(updated: Tue Sep 26 13:48:21 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

  
  ----HG------ET----RTRG------   L                   +--------------5v0l_A    
                                           +---------2 
  ----HG----ITEC----RCRG------   L     +---4         +--------------5nj8_D    
                                       !   ! 
  ----HGNT--LGEC----RCRC------   L     !   +------------------------5i50_B    
                                     +-5 
  --QG------VTEC----RCRG----QG   L   ! !          +-----------------1an4_A    
                                     ! +----------3 
  --------HGST--ITET----RCRG--   L --6            !             +---4h10_A    
                                     !            +-------------1 
  RT--STRT----AT----RGRG------       !                          +---4zpr_B    
                                     ! 
  ----HG------ET----RCRG------   L   +-----------------------------5gnj_I    
                                   


> 1a3q_A:HUMAN NF-KAPPA-B P52 BOUND TO DNA

  
  RGRGYTCCEC--HG--KG------   L      +-1a3q_A    
                                 +--2 
  RGRGYTCCEC--HTKTKTPTKTRG   L   !  +-1nfk_A    
                               --3 
  RGRGYTCTECSG----RT------   L   !   +2i9t_A    
                                 +---1 
  RGRGYTCTEC------RT------   L       +1gji_A    
                               


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

  
  RGRGYT--ECRA--KTRTTT----QART   L                  +------------1a66_A    
                                                +---3 
  RGRGYTCT----------------RT--   L              !   !           +2i9t_A    
                                                !   +-----------1 
  RGRGYTCTEC------------------   L   +----------4               +1gji_A    
                                     !          ! 
  RGRG----EG------------------   L   !          !             +--1bvo_A    
                                   --5          +-------------2 
  RGRGYTCCEC--KT----------KT--   L   !                        +--1nfk_A    
                                     ! 
  --------------------RGAT----       +---------------------------5kbd_B    
                                   


> 1a6y_A:REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX

  
  --ECKA--RGRG--   L   +----------------------4nqa_I    
                       !  
  --ECKG--KGRA--   L   !                     +5l0m_A    
                       !                   +-4 
  --ECKG----RA--   L   !                   ! +5krb_G    
                     -10    +--------------7 
  --EAKG--KTRG--   L   !    !              ! +-4cn3_D    
                       !    !              +-5 
  ----KGVT--RG--   L   !    !                ! +5cbz_E    
                       !    !                +-2 
  ----KAVA--RA--   L   +----9                  +5e69_A    
                            ! 
  --ECKG--RGRG--   L        !        +--------2nll_B    
                            !        ! 
  --ECKGAG--RG--   L        !        !          +4ond_A    
                            +--------8        +-1 
  ----KGVG--RG--   L                 !      +-3 +4tnt_B    
                                     !      ! ! 
  ----KGVT--RG--                     +------6 +5emc_A    
                                            ! 
  YGECKGAG--KGRG   L                        +-4oln_B    
                     


> 1ais_A:TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI

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


> 1ais_B:TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI

  
  ----VCRG----------                                       +1c9b_M    
                                       +-------------------1 
  ACRC--------------   L     +---------2                   +4roc_A    
                             !         ! 
  ----------YG------       +-3         +-------------------3irr_C    
                           ! ! 
  --------NT--NAIARG   L --4 +-----------------------------4cyc_B    
                           ! 
  ----------YG------       +-----------------------------1sfu_A    
                         


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

  
  ------------HGNT--LGEC----RCRC   L                      +--5i50_B    
                                          +---------------2 
  --------HG------ET----RCRG----   L      !               +--5gnj_I    
                                       +--4 
  --RT------NT--RGEC----RCQT----       !  !                  +2ypa_A    
                                       !  !             +----1 
  ----ST------AT----RTRG--------     --5  +-------------3    +4zpk_B    
                                       !                ! 
  ST------AT----RTRG------------       !                +----5sy7_B    
                                       ! 
  ------HG------ET----RTRG------   L   +---------------------5v0l_A    
                                     


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

  
  ----QG----VTECRCRGQG   L                        +----1an4_A    
                                       +----------2 
  RT----STRT--ATRGRG--                 !          +----4zpr_B    
                                  +----4 
  --RT----NTRGECRCQT--            !    !       +-------2ypa_A    
                                  !    +-------3 
  ------HG--ITECRCRG--   L   +----5            +-------5nj8_D    
                             !    ! 
  --------NT--ETRCMT--       !    !                   +2ql2_D    
                           --6    +-------------------1 
  ------RTNT--ECRCRG--   L   !                        +4h10_B    
                             ! 
  --RG--HGKT--EARCRC--   L   +-------------------------1a0a_B    
                           


> 1au7_A:PIT-1 MUTANT/DNA COMPLEX

  
  ----RT----VAQTNA------   L   +----------------------5hod_A    
                               !  
  ----RT----IAQTNA----KT   L   !                          +4rdu_A    
                               !                        +-1 
  ----RA--RTITQCNA------   L   !                      +-3 +5eea_B    
                               !                      ! ! 
  --YART----IAQTNA------   L   !               +------6 +5lty_K    
                               !               !      ! 
  ----RT--RTIAQCNA------   L -13               !      ! +5jlw_D    
                               !           +---9      +-2 
  --YARA----IAQTNA------   L   !           !   !        +5lux_L    
                               !           !   ! 
  ----RA----IAQCNAMC----   L   !      +---10   +------4cyc_A    
                               !      !    !  
  ----RA----IA--NA------       !      !    !         +4xrs_G    
                               !      !    +---------8 
  ----------IA--NA------       +-----12              +4qtr_D    
                                      !  
  ----RT----IAQTNAMC----   L          !               +2h1k_B    
                                      !   +-----------5 
  RT--RA----IAQCNAMG----   L          !   !           +2r5z_A    
                                      +--11  
  ----------TAQCNAMC----                  !            +4rbo_D    
                                          !          +-4 
  ------RT--NT--NAIARG--   L              +----------7 +4cyc_B    
                                                     ! 
  ----------NCICNARGRG--   L                         +4xrm_B    
                             


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

  
  ------DCKT--RG--RGYA--------   L            +------1dux_F    
                                              ! 
  --------STVT----RGQTNT--MT--   L          +-6       +5d5v_B    
                                            ! !     +-4 
  --------ST------RTQT--MT----   L          ! !     ! ! +5d8k_B    
                                            ! +-----5 +-2 
  --KTHG----------------------       +------7       !   +5hdn_C    
                                     !      !       ! 
  --------ST------RTQT----KG--       !      !       +5d5w_B    
                                     !      ! 
  ------DCKT--RGSTRGYC--------   L   !      !        +4uno_A    
                                   --9      +--------1 
  ------DCKT--RGATRCYA--------   L   !               +5e8i_D    
                                     ! 
  ------DCKT--RGSTRGYA--------   L   !              +4bnc_A    
                                     !    +---------3 
  --------KT--RGATRGYA--------   L   +----8         +4iri_A    
                                          ! 
  RC------QG----------------SG            +----------4qlc_U    
                                   


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

  
  WGFTRTNTKGFT------KTTGYCNGRT------------------------   L                          +1b3t_A    
                                                                             +------1 
  WCFT----KG--------KGTAYCNGRT------------------------   L          +--------2      +5t7x_B    
                                                                    !        ! 
  --------KG------------------------------------------   L   +------3        +------4uzb_B    
                                                             !      ! 
  ----------------------KGCGFT------------------------   L --4      +---------------2bop_A    
                                                             ! 
  ------------TAFCSG----------LATGSGVGFARAECACKCSCTAKC   L   +----------------------5tkz_B    
                                                           


