
  RA----RA------------------IAQTNAMC------   L                                   !   +1puf_A    
                                                                                 !  
  RA----RT------------------IAQTNA------KT   L                                +-14    +4rdu_A    
                                                                              !  !  +-2 
  ------RT------------------IAQCNAMG------   L                                !  !  ! +1b72_A    
                                                                              !  !  !  
  ------RT------------------VAQTNA--------   L                                !  +-13    +5hod_A    
                                                                              !     !  +-8 
  RA----RT------------------VASGNA--------   L                             +-15     !  ! ! +3cmy_A    
                                                                           !  !     +-10 +-3 
  RA----RT------------------VA--NAQT------   L                             !  !        !   +3d1n_M    
                                                                           !  !        !  
  ----YARA------------------IAQTNA--------   L                          +-16  !        +5lux_L    
                                                                        !  !  !  
  ------RT------------------NT--NAIARG----   L                          !  !  +----1puf_B    
                                                                        !  !  
  RT----RT------------------VAQTNA--------   L                       +-18  !    +1fjl_B    
                                                                     !  !  +----4 
  ------RT------------------VASCNAQA------   L                       !  !       +1gt0_C    
                                                                     !  !  
  ------RA----------------RCVTCTNAQTRC----   L                       !  +-------1au7_A    
                                                                  +-19  
  ------RT--------------------KGNA--------   L                    !  !        +2hos_A    
                                                                  !  !  +-----6 
  RT--RT--------------VT--KTIAQTNA------RT   L                    !  !  !     +2me6_A    
                                                                  !  +-17  
  ------------------------RTVAIANAMCRG----   L                    !     !     +1le8_A    
                                                                  !     !   +-7 
  ------RA----------RCET----SAQAKG--------   L                    !     +--12 +5lxu_A    
                                                               +-21         !  
  ------RT----------STVC--KGDCRG----------   L                 !  !         +-1w0t_A    
                                                               !  !  
  ------RT------------------IAKGNA--------   L                 !  !             +2hdd_A    
                                                               !  !           +-5 
  --------HTRT--------------NCSTNARG------   L                 !  !         +-9 +1k61_B    
                                                 +------------22  !         ! ! 
  --------RT----------------NT--NAIARG----   L   !             !  !  +-----11 +4cyc_B    
                                                 !             !  !  !      !  
  --------NGRGTG--LG--LCRG----------------       !             !  +-20      +-4ew0_A    
                                               -23             !     !  
  ----------------------------KG--NA--EC--   L   !             !     +--------1xpx_A    
                                                 !             !  
  ------------------YTVC--KGDCKC----------   L   !             +-------------2qhb_A    
                                                 !  
  ----------QGCGTALC----------------------       +---------------------------1orn_A    
                                               


> 1nkp_A:CRYSTAL STRUCTURE OF MYC-MAX RECOGNIZING DNA

  
  ----HGNT--LGECRCRC   L                               +-5i50_B    
                                                     +-5 
  KT--HGNT----ECRCRG   L                           +-7 +-1nkp_A    
                                                   ! ! 
  ----HGNT----ECRCRG   L               +----------10 +--1nkp_E    
                                       !           !  
  ----HGNT--IAECYCRG   L               !           !   +1am9_A    
                                       !           +---3 
  ----HGNT--MTEARCRG   L               !               +1nlw_D    
                                       !  
  ----HGNT--LCECRCRG   L               !                +1hlo_B    
                               +------14             +--4 
  ----HGNT--IAECRCRT   L       !       !     +-------9  +4ati_B    
                               !       !     !       ! 
  --RT--NT--RGECRCQT           !       !     !       +---2ypa_A    
                               !       !  +-11  
  --RG--TT--RAECRC--           !       !  !  !        +--1mdy_C    
                               !       !  !  +--------8 
  ----HGST--ITETRCRG   L       !       +-12           !  +4h10_A    
                           +--15          !           +--2 
  ----HG----ITECRCRG   L   !   !          !              +5nj8_D    
                           !   !          !  
  ----HG------ETRTRG   L   !   !          +--------------5v0l_A    
                           !   !  
  ----RTNT----ECRCRG   L   !   !                       +4h10_B    
                         -16   !       +---------------1 
  ----ST------ATRTRG       !   !       !               +4zpk_B    
                           !   +------13  
  ------NT----ETRCMT       !           !             +-2ql2_D    
                           !           +-------------6 
  --------NG--SCHTRC       !                         +-5nj8_C    
                           !  
  ----HG------ETRCRG   L   +---------------------------5gnj_I    
                         


> 1nkp_E:CRYSTAL STRUCTURE OF MYC-MAX RECOGNIZING DNA

  
  HGNT--EC--RCRG------   L                        +1nkp_E    
                                                +-1 
  HGNTLGEC--RCRC------   L                  +---3 +5i50_B    
                                            !   ! 
  HGNT--EC--RCRG------   L                  !   +1nkp_A    
                                         +--6 
  HGNTMTEA--RCRG------   L               !  !     +1nlw_D    
                                         !  ! +---2 
  --------HG----ECYCRG   L               !  +-5   +1am9_A    
                             +-----------7    ! 
  HGNTIAEC--RCRT------   L   !           !    +---4ati_B    
                             !           ! 
  --NTRGEC--RCQT------     --8           !    +--2ypa_A    
                             !           +----4 
  HGSTITET--RCRG------   L   !                +--4h10_A    
                             ! 
  HGKT--EA--RCRC------   L   +-------------------1a0a_B    
                           


> 1nlw_D:CRYSTAL STRUCTURE OF MAD-MAX RECOGNIZING DNA

  
  --------HGNT--IAEC----YCRG--   L                          +1am9_A    
                                                         +--2 
  ----HGNT--LGEC----RCRC------   L                       !  +5i50_B    
                                                +--------5 
  ----HGNT--MTEA----RCRG------   L              !        !   +1nlw_D    
                                                !        ! +-1 
  ----HGNT----EC----RCRG------   L              !        +-3 +1nkp_A    
                                                !          ! 
  ----HGNT----EC----RCRG------   L        +-----8          +-1nkp_E    
                                          !     ! 
  ----HGNT--IAEC----RCRT------   L        !     !        +---4ati_B    
                                          !     !      +-6 
  RT----NT--RGEC----RCQT------            !     !      ! +---2ypa_A    
                                     +----9     +------7 
  ----HGST--ITET----RCRG------   L   !    !            !  +--4h10_A    
                                     !    !            +--4 
  --QG------VTEC----RCRG----QG   L -10    !               +--1an4_A    
                                     !    ! 
  RG--HGKT----EA----RCRC------   L   !    +------------------1a0a_B    
                                     !  
  --------NG--SC----HTRC------       +-----------------------5nj8_C    
                                   


> 1nwq_C:CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX

  
  --------RG------NC--YGAT--CTRG   L     +------2wt7_B    
                                         ! 
  ----RC----NC----AAAT--CTRC----   L     !          +2wt7_A    
                                         !        +-1 
  ----------------NTRTATAT--CTRA   L   +-5      +-2 +5vpe_D    
                                       ! !      ! ! 
  RG----NC----YGAT----RC--------   L   ! !    +-3 +4eot_A    
                                       ! !    ! ! 
  --RG--QGNART--AGQT--FTRG------   L --6 +----4 +-1gd2_G    
                                       !      ! 
  ----------RA----NA--AAVT--STRG   L   !      +-1nwq_C    
                                       ! 
  ----------------NCTT--AT----RG   L   +--------2dgc_A    
                                     


> 1oe4_B:XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE

  
  VGRG------PG------NG          +--------------1oe4_B    
                             +--2 
  ------RANT--QGTCRC--   L   !  +--------------2dp6_A    
                           --3 
  KT--TT--------------       !              +--4yig_E    
                             +--------------1 
  ----------PALA------                      +--4uqm_A    
                           


> 1orn_A:STRUCTURE OF A TRAPPED ENDONUCLEASE III-DNA COVALENT INTERMEDIATE: ESTRANGED-GUANINE COMPLEX

  
  ----QGCGTA----LC------------------------                                +-1orn_A    
                                                                   +------6 
  ----------------YG--------------------RG   L                     !      +-5kn8_A    
                                                                   ! 
  ----NCNANARC--------YGRC----------------                 +-------9     +---2xhi_A    
                                                           !       ! +---7 
  ----NG--RG--------FGRC------------------                 !       ! !   !   +4ejy_A    
                                                           !       ! !   +---1 
  ----NA--RA--------FGRC------------------   L             !       +-8       +3i0w_A    
                                                           !         ! 
  ----QTLAHGAT--------KT------------------           +----10         !      +3s6i_A    
                                                     !     !         +------4 
  --QGKGLGSGAG--SC--LTKC------------------           !     !                +4b21_A    
                                                     !     !  
  --NGRGTG------LG----LCRG----------------           !     !                 +4ew0_A    
                                                 +--11     !               +-2 
  LTNGRGTG------LC----LCRG--------YTNTKT--       !   !     +---------------3 +4ofa_A    
                                                 !   !                     ! 
  --NGRGTG------LG----LCRG----------------       !   !                     +4e9f_A    
                                               -12   !  
  --AA--LA----ITHT----KT------------------       !   +----------------------2ofi_A    
                                                 !  
  ------------------------IAQCNAYA--------   L   !                         +1nk3_P    
                                                 +-------------------------5 
  ------------------------VASGNA----------   L                             +3cmy_A    
                                               


> 1p7h_L:STRUCTURE OF NFAT1 BOUND AS A DIMER TO THE HIV-1 LTR KB ELEMENT

  
  RG--YTTTECRGRCQA----KARC   L            +-------------------1p7h_L    
                                          ! 
  RGRGYTEC------RT--------   L   +--------3                 +-1gji_A    
                                 !        !               +-1 
  ----------------PTRG----   L   !        +---------------2 +-1nfk_A    
                               --4                        ! 
  RGRGYTEC--HG--KG--------   L   !                        +---1a3q_A    
                                 ! 
  --------------------RT--       +----------------------------4oi8_B    
                               


> 1pp7_U:CRYSTAL STRUCTURE OF THE T. VAGINALIS INITIATOR BINDING PROTEIN BOUND TO THE FERREDOXIN INR

  
  KTHG----------------                    +5hdn_C    
                             +------------1 
  ------STRTQTMT------   L   !            +5d8k_B    
                           --3 
  ------KTRGYA--------   L   ! +------------1bc8_C    
                             +-2 
  ----KATGLTRT--KAFTYT   L     +------------2p7c_B    
                           


> 1pue_E:PU.1 ETS DOMAIN-DNA COMPLEX

  
  ----DCKTRG----RGYA------   L                        +1dux_F    
                                                    +-1 
  ------KTRGAT--RGYA------   L                    +-4 +1bc8_C    
                                                  ! ! 
  ------KTRGSA--RGQA----RA   L          +---------5 +1yo5_C    
                                        !         ! 
  ------KTRGAT--RGYT------   L   +------7         +-1awc_A    
                                 !      ! 
  KTHG--------------------       !      !          +5hdn_C    
                                 !      +----------2 
  ------ST------RTQT--MT--   L --8                 +5d8k_B    
                                 ! 
  ----KG--ATNT--CT----SC--   L   !                  +2irf_L    
                                 !                +-3 
  --------NT--RGCT--NGST--   L   +----------------6 +1if1_B    
                                                  ! 
  --------------------RG--                        +-4hly_B    
                               


> 1puf_A:CRYSTAL STRUCTURE OF HOXA9 AND PBX1 HOMEODOMAINS BOUND TO DNA

  
  RA----RA----------IAQTNAMC------   L            +----1puf_A    
                                               +-16  
  ------RT----------IAQCNAMG------   L         !  +----1b72_A    
                                               !  
  --KG--RC----------IAQCNAYA------   L         !        +1nk3_P    
                                               !     +-10  
  RA----RT----------IAQTNA------KT   L      +-18     !  ! +4rdu_A    
                                            !  !     !  +-9 
  ----YARA----------IAQTNA--------   L      !  !  +-11    +5lux_L    
                                            !  !  !  !  
  ------RT----------VAQTNA--------   L      !  !  !  ! +5hod_A    
                                            !  !  !  +-7 
  RA----RT----------VASGNA--------   L      !  +-14    ! +3cmy_A    
                                            !     !    +-2 
  RA----RT----------VA--NAQT------   L      !     !      +3d1n_M    
                                            !     !  
  RT----RT----------VAQTNA--------   L      !     !  +1fjl_B    
                                            !     +--1 
  ------RT----------VASCNAQA------   L   +-19        +1gt0_C    
                                         !  !  
  ------RT------------KGNA--------   L   !  !          +2hos_A    
                                         !  !        +-3 
  ------RA--------RCVTCTNAQTRC----   L   !  !     +--6 +1au7_A    
                                         !  !     !  ! 
  ------RT----------IAKGNA--------   L   !  !     !  +2hdd_A    
                                         !  !     !  
  --------HTRT------NCSTNARG------   L   !  !  +-13      +1k61_B    
                                         !  !  !  !    +-5 
  ------RT----------NT--NA--------   L -20  !  !  !  +-8 +1puf_B    
                                         !  !  !  !  ! ! 
  --------RT--------NT--NAIARG----   L   !  +-17  +-12 +4cyc_B    
                                         !     !     !  
  ------RA----RCET--SAQAKG--------   L   !     !     +5lxu_A    
                                         !     !  
  ----------------RTVAIANAMCRG----   L   !     !    +1le8_A    
                                         !     +----4 
  --------------------KG--NA--EC--   L   !          +1xpx_A    
                                         !  
  ------RT----STVCKGDCRG----------   L   !      +--1w0t_A    
                                         +-----15  
  --------------VTKTIAQTNA------RT   L          +--2me6_A    
                                       


> 1puf_B:CRYSTAL STRUCTURE OF HOXA9 AND PBX1 HOMEODOMAINS BOUND TO DNA

  
  ------RT------------------------NT------NA----IARG------   L                               +-----1puf_B    
                                                                                             !  
  --KG--RC------------------------IA----QCNA----YA--------   L                               !                +1nk3_P    
                                                                                             !              +-6 
  ------RA------------------------IA----QTNA------------MC   L                               !              ! +1puf_A    
                                                                                             !           +-12  
  RA----RT------------------------IA----QTNA----------KT--   L                               !           !  ! +4rdu_A    
                                                                                             !        +-13  +-5 
  ------RT------------------------IA----QCNA----MG--------   L                               !        !  !    +1b72_A    
                                                                                             !        !  !  
  ----YARA------------------------IA----QTNA--------------   L                               !        !  +5lux_L    
                                                                                          +-19     +-16  
  RA----RT------------------------VA----SGNA--------------   L                            !  !     !  !    +3cmy_A    
                                                                                          !  !     !  !  +-1 
  ------RT------------------------VA----QTNA--------------   L                            !  !     !  !  ! +5hod_A    
                                                                                          !  !     !  +--9 
  RT----RT------------------------VA----QTNA--------------   L                            !  !     !     ! +1fjl_B    
                                                                                          !  !  +-17     +-4 
  RA----RT------------------------VA------NA----QT--------   L                            !  !  !  !       +3d1n_M    
                                                                                          !  !  !  !  
  --------HTRT--------------------NC----STNA----RG--------   L                            !  !  !  !     +1k61_B    
                                                                                       +-20  !  !  !  +-11  
  --------RT----------------------NT------NA----IARG------   L                         !  !  +-18  !  !  +4cyc_B    
                                                                                       !  !     !  +-15  
  ------RT------------------------IA----KGNA--------------   L                         !  !     !     ! +2hdd_A    
                                                                                       !  !     !     +-3 
  ------RA----------------------RCVT----CTNA----QTRC------   L                         !  !     !       +1au7_A    
                                                                                       !  !     !  
  ------RT------------------------VA----SCNA----QA--------   L                         !  !     +-----1gt0_C    
                                                                             +--------21  !  
  ------RA--------------RCET------SA----QAKG--------------   L               !         !  !     +5lxu_A    
                                                                             !         !  +----14  
  ------RT------------------------------KGNA--------------   L               !         !        ! +2hos_A    
                                                                             !         !        +-2 
  ----------------------YTVC----KGDC----KC----------------   L               !         !          +2qhb_A    
                                                                         +--22         !  
  ------------------------------RTVA----IANA----MCRG------   L           !   !         !       +1le8_A    
                                                                         !   !         +-------7 
  --------------------------------------KG------NA--EC----   L           !   !                 +1xpx_A    
                                                                         !   !  
  --------NGRGTG----LG----LCRG----------------------------          +---23   !                  +4ew0_A    
                                                                    !    !   !                +-8 
  --------NGRGTG----LC----LCRG----------------------------          !    !   +---------------10 +4ofa_A    
                                                                    !    !                    !  
  --------NGRGTG----LG----LCRG----------------------------       +-24    !                    +4e9f_A    
                                                                 !  !    !  
  ------KA--------------------NA----RGDC----RGKT----------   L   !  !    +---------------------1ign_A    
                                                               -25  !  
  ------------RALTPT--DCHGTCTC--LTHT----------------------   L   !  +--------------------------1j1v_A    
                                                                 !  
  --------------------TGKG--------------------------------   L   +----------------------------4pxi_B    
                                                               


> 1qbj_C:CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX

  
  --------------------TT--PTTC--STNT--------------------RT------   L                                  +---4lln_I    
                                                                                             +-------10  
  ----------------------RGSTRT--STHG--------------------RA------   L                         !        +---3zpl_B    
                                                                                             !  
  --------------SGQG----YCNC------------------------------------                             !                +2ve9_C    
                                                                                             !              +-1 
  ------------------------KGTA----TA------RG--------------------   L                         !            +-7 +1xsd_A    
                                                                                         +--18            ! ! 
  ------------TT----------KATT--QTTG----LTRT----KA----------FTYT   L                     !   !       +----9 +2p7c_B    
                                                                                         !   !       !    ! 
  --------------------------------------YGRG--------------------                         !   !    +-14    +4wcg_B    
                                                                                         !   !    !  !  
  --------------------------------------YG----------------------                         !   !    !  !     +4lb5_B    
                                                                                         !   !    !  +-----5 
  --------------------DCSA--TA--TT--------RT------------RA------   L                     !   +---15        +1z9c_A    
                                                                                         !        !  
  --------------------------------------YG----------------------                         !        !       +2heo_D    
                                                                                      +-20        !   +---4 
  --------------------STQASGAT--STQT--------------------QA------   L                  !  !        +--12   +4on0_B    
                                                                                      !  !            !  
  --------------------STKTPTTT--FT----------------------RA------   L                  !  !            +---4aso_F    
                                                                                      !  !  
  --------------------------------------YG----------------------                      !  !                 +4ka4_B    
                                                                                   +-22  !               +-2 
  ------------------------HT----RTITYT--------------------------   L               !  !  !     +---------8 +4kfc_B    
                                                                                   !  !  !     !         ! 
  ----------------------RG----DTVT----ST------------RC----------   L               !  !  +----17         +4nhj_A    
                                                                                   !  !        !  
  ------------------------NTVC--ECSTYT--STYC--------RA----------   L               !  !        +----------5ed4_A    
                                                                                   !  !  
  MTPT--------------RT------------------------------------------   L            +-23  +------------------5fmf_V    
                                                                                !  !  
  --------------RG----STRGMCTT--RT------------------------------   L            !  !                   +4u0y_B    
                                                                                !  !               +---6 
  --------------------TTLTECTA--STRG----------------------------   L            !  !  +-----------11   +4i2o_B    
                                                                                !  !  !            !  
  --------------------ITRGECSC--SGKG----------------------------   L         +-24  +-21            +---5i2d_R    
                                                                             !  !     !  
  ------------------------RGRG--YC------------------------------   L         !  !     !                +1cf7_A    
                                                                             !  !     +----------------3 
  ----TTQT------------------------------------------------------   L         !  !                      +3gpl_A    
                                                                             !  !  
  --------------------------------------------------------ITHG--   L      +-25  +---------------------5iyc_T    
                                                                          !  !  
  --------------------------------NA----HT--STLT----------------   L      !  !                +-----2a07_K    
                                                                          !  !           +---13  
  ------------------------------NAST--RTHT--ST------------------   L      !  !      +---16    +-----3l2c_A    
                                                                       +-26  !      !    !  
  --------KAFA------------------------------------YANAKTFGMC----       !  !  +-----19    +----------3aaf_B    
                                                                       !  !         !  
  --------------YC----KTHGSTQT--YTPT----------------------------   L -27  !         +---------------5x11_A    
                                                                       !  !  
  ------------ST------STQAQGST--SART--------------------KT------   L   !  +-----------------------5trd_B    
                                                                       !  
  --------------------TT--RGRT--------------------------KT------   L   +-------------------------2v1u_A    
                                                                     


> 1qna_B:CRYSTAL STRUCTURE OF THE T(-30) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.

  
  NTVTFT--LTFAVATTNAVTFTPALTFAVATA   L                      +1qna_B    
                                                   +--------3 
  NTVAFT--LTFAVATTNAVTFAPALAFTVATA   L             !        ! +1cdw_A    
                                                   !        +-1 
  NTVAFC--LTFAVATTNAVTFTPALTFTVATA   L     +-------4          +4wzs_D    
                                           !       ! 
  NTVTFA--LAFTVATTNAVTFTPALTFAVTTA   L     !       !         +5n9g_G    
                                         +-5       +---------2 
  NAVTFTPALTFAVATANTVTFTPALTFAVAST   L   ! !                 +1ais_A    
                                       --6 ! 
  NTVAFT--LTFAVATTNAVAFAPALTFTVATA   L   ! +-----------------1rm1_A    
                                         ! 
  NAVTFT--LTFAVATANTVTFAPALAFTVATA   L   +-------------------1ytb_A    
                                       


> 1qpi_A:CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX

  
  --RC----PTTC--WC   L     +--------------1qpi_A    
                         +-7 
  TTHTRTQAATSCYTYT   L   ! !     +--------5dy0_D    
                         ! +-----4 
  ----TGKG----YCFA   L   !       +--------4pxi_B    
                         ! 
  ----SCKGSG--IGYC   L --8     +----------2yvh_A    
                         !   +-5 
  --EC--KGQCTGYGRC   L   !   ! !       +--4jl3_B    
                         !   ! +-------3 
  TA--AT----LCFGHA       !   !         +--4i6z_B    
                         +---6 
  TA----ECAC--YCRA           !              +5haw_A    
                             !            +-1 
  TA--STECAGATYTRG   L       +------------2 +4gck_A    
                                          ! 
  VT--AGDT--TTYTLA   L                    +5gpc_B    
                       


> 1qpz_A:PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

  
  ----SG--TC------RG------LCKA   L             +1qpz_A    
                                     +---------2 
  ITYTSGMTAA--STRG--NT--AGLCAT   L   !         ! +3oqm_C    
                                   --3         +-1 
  IT--ST--ATTTSTRG----VTAGLCAC   L   !           +1rzr_C    
                                     ! 
  LTYCSGYGQC--STRG--HT--AGLGAC   L   +----------1efa_B    
                                   


> 1qrv_A:CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA

  
  ----STYGLASGLA--TGTCIT--   L   +-----------------3tq6_B    
                                 ! 
  RTTASTYAFALT----PTATSTRA   L --4 +---------------5jh0_D    
                                 ! ! 
  RT--NTFTMA--RT--NG--SA--   L   +-3              +4y60_C    
                                   !            +-1 
  KC--NT--MAMA--EGSAACNT--   L     +------------2 +2lef_A    
                                                ! 
  RC--NTFTMA--RAHGNT--SA--   L                  +--3f27_D    
                               


> 1qzh_E:CRYSTAL STRUCTURE OF POT1 (PROTECTION OF TELOMERE)- SSDNA COMPLEX

  
  --------DGTGFGYGKT------YT----KG------------FGIGHG--RGYGQG------   L     +-----------------------2i0q_A    
                                                                         +-2 
  --------------------------YTFT----NT--SG--WG--------KGFGEGKG--KG       ! +-----------------------3u58_C    
                                                                       --3 
  ------KGFG--------STTTDT------TGTG--LA--FA----------QGYGQG--IA--   L   !    +--------------------3kjp_A    
                                                                         +----1 
  EGTGYG----------------------------KG--------------KT--YG--------   L        +--------------------1s40_A    
                                                                       