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

  
  HT----RA----IAQCNA----MG----   L                     +2r5z_A    
                                                     +-4 
  ------RT----VAQTNA----------   L                +--7 +5hod_A    
                                                  !  ! 
  ------RA----IA--NA----------                 +--9  +4xrs_G    
                                               !  ! 
  ------RA----IAQCNA----MC----   L         +--11  +---4cyc_A    
                                           !   !  
  ------------IA--NA----------             !   !    +-4qtr_D    
                                           !   +----8 
  ------------NCIC--RGRG------   L         !        +-4xrm_B    
                                           !  
  --RA--RT----IAQTNA--------KT   L   +----12             +4rdu_A    
                                     !     !           +-1 
  ------RA--RTITQCNA----------   L   !     !         +-3 +5eea_B    
                                     !     !         ! ! 
  ----YART----IAQTNA----------   L   !     !     +---6 +5lty_K    
                                     !     !     !   ! 
  --KT--RT----IAQTNA----MC----   L -13     +----10   +2h1k_B    
                                     !           !  
  ------RT--RTIAQCNA----------   L   !           !    +5jlw_D    
                                     !           +----2 
  ----YARA----IAQTNA----------   L   !                +5lux_L    
                                     !  
  ------------TAQCNA----MC----       !                +4rbo_D    
                                     +----------------5 
  --------RT--NT--NA----IARG--   L                    +4cyc_B    
                                   


> 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

  
  ------DCKT--RGAT--RCYA--------   L                                  +5e8i_D    
                                                               +------1 
  --------KT--RGAT--RGYA--------   L                           !      +4iri_A    
                                                             +-7 
  --------STVT------RGQTNT--MT--   L                         ! !     +5d5v_B    
                                                             ! +-----4 
  --------ST--------RTQT--MT----   L                         !       ! +5d8k_B    
                                                          +--8       +-3 
  --KTHG------------------------                          !  !         +5hdn_C    
                                                          !  ! 
  ------DCKT--RGST--RGYA--------   L                      !  !       +4bnc_A    
                                                +---------9  +-------2 
  ------DCKT--RGST--RGYC--------   L            !         !          +4uno_A    
                                                !         ! 
  ------DCKT--RG----RGYA--------   L            !         !    +-----1dux_F    
                                       +-------10         +----6 
  --------ST--------RTQT--KG----       !        !              +-----5d5w_B    
                                       !        !  
  ----------NA----RAHT--STLT----   L -11        !                 +--2a07_K    
                                       !        +-----------------5 
  RC------QG------------------SG       !                          +--4qlc_U    
                                       !  
  ------------ST--RGHT--ST------   L   +-----------------------------3g73_A    
                                     


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

  
  KCEC--STNTVGSTQT   L                              +1bf5_A    
                                           +--------1 
  ------STNT----QT       +-----------------2        +1bg1_A    
                         !                 ! 
  ----KAVTHG--NTQT   L --3                 +--------4y5w_B    
                         ! 
  ------ATCT----RG   L   +--------------------------3q05_B    
                       


> 1bg1_A:TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX

  
  ------------STNT----QT                                   +1bg1_A    
                                                  +--------1 
  --------KC--STNTVGSTQT   L     +----------------2        +1bf5_A    
                                 !                ! 
  ----------KAVTHG--NTQT   L   +-3                +---------4y5w_B    
                               ! ! 
  ------------ATCT----RG   L --4 +--------------------------3q05_B    
                               ! 
  NGATSTRG--------------       +----------------------------5szx_B    
                             


> 1bvo_A:DORSAL HOMOLOGUE GAMBIF1 BOUND TO DNA

  
  RGRG----EGRG----------   L                            +1bvo_A    
                                    +-------------------2 
  RGRGYTCTEC------------   L        !                   ! +1gji_A    
                               +----3                   +-1 
  RGRGYTCTEC--SG--------   L   !    !                     +2i9t_A    
                             --4    ! 
  RGRGYTCCEC----HTKT----   L   !    +--------------------1nfk_A    
                               ! 
  RGRGYT--EC--------KTTT   L   +-------------------------1a66_A    
                             


> 1c9b_M:CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP)

  
  ACRC--------------   L   +-----------------------4roc_A    
                           ! 
  ----------YG------     --3                       +3irr_C    
                           !     +-----------------1 
  ----KGEA----RGLGNC   L   +-----2                 +5kbj_B    
                                 ! 
  --------RGYG------             +-----------------1qbj_C    
                         


> 1cdw_A:HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA

  
  NTVAFTLTFAVATTNAVTFAPALAFTVATA   L         +1cdw_A    
                                           +-1 
  NAVTFTLTFAVATANTVTFAPALAFTVATA   L     +-2 +1ytb_A    
                                         ! ! 
  NTVAFTLTFAVATTNAVAFAPALTFTVATA   L   +-3 +1rm1_A    
                                       ! ! 
  NTVAFCLTFAVATTNAVTFTPALTFTVATA   L --4 +4wzs_D    
                                       ! 
  NTVTFALAFTVATTNAVTFTPALTFAVTTA   L   +5n9g_G    
                                     


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

  
  RC------------------EGRTRGRG--YT------------------------   L                        +-------------------------4yo2_A    
                                                                                      !  
  --------------------HT--STAT--STRG----------------------   L                     +-21   +---------------------5lej_A    
                                                                                   !  !   !  
  --------------ETNT--SCRGHC----RT------------------QA----   L                     !  +--17                     +5d4s_B    
                                                                                   !      !        +------------1 
  ----------------RG--STRGMCTT--RT------------------------   L                     !      !        !            +4u0y_B    
                                                                                   !      +-------12  
  --------------------ITRGECSC--SGKG----------------------   L                     !               !          +-5i2d_R    
                                                                                   !               +----------6 
  --------------------STRGECTA--NGKG----------------------   L                     !                          +-3mzh_A    
                                                                                   !  
  --------------------------------------YGRG--------------                         !                             +4wcg_B    
                                                                                   !              +--------------5 
  --------------ST----STQAQGST--SART--------------------KT   L                  +-23         +---13              +5trd_B    
                                                                                !  !         !    !  
  ----------------YA--KTPTPG----YTRG----------------------   L                  !  !     +--16    +---------------4mte_D    
                                                                                !  !     !   !  
  --------------------SG--AT----YTRG----------------------   L                  !  !  +-18   +--------------------4rb3_D    
                                                                                !  !  !  !  
  --------------------ST--SAYT--ECQT--------------RT--PT--   L                  !  !  !  !        +---------------4hf1_A    
                                                                                !  !  !  +-------15  
  ----------------RG--TTRGTTTT--RTET----------------HA----   L                  !  !  !           +---------------4p9u_B    
                                                                                !  !  !  
  --KC------------------YAQTTC----QC----------------------   L                  !  !  !                            +5k5q_D    
                                                                                !  !  !                        +---2 
  ----------------------SANCTG--TTPT--------------------RT   L                  !  !  !                        !   +5hlg_E    
                                                                                !  +-22               +--------8 
  --------------------------------------YG----------------                      !     !               !        !  +4lb5_B    
                                                                                !     !               !        +--3 
  --------------------DCLT--AG--TTRG------RG------------RA   L               +-24     !            +-11           +5h3r_A    
                                                                             !  !     !            !  !  
  ----------YA--------PTATPARA--YA------------------------   L               !  !     !            !  !           +5bpd_A    
                                                                             !  !     !  +--------14  +-----------4 
  --------------NT----KTPTQTSC----KA----------------------   L               !  !     !  !         !              +5bmz_D    
                                                                             !  !     +-20         !  
  ----------------------RGSTRT--STHG--------------------RA   L               !  !        !         +---------------3zpl_B    
                                                                             !  !        !  
  ------------------------AT------------------------------                   !  !        +-------------------------5fyw_R    
                                                                             !  !  
  ------------RC------------QG--------------------------SG                +-25  !                       +---4qlc_U    
                                                                          !  !  !                  +----7 
  ------------------------------NAST--RGHT--STFT----------   L            !  !  !                  !    +---5x07_F    
                                                                          !  !  !  +--------------10  
  --------------------------SA----------------------------   L            !  !  !  !               ! +------5npk_d    
                                                                          !  !  +-19               +-9 
  --------------------------SG----------------------------             +-26  !     !                 +------5iwi_C    
                                                                       !  !  !     !  
  ------------------------NTVC--ECSTYT--STYC--------RA----   L         !  !  !     +------------------------5ed4_A    
                                                                       !  !  !  
  --------------------TTNATT--ECVT----HT------------RT----   L      +-27  !  +----------------------------4s04_B    
                                                                    !  !  !  
  --------KC------------MGSGTT--TTYC----------------------   L      !  !  +-----------------------------5f7q_C    
                                                                 +-28  !  
  --SGITMTPT--------RT------------------------------------   L   !  !  +-----------------------------5fmf_V    
                                                               -29  !  
  ------------------------SC----RGKC------------RA--------       !  +-----------------------------5fur_G    
                                                                 !  
  ------RC------------------------------------------------   L   +-----------------------------4roc_A    
                                                               