> 1r4i_A:CRYSTAL STRUCTURE OF ANDROGEN RECEPTOR DNA-BINDING DOMAIN BOUND TO A DIRECT REPEAT RESPONSE ELEMENT

  
  ----EC--KG--KGRG--   L         +-1dsz_B    
                                 !  
  --HGECAGKGAAKGRT--   L      +-12     +1lo1_A    
                              !  !  +-10  
  ----EC--KG--KGRA--   L      !  +-11  +5l0m_A    
                              !     !  
  ----EC--KG--KGRG--   L   +-16     +-2ff0_A    
                           !  !  
  --------KGVT--RG--   L   !  !     +2c7a_B    
                           !  !   +-2 
  ----EC--KA--RGRG--   L   !  !   ! +4nqa_I    
                           !  +---8 
  --------KGVT--RG--   L   !      ! +5cbz_E    
                           !      +-1 
  ----EA--KG--RTRTRT       !        +2han_B    
                           !  
  --------KAVA--RA--   L   !          +5e69_A    
                         -17        +-3 
  --------VG--RG----   L   !     +--4 +3g6t_A    
                           !     !  ! 
  ----EC--KG--RGRG--   L   !     !  +2nll_B    
                           !     !  
  ----ET--KGAT--RG--   L   !     !        +1lat_A    
                           !  +-14      +-5 
  --HAEC--KG--RGRG--   L   !  !  !    +-7 +1a6y_A    
                           !  !  !    ! ! 
  ----EA--KG--RTRG--   L   !  !  !  +-9 +1kb2_B    
                           !  !  !  ! ! 
  ----DG--KG--RTRG--   L   +-15  !  ! ! +3cbb_A    
                              !  +-13 +-6 
  CA--EC--KG--KGRG--   L      !     !   +1cit_A    
                              !     !  
  --HC----KGVT--RG--          !     +-3g9m_B    
                              !  
  --------KGVT--RG--          +---5emc_A    
                         


> 1r71_C:CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF KORB IN COMPLEX WITH THE OPERATOR DNA

  
  --STPTAAFTTTQC--DGTC--RG----   L                   +----1r71_C    
                                     +---------------2 
  ETSGRGAT--ATNTRT----KCVTRTEC   L   !               +----4umk_D    
                                   --3 
  --SGRAAT--TTRG--------------   L   !                    +3vwb_A    
                                     +--------------------1 
  --SGQAAT--TTRG--------------   L                        +1zx4_A    
                                   


> 1r8d_B:CRYSTAL STRUCTURE OF MTAN BOUND TO DNA

  
  RGHTHCYG   L                   +1r8d_B    
                 +---------------3 
  KCRT--YC       !               +1r8e_A    
                 ! 
  KGRT----   L --5                 +5i44_I    
                 !               +-1 
  RART----       !        +------2 +4r24_B    
                 !        !      ! 
  RGRTYTRT   L   +--------4      +4r4e_B    
                          ! 
  KGRTFCYG   L            +-------4wls_B    
               


> 1r8e_A:CRYSTAL STRUCTURE OF BMRR BOUND TO DNA AT 2.4A RESOLUTION

  
  KCRT--YC--               +--------------------1r8e_A    
                           ! 
  RGHTHCYG--   L   +-------5        +-----------1r8d_B    
                   !       !        ! 
  KGQGRT----   L   !       !        !            +5i44_I    
                   !       +--------4          +-1 
  RART------       !                !      +---2 +4r24_B    
                 --6                !      !   ! 
  RGRTYTRT--   L   !                +------3   +4r4e_B    
                   !                       ! 
  KGRTFCYG--   L   !                       +----4wls_B    
                   ! 
  --------RG   L   +----------------------------1nlw_D    
                 


> 1rep_C:CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI-F PLASMID COMPLEXED WITH AN ITERON DNA

  
  ------SGAAECSAKGRGRG--STYGRTPGDCRGRG--RC   L                          +--1rep_C    
                                                 +----------------------1 
  ----TT--SGLTYART--------YT--PCITRGDCKT--   L   !                      +--2nra_C    
                                               --4 
  ----TT--PTTCSTNT----RT------------------   L   !        +----------------4lln_I    
                                                 ! +------2 
  --------RGRGYC--------------------------   L   +-3      +----------------1cf7_A    
                                                   ! 
  LTETTTRAECRCRCQC------------------------   L     +-----------------------3n97_A    
                                               


> 1rio_A:STRUCTURE OF BACTERIOPHAGE LAMBDA CI-NTD IN COMPLEX WITH SIGMA-REGION4 OF THERMUS AQUATICUS BOUND TO DNA

  
  KGKG------QASG----------NG   L                +-1rio_A    
                                      +---------2 
  KGKG--ET--QASG----------NG   L      !         +-1lmb_4    
                                   +--4 
  ----QT--STNTVTATSTQTRTETTT   L   !  !          +2r1j_L    
                                   !  !      +---1 
  ----------SCATRTNCQT----HT   L --5  +------3   +4jcy_A    
                                   !         ! 
  ------AT--QAAT--SA--------       !         +----4z5h_A    
                                   ! 
  --------TT----ATYTQTQT----   L   +--------------3qws_B    
                                 


> 1rio_H:STRUCTURE OF BACTERIOPHAGE LAMBDA CI-NTD IN COMPLEX WITH SIGMA-REGION4 OF THERMUS AQUATICUS BOUND TO DNA

  
  LTEGTT--ETRC--RC----------   L              +-------------------------6b6h_F    
                                          +---7 
  YG--------TG--RGSG--FTRG--   L          !   +-------------------------2h27_A    
                                          ! 
  LTETTTRAECRC--RCQC--------   L          !                          +--3n97_A    
                                          !                        +-1 
  ----TT--PTTC--STNT--------   L        +-8             +----------3 +--4lln_I    
                                        ! !             !          ! 
  ------RGSTRT--STHG--------   L        ! !       +-----5          +----3zpl_B    
                                        ! !       !     ! 
  ----STKTPTTT--FT----------   L        ! !       !     +---------------4aso_F    
                                        ! +-------6 
  TT------KATT--QTTG--LTRTKA   L      +-9         !                 +---2p7c_B    
                                      ! !         !               +-2 
  ----TT--RG----ST----------   L      ! !         +---------------4 +---2qby_A    
                                      ! !                         ! 
  ----ST--RG----------------   L   +-10 !                         +-----2qby_B    
                                   !  ! ! 
  ----TT--SGLT--YART--------   L   !  ! +-----------------------------2nra_C    
                                 -11  !  
  ------RG----DTVT--STRG----   L   !  +-----------------------------4nhj_A    
                                   !  
  ------------RGAC--LG------       +-----------------------------4wx9_A    
                                 


> 1rpe_R:THE PHAGE 434 OR2/R1-69 COMPLEX AT 2.5 ANGSTROMS RESOLUTION

  
  ------SCATRTNCQT----HT   L           +----------4jcy_A    
                                 +-----4 
  QT--STNTVTATSTQTRTETTT   L     !     !       +--2r1j_L    
                                 !     +-------2 
  ------QASG----------NG   L   +-5             ! +-1rio_A    
                               ! !             +-1 
  --ET--QASG----------NG   L   ! !               +-1lmb_4    
                             --6 ! 
  ----TT----ATYTQTQT----   L   ! +----------------3qws_B    
                               ! 
  --AT--QAAT--SA--------       !         +-------4z5h_A    
                               +---------3 
  ----TTQA--LTSAET------   L             +-------2o4a_A    
                             


> 1rxw_A:CRYSTAL STRUCTURE OF A. FULGIDUS FEN-1 BOUND TO DNA

  
  ----------ICIC--QG--TGLGKGSG----------------------RC                       +-1rxw_A    
                                                             +---------------1 
  --------IA--AGVG--QC--LCQCMG------------KCKA------RC       !               +-5k97_A    
                                                           --4 
  CTHTKA------------------------RT------RC----RG------       !    +------------5v07_Z    
                                                             ! +--2 
  ITYTQT--KTAA----------------------------------------       +-3  +------------4q0w_A    
                                                               ! 
  ------FCRT------------------LT--TGEGEG--------FTRT--   L     +---------------5hp4_A    
                                                           


> 1rzr_C:CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR- PHOSPHOPROTEIN-DNA COMPLEX

  
  IT--ST--ATTTSTRG----VTAGLCAC   L               +1rzr_C    
                                               +-1 
  ITYTSGMTAA--STRG--NT--AGLCAT   L   +---------2 +3oqm_C    
                                     !         ! 
  ----SG--TC------RG------LCKA   L --3         +1qpz_A    
                                     ! 
  LTYCSGYGQC--STRG--HT--AGLGAC   L   +---------1efa_B    
                                   


> 1s40_A:SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH A SINGLE-STRANDED TELOMERIC DNA 11-MER

  
  EGTGYG--SG--DGKGATFTSGVGNGYTLGYGYGKG--YT--RGDGNG--KT--YG--NGAG--RT--   L      +----------------1s40_A    
                                                                             +--1 
  ----YT--------------------------------YGDG----------------------RT--   L   !  +----------------3kjp_A    
                                                                           --3 
  ----QT------------------------------RT----------LTTTKTFTQT----ST--HT       !  +----------------4gnx_B    
                                                                             +--2 
  ------KG--WGYT--------YCFA--MA--RGRTIGWGDG--------------------------   L      +----------------4hja_A    
                                                                           


> 1sax_A:THREE-DIMENSIONAL STRUCTURE OF S.AUREUS METHICILLIN-RESISTANCE REGULATING TRANSCRIPTIONAL REPRESSOR MECI IN COMPLEX WITH 25-BP DS- DNA

  
  ----------------KGTA--TA----RG----------------   L                 +-----------1xsd_A    
                                                                     !  
  ----TT----------KATTQTTG--LTRT----KA----FT--YT   L         +------13        +---2p7c_B    
                                                             !       !      +-6 
  --------------SANCTGTTPT----------------RT----   L         !       +------8 +---5hlg_E    
                                                             !              ! 
  ------------DCSA--TATT------RT----------RA----   L         !              +----1z9c_A    
                                                             !  
  ----------------------NA--HT--STLT------------   L         !              +-----2a07_K    
                                                          +-15           +-10  
  --------------------NASTRTHT--ST--------------   L      !  !  +-------11  +-----3l2c_A    
                                                          !  !  !        !  
  KAFA--------------------------------------MC--          !  !  !        +--------3aaf_B    
                                                          !  !  !  
  --------------------------YG------------------          !  !  !                  +4lb5_B    
                                                          !  !  !                +-2 
  ----ST------STQAQGSTSART------------KT--------   L      !  +-14     +----------5 +5trd_B    
                                                          !     !     !          ! 
  ------SG--QG--YCNC----------------------------          !     !     !          +2ve9_C    
                                                          !     !     !  
  --------------------------YG------------------       +-16     !     !               +4ka4_B    
                                                       !  !     !     !             +-1 
  --------------------------YGRG----------------       !  !     +----12           +-3 +4wcg_B    
                                                       !  !           !           ! ! 
  ----------------RGRGYC------------------------   L   !  !           !       +---4 +1cf7_A    
                                                       !  !           !       !   ! 
  ------------ST--PTTC--QG----RG----------------   L   !  !           !     +-7   +1f5t_A    
                                                     -17  !           !     ! ! 
  --------------------------YG------------------       !  !           +-----9 +----2heo_D    
                                                       !  !                 ! 
  --------RG--STRGMCTTRT------------------------   L   !  !                 +-----4u0y_B    
                                                       !  !  
  ------YC----KTHGSTQTYTPT--------------LG------   L   !  +----------------------5x11_A    
                                                       !  
  ----------------DCKT--RG--RGYA----------------   L   +------------------------1dux_F    
                                                     


> 1sfu_A:CRYSTAL STRUCTURE OF THE VIRAL ZALPHA DOMAIN BOUND TO LEFT- HANDED Z-DNA

  
  --------ST------STQAQGST--SART--------------KT------   L            +------------------------5trd_B    
                                                                      !  
  --------------------RGRG--YC------------------------   L            !                              +--1cf7_A    
                                                                      !                         +----7 
  --------------------------------YG------------------                !                         !    !  +2heo_D    
                                                                      !                         !    +--2 
  ----------------ST--PTTC----QG----RG----------------   L            !                         !       +1f5t_A    
                                                                      !                    +---11  
  --------------------------------YGRG----------------                !                    !    !      +4wcg_B    
                                                                      !                    !    !    +-5 
  ----------SGQG----YCNC------------------------------                !                    !    !    ! +2ve9_C    
                                                                      !                    !    +----6 
  --------------------------------YG------------------                !                    !         ! +4ka4_B    
                                                                      !                    !         +-3 
  --------TT----------KATT--QTTG--LTRT----KA------FTYT   L            !              +----15           +2p7c_B    
                                                                      !              !     !  
  --------------------------------YG------------------                !              !     !               +4lb5_B    
                                                                      !              !     !           +---1 
  ----------------TT--PTTC--STNT--------------RT------   L            !              !     !     +-----8   +4lln_I    
                                                                      !              !     !     !     ! 
  ------------------RGSTRT--STHG--------------RA------   L         +-22              !     !  +-12     +---3zpl_B    
                                                                   !  !           +-17     !  !  !  
  --------------------KGTA----TA----RG----------------   L         !  !           !  !     +-14  +---------1xsd_A    
                                                                   !  !           !  !        !  
  ----------------STKTPTTT--FT----------------RA------   L         !  !           !  !        +-----------4aso_F    
                                                                   !  !           !  !  
  ----------RG----STRGMCTT--RT------------------------   L         !  !        +-18  !                 +4u0y_B    
                                                                   !  !        !  !  !              +--4 
  ----------------TTLTECTA--STRG----------------------   L         !  !        !  !  +--------------9  +4i2o_B    
                                                                   !  !        !  !                 ! 
  ----------------ITRGECSC--SGKG----------------------   L         !  !        !  !                 +---5i2d_R    
                                                                   !  !        !  !  
  ------------------RG----DTVT--STRG--------RC--------   L         !  !     +-19  +--------------------4nhj_A    
                                                                +-23  !     !  !  
  ----------------------------NA--HT--STLT------------   L      !  !  !     !  !               +-----2a07_K    
                                                                !  !  !     !  !          +---10  
  --------------------------NASTRTHT--ST--------------   L      !  !  !     !  !     +---13    +-----3l2c_A    
                                                                !  !  !  +-20  !     !    !  
  ----KAFA------------------------------------FG------          !  !  !  !  !  +----16    +----------3aaf_B    
                                                                !  !  !  !  !        !  
  ----------YC----KTHGSTQT--YTPT----------------------   L   +-24  !  +-21  !        +---------------5x11_A    
                                                             !  !  !     !  !  
  ITPT----------RT------------------------------------   L   !  !  !     !  +----------------------5fmf_V    
                                                             !  !  !     !  
  ----------------------------------------------HG----   L   !  !  !     +-----------------------5iyc_T    
                                                           -25  !  !  
  --KC--------------MGSGTT--TTYC----------------------   L   !  !  +-------------------------5f7q_C    
                                                             !  !  
  ----------------------AA----ET--------------RG------   L   !  +----------------------------5eix_A    
                                                             !  
  --------------------FT------------------------------   L   +-----------------------------1u8b_A    
                                                           