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

  
  --------NG--RGRGYC--------------   L                           +------1cf7_B    
                                                         +-------2 
  RC------------QG--------------SG                       !       +------4qlc_U    
                                               +---------3 
  ----------------------YGRG------             !         !             +4wcg_B    
                                             +-4         +-------------1 
  ------------------RG--YG--------           ! !                       +1qbj_C    
                                           +-5 ! 
  ----------------NA--RAHT--STLT--   L     ! ! +------------------------2a07_K    
                                         +-6 ! 
  --QGVCRC------------------------   L   ! ! +--------------------------5dwa_A    
                                       --7 ! 
  ----------NAST------RGHT--STFT--   L   ! +--------------------------1vtn_C    
                                         ! 
  ----------------NASTRGHT--ST----   L   +---------------------------3g73_A    
                                       


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

  
  --ECKG----RA----PARC   L                  +--5krb_G    
                                     +------6 
  --EAKG--KTRG--------   L           !      ! +-4cn3_D    
                                     !      +-4 
  ----KAVA--RA--------   L   +-------8        ! +5e69_A    
                             !       !        +-1 
  ----KGVT--RG--------   L   !       !          +5cbz_E    
                             !       ! 
  --ECKG--KGRART------   L   !       +---------5l0m_A    
                           -10  
  --ECKG--RGRG--KA----   L   !            +-----2nll_B    
                             ! +----------7 
  --ECKA--RGRG--------   L   ! !          +-----4nqa_I    
                             ! ! 
  --ECKGAG--RG--------   L   +-9                  +4ond_A    
                               !                +-2 
  ----KGVG--RG--------   L     !              +-3 +4tnt_B    
                               !              ! ! 
  ----KGVT--RG--------         +--------------5 +5emc_A    
                                              ! 
  YGECKGAGKGRG--------   L                    +-4oln_B    
                           


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

  
  --------NT----ATAT----STRG   L                      +1dh3_C    
                                                    +-1 
  --RC----NC----AAAT----CTRC   L   +----------------2 +2wt7_A    
                                   !                ! 
  ----NT--ATAT------RG------   L   !                +5t01_B    
                                 --5 
  RA--NA--AAVT----STRG------   L   !             +----1nwq_C    
                                   !           +-3 
  ------NG----AT------STRG--       +-----------4 +----5szx_B    
                                               ! 
  --------NCTT----AT------RG   L               +-----2dgc_A    
                                 


> 1dmu_A:CRYSTAL STRUCTURE OF THE RESTRICTION ENDONUCLEASE BGLI (E.C.3.1.21.4) BOUND TO ITS DNA RECOGNITION SEQUENCE

  
  KG----DC----------KG--KTRG----   L                +-----------1dmu_A    
                                       +------------1 
  --------ECRG----QTKGSC--RGRGYT   L   !            +-----------2ezv_A    
                                     --3 
  ----NC--------TT--------------   L   !       +----------------1sx5_A    
                                       +-------2 
  --RA--------NTPADA------------   L           +----------------5tgx_A    
                                     


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

  
  --ECKG--KGRA   L                    +-5l0m_A    
                                    +-5 
  --ECKG----RA   L                  ! +-5krb_G    
                          +---------7 
  ----KGVT--RG   L        !         !  +5cbz_E    
                          !         +--3 
  ----KAVA--RA   L   +----9            +5e69_A    
                     !    ! 
  --EAKG--KTRG   L   !    !             +4cn3_D    
                     !    +-------------1 
  --ECKA--RGRG   L -10                  +4nqa_I    
                     !  
  --ECKG--RGRG   L   !         +--------2nll_B    
                     !         ! 
  --ECKGAG--RG   L   !         !          +4ond_A    
                     +---------8        +-2 
  ----KGVG--RG   L             !      +-4 +4tnt_B    
                               !      ! ! 
  ----KGVT--RG                 +------6 +5emc_A    
                                      ! 
  YGECKGAGKGRG   L                    +-4oln_B    
                   


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

  
  --ECKA--RGRG   L   +----------------------4nqa_I    
                     !  
  --EAKG--KTRG   L   !                      +4cn3_D    
                     !                  +---1 
  --ECKG--RGRG   L   !                  !   +2nll_B    
                     !                  ! 
  --ECKG--KGRA   L -10      +-----------8    +5l0m_A    
                     !      !           ! +--5 
  --ECKG----RA   L   !      !           ! !  +5krb_G    
                     !      !           +-7 
  ----KGVT--RG   L   !      !             !  +5cbz_E    
                     !      !             +--3 
  ----KAVA--RA   L   +------9                +5e69_A    
                            ! 
  --ECKGAG--RG   L          !                 +4ond_A    
                            !               +-2 
  ----KGVG--RG   L          !             +-4 +4tnt_B    
                            !             ! ! 
  ----KGVT--RG              +-------------6 +5emc_A    
                                          ! 
  YGECKGAGKGRG   L                        +-4oln_B    
                   


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

  
  ------------KT--RGATRGYA------   L                                 +1bc8_C    
                                                             +-------1 
  ----------DCKT--RGATRCYA------   L                         !       +5e8i_D    
                                                             ! 
  ------------STVT----RGQTNT--MT   L        +----------------8       +5d5v_B    
                                            !                !     +-4 
  ------------ST------RTQT--MT--   L        !                !     ! ! +5d8k_B    
                                            !                +-----5 +-2 
  --KTHG------------------------          +-9                      !   +5hdn_C    
                                          ! !                      ! 
  ------------ST------RTQT--KG--          ! !                      +-5d5w_B    
                                          ! ! 
  RC----------QG----------------       +-10 !                 +------4qlc_U    
                                       !  ! +-----------------7 
  --------YA--TC--QC------------   L   !  !                   +------5k5q_D    
                                       !  !  
  --------KGEA------------------   L -11  +-------------------------5kbj_B    
                                       !  
  ------ITRGECSCSGKG------------   L   !                           +5i2d_R    
                                       !                         +-3 
  ------HT--STATSTRG------------   L   +-------------------------6 +5lej_A    
                                                                 ! 
  ------STRGECTANGKG------------   L                             +--3mzh_A    
                                     