> 1t2k_D:STRUCTURE OF THE DNA BINDING DOMAINS OF IRF3, ATF-2 AND JUN BOUND TO DNA

  
  --RC----NC----AAAT--CTRC----------   L                       +2wt7_A    
                                                             +-1 
  --RG----NC----YGAT----RC----------   L                     ! +4eot_A    
                                                     +-------5 
  RG--QGNART--AGQT--FTRG------------   L             !       ! +1gd2_G    
                                                     !       +-3 
  ----------------RG----NC--YGATCTRG   L           +-7         +2wt7_B    
                                                   ! ! 
  --RG----NT----ATAT----RG----------   L           ! !        +5vpe_C    
                                           +-------8 +--------2 
  --------------NTRTATAT--CTRA------   L   !       !          +5vpe_D    
                                           !       ! 
  --------NCRT--ATAT--STRG----------   L   !       !        +1t2k_D    
                                         --9       +--------4 
  --------RA----NA--AAVT--STRG------   L   !                +1nwq_C    
                                           ! 
  ----------------NT--ATAT--STRG----   L   !             +---1dh3_C    
                                           +-------------6 
  --------NCTT----AT----RG----------   L                 +---2dgc_A    
                                         


> 1t38_A:HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAINING O6-METHYLGUANINE

  
  RGAC--                               +--1t38_A    
               +-----------------------2 
  RAAC--       !                       !  +1yfh_A    
             --3                       +--1 
  RGACLG       !                          +4wx9_A    
               ! 
  ----YG       +--------------------------2heo_D    
             


> 1t9i_B:I-CREI(D20N)/DNA COMPLEX

  
  STITQANG------ST--------RG--RG--YCTCYC--RG------VCQT------KGTC--   L                              +3mxb_R    
                                                                                                  +-1 
  STITQAKG--RG--STNT------QT--ST--ATTC----YT--SC--VCDTRGST--KGTG--   L                      +-----6 +3mxb_B    
                                                                                            !     ! 
  SAYCLCIT--RGDCYA--------QG--------IG--NA--RG--DTIC--RG----------   L                   +-10     +2fld_B    
                                                                                         !  !  
  STITQAKG--RG--STNT------QG--ST--ATTC----YT--SC--VCDTRGST--KGTG--   L                   !  !    +-2xe0_B    
                                                                                         !  +----8 
  SANCSCKG--LT----------------DAECNATG----RC------------DAQA----QC   L                   !       +-2ex5_A    
                                                                                         !  
  ST--NAVT--HG--TCNA------AT--LCYCECAT----YG--NA--TCKTKGSA--------   L                   !          +4lq0_A    
                                                                                     +--11        +-2 
  SGMGRGRG------KTYA------LT--VT----TT----KTSC--------RGEC--------   L               !   !      +-5 +4lox_A    
                                                                                     !   !      ! ! 
  STMG----------KGYC------RT----RGVTSA----FCMC----STQTRGEC--------   L               !   !      ! +5esp_A    
                                                                                     !   !    +-7 
  ------RA--RG----------RTRG--STRTQGTA------SC----ATMCRGTC--------   L               !   !    ! !   +5t2h_A    
                                                                                  +-12   !    ! ! +-3 
  SCMCRG--RG--------------YT--ST--ECTT------RG----TTRG------------   L            !  !   +----9 +-4 +5thg_A    
                                                                                  !  !        !   ! 
  STIGRGRG--------MC------LT--EC--STKG----TTNA------MGRTSC--------   L            !  !        !   +5t2n_A    
                                                                         +-------13  !        ! 
  CGRGST--------------TTKARG--QTFAQGNG----HCSC----LAQGRGQA--------   L   !        !  !        +--4yit_A    
                                                                         !        !  !  
  YCSTTC------------KG----YC--TGET--EC----RG--RG--MA--RGRG--------   L -14        !  +-----------3uvf_B    
                                                                         !        !  
  SAYCKTIT--RGDCYA------------------IG------RG--DTIC----IA--------   L   !        +--------------1m5x_B    
                                                                         !  
  --YT--------------------RGSGECRGVTTGQG--VG------RTEARGSC--------   L   +-----------------------2vs7_A    
                                                                       


> 1tc3_C:TRANSPOSASE TC3A1-65 FROM CAENORHABDITIS ELEGANS

  
  RT----HGSGRGHG--RT----   L                         +1tc3_C    
                                      +--------------1 
  --RTQG----PTSGTCSTTC--   L     +----2              +1hlv_A    
                                 !    ! 
  ------------NG----NA--   L   +-3    +---------------2kdz_A    
                               ! ! 
  NG------STHG--CTSTKG--   L --4 +--------------------1pdn_C    
                               ! 
  ----------YTVC--KGDCKC   L   +----------------------2qhb_A    
                             


> 1tez_B:COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

  
  --RT--------ETWTYT------------PA--------               +-1tez_B    
                                                       +-1 
  --------------------------HCQC--FCRG----   L   +-----2 +-2wq7_A    
                                                 !     ! 
  --RT--WTFT--ETWT------NT------ETDTRTYTHT   L --3     +---2vtb_A    
                                                 ! 
  HGRTNT----ET--WT--YTMT--WT--------RT----   L   +---------2xrz_B    
                                               


> 1tf6_A:CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION

  
  KG--WTKA--------HCHG--RGTA--ACNAKGRGLTSTRG--RG   L               +---------------1tf6_A    
                                                                   ! 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG------------   L               !             +-5kl3_A    
                                                                 +-5           +-2 
  QA--TTNA--STQAQTATSTNTATTTLAHGTCRG------------   L             ! !           ! ! +1g2f_F    
                                                                 ! !   +-------3 +-1 
  RG--DCHG--------KGDC--RGQARGATNA--------------   L             ! !   !       !   +2i13_A    
                                                       +---------6 +---4       ! 
  EC--SCKGRG----TCYCKA--RGQA----TC--------------   L   !         !     !       +---5yeg_A    
                                                       !         !     ! 
  ----TTSGRG--LT--ETYC----NTYGQG----------------   L --7         !     +-----------4f6m_A    
                                                       !         ! 
  ------------RG--DGEC--RGRGSGDCHA--------------   L   !         +----------------2wbs_A    
                                                       ! 
  ------TG----RA--SCDC----------------QG--LGLC--   L   +--------------------------5yel_A    
                                                     


> 1u8r_B:CRYSTAL STRUCTURE OF AN IDER-DNA COMPLEX REVEALS A CONFORMATIONAL CHANGE IN ACTIVATED IDER FOR BASE-SPECIFIC INTERACTIONS

  
  ------------ST--PTTCSTQC----RC------------   L                   +-----------1u8r_B    
                                                             +----14  
  ------------ST--PTTC--QG----RG------------   L             !     +-----------1f5t_A    
                                                             !  
  ------------TT--PTTCSTNT------------------   L             !                +4lln_I    
                                                          +-16             +--6 
  ------------DCSA--TATT------RT------------   L          !  !             !  +1z9c_A    
                                                          !  !        +----7 
  --------------RGTCTA--RGNT----------------   L          !  !        !    !  +4fx4_B    
                                                          !  +-------12    +--4 
  --------------RGSTRTSTHG------------------   L          !           !       +3zpl_B    
                                                          !           !  
  ----------------QC------------------------              !           +--------5hso_A    
                                                          !  
  RC--------------RGRGYC--------------------   L          !            +----1cf7_A    
                                                          !          +-8 
  ------ST----STQAQGSTSART------------------   L   +-----17     +---11 +----5trd_B    
                                                   !      !     !    !  
  ------------STKTPTTTFT--------------------   L   !      !     !    +------4aso_F    
                                                   !      !     !  
  --------------------------YG--------------       !      !     !            +2heo_D    
                                                   !      !  +-13          +-1 
  --------------------------YGRG------------       !      !  !  !          ! +4wcg_B    
                                                   !      !  !  !     +----5 
  --------------------------YG--------------       !      !  !  !     !    !   +4ka4_B    
                                                   !      !  !  !     !    ! +-2 
  ----------------KGTA--TA----RG------------   L -18      !  !  +----10    +-3 +1xsd_A    
                                                   !      +-15        !      ! 
  --------SGQG--YCNC------------------------       !         !        !      +2ve9_C    
                                                   !         !        !  
  --------RG--STRGMCTTRT--------------------   L   !         !        +-----4u0y_B    
                                                   !         !  
  ------TT--------KATTQTTG--LTRTKA------FTYT   L   !         !         +----2p7c_B    
                                                   !         +---------9 
  ------------STQASGATSTQT------------QA----   L   !                   +----4on0_B    
                                                   !  
  --KAFA--------------------------FGMC------       +------------------------3aaf_B    
                                                 


> 1uaa_B:E. COLI REP HELICASE/DNA COMPLEX

  
  ----HTDTKTRTATFTLTDTQTFT----WTRTRTHTHTSTST------   L                +----------1uaa_B    
                                                         +------------2 
  FT--HT------------ST--FT----WGRTRTHGSTMT--RTEGEG       !            !    +-----2is6_B    
                                                       --3            +----1 
  FTTTHT----------------FTDTYTWTRTRT--------------   L   !                 +-----2pjr_A    
                                                         ! 
  ----------------------------VT----HT------------   L   +-----------------------3gpl_A    
                                                       


> 1ubd_C:CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT

  
  ----KGDCRG--QARGATNA----QA--ATHG--RG--DCNATT   L            +--------2i13_A    
                                                     +--------3 
  ------KGRG----TCYCKA--RGQA----TC--RA--SCDCVT   L   !        +--------5yeg_A    
                                                     ! 
  RGSTDAHARG--RGSTDCHG--TTRG--DAEGRG----------   L   !                  +5kl3_A    
                                                   --6          +-------1 
  KG----KA--------HCHG--RGTA--ACNAKG----------   L   !        +-2       +1tf6_A    
                                                     !        ! ! 
  ----------STQAQTATSTNTATTTLAHGTCRG----------   L   ! +------4 +-------1g2f_F    
                                                     ! !      ! 
  ----TTSGRG--LT--ETYC----NTYGQG--------------   L   +-5      +---------4f6m_A    
                                                       ! 
  ------------------------RG--DGECRGRGSGDCHA--   L     +----------------2wbs_A    
                                                   


> 1vtn_C:CO-CRYSTAL STRUCTURE OF THE HNF-3/FORK HEAD DNA-RECOGNITION MOTIF RESEMBLES HISTONE H5

  
  --------------------------NA----RAHT--STLT------------   L                                    +------2a07_K    
                                                                                              +-4 
  --------------------------NAST--RTHT--ST--------------   L                               +--5 +------3l2c_A    
                                                                                           !  ! 
  --------------------KGTA----TA------RG----------------   L                            +--7  +-------1xsd_A    
                                                                                        !  ! 
  ------------------RGSTRT--STHG--------------------RA--   L                            !  +----------3zpl_B    
                                                                                        ! 
  --------SGQG------YCNC--------------------------------                          +-----8             +2ve9_C    
                                                                                  !     !           +-1 
  ------TT------------KATT--QTTG----LTRT----KA----------   L                      !     !   +-------2 +2p7c_B    
                                                                                  !     !   !       ! 
  ----------------------------------YG------------------                          !     +---6       +-4lb5_B    
                                                                               +-10         ! 
  RC------------------RGRG--YC--------------------------   L                   !  !         !     +---1cf7_A    
                                                                               !  !         +-----3 
  ----------------------------------YG------------------                       !  !               +---2heo_D    
                                                                            +-11  !  
  ------------RT----------------------------------------   L                !  !  +-------------------5fmf_V    
                                                                            !  !  
  --KAFA----------------------------------------YA--FGMC                +--12  !     +---------------3aaf_B    
                                                                        !   !  +-----9 
  ----------------------NG----RGRG----------------------   L            !   !        +---------------1cf7_B    
                                                                     +-13   !  
  --------YC------KTHGSTQT--YTPT------------------LG----   L         !  !   +------------------------5x11_A    
                                                                  +-14  !  
  --------------------SGTT--TTYC------------------------   L      !  !  +----------------------------5f7q_C    
                                                               +-15  !  
  --------------DCKGRGNA--RT--------KT--------------KGRA   L   !  !  +----------------------------5ddg_A    
                                                             -16  !  
  ----------------TT----RT--------------------SGRT--KT--   L   !  +----------------------------2v1u_A    
                                                               !  
  ------------------------ST--------------------------RA       +-----------------------------5bs8_A    
                                                             


> 1w0t_A:HTRF1 DNA-BINDING DOMAIN IN COMPLEX WITH TELOMERIC DNA.