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

  
  --SGQATT--STRG--LTNT--------RTVASTNAQA----   L                  +---------------1e3o_C    
                                                                  !  
  ----------------------RT--RT--IAQCNA------   L               +-14                +5jlw_D    
                                                               !  !              +-1 
  ----------------------RT------VAQTNA------   L               !  !              ! +5hod_A    
                                                               !  +--------------6 
  ------------------------------IA--NA------                   !                 ! +4qtr_D    
                                                               !                 +-3 
  --------------------YARA------IAQTNA------   L               !                   +5lux_L    
                                                               !  
  ----------------------RT------IAQTNAMC----   L               !                  +2h1k_B    
                                                   +----------15     +------------5 
  ----------------------RA------IAQCNAMG----   L   !           !     !            +2r5z_A    
                                                   !           !     !  
  ----------------------RA--RT--ITQCNA------   L   !           !     !               +5eea_B    
                                                   !           !  +-12             +-2 
  ----------------------RT------IAQTNA----KT   L   !           !  !  !           +-4 +4rdu_A    
                                                   !           !  !  !           ! ! 
  --------------------YART------IAQTNA------   L   !           !  !  !      +----7 +5lty_K    
                                                   !           !  !  !      !    ! 
  ----------------------RA------IA--NA------       !           !  !  +-----10    +4xrs_G    
                                                 -16           +-13         !  
  ------------------------RT----NT--NAIARG--   L   !              !         !   +-4cyc_B    
                                                   !              !         +---8 
  ----------------------RA------IAQCNAMC----   L   !              !             +-4cyc_A    
                                                   !              !  
  ------------------------------NCICNARGRG--   L   !              !        +-----4xrm_B    
                                                   !              +-------11  
  ------------------------------TAQCNAMC----       !                       +-----4rbo_D    
                                                   !  
  AT--QAAT--SA------------------------------       !                       +----4z5h_A    
                                                   +-----------------------9 
  ----QASTCTSARTET--------------------------   L                           +----5j2y_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    
                                   --4                      ! 
  ----SG--TC------RG------LCKA   L   !                      +1qpz_A    
                                     ! 
  LCYCSGVTAT--ST----HT--AGLCAC   L   +-----------------------2bjc_A    
                                   


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

  
  --------PTLA------                     +1emh_A    
                           +-------------1 
  --------PALA------       !             +4uqm_A    
                         --4 
  KT----TT------RA--       ! +-------------4yig_E    
                           +-3 
  ----KT--CGACQT--PG         !            +4z47_A    
                             +------------2 
  --SGKT--CGACQT--PG   L                  +5hf7_A    
                         


> 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       +--------3thx_A    
                       


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

  
  --RTTT------KT--------TT--ATKTFT--RTFT--ITYT----RT------ET--WTRT   L                               +-2vw9_A    
                                                                         +---------------------------1 
  NT----------RT--MT--VTET--------RTSTLT----------TT--ETYTRTQT----   L   !                           +-3udg_C    
                                                                       --3 
  ------DGTGFGYGKT--YT----KG--------------FG--IGHG----------------   L   !     +-----------------------2i0q_A    
                                                                         +-----2 
  ----------RTWT----------------------FTNT----------RT--------KT--   L         +-----------------------4gnx_Z    
                                                                       


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

  
  ------RG--DCEC--RGRG--DCHG------   L                        +1f2i_J    
                                                         +----5 
  PCYC--RG--DA----RGRG--DCHG------   L                 +-6    +2prt_A    
                                                       ! ! 
  ------RA----NC------ATSGDC--KG--   L           +-----7 +-----2gli_A    
                                                 !     ! 
  ----RGDC--SCNA----NCKTSAHG--RG--   L           !     !       +5ei9_F    
                                                 !     +-------3 
  ------DG--YCKG--RGQA----TC------   L           !             +5kkq_D    
                                             +---9 
  ------QASTSCDC--KGRG--DCHA--RG--   L       !   !               +1mey_C    
                                             !   !             +-1 
  ------RGSTDTEG--RGRGSGDCHG--TT--   L       !   ! +-----------4 +4x9j_A    
                                             !   ! !           ! 
  ------RGSTDAHA--RGRGSTDCHG--TT--   L   +--10   +-8           +5kl3_A    
                                         !   !     ! 
  ----RGST--YGYC----QC--TGSTRGYT--   L   !   !     !           +4is1_C    
                                         !   !     +-----------2 
  ------DC--YCKG--RGQA----TC------   L -11   !                 +5k5i_A    
                                         !   !  
  ----------HCHG--RGTA--ACNA--KGRG   L   !   +-----------------1tf6_A    
                                         !  
  ------RGSTDCHGTTTTRG--DAEC--RG--   L   +---------------------1llm_D    
                                       


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

  
  RTLANTHGTTETYTRG------------------   L                   +------1f4k_B    
                                              +------------3 
  ----TT--RGRT------------SGRT----KT   L      !            +------2v1u_A    
                                              ! 
  ------------NASTRGHTSTFT----------   L      !                    +1vtn_C    
                                              !         +----------1 
  ------------NASTRGHTSTFT----------   L   +--7         !          +5x07_F    
                                           !  !   +-----4 
  ------------NA--RAHTSTLT----------   L   !  !   !     !       +--2a07_K    
                                           !  ! +-5     +-------2 
  ----------QG----------------------       !  ! ! !             +--4qlc_U    
                                         --8  +-6 ! 
  ------YAQTTC--QC------------------   L   !    ! +----------------5k5q_D    
                                           !    ! 
  ------------NASTRGHTST------------   L   !    +------------------3g73_A    
                                           ! 
  ----DCKGRG----NARTKT--------KGRA--   L   +----------------------5ddg_A    
                                         


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

  
  ------YAQTTC--QC----------------   L                                +5k5q_D    
                                                  +-------------------2 
  ST--STQAQGSTSART----------------   L            !                   +5trd_B    
                                                  ! 
  ------RGSTRTSTHG----------------   L      +-----8              +-----3zpl_B    
                                            !     !     +--------5 
  ----DCLT--AGTTRG----RG----------   L      !     !     !        !   +-5h3r_A    
                                            !     +-----7        +---3 
  NT--KTPTQTSC--KA------------RT--   L      !           !            +-5bmz_D    
                                            !           ! 
  --------QC----------------------       +-10           +--------------5hso_A    
                                         !  !  
  ------------------YGRG----------       !  !                       +--4wcg_B    
                                         !  !  +--------------------4 
  ----------QG--------------------       !  !  !                    +--4qlc_U    
                                         !  +--9 
  ETNTSCRGHC--RT------------QA----   L -11     !                       +5d4s_B    
                                         !     !            +----------1 
  --RGSTRGMCTTRT------------------   L   !     +------------6          +4u0y_B    
                                         !                  ! 
  ----ST--SAYTECQT--------RT--PT--   L   !                  +----------4hf1_A    
                                         !  
  --------SAQT----RGQT--NG------QT   L   +-----------------------------3wgi_D    
                                       