  
  RT------------VA--NA--QT   L          +-------------------3d1n_M    
                                        !  
  ------YTVC--KGDCKC------   L          !   +---------------2qhb_A    
                                        !   !  
  RC------------IAQCNA--YA   L          !   !                       +1nk3_P    
                                        !   !                     +-2 
  RA------------IAQTNA--MC   L          !   !                   +-8 +1puf_A    
                                        !   !                   ! ! 
  RT------------VAQTNA----   L   +-----20   !                +-10 +5hod_A    
                                 !      !   !                !  !  
  RA------------IAQTNA----   L   !      !   !             +-11  +5lux_L    
                                 !      !   !             !  !  
  RT------------IAQTNA----   L   !      !   !             !  ! +4rdu_A    
                                 !      !   !             !  +-1 
  RT------------IAQCNA--MG   L   !      !   !             !    +1b72_A    
                                 !      !   !             !  
  RT----STVC--KGDCRG------   L   !      !   !             !        +1w0t_A    
                                 !      +--19         +--15      +-3 
  RT------------VAQTNA----   L   !          !         !   !    +-4 +1fjl_B    
                                 !          !         !   !    ! ! 
  RT------------VASGNA----   L   !          !         !   !  +-9 +3cmy_A    
                                 !          !         !   !  ! ! 
  RT------------VASCNA--QA   L   !          !         !   !  ! +1gt0_C    
                                 !          !      +-16   +-12  
  RT------------IAKGNA----   L -21          !      !  !      !   +2hdd_A    
                                 !          !      !  !      ! +-5 
  RT--------------KGNA----   L   !          !      !  !      +-7 +2hos_A    
                                 !          !      !  !        ! 
  --------VT--KTIAQTNA----   L   !          !  +--17  !        +2me6_A    
                                 !          !  !   !  !  
  ----------------KG----NA   L   !          !  !   !  +-------1xpx_A    
                                 !          !  !   !  
  RA----RCET----SAQAKG----   L   !          !  !   !       +-5lxu_A    
                                 !          +-18   +------13  
  ------------RTVAIANA--MC   L   !             !           ! +1le8_A    
                                 !             !           +-6 
  KAHG----NCSCRGHCRG--YC--   L   !             !             +1ign_A    
                                 !             !  
  RA----------RCVTCTNA--QT   L   !             +-------------1au7_A    
                                 !  
  --------KG--RTEC--------   L   !                       +--1h89_C    
                                 +----------------------14  
  ----NA--RTQT--EC--------   L                           +--2kdz_A    
                               


> 1w36_B:RECBCD:DNA COMPLEX

  
  ----HTDTKTRTFT----WTRTRT----HTSTST----------------------------   L                   +----------------1uaa_B    
                                                                                       !  
  ----HT------FT----FTRTRTNTATHT----ET----ET--------------------          +-----------11              +-4c2u_D    
                                                                          !            !           +--6 
  FT--HT------FT----WGRTRT----HG------RTEGEG--------------------          !            +-----------8  +-2is6_B    
                                                                          !                        ! 
  FTTTHT------FTDTYTWTRTRT--------------------------------------   L      !                        +----2pjr_A    
                                                                          !  
  --------------------------------------------RT----IAQTNAMC----   L      !                               +2h1k_B    
                                                                          !                  +------------4 
  ------------------------------------------RA------IAQTNA------   L      !                  !            +5lux_L    
                                                                          !                  !  
  ------------------------------------------YART----VTQTNAMTKTRT   L      !                  !              +1jgg_B    
                                                                          !                  !            +-2 
  --------------------------------------------------VAQTNA------   L      !            +----10         +--5 +5hod_A    
                                                                       +-16            !     !         !  ! 
  ------------------------------------------------RTVAIANAMCRG--   L   !  !            !     !         !  +1le8_A    
                                                                       !  !            !     !  +------7 
  --------------------------------------------------IA--NA------       !  !            !     !  !      !     +4qtr_D    
                                                                       !  !            !     !  !      !   +-1 
  ----------------------------------------------------KGNA------   L   !  !        +--12     +--9      +---3 +2hos_A    
                                                                       !  !        !   !        !          ! 
  ------------------------------------------RT------IAKGNA------   L   !  !        !   !        !          +2hdd_A    
                                                                       !  !        !   !        ! 
  --------------------------------------------RTRT--IAQCNA------   L -17  !     +-13   !        +----------5jlw_D    
                                                                       !  !     !  !   !  
  ------------------------------------------RT----KTIAQCNA----RT   L   !  !     !  !   +-------------------1ig7_A    
                                                                       !  !  +-14  !  
  ------------------------------------------RT------VAQTNA------   L   !  !  !  !  +-----------------------3lnq_A    
                                                                       !  +-15  !  
  ------------------------------------------RA--------IA--NA----       !     !  +--------------------------4xrs_G    
                                                                       !     !  
  --------------------------------------------------IAQCNAMG----   L   !     +--------------------------2r5z_A    
                                                                       !  
  --------------------------------------------RC----IAQCNAYC----   L   +-----------------------------3rkq_B    
                                                                     


> 1w36_C:RECBCD:DNA COMPLEX

  
  ----HTDT--RTHT----------------   L                       +-----------1uaa_B    
                                         +-----------------3 
  FTTT----DTRT------------------   L     !                 +-----------2pjr_A    
                                       +-4 
  --------------RT----NT--NAIARG   L   ! !                             +4cyc_B    
                                       ! !                          +--1 
  --------------------NT--NAIARG   L --5 +--------------------------2  +1puf_B    
                                       !                            ! 
  --------------HTRT--NCSTNARG--   L   !                            +--1k61_B    
                                       ! 
  ------------------RTIAQCNA----   L   +-----------------------------5jlw_D    
                                     


> 1wb9_A:CRYSTAL STRUCTURE OF E. COLI DNA MISMATCH REPAIR ENZYME MUTS, E38T MUTANT, IN COMPLEX WITH A G.T MISMATCH

  
  MGDAFGTTRCMC--PT--   L                              +--1wb9_A    
                                                    +-1 
  ----FGET----------                              +-2 +--1ewq_A    
                                                  ! ! 
  --YGKA------SAPA--                           +--3 +----3thx_B    
                                               !  ! 
  VCKCFGET------PG--       +-------------------4  +-----2o8b_B    
                           !                   ! 
  --DGFG------VGSG--     --5                   +--------3thx_A    
                           ! 
  ----------------RT       +----------------------------1jfi_B    
                         


> 1x9m_A:T7 DNA POLYMERASE IN COMPLEX WITH AN N-2- ACETYLAMINOFLUORENE-ADDUCTED DNA

  
  ------------------KT----------RTNGQG------------YA----------------------QA----                         +------------1x9m_A    
                                                                                                         ! 
  --------------------YG--------RGNG--NGRC----YG--YAIGSCYC--NG--RC--------QA--HG                         !            +-4yfu_D    
                                                                                                         !          +-1 
  --LC----MGRCEG----------SGHGVC------------------------------------------------           +-------------5        +-2 +-1kln_A    
                                                                                           !             !        ! ! 
  --------------KC--------------RGNG--NG----TGFG--YGMG----RG--------------QG--HG   L       !             !      +-3 +---4bwj_A    
                                                                                           !             !      ! ! 
  ----------------KA------------RG--NT------QC------MC------QC------------------         +-7             +------4 +----4x0q_B    
                                                                                         ! !                    ! 
  ------------------------------RG--------EG--YGAC--AC----RC------------------HC   L     ! !                    +-----4xvk_A    
                                                                                         ! ! 
  ----------------------EG------------------QG--TGYGVG--------EG------RG--------   L   +-8 !           +--------------4boc_A    
                                                                                       ! ! +-----------6 
  ----------------------------------------------TT--------QG----------------HT--   L   ! !             +--------------1msw_D    
                                                                                     --9 ! 
  ------------------NG----------RT----------IGYG------------------EGMCTCNGQT----       ! +----------------------------4ztu_A    
                                                                                       ! 
  TT--NTFT----------------------------------------------------------------------       +----------------------------2py5_B    
                                                                                     


> 1xo0_B:HIGH RESOLUTION STRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-SPECIFIC RECOMBINATION

  
  HTTTKGMT--ST----KATT----QT----QT--------------KA--RARTKTST--RG--EA----RA------------   L                                +1xo0_B    
                                                                                                               +----------1 
  HTTAECMA--ST----KTTT--QTQT--CTRA--MT----------KA--RARTRCSA--YA--QG----RA------------   L                +----2          +5u91_B    
                                                                                                          !    ! 
  KATT--AAYT--WTTTKATTQTSTLTLTNT--ST--LTLT------------------------QA------DC--KCTC--IC   L         +------3    +----------2a3v_C    
                                                                                                   !      ! 
  --------------------------------------------------------TTQAATYGYAKT----------------   L       +-4      +---------------5jk0_B    
                                                                                                 ! ! 
  ----------------------------------------FCKC----KC----------NT--RGSTKT--------------   L   +---5 +----------------------1flo_A    
                                                                                             !   ! 
  --------------------------------------------KTDA------------------TT----------------   L --6   +------------------------2b9s_A    
                                                                                             ! 
  ------------------------------------------------------------------------NGRG--TTRGKT   L   +----------------------------5ds9_A    
                                                                                           


> 1xpx_A:STRUCTURAL BASIS OF PROSPERO-DNA INTERACTION; IMPLICATIONS FOR TRANSCRIPTION REGULATION IN DEVELOPING CELLS

  
  ----------KG--NA--EC--   L   +-----------------1xpx_A    
                               !  
  --------IAQTNA------KT   L   !                   +4rdu_A    
                               !                 +-1 
  --------IAQCNAYA------   L   !              +--3 +1nk3_P    
                               !              !  ! 
  --------IAQTNAMC------   L   !              !  +1puf_A    
                               !              !  
  ----------KGNA--------   L   !              !            +2hos_A    
                               !              !          +-4 
  --------VAQTNA--------   L   !              !        +-7 +5hod_A    
                             -16              !        ! ! 
  --------IAQTNA--------   L   !              !        ! +5lux_L    
                               !        +----14     +-10  
  ------RTVAIANAMCRG----   L   !        !     !     !  !   +1le8_A    
                               !        !     !     !  ! +-2 
  --------IAKGNA--------   L   !        !     !     !  +-5 +2hdd_A    
                               !        !     !  +-11    ! 
  --------IAQCNAMG------   L   !        !     !  !  !    +1b72_A    
                               !        !     !  !  !  
  --------VASGNA--------   L   !        !     !  !  ! +3cmy_A    
                               !        !     !  !  +-9 
  --------VAQTNA--------   L   +-------15     +-13    +1fjl_B    
                                        !        !  
  --------NT--NAIARG----   L            !        !      +4cyc_B    
                                        !        !    +-6 
  --------NT--NAIARG----   L            !        !  +-8 +1puf_B    
                                        !        !  ! ! 
  RT------NCSTNARG------   L            !        +-12 +1k61_B    
                                        !           !  
  --RCET--SAQAKG--------   L            !           +-5lxu_A    
                                        !  
  ------KGDCRG----------   L            +--------1w0t_A    
                             