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

  
  --RT--RA------------------------IAQCNAMG--   L                             +2r5z_A    
                                                                           +-1 
  ------RT------------------------VAQTNA----   L                 +---------7 +5hod_A    
                                                                 !         ! 
  ----YARA------------------------IAQTNA----   L                 !         +5lux_L    
                                                            +---11  
  KT----RT------------------------IAQTNAMC--   L            !    !         +2h1k_B    
                                                            !    !         ! 
  ------RA------------------RT----ITQCNA----   L            !    +---------6   +5eea_B    
                                                            !              ! +-2 
  RA----RT------------------------IAQTNA----   L            !              +-3 +4rdu_A    
                                                            !                ! 
  ----YART------------------------IAQTNA----   L         +-13                +5lty_K    
                                                         !  !  
  ------RA------------------------IA--NA----             !  !               +4xrs_G    
                                                         !  !             +-8 
  --------------------------------IA--NA----             !  !   +---------9 +4qtr_D    
                                                         !  !   !         ! 
  --------------------------------NCICNARGRG   L         !  +--12         +4xrm_B    
                                                      +-14      !  
  ------RT------------------RT----IAQCNA----   L      !  !      !          +5jlw_D    
                                                      !  !      +----------4 
  ------RA------------------------IAQCNAMC--   L      !  !                 +4cyc_A    
                                                      !  !  
  --------------------------------TAQCNAMC--       +-15  !                 +4rbo_D    
                                                   !  !  !         +-------5 
  --------RT----------------------NT--NAIARG   L   !  !  +--------10       +4cyc_B    
                                                   !  !            !  
  --------NGRGTG--------LC--LCRG------------     -16  !            +-------4ofa_A    
                                                   !  !  
  ----------KA------------SGAT--YTRG--------   L   !  +--------------------4rb3_D    
                                                   !  
  --------------IGYGYGFG--------------------       +---------------------4ztu_A    
                                                 


> 1flo_A:FLP RECOMBINASE-HOLLIDAY JUNCTION COMPLEX I

  
  --AATAYGTTKGRAFCKC--KC------NT----RGST--KT--   L         +---------------------1flo_A    
                                                     +-----2 
  LTNTTT------------------TTQAATYG--YAKT------   L   !     !    +----------------5jk0_B    
                                                   --3     +----1 
  ------------------KA----SA--------QG------RA   L   !          +----------------5u91_B    
                                                     ! 
  ----------------------KA------RTLT----RT----   L   +---------------------------4e0p_A    
                                                   


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

  
  QANARGQGDTNTWCNGNCECSAKGRGMG----------------------------------   L          +------------------------1fok_A    
                                                                              !  
  ----------------------------------------------YGRG------------          +--14                        +4wcg_B    
                                                                          !   !  +---------------------7 
  ----------------------------------------------YG--------------          !   !  !                     +4lb5_B    
                                                                          !   +-13  
  --------------------------------RGSTRGMCTTRT------------------   L   +-15      !                +-----4u0y_B    
                                                                       !  !      +----------------9 
  ----------------------------------ST--SAYTECQT----------RT----   L   !  !                       +-----4hf1_A    
                                                                       !  !  
  ----------------------------------------------------------RTEG       !  +----------------------------5gke_A    
                                                                       !  
  --------------------------------------------TAQCNAMC----------       !                                +4rbo_D    
                                                                       !                              +-1 
  ----------------------------RT--------RT----IAQCNA------------   L   !                            +-2 +5jlw_D    
                                                                       !                            ! ! 
  ------------------------------RA------RT----ITQCNA------------   L -16                +-----------5 +5eea_B    
                                                                       !                !           ! 
  --------------------------------------------IAQTNA----KT------   L   !                !           +4rdu_A    
                                                                       !                !  
  --------------------------------------------NT--NAIARG--------   L   !                !           +4cyc_B    
                                                                       !             +-11         +-6 
  --------------------------------------------NCICNARGRG--------   L   !             !  !         ! +4xrm_B    
                                                                       !             !  !   +-----8 
  --------------------------------------------IA--NA------------       !             !  !   !     ! +4qtr_D    
                                                                       !             !  !   !     +-4 
  --------------------------------------------VAQTNA------------   L   +------------12  +--10       +5hod_A    
                                                                                     !      !  
  --------------------------------------------IA--NA------------                     !      !       +4xrs_G    
                                                                                     !      +-------3 
  --------------------------------------------IAQTNAMC----------   L                 !              +2h1k_B    
                                                                                     !  
  ----------------------------RTRA------------IAQCNAMG----------   L                 +--------------2r5z_A    
                                                                     


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

  
  KG--WTKA--------HCHGRGTA--ACNA--KGRG   L             +---------------1tf6_A    
                                                       ! 
  RGSTDTEGRG--RGSGDCHGTTRG--DAEG--RG--   L        +----4                +4x9j_A    
                                                  !    !              +-2 
  RGSTDAHARG--RGSTDCHGTTRG--DAEG--RG--   L        !    +--------------3 +5kl3_A    
                                             +----5                   ! 
  DC--YCKGRG--QA----TC--RC--SCDC--VT--   L   !    !                   +5k5i_A    
                                             !    ! 
  ECVASCKGRG--DG--YCKGRGQA----TC------   L --6    !                    +5kkq_D    
                                             !    +--------------------1 
  DA--SCHGRGRGDC--SCNA--NCKTSAHG--RG--   L   !                         +5ei9_F    
                                             ! 
  ----------RGST--YGYC--QC--TGSTRGYT--   L   +-------------------------4is1_C    
                                           


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

  
  KG--WTKA--------HCHGRGTA--ACNA--KGRG   L            +---------------1tf6_A    
                                                      ! 
  RGSTDTEGRG--RGSGDCHGTTRG--DAEG--RG--   L          +-5                +4x9j_A    
                                                    ! !              +-2 
  RGSTDAHARG--RGSTDCHGTTRG--DAEG--RG--   L          ! +--------------3 +5kl3_A    
                                             +------6                ! 
  DC--YCKGRG--QA----TC--RC--SCDC--VT--   L   !      !                +5k5i_A    
                                             !      ! 
  ECVASCKGRG--DG--YCKGRGQA----TC------   L   !      !                +5kkq_D    
                                           --7      +----------------1 
  DA--SCHGRGRGDC--SCNA--NCKTSAHG--RG--   L   !                       +5ei9_F    
                                             ! 
  ----TTSGRG--LT--ETYC--NTYGQG--------   L   !            +----------4f6m_A    
                                             +------------4 
  ----------RGST--YGYC--QC--TGSTRGYT--   L                +----------4is1_C    
                                           


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

  
  ----NT--ATAT----RG----   L     +-----------------------------5t01_B    
                               +-2 
  --RG----NC--YGAT--CTRG   L   ! !                            +3a5t_B    
                             --3 +----------------------------1 
  ----RA--NA--AAVT--STRG   L   !                              +1nwq_C    
                               ! 
  RCNC--AAAT--CTRC------   L   +-----------------------------2wt7_A    
                             


> 1gdt_A:CRYSTAL STRUCTURE OF A SITE-SPECIFIC RECOMBINASE, GAMMA- DELTA RESOLVASE COMPLEXED WITH A 34 BP CLEAVAGE SITE

  
  IT--RTTTRAFTRA--ACRGSGTC--YTKT   L              +-------1gdt_A    
                                              +---1 
  IT----------RTPAAGLASTTGLT--KA   L   +------2   +-------4m6f_A    
                                       !      ! 
  --LG--------------------------   L --3      +-----------5cy1_B    
                                       ! 
  ------QT----------------------   L   +------------------2r0q_E    
                                     


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

  
  --------------------------RT----VAQTNA----   L        +---------------------5hod_A    
                                                        !  
  ----------------------RA--RT----VTKGNA--KA   L        !                       +2lkx_A    
                                                        !                     +-1 
  --------------------------RA--RTITQCNA----   L        !                 +---2 +5eea_B    
                                                        !                 !   ! 
  --------------------RA----RT----IAQTNA----   L        !                 !   +4rdu_A    
                                                        !        +-------11  
  --------------------------RA----IA--NA----            !        !        !     +4xrs_G    
                                                   +---15        !        !   +-3 
  ------------------------YARA----IAQTNA----   L   !    !        !        +---4 +5lux_L    
                                                   !    !        !            ! 
  ------------------------YART----IAQTNA----   L   !    !    +--13            +5lty_K    
                                                   !    !    !   !  
  --------------------------RT--RTIAQCNA----   L   !    !    !   !             +5jlw_D    
                                                   !    !    !   !           +-5 
  SGQATT----STRG--LTNT----------------------   L   !    !    !   +-----------8 +1e3o_C    
                                                   !    !    !               ! 
  --------------------------------IA--NA----       !    +---14               +4qtr_D    
                                                   !         !  
  ----------------------RT--RT----VAQTNA----   L -16         !                 +3lnq_A    
                                                   !         !               +-7 
  ----------------------RT--RA----IAQCNAMG--   L   !         !          +----9 +2r5z_A    
                                                   !         !          !    ! 
  --------------------------RA----IAQCNAMC--   L   !         !          !    +4cyc_A    
                                                   !         +---------12  
  --------------------------------TAQCNAMC--       !                    !      +4rbo_D    
                                                   !                    !    +-6 
  ----------------------------RT--NT--NAIARG   L   !                    +---10 +4cyc_B    
                                                   !                         !  
  --------------------------------NCICNARGRG   L   !                         +4xrm_B    
                                                   !  
  NTQASTHTSTQT--TT--------------------------   L   +--------------------------2h8r_B    
                                                 


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

  
  RTNGFTIA--RA--NASG--STYAPGRG   L   +-----------1j47_A    
                                     ! 
  RTNTFTMA--RA--NGAC--STYA----   L   !            +4s2q_D    
                                   --6          +-1 
  RCNTFTMA--RAHTNTAT--SAYA----   L   !  +-------3 +3u2b_C    
                                     !  !       ! 
  RTNTFTMA--RT--NG----SAYA----   L   !  !       +4y60_C    
                                     +--5 
  --------VT----FG--FCSA------          !        +4qr9_A    
                                        !    +---2 
  RTSAYCMT------FT------------   L      +----4   +1j5n_A    
                                             ! 
  ----FTIA--RT--QTLA--MT------   L           +---5jh0_D    
                                   


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

  
  ----------NTVC--ECSTYTSTYC------RA--   L          +-----------------------------5ed4_A    
                                                    ! 
  ----------TTNATT--ECVT--HT------RT--   L          !    +------------------------4s04_B    
                                                  +-8    ! 
  --------------------------YG--------            ! !    !                        +4lb5_B    
                                                  ! !    !           +------------1 
  KA--------AT----YTRG----------------   L        ! +----7           !            +4rb3_D    
                                                  !      !   +-------5 
  ----------------------------RG------            !      !   !       !           +4wcg_B    
                                                  !      !   !       +-----------3 
  ----YAKTPTPG----YTRG----------------   L      +-9      +---6                   +4mte_D    
                                                ! !          ! 
  ----RGSTRGMCTT--RT------------------   L      ! !          !                    +4u0y_B    
                                                ! !          !          +---------2 
  --ETNTSCRGHC----RT--------------QA--   L      ! !          +----------4         +5d4s_B    
                                             +-10 !                     ! 
  ----------------KGEA----------RGLGNC   L   !  ! !                     +---------5kbj_B    
                                             !  ! ! 
  ------------RGAC----LG--------------     -11  ! +-----------------------------4wx9_A    
                                             !  !  
  ----------KGTC--KGTCHT--------------   L   !  +-----------------------------4wuh_B    
                                             !  
  ----------KGTG--KANGYAST------------   L   +-----------------------------1zlk_A    
                                           


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

  
  ----RGTGRGTG--RTET----HA----   L                      +---1h9t_B    
                                     +------------------3 
  ----RGTTRGTTTTRTET----HA----   L   !                  +---4p9u_B    
                                     ! 
  ----RGSTRGMCTTRT------------   L   !                      +4u0y_B    
                                   --7               +------1 
  --ETNTSCRGHC--RT------QA----   L   !      +--------5      +5d4s_B    
                                     !      !        ! 
  ------ST--SAYTECQT----RT--PT   L   !      !        +------4hf1_A    
                                     +------6 
  ------------------YG--------              !             +-4lb5_B    
                                            !          +--2 
  RC----------QG----------SG--              +----------4  +-4qlc_U    
                                                       ! 
  ------------------YGRG------                         +----4wcg_B    
                                   


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

  
  ----KGVG--RG   L                    +4tnt_B    
                                    +-1 
  --ECKGAG--RG   L                +-2 +4ond_A    
                                  ! ! 
  ----KAVA--RA   L     +----------3 +5e69_A    
                       !          ! 
  --ECKG--KGRA   L     !          +5l0m_A    
                     +-9 
  --ECKG--RGRG   L   ! !  +-------2nll_B    
                     ! !  ! 
  --EAKG--KTRG   L   ! +--8    +--4cn3_D    
                     !    !    ! 
  ----KGVT--RG       !    +----7   +5emc_A    
                   -10         ! +-5 
  --ECKG----RA   L   !         +-6 +5krb_G    
                     !           ! 
  YGECKGAGKGRG   L   !           +4oln_B    
                     !  
  ----KGVT--RG   L   !           +5cbz_E    
                     +-----------4 
  --ECKA--RGRG   L               +4nqa_I    
                   


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

  
  ----HGNTLGECRCRC   L                       +-5i50_B    
                              +--------------4 
  ----HG----ETRCRG   L        !              +-5gnj_I    
                              ! 
  KT--HGNT--ECRCRG   L     +--7             +--1nkp_A    
                           !  !        +----5 
  ----HGNT--ECRCRG   L     !  !        !    +--1nkp_E    
                           !  +--------6 
  --RT--NTRGECRCQT       +-8           !       +2ypa_A    
                         ! !           +-------1 
  ----ST----ATRTRG       ! !                   +4zpk_B    
                         ! ! 
  ------NT--ETRCMT     --9 !                  +2ql2_D    
                         ! +------------------3 
  RT--STRT--ATRGRG       !                    +4zpr_B    
                         ! 
  ----HG--ITECRCRG   L   !                    +5nj8_D    
                         +--------------------2 
  ----HG----ETRTRG   L                        +5v0l_A    
                       


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

  
  NTQASTHTSTQT--TTRAYT----NAKG   L                          +2h8r_B    
                                                   +--------1 
  ----------------RT--IAQTNAMC   L                 !        +2h1k_B    
                                     +-------------3 
  --------------------IA--NA--       !             !        +4qtr_D    
                                   --4             +--------2 
  ----------------RA--IA--NA--       !                      +4xrs_G    
                                     ! 
  --QASTCT--SARTET------------   L   +----------------------5j2y_A    
                                   


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

  
  --KTRGAT--RGYA----   L                            +4iri_A    
                                     +--------------3 
  DCKTRGST--RGYC----   L             !              ! +4uno_A    
                                     !              +-2 
  DCKTRGAT--RCYA----   L   +---------6                +5e8i_D    
                           !         ! 
  DCKTRGST--RGYA----   L   !         !           +---4bnc_A    
                           !         +-----------4 
  DCKTRG----RGYA----   L --7                     +---1dux_F    
                           ! 
  ----NA--RAHT--STLT   L   !                         +2a07_K    
                           !          +--------------1 
  ----NASTRGHT--STFT   L   +----------5              +5x07_F    
                                      ! 
  ----NASTRGHT--ST--   L              +--------------3g73_A    
                         