> 1xsd_A:CRYSTAL STRUCTURE OF THE BLAI REPRESSOR IN COMPLEX WITH DNA

  
  ------------KGTA--TA----RG----------------   L                  +------------1xsd_A    
                                                               +-14  
  TT----------KATTQTTG--LTRT----KA------FTYT   L               !  !       +----2p7c_B    
                                                               !  +-------9 
  --------TT--PTTCSTNT------------------RT--   L               !          ! +----4lln_I    
                                                               !          +-8 
  ----------SANCTGTTPT------------------RT--   L               !            ! +--5hlg_E    
                                                               !            +-7 
  ----------RGSTRTSTHG------------------RA--   L            +-15              +--3zpl_B    
                                                            !  !  
  --SG--QG--YCNC----------------------------                !  !            +2ve9_C    
                                                            !  !        +---4 
  ST------STQAQGSTSART------------KT--------   L            !  !        !   +5trd_B    
                                                            !  !   +---10  
  ----------------------YG------------------                !  !   !    !   +4lb5_B    
                                                            !  +--13    +---3 
  --------DCSA--TATT------RT------------RA--   L            !      !        +1z9c_A    
                                                       +---16      !  
  --------STKTPTTTFT----------------RA------   L       !    !      +---------4aso_F    
                                                       !    !  
  ----------------------YG------------------           !    !                 +4ka4_B    
                                                       !    !               +-5 
  --------ST--PTTC--QG----RG----------------   L       !    !               ! +1f5t_A    
                                                       !    !         +-----6 
  ----------------------YG------------------           !    !         !     !   +2heo_D    
                                                       !    !         !     ! +-1 
  ----------------------YGRG----------------       +--18    +--------12     +-2 +4wcg_B    
                                                   !   !              !       ! 
  ------------RGRGYC------------------------   L   !   !              !       +1cf7_A    
                                                   !   !              !  
  ----RG--STRGMCTTRT------------------------   L   !   !              +------4u0y_B    
                                                   !   !  
  ----------------NA--RAHT--STLT------------   L -19   !               +-----2a07_K    
                                                   !   !  +-----------11  
  ----------------NASTRTHT--ST--------------   L   !   +-17            +-----3l2c_A    
                                                   !      !  
  --YC----KTHGSTQTYTPT----------------LG----   L   !      +------------------5x11_A    
                                                   !  
  ------------DCKT--RG--RGYA----------------   L   +-------------------------1dux_F    
                                                 


> 1yo5_C:ANALYSIS OF THE 2.0A CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX OF HUMAN PDEF ETS DOMAIN BOUND TO THE PROSTATE SPECIFIC ANTIGEN REGULATORY SITE

  
  ------KT--RGSA--RGQA--------RA   L                           +1yo5_C    
                                                             +-3 
  ------KT--RGAT--RGYA----------   L                         ! +1bc8_C    
                                                    +--------5 
  ----DCKT--RG----RGYA----------   L                !        ! +1dux_F    
                                                    !        +-1 
  ------KT--RGAT--RGYT----------   L          +-----6          +1awc_A    
                                              !     ! 
  KTHG--------------------------              !     !          +5hdn_C    
                                           +--7     +----------2 
  ------ST--------RTQT--MT------   L       !  !                +5d8k_B    
                                           !  ! 
  ----KG----ATNT--CT----SC------   L   +---8  !               +2irf_L    
                                       !   !  +---------------4 
  ------------NT--CT--NGST------   L   !   !                  +1if1_B    
                                     --9   ! 
  --------NA----RAHT--STLT------   L   !   +-------------------2a07_K    
                                       ! 
  ------------------------KGKG--   L   +-----------------------5xfr_B    
                                     


> 1z19_B:CRYSTAL STRUCTURE OF A LAMBDA INTEGRASE(75-356) DIMER BOUND TO A COC' CORE SITE

  
  KGTA--NAYASG--ATST----LT--------------------------------KT--RCST----TTSTRGYC----TT--QT   L                     +-------1z19_B    
                                                                                                              +--1 
  KATT--AAYT--WT--TTKATTQTSTLT--LTNT----STLTLTITFTRT------KA------------QA------DCKCTCIC   L              +---2  +-------2a3v_C    
                                                                                                          !   ! 
  HTTAECMA--ST--------KTTT--QTQT----CTRA----------------KA------SA--YA--QG--------------   L      +-------3   +----------5u91_B    
                                                                                                  !       ! 
  --------------AATA--KGNA----IT--------------------------------TTQAATYGYAKT--------TT--   L   +--4       +--------------5jk0_B    
                                                                                               !  ! 
  --------------------------------------------------RAFC--KC--------NT--RGST--KT--------   L --5  +----------------------1flo_A    
                                                                                               ! 
  --------------------------------------------------------KTDA------TT------------------   L   +-------------------------2b9s_A    
                                                                                             


> 1z63_B:SULFOLOBUS SOLFATARICUS SWI2/SNF2 ATPASE CORE IN COMPLEX WITH DSDNA

  
  ------RC----                   +-----------------1z63_B    
                           +-----1 
  --------NT--   L     +---2     +-----------------5vvr_M    
                       !   ! 
  ----------NA   L   +-3   +-----------------------3v4r_B    
                     ! ! 
  ----------QA   L --4 +---------------------------4qqw_A    
                     ! 
  RAYTEC------       +----------------------------2p6r_A    
                   


> 1z9c_A:CRYSTAL STRUCTURE OF OHRR BOUND TO THE OHRA PROMOTER: STRUCTURE OF MARR FAMILY PROTEIN WITH OPERATOR DNA

  
  ------DCSA--TATT------RT----RA----   L                      +1z9c_A    
                                                          +---5 
  ------TT--PTTCSTNT----------RT----   L                  !   +4lln_I    
                                                     +----8 
  --------RGTCTA--RGNT--------RT----   L             !    !    +4fx4_B    
                                                     !    ! +--2 
  --------RGSTRTSTHG----------RA----   L   +--------11    +-7  +3zpl_B    
                                           !         !      ! 
  --------SANCTGTTPT----------RT----   L   !         !      +--5hlg_E    
                                           !         !  
  ----------QC----------------------       !         +--------5hso_A    
                                           !  
  ------STKTPTTTFT------------RA----   L   !              +-----4aso_F    
                                           !           +-10  
  ------STQASGATSTQT----------QA----   L   !     +----12  +-----4on0_B    
                                           !     !     !  
  ST----STQAQGSTSART--------KT------   L -16     !     +--------5trd_B    
                                           !     !  
  TT--------KATTQTTG--LTRTKA----FTYT   L   !  +-14          +---2p7c_B    
                                           !  !  !    +-----9 
  --------------------YG------------       !  !  !    !     !   +4lb5_B    
                                           !  !  !    !     +---3 
  ----------KGTA--TA----RG----------   L   !  !  +---13         +1xsd_A    
                                           !  !       !  
  --SGQG--YCNC----------------------       !  !       !       +-2ve9_C    
                                           +-15       +-------6 
  --------------------YG------------          !               ! +4ka4_B    
                                              !               +-4 
  --------------------YG------------          !                 ! +2heo_D    
                                              !                 +-1 
  --------------------YGRG----------          !                   +4wcg_B    
                                              !  
  ------ST--PTTC--QG----RG----------   L      +----------------1f5t_A    
                                         


> 1zlk_A:CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS HYPOXIC RESPONSE REGULATOR DOSR C-TERMINAL DOMAIN-DNA COMPLEX

  
  ------KGTGKANGYAST------   L                                +1zlk_A    
                                                            +-1 
  ------SCTAKTVCHTKG------   L               +--------------2 +1je8_F    
                                             !              ! 
  ------KGTCKGTCHT--------   L            +--7              +4wuh_B    
                                          !  ! 
  ------RG--DTVT--STRG----   L            !  +--------------4nhj_A    
                                      +---8 
  TT----KATTQTTG----LTRTKA   L        !   !             +---2p7c_B    
                                      !   !     +-------5 
  ----SANCTG--TTPT--------   L        !   !     !       +---5hlg_E    
                                      !   +-----6 
  ------------------YG----       +----9         !         +-4ka4_B    
                                 !    !         +---------4 
  ----RGTCTA--RGNT--------   L   !    !                   ! +4fx4_B    
                                 !    !                   +-3 
  --DCSA--TATT--------RT--   L -10    !                     +1z9c_A    
                                 !    ! 
  --ST--RG----------------   L   !    +---------------------2qby_B    
                                 !  
  ----YTNT--RGVT--RTET----   L   +--------------------------1l3l_A    
                               


> 1zq3_P:NMR SOLUTION STRUCTURE OF THE BICOID HOMEODOMAIN BOUND TO THE CONSENSUS DNA BINDING SITE TAATCC

  
  --RA--RA----------------IAQTNA--MC------   L                                  +------1puf_A    
                                                                                !  
  --KG--RC----------------IAQCNA--YA------   L                                  !                 +1nk3_P    
                                                                                !              +-10  
  ------RT----------------VAQTNA----------   L                                  !              !  ! +5hod_A    
                                                                                !              !  +-8 
  RA----RT----------------VASGNA----------   L                                  !           +-11    ! +3cmy_A    
                                                                                !           !  !    +-2 
  RA----RT----------------VA--NA--QT------   L                                  !           !  !      +3d1n_M    
                                                                             +-17        +-12  !  
  ----YARA----------------IAQTNA----------   L                               !  !        !  !  +-5lux_L    
                                                                             !  !        !  !  
  RA----RT----------------IAQTNA--------KT   L                               !  !        !  ! +4rdu_A    
                                                                             !  !     +-14  +-1 
  ------RT----------------IAQCNA--MG------   L                               !  !     !  !    +1b72_A    
                                                                             !  !     !  !  
  RT----RT----------------VAQTNA----------   L                               !  !  +-15  !  +1fjl_B    
                                                                             !  !  !  !  +--3 
  ------RT----------------NT--NA--IARG----   L                               !  !  !  !     +1puf_B    
                                                                             !  +-16  !  
  ------RT----------------VASCNA--QA------   L                            +-18     !  +----1gt0_C    
                                                                          !  !     !  
  ------RT------------------KGNA----------   L                            !  !     !    +2hos_A    
                                                                          !  !     +----4 
  ------RA--------------RCVTCTNA--QTRC----   L                            !  !          +1au7_A    
                                                                          !  !  
  ------RT----------------IAKGNA----------   L                            !  !         +2hdd_A    
                                                                          !  !       +-5 
  --------HTRT------------NCSTNA--RG------   L         +-----------------19  !     +-9 +1k61_B    
                                                       !                  !  !     ! ! 
  --------RT--------------NT--NA--IARG----   L         !                  !  +----13 +4cyc_B    
                                                       !                  !        !  
  ----------------------RTVAIANA--MCRG----   L         !                  !        ! +1le8_A    
                                                       !                  !        +-6 
  --------------------------KG----NA--EC--   L      +-20                  !          +1xpx_A    
                                                    !  !                  !  
  ------RT--------STVC--KGDCRG------------   L      !  !                  !         +1w0t_A    
                                                    !  !                  +---------7 
  ------RA------------RCET--SA--QAKG------   L   +-21  !                            +5lxu_A    
                                                 !  !  !  
  ----------------RGKG--SGSAQAVC--RT------   L   !  !  +----------------------------5gzb_A    
                                               -22  !  
  ----------------------RTRA--TAEGWA--NG--       !  +-----------------------------2p6r_A    
                                                 !  
  --PTRT------HGSGRGHG--RT----------------   L   +-----------------------------1tc3_C    
                                               


> 1zrf_A:4 CRYSTAL STRUCTURES OF CAP-DNA WITH ALL BASE-PAIR SUBSTITUTIONS AT POSITION 6, CAP-[6C;17G]ICAP38 DNA

  
  QT--STRGEC----RG--   L                          +1zrf_A    
                                                +-1 
  ----STRGECTANGKG--   L                      +-3 +3mzh_A    
                                              ! ! 
  ----HT--STATSTRG--   L   +------------------6 +-5lej_A    
                           !                  ! 
  ----ITRGECSCSGKG--   L   !                  ! +--5i2d_R    
                           !                  +-4 
  ----TTLTECTASTRG--   L   !                    +--4i2o_B    
                         --9 
  RG--STRGMCTTRT----   L   !              +-------4u0y_B    
                           !           +--7 
  --------RGRGYC----   L   !           !  +-------1cf7_A    
                           +-----------8 
  ----------------YG                   !         +2heo_D    
                                       !      +--2 
  SGQG--YCNC--------                   +------5  +2ve9_C    
                                              ! 
  ----------------YG                          +---4lb5_B    
                         


> 2a07_K:CRYSTAL STRUCTURE OF FOXP2 BOUND SPECIFICALLY TO DNA.