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

  
  RT--RA----------------------IA--QCNAMG----   L                               +2r5z_A    
                                                                             +-1 
  ----RT----------------------VA--QTNA------   L                  +----------6 +5hod_A    
                                                                  !          ! 
  --YARA----------------------IA--QTNA------   L      +----------12          +5lux_L    
                                                      !           !  
  --YART----------------------IA--QTNA------   L      !           +-----------5lty_K    
                                                      !  
  ----RT----------------------IA--QTNAMC----   L      !                        +2h1k_B    
                                                      !                      +-5 
  ----RT----------------------IA--QTNA----KT   L      !                      ! ! +4rdu_A    
                                                      !                      ! +-2 
  ----RA----------------RT----IT--QCNA------   L      !               +------9   +5eea_B    
                                                      !               !      ! 
  ----RA----------------------IA----NA------          !               !      ! +-4xrs_G    
                                                      !           +--10      +-8 
  ----------------------------IA----NA------       +-16           !   !        +-4qtr_D    
                                                   !  !           !   !  
  ----RT----------------RT----IA--QCNA------   L   !  !           !   !         +5jlw_D    
                                                   !  !           !   +---------3 
  ----RA----------------------IA--QCNAMC----   L   !  !      +---13             +4cyc_A    
                                                   !  !      !    !  
  ----------------------------TA--QCNAMC----       !  !      !    !             +4rbo_D    
                                                   !  !      !    !           +-4 
  ------RT--------------------NT----NAIARG--   L   !  !      !    !  +--------7 +4cyc_B    
                                                 -17  !   +-14    !  !        ! 
  ----------------------------NC--RG--------   L   !  !   !  !    +-11        +-4xrm_B    
                                                   !  !   !  !       !  
  ------NGRGTG------LC--LCRG----------------       !  +--15  !       +----------4ofa_A    
                                                   !      !  !  
  --------KA----------SGAT--YTRG------------   L   !      !  +------------------4rb3_D    
                                                   !      !  
  ------------IGYGFG------------------------       !      +-------------------4ztu_A    
                                                   !  
  --------------------------RTNAQAIASCRTVA--   L   +-------------------------5b7j_A    
                                                 


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

  
  --VTKGDCRGTA--------------   L                           +-3sjm_A    
                                             +-------------3 
  ------TAQCNAMC------------                 !             +-4rbo_D    
                                             ! 
  ----------------RTNTNAIARG   L   +---------6             +-1puf_B    
                                   !         !        +----4 
  RT----NT--NAIARG----------   L   !         !        !    ! +4cyc_B    
                                   !         !        !    +-1 
  ----ICNARGRG--------------   L   !         +--------5      +4xrm_B    
                                 --7                  ! 
  ------IA--NA--------------       !                  !     +4qtr_D    
                                   !                  +-----2 
  ------IA--NA--------------       !                        +4xrs_G    
                                   ! 
  ------IAQCNAYC------------   L   +-------------------------3rkq_B    
                                 


> 1imh_C:TONEBP/DNA COMPLEX

  
  RG--YTTTEC----RG--------QA--   L        +-----------1imh_C    
                                        +-3 
  RGRGYT--EC----RA--KTRTTTQA--   L      ! +-----------1a66_A    
                                     +--4 
  RGRGYTCC------HTKT--------RG   L   !  !        +----1nfk_A    
                                     !  +--------2 
  RGRGYTEC----SG--------------   L --5           !    +2i9t_A    
                                     !           +----1 
  RGRGYTEC--------------------   L   !                +1gji_A    
                                     ! 
  RGRG--EG--RG----------------   L   +----------------1bvo_A    
                                   


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

  
  RALTPTDCHGTCTCLTHT--------   L                +------------1j1v_A    
                                             +--2 
  ----------------NT--NAIARG   L             !  !           +1puf_B    
                                   +---------3  +-----------1 
  ----------------NT--NAIARG   L   !         !              +4cyc_B    
                                 --4         ! 
  ----------------IA--NA----       !         +---------------4xrs_G    
                                   ! 
  ----------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--RGNC----SALT------YAKTEAKA   L   +---------------------2gzk_A    
                                                 ! 
  --RC--NTFTMA--RANGSC--ST--------YA--RG--   L   !                    +1gt0_D    
                                                 !             +------3 
  --RT--NTFTMA--RANGAC--ST--------YA------   L --7             !      +4s2q_D    
                                                 !  +----------5 
  ------------VT--FG--FCSA----------------       !  !          !        +4qr9_A    
                                                 !  !          !      +-1 
  KCRC----YTMALTRAVCTG--AA----VCEC--------   L   !  !          +------2 +1qrv_A    
                                                 +--6                 ! 
  --RTTASTYAFALT--PTAT--ST--RA------------   L      !                 +5jh0_D    
                                                    ! 
  --RT--NTFTMA--RTNG----SA--------YA------   L      !               +--4y60_C    
                                                    +---------------4 
  ------STYGLASGLATGTC--IT----------------   L                      +--3tq6_B    
                                               


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

  
  VGTTRTTGRTRT--SAYCMT------FT--------   L              +-----1j5n_A    
                                               +--------4 
  ----------RTTASTYAFALT----PTAT--STRA   L     !        +-----5jh0_D    
                                             +-5 
  ----------RC--NTFTMA--RAHTNTAT--SA--   L   ! !              +3u2b_C    
                                             ! +--------------2 
  ----------RT--NTFTMA--RA--NGAC--ST--   L --6                +4s2q_D    
                                             ! 
  --------------------VT----FG--FCSA--       !                  +4qr9_A    
                                             !                +-1 
  ----------RT--NTFTMA--RT--NG----SA--   L   +----------------3 +4y60_C    
                                                              ! 
  ----------RT--NGFTIA--RA--NASG--ST--   L                    +1j47_A    
                                           


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

  
  --KGTCKGTCHT----   L                              +4wuh_B    
                                           +--------1 
  --SCTAKTVCHTKG--   L          +----------2        +1je8_F    
                                !          ! 
  QAPCSTVT--------   L        +-3          +---------4aik_A    
                              ! ! 
  --KGTGKANGYAST--   L     +--4 +--------------------1zlk_A    
                           !  ! 
  YTNT--RGVT--RTET   L   +-5  +----------------------1l3l_A    
                         ! ! 
  --------------YG     --6 +-------------------------3eyi_B    
                         ! 
  --RTTTDAVT--RGRG   L   +--------------------------1gxp_A    
                       


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

  
  ------RT--                       +5b0z_C    
                              +----8 
  --------RT                  !    +5b31_G    
                            +-9 
  ------RART                ! !       +3x1t_G    
                            ! !     +-1 
  ------RT--          +----11 +-----5 +5gt0_C    
                      !     !       ! 
  ------RG--          !     !       +4jjn_G    
                      !     !  
  IT--------       +-12     +-------5b0z_D    
                   !  !  
  ----RT----       !  !      +------4jjn_F    
                   !  +-----10  
  ------RG--       !         !      +5t5k_E    
                 -13         +------2 
  IT--------       !                +5b1m_D    
                   !  
  ------RT--       !             +4x23_O    
                   !             ! 
  --LT--RC--       +-------------7 +5av9_A    
                                 ! ! 
  --LT--RA--                     +-6   +5ay8_E    
                                   ! +-3 
  --LT------                       +-4 +4z5t_A    
                                     ! 
  --LC--RG--                         +4jjn_A    
                 