  
  --------------------------NA----RAHT--STLT----------------   L                                     +-----2a07_K    
                                                                                                  +-10  
  --------------ST----------NAST--RTHT--ST------------------   L                            +----13  +-----3l2c_A    
                                                                                            !     !  
  --KAFA--------------------------------------YANAKTFGMC----                                !     +--------3aaf_B    
                                                                                         +-17  
  ------TT------------KATT--QTTG----LTRT----KA----------FTYT   L                         !  !             +2p7c_B    
                                                                                         !  !     +-------4 
  --------------------KGTA----TA------RG--------------------   L                         !  +----14       +1xsd_A    
                                                                                         !        !  
  ----------------RGSTRT--STHG----------------------RA------   L                         !        +--------3zpl_B    
                                                                                         !  
  --------------STKTPTTT--FT------------------------RA------   L                         !          +-------4aso_F    
                                                                                  +-----19     +---12  
  ----------------------------------YG----------------------                      !      !     !    !       +4lb5_B    
                                                                                  !      !     !    +-------1 
  ------ST--------STQAQGST--SART----------------------------   L                  !      !     !            +5trd_B    
                                                                                  !      !  +-16  
  RC------------------RGRG--YC------------------------------   L                  !      !  !  !         +---1cf7_A    
                                                                                  !      !  !  !       +-8 
  ----------------------------------YG----------------------                      !      !  !  !       ! !   +2heo_D    
                                                                               +-21      !  !  +-------9 +---2 
  ----------------------------------YG----------------------                   !  !      +-18          !     +4ka4_B    
                                                                               !  !         !          ! 
  ------------RT--------------------------------------------   L               !  !         !          +----5fmf_V    
                                                                               !  !         !  
  --------SGQG----YCNC--------------------------------------                   !  !         !             +-2ve9_C    
                                                                            +-22  !         +-------------6 
  --------------TT--RG----ST--------------------------------   L            !  !  !                       +-2qby_A    
                                                                            !  !  !  
  --------YC------KTHGSTQT--YTPT----------------------------   L            !  !  +------------------------5x11_A    
                                                                            !  !  
  --------------------------------------------KG------------   L            !  !  +-----------------------5xfr_B    
                                                                         +-23  +-20  
  --------------NG----RGRG--YC------------------------------   L         !  !     +-----------------------1cf7_B    
                                                                         !  !  
  ----------------------KT----RGAT--RGYA--------------------   L         !  !                        +-1bc8_C    
                                                                         !  !               +--------7 
  ----------------------KT----RG----RGYA--------------------   L         !  !               !        ! +1dux_F    
                                                                         !  +--------------15        +-3 
  ----------------------KT----RGSA--RGQA--------------RA----   L      +-24                  !          +1yo5_C    
                                                                      !  !                  !  
  ----------------------------NT--RGCT--NGST----------------   L      !  !                  +----------1if1_B    
                                                                      !  !  
  --------------------AA----ET----------------------RG------   L      !  !                         +-5eix_A    
                                                                   +-25  !                    +----5 
  --------------------SA------------------------------------   L   !  !  +-------------------11    +-5npk_d    
                                                                   !  !                       !  
  --------------------SG------------------------------------     -26  !                       +------5iwi_C    
                                                                   !  !  
  ----------------------------------------------TGAG--ATTT--       !  +----------------------------2wwy_B    
                                                                   !  
  --------------DCKGRGNA--RT--------KT----------------------   L   +----------------------------5ddg_A    
                                                                 


> 2b9s_A:CRYSTAL STRUCTURE OF HETERODIMERIC L. DONOVANI TOPOISOMERASE I- VANADATE-DNA COMPLEX

  
  KANT--RGMGYAMCKT--NC--KTDA------TT--   L                             +2b9s_A    
                                                    +------------------1 
  ----ECRA--YAMCKT--NT--KT------------       +------3                  +1k4t_A    
                                             !      ! 
  ----------------RG--------RG--------   L --4      +-------------------3m4a_A    
                                             ! 
  --------------------KA------QG------   L   !         +----------------5u91_B    
                                             +---------2 
  ----------------------------TTQAYAKT   L             +----------------5jk0_B    
                                           


> 2bcq_A:DNA POLYMERASE LAMBDA IN COMPLEX WITH A DNA DUPLEX CONTAINING AN UNPAIRED DTMP

  
  WC--LC----KA--YCAGNGRCRGEGKTPT                      +--2bcq_A    
                                                    +-2 
  --SALTAART------RGEGRGRG------                    ! +--4qz9_A    
                                          +---------3 
  HC--------KG--YCDCNCKGRG------          !         ! +-4kli_A    
                                          !         +-1 
  ----LC--RCRAFT--KTQTRARA------       +--5           +-5vzi_A    
                                       !  ! 
  --------------YA--------------       !  !  +---------3v7j_A    
                                     --6  +--4 
  ----------KC----KA--VARA------       !     +---------4p4m_A    
                                       ! 
  ----------KT--HCVGLCIGRG------       +---------------5hrb_A    
                                     


> 2bop_A:CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVIRUS-1 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET

  
  ------KGCGFT----------------   L                        +---2bop_A    
                                       +------------------2 
  ----NCKGCAYGRA--------------   L     !                  !   +2ayg_A    
                                     +-3                  +---1 
  --KTTGYCNGRT----------------   L   ! !                      +1b3t_A    
                                   --4 ! 
  --------------------------RG   L   ! +----------------------3qfq_B    
                                     ! 
  KG------------NTECKCDGHGYT--   L   +------------------------1lwt_A    
                                   


> 2bzf_A:STRUCTURAL BASIS FOR DNA BRIDGING BY BARRIER-TO- AUTOINTEGRATION FACTOR (BAF)

  
  ----RT------------------          +-----------------------------4p0p_A    
                                    !  
  ------------NT--NAIARG--   L      !                               +4cyc_B    
                                    !                             +-3 
  ------------NT--NAIARG--   L      !                          +--8 +1puf_B    
                                    !                          !  ! 
  RT----------NCSTNARG----   L      !                          !  +1k61_B    
                                 +-15                          !  
  --------------KGNA------   L   !  !                          !              +2hos_A    
                                 !  !                          !            +-1 
  ------------IAQCNAYA----   L   !  !                          !          +-7 +1nk3_P    
                                 !  !                          !          ! ! 
  ------------IAQTNAMC----   L   !  !                          !        +-9 +1puf_A    
                                 !  !                          !        ! ! 
  ------------VASGNA------   L   !  +-------------------------14        ! ! +3cmy_A    
                                 !                             !        ! +-4 
  ------------VAQTNA------   L   !                             !     +-10   +5hod_A    
                                 !                             !     !  !  
  ------------IAKGNA------   L   !                             !     !  !   +2hdd_A    
                               -16                             !     !  ! +-2 
  ------------IAQTNA----KT   L   !                             !  +-12  +-6 +4rdu_A    
                                 !                             !  !  !    ! 
  ------------IAQCNAMG----   L   !                             !  !  !    +1b72_A    
                                 !                             !  !  !  
  RA----------IAQTNA------   L   !                             +-13  +5lux_L    
                                 !                                !  
  ----------RTVAIANAMCRG--   L   !                                !    +1le8_A    
                                 !                                !  +-5 
  ------------VAQTNA------   L   !                                +-11 +1fjl_B    
                                 !                                   !  
  ------RCET--SAQAKG------   L   !                                   +5lxu_A    
                                 !  
  --RT--------------------       +-----------------------------3n4m_B    
                               


> 2c6y_A:CRYSTAL STRUCTURE OF INTERLEUKIN ENHANCER-BINDING FACTOR 1 BOUND TO DNA

  
  ----------------------NASTRGHT--STLT--------------KA----   L                                      +---2c6y_A    
                                                                                           +-------10  
  ----------------------NASTRGHT--STFT--------------------   L                             !        !   +1vtn_C    
                                                                                       +--15        +---1 
  ------------TT----RT----------------------SGRT----KT----   L                         !   !            +2v1u_A    
                                                                                       !   !  
  ------------TT--RG----ST--------------------------KT----   L                         !   +------------2qby_A    
                                                                                       !  
  ----------------------NASTRGHT--STFT--------------------   L                      +-18               +--5x07_F    
                                                                                    !  !         +-----7 
  ----------------------NA--RAHT--STLT--------------------   L                      !  !  +-----12     +--2a07_K    
                                                                                    !  !  !      !  
  --------------------------------------KGKG--------------   L                      !  +-17      +--------5xfr_B    
                                                                                    !     !  
  --------------RGSTRT--STHG------------------------RA----   L                      !     +---------------3zpl_B    
                                                                                    !  
  ----------------------NASTRTHTNTSTLT--------------------   L                   +-19                  +3co6_C    
                                                                                 !  !       +----------2 
  ----------ST----------NASTRTHT--ST----------------------   L                   !  !       !          +3l2c_A    
                                                                                 !  !       !  
  ----------------------------YG--------------------------                       !  !   +--13         +4lb5_B    
                                                                                 !  !   !   !       +-5 
  ----TT----------KATT--QTTG--LTRT----KA----------------FT   L                   !  !   !   !       ! +2p7c_B    
                                                                                 !  !   !   +-------8 
  ------SGQG----YCNC--------------------------------------                    +-20  +--16           !  +2ve9_C    
                                                                              !  !      !           +--3 
  ----------------KGTA----TA----RG------------------------   L                !  !      !              +1xsd_A    
                                                                              !  !      !  
  ----------------RGRG--YC--------------------------------   L                !  !      !        +-----1cf7_A    
                                                                          +--21  !      +-------11  
  ------------STRGMCTT--RT--------------------------------   L            !   !  !               +-----4u0y_B    
                                                                          !   !  !  
  KAFA----------------------------------------YANA--FGMC--                !   !  +------------------3aaf_B    
                                                                       +-22   !  
  ------------STKTPTTT--FT--------------------------RA----   L         !  !   !        +-----------4aso_F    
                                                                       !  !   +-------14  
  ------------RT------------------------------------------   L         !  !            +-----------5fmf_V    
                                                                    +-23  !  
  ------YC----KTHGSTQT--YTPT----------------------LG------   L      !  !  +------------------------5x11_A    
                                                                    !  !  
  ------------------SA------------------------------RG----   L      !  !                      +---5npk_d    
                                                                    !  +----------------------9 
  ------------------SG------------------------------RT----       +-24                         !  +5iwi_C    
                                                                 !  !                         +--4 
  ------------------AA----ET------------------------RG----   L   !  !                            +5eix_A    
                                                                 !  !  
  ------------------DCKGRGNARTKT------------------KGRA----   L -25  !                         +-5ddg_A    
                                                                 !  +-------------------------6 
  ------------------QC--KGSGRTRG--------------------------   L   !                            +-3gz6_A    
                                                                 !  
  ----------------------------------RG--------------------       +----------------------------4hly_B    
                                                               


> 2c7a_B:STRUCTURE OF THE PROGESTERONE RECEPTOR-DNA COMPLEX

  
  ----EC--KA--RGRG----   L   +---------------------4nqa_I    
                             !  
  --------KGVT--RG--RC   L   !                               +2c7a_B    
                             !                             +-5 
  ----EC--KG--KGRG----   L   !                           +-7 +1dsz_B    
                             !                           ! ! 
  ----EA--KG--RTRTRT--       !                         +-9 +2han_B    
                             !                         ! ! 
  ----EC--KG--RGRG----   L   !                         ! +2nll_B    
                             !                      +-12  
  --------KGVT--RG----   L   !                      !  !   +5cbz_E    
                             !                      !  ! +-2 
  --HGECAGKGAAKGRT----   L   !                      !  ! ! +1lo1_A    
                           -16                      !  +-8 
  --------KAVA--RA----   L   !                      !    ! +5e69_A    
                             !                      !    +-1 
  ----EC--KG--KGRA----   L   !                   +-13      +5l0m_A    
                             !                   !  !  
  --HC----KGVT--RG--RT       !                   !  !     +-3g9m_B    
                             !                   !  !     !  
  ----DG--KG--RTRG----   L   !                   !  !  +-10   +3cbb_A    
                             !                   !  !  !  ! +-3 
  ----EA--KG--RTRG----   L   !                +-14  !  !  +-4 +1kb2_B    
                             !                !  !  +-11    ! 
  CA--EC--KG--KGRG----   L   !                !  !     !    +1cit_A    
                             !                !  !     !  
  --HAEC--KG--RGRG----   L   !                !  !     +-1a6y_A    
                             +---------------15  !  
  ----ET--KGAT--RG----   L                    !  !   +1lat_A    
                                              !  +---6 
  --------KGVT--RG----                        !      +5emc_A    
                                              !  
  ----EC--KG--KGRG----   L                    +----2ff0_A    
                           


> 2d5v_B:CRYSTAL STRUCTURE OF HNF-6ALPHA DNA-BINDING DOMAIN IN COMPLEX WITH THE TTR PROMOTER

  
  --TTQA--LTSAET--------------------------------   L                     +-----------2o4a_A    
                                                       +----------------17  
  QTSTNTVTATSTQTRTETTT--------------------------   L   !                 +-----------2r1j_L    
                                                       !  
  ----------------------RT----------IAKGNA------   L   !                                     +2hdd_A    
                                                       !                                   +-1 
  ------------------------HTRT------NCSTNARG----   L   !                                 +-4 +1k61_B    
                                                       !                                 ! ! 
  ----------------------RT----------NT--NAIARG--   L   !                               +-8 +1puf_B    
                                                       !                               ! ! 
  ------------------------RT--------NT--NAIARG--   L   !                            +-11 +4cyc_B    
                                                       !                            !  !  
  --------------------------------RTVAIANAMCRG--   L   !                            !  +1le8_A    
                                                       !                            !  
  ----------------------RT------------KGNA------   L   !                            !               +2hos_A    
                                                     -18                            !             +-2 
  ----------------------RT----------VAQTNA------   L   !                            !           +-3 +5hod_A    
                                                       !                            !           ! ! 
  ----------------------RC----------IAQCNAYA----   L   !                         +-13         +-5 +1nk3_P    
                                                       !                         !  !         ! ! 
  ----------------------RA----------IAQTNAMC----   L   !                         !  !       +-7 +1puf_A    
                                                       !                         !  !       ! ! 
  ----------------------RT----------VASGNA------   L   !                         !  !     +-9 +3cmy_A    
                                                       !                         !  !     ! ! 
  ----------------------RT----------IAQTNA----KT   L   !                         !  !  +-10 +4rdu_A    
                                                       !                      +-15  !  !  !  
  --------------------YARA----------IAQTNA------   L   !                      !  !  +-12  +5lux_L    
                                                       !                      !  !     !  
  ----------------------RT----------VAQTNA------   L   !                      !  !     ! +1fjl_B    
                                                       !                      !  !     +-6 
  --SGQATT--STRG--------------------------------   L   +---------------------16  !       +1gt0_C    
                                                                              !  !  
  ----------------------RT----------IAQCNAMG----   L                          !  +---1b72_A    
                                                                              !  
  ----------------------RT----STVCKGDCRG--------   L                          !   +--1w0t_A    
                                                                              +--14  
  ------------------------------VTKTIAQTNA----RT   L                              +--2me6_A    
                                                     


> 2dgc_A:GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA

  
  ------NCTT--AT--RG   L                             +2dgc_A    
                                                  +--1 
  RG----NC--YGATCTRG   L                          !  +2wt7_B    
                                                +-5 
  RC----NC--AAATCTRC   L                        ! !  +2wt7_A    
                                                ! +--2 
  RG----NC--YGAT--RC   L   +--------------------6    +4eot_A    
                           !                    ! 
  RG--QGNARTAGQTFTRG   L   !                    !  +-1gd2_G    
                           !                    +--4 
  --RA--NA--AAVTSTRG   L --7                       ! +1nwq_C    
                           !                       +-3 
  ------NTRTATATCTRA   L   !                         +5vpe_D    
                           ! 
  ------NG--AT--STRG       +-------------------------5szx_B    
                         


> 2dp6_A:CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE IN COMPLEX WITH AP:C CONTAINING DNA

  
  RC--RA--RCQTNT--QGTCRC--   L       +-------------2dp6_A    
                                 +---2 
  --------------PG------NG       !   +-------------1oe4_B    
                               --3 
  --------PALA------------       !             +---4uqm_A    
                                 +-------------1 
  --KT--TT----------------                     +---4yig_E    
                               


> 2drp_D:THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXTENSION TO THE RULES FOR ZINC-FINGER/DNA RECOGNITION

  
  ------TTSG--RGLT--ETYC--   L          +--------4f6m_A    
                                        ! 
  STQAQTATSTNTATTTLAHGTCRG   L        +-3        +1g2f_F    
                                      ! !  +-----1 
  ------KGDC--RGQARGATNA--   L        ! +--2     +2i13_A    
                                 +----4    ! 
  --RGSTDCHG--TTRG--DAEGRG   L   !    !    +-----5kl3_A    
                               --5    ! 
  --QA----TC----RA--SCDCVT   L   !    +---------5yeg_A    
                                 ! 
  --RG--DGEC--RGRGSGDCHA--   L   +--------------2wbs_A    
                               


> 2e1c_A:STRUCTURE OF PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR PH1519/DNA COMPLEX

  
  LTAGETSGTTHT--------------------------   L           +-----------------2e1c_A    
                                               +-------2 
  --------------TAFCSG--------LATGSGVGFA   L   !       !        +--------5tkz_B    
                                             --3       +--------1 
  --------------------KTTGYCNG----------   L   !                +--------1b3t_A    
                                               ! 
  ------------YG------------------------       +-------------------------2heo_D    
                                             


> 2e42_A:CRYSTAL STRUCTURE OF C/EBPBETA BZIP HOMODIMER V285A MUTANT BOUND TO A HIGH AFFINITY DNA FRAGMENT

  
  RG--QGNARTAGQT----FTRG--------------   L             +1gd2_G    
                                                     +-2 
  --------------RG------NC----YGATCTRG   L           ! +2wt7_B    
                                                 +---4 
  ----------NTRT--ATAT----CTRA--------   L       !   ! +5vpe_D    
                                                 !   +-1 
  --------------RG------NC----YGAT--RC   L   +---5     +4eot_A    
                                             !   ! 
  ------RA--NA----AAVT----STRG--------   L   !   !    +1nwq_C    
                                           --6   +----3 
  --RC----NC--AAAT----CTRC------------   L   !        +2wt7_A    
                                             ! 
  ----------NCTT----AT------RG--------   L   +--------2dgc_A    
                                           


> 2ex5_A:GROUP I INTRON-ENCODED HOMING ENDONUCLEASE I-CEUI COMPLEXED WITH DNA

  
  SANCSCKGLT----------DAECNATG------RC--KGST--------------DA--QA----QCNT   L                +-----------2ex5_A    
                                                                                            !  
  SAYCLCITRGDCYA--QG--------IG--NA--RG------RG--DTIC--RG----------------   L                !         +--2fld_B    
                                                                                            !    +----7 
  STITQAKGRG--STNTQT--ST--ATTC------------YT--SC--VCDTRG--ST----KGTG----   L                !    !    +--3mxb_B    
                                                                                            !    ! 
  CTFTSTYAST--KTSTAT--QA--KTTG--RA--ET----RG------ATDT----TA------------   L                !    !          +4lq0_A    
                                                                               +-----------10    !        +-2 
  SAKGIGKT----SGITQA--IA--QATC------EC----DT--RG--WTYC----TC------------   L   !            ! +--8      +-4 +4lox_A    
                                                                               !            ! !  !      ! ! 
  CTSTVAFTST--TCSCAT--KA--ITTC------ST------DA--RGTC--KT--TG------------   L   !            ! !  !      ! +5esp_A    
                                                                               !            ! !  !    +-5 
  TTYTHG----------YC--RGRGIT--------QC------------MCHT----TGKT----------   L   !            ! !  !    ! !   +5thg_A    
                                                                               !            ! !  !    ! ! +-1 
  HC--NAKT--------YA----RG--SA----RT--KG--KG----FTWTECET--TT------------   L -11            +-9  +----6 +-3 +5t2h_A    
                                                                               !              !       !   ! 
  HT--NCWCRG----------QG----ST--YG--LA--KG--RG--LTWC--RG--TG------------   L   !              !       !   +5t2n_A    
                                                                               !              !       ! 
  CCMT--ACST--AT--QA--YA--ICTA--RT------------KGRTVAEC--QT--------------   L   !              !       +--4yit_A    
                                                                               !              ! 
  CCSTYG------NT--YT--ITSTDT--AT--------YA------TTCCRTKT--TA------------   L   !              +----------3uvf_B    
                                                                               !  
  --YT------------RGSGECRGVTTG--------QG--VG------RTEARG--SC------------   L   +------------------------2vs7_A    
                                                                             


> 2f8n_G:2.9 ANGSTROM X-RAY STRUCTURE OF HYBRID MACROH2A NUCLEOSOMES

  
  --KT----------RT--   L                  +2f8n_G    
                                    +-----1 
  KT------------RA--                !     +1kx5_G    
                               +---10  
  --------------RT--           !    !      +5b0z_C    
                               !    !    +-2 
  --------------RT--           !    +----5 +5gt0_C    
                               !         ! 
  --------------RG--       +--14         +4jjn_G    
                           !   !  
  --------------RART       !   !  +----------3x1t_G    
                           !   !  !  
  --------IT--------       !   !  !         +3wkj_D    
                           !   +-13       +-7 
  ------RAAANA------       !      !   +---8 +1jfi_B    
                           !      !   !   ! 
  --------AT--------       !      !   !   +--4awl_B    
                           !      +--12  
  ----------RT------       !          !  +------4jjn_F    
                         -15          !  !  
  ----RA--ET--RT----       !          !  !     +4ne1_p    
                           !          +-11 +---6 
  --------LC----RG--       !             ! !   ! +4jjn_A    
                           !             ! !   +-4 
  --------LT----RC--       !             +-9     +5av9_A    
                           !               ! 
  --------------RG--       !               !    +5t5k_E    
                           !               +----3 
  --------------RC--       !                    +1kx5_B    
                           !  
  ----------------RT       +--------------5b31_G    
                         


> 2fdc_B:STRUCTURAL BASIS OF DNA DAMAGE RECOGNITION AND PROCESSING BY UVRB: CRYSTAL STRUCTURE OF A UVRB/DNA COMPLEX

  
  ----SGYGYGQCPCYCFCMAFASAICECLCQAMGRG----FT--                                  +--2fdc_B    
                                                         +----------------------1 
  --------YT--PTYT--------------QTMGRT--NAFALA   L     +-2                      +--3v4r_B    
                                                       ! ! 
  --------------------------------------RT----   L   +-3 +-------------------------5vvr_M    
                                                     ! ! 
  FTTT--------------------------------RT------   L --4 +---------------------------2pjr_A    
                                                     ! 
  ------------------------------DA------QA----   L   +----------------------------4qqw_A    
                                                   


> 2ff0_A:SOLUTION STRUCTURE OF STEROIDOGENIC FACTOR 1 DNA BINDING DOMAIN BOUND TO ITS TARGET SEQUENCE IN THE INHIBIN ALPHA- SUBUNIT PROMOTER

  
  ----EC--KG--KGRG--RCRC   L         +2ff0_A    
                               +-----9 
  ----EC--KG--KGRA--RTRC   L   !     +5l0m_A    
                               !  
  --HGECAGKGAAKGRT--RTRC   L   !     +--1lo1_A    
                               !  +-13  
  CA--EC--KG--KGRG------   L   !  !  +--1cit_A    
                             -16  !  
  ----EC--KG--KGRG------   L   !  !     +-1dsz_B    
                               !  !     !  
  ----DG--KG--RTRG------   L   !  !     !    +3cbb_A    
                               !  !     !  +-1 
  ----EA--KG--RTRTRT----       !  !  +-12  ! +2han_B    
                               +-15  !  !  !  
  --------KGVT--RG------   L      !  !  !  !        +5cbz_E    
                                  !  !  !  !      +-5 
  ----EC--KA--RGRG------   L      !  !  !  !      ! +4nqa_I    
                                  !  !  +-11    +-7 
  --------KAVA--RA------   L      !  !     !    ! ! +5e69_A    
                                  !  !     !  +-8 +-2 
  --------KGVT--RG------   L      !  !     !  ! !   +2c7a_B    
                                  +-14     !  ! ! 
  --HAEC--KG--RGRG------   L         !     !  ! +1a6y_A    
                                     !     +-10  
  ----ET--KGAT--RG------   L         !        !   +1lat_A    
                                     !        ! +-3 
  ----EA--KG--RTRG------   L         !        +-4 +1kb2_B    
                                     !          ! 
  ----EC--KG--RGRG------   L         !          +2nll_B    
                                     !  
  --------KGVT--RG------             !  +5emc_A    
                                     +--6 
  --HC----KGVT--RG------                +3g9m_B    
                             


> 2fld_B:I-MSOI RE-DESIGNED FOR ALTER