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

  
  --RT----               +-------4jjn_F    
                 +-------8 
  IT------       !       !       +5b1m_D    
                 !       +-------3 
  IT------       !               +5b0z_D    
                 !  
  ----RG--       !               +5t5k_E    
               -11       +-------2 
  LT------       !       !       +4z5t_A    
                 !  +----9 
  LC--RG--       !  !    !       +4jjn_A    
                 !  !    +-------1 
  LT--RC--       !  !            +5av9_A    
                 +-10  
  ----RART          !               +3x1t_G    
                    !             +-4 
  ----RT--          !           +-5 +5gt0_C    
                    !           ! ! 
  ----RG--          +-----------7 +4jjn_G    
                                ! 
  ------RT                      ! +5b31_G    
                                +-6 
  ----RT--                        +5b0z_C    
               


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

  
  --RT------------------------IAQTNAMC----   L                               +2h1k_B    
                                                                           +-2 
  --RA------------------------IAQCNAMG----   L                             ! +2r5z_A    
                                                                           ! 
  --RA------------------------IA--NA------                            +----9     +4xrs_G    
                                                                      !    !   +-5 
  --RT------------------RT----IAQCNA------   L                        !    ! +-7 +5jlw_D    
                                                                      !    ! ! ! 
  ----------------------------IA--NA------                            !    +-8 +4qtr_D    
                                                                 +---10      ! 
  ----------------------------NCICNARGRG--   L                   !    !      +4xrm_B    
                                                                 !    !  
  --RA------------------RT----ITQCNA------   L                   !    !       +5eea_B    
                                                                 !    !     +-3 
  --RT------------------------IAQTNA----KT   L             +----12    +-----6 +4rdu_A    
                                                           !     !          ! 
  --RA------------------------IAQCNAMC----   L             !     !          +4cyc_A    
                                                           !     !  
  ----------------------------TAQCNAMC----              +-14     !           +4rbo_D    
                                                        !  !     +-----------4 
  ----RT----------------------NT--NAIARG--   L          !  !                 +4cyc_B    
                                                     +-15  !  
  ------KA------------SGAT--YTRG----------   L       !  !  +-----------------4rb3_D    
                                                     !  !  
  ----------IGYGYGFG----------------------       +--16  +-------------------4ztu_A    
                                                 !   !  
  ----NGRGTG--------LC--LCRG--------------       !   !              +-------4ofa_A    
                                                 !   +-------------11  
  --------------------YG------------------   L -17                  +-------5kn8_A    
                                                 !  
  YARA------------------------IAQTNA------   L   !                          +5lux_L    
                                                 !           +--------------1 
  YART------------------------IAQTNA------   L   +----------13              +5lty_K    
                                                             !  
  --RT------------------------VAQTNA------   L               +--------------5hod_A    
                                               


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

  
  --------------------KGCG--------------------------------   L                            +----------2bop_A    
                                                                       +------------------9 
  ----------------KGTAYCNG--------------------------------   L         !                  +----------5t7x_B    
                                                                    +-11  
  ----DG--IC--LG--WG--------QG--KT------------KGFGFG--RGPC   L      !  !                        +----4y0f_A    
                                                                 +-12  +------------------------8 
  ----TA--FC--SG----------LAKA--------------TGSGVGFA------   L   !  !                           +----5tkz_B    
                                                                 !  !  
  TC------------------------------------------------------   L   !  +-----------------------------4fb3_A    
                                                                 !  
  --QA----------TA--------YAKG--KG--KG----FT--WCEA--------   L   !                            +4yhx_A    
                                                                 !                            ! 
  --RG--KG--TT--TC------------IG--AC--NA------AT----------   L   !                            !     +5t8d_A    
                                                               -13                         +--5   +-1 
  --EC------ST--KG----------------TT--NA--------MG--SC----   L   !                         !  ! +-2 +5t2n_A    
                                                                 !                         !  ! ! ! 
  --ST------EC--TT--------------------RG------TTRG--------   L   !                         !  +-4 +5thg_A    
                                                                 !      +------------------7    ! 
  --RG----------------------------TA--AA------VAQT--------   L   !      !                  !    +5t2o_A    
                                                                 !      !                  ! 
  --QT--FA--QG--NG----------------HC--SC------LAQG--QA----   L   !      !                  !   +4yit_A    
                                                                 +-----10                  ! +-3 
  ------RG--VT--SA----------------FC--MC------STQT--EC----   L          !                  +-6 +5esp_A    
                                                                        !                    ! 
  --KG--VT------------------------HC--HG--------QT--DC----   L          !                    +-4yis_A    
                                                                        !  
  --RT----------FA----------------RG--RGNTDT--MCEA--------   L          +----------------------5a77_B    
                                                               


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

  
  LG----KG--STYTHT   L                  +--4l62_M    
                               +--------3 
  ----TCKGAG--YTHA           +-7        +--5k7z_A    
                             ! ! 
  MTRGAAVT--TTYT--   L       ! +-----------5fmp_B    
                             ! 
  TA--STECAGATYTRG   L   +---8               +4gck_A    
                         !   !             +-1 
  VT--AGDT--TTYTLA   L   !   !          +--2 +5gpc_B    
                         !   !          !  ! 
  TA----ECAC--YCRA       !   +----------4  +5haw_A    
                       --9              ! 
  --EC--KGQCTGYGRC   L   !              +--4jl3_B    
                         ! 
  TA--AT----LCFGHA       !           +-----4i6z_B    
                         !       +---5 
  ----TGKG----YCFA   L   +-------6   +-----4pxi_B    
                                 ! 
  TTHTRTQAATSCYTYT   L           +---------5dy0_D    
                       


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

  
  QALGYA------------------RG               +-1k3x_A    
                                     +-----3 
  RTMTET--RC--------------RT         !     ! +4pd2_A    
                                   +-5     +-1 
  --MG------RC--FCKGDGACQTRG   L   ! !       +1k82_A    
                                   ! ! 
  --MG--ITRC--FG------HG--RG   L   ! +-------5itu_A    
                                 --6 
  RA--------FT------------RA   L   !        +3gpu_A    
                                   !      +-2 
  RGMG------FC------------RG   L   +------4 +3u6p_A    
                                          ! 
  --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--RG--MG--YAMCKT--NC----KTDA----TT------   L        !                +------2b9s_A    
                                                   +----3 
  ------RA--QAYC----RTKGKG--KT----ETRGYG----   L   !    ! +----------------------2h7g_X    
                                                 --4    +-2 
  ------------------------KA----RA----------   L   !      +----------------------5u91_B    
                                                   ! 
  --------------------------------------NT--       +----------------------------2b9s_B    
                                                 


> 1k61_B:MATALPHA2 HOMEODOMAIN BOUND TO DNA

  
  --------------------NC--ICNARGRG--   L                        +----4xrm_B    
                                                                !  
  --RT----------------NT----NAIARG--   L                  +----11 +--4cyc_B    
                                                          !     ! ! 
  RT------------RT----IA--QCNA------   L                  !     +-9    +5jlw_D    
                                                          !       !  +-1 
  RA------------------IA--QTNA------   L               +-12       +--3 +5lux_L    
                                                       !  !          ! 
  RT------------------IA--QTNA------   L               !  !          +5lty_K    
                                                       !  !  
  RA------------------IA--QCNAMG----   L               !  !          +2r5z_A    
                                                       !  +----------2 
  RT------------------VA--QTNA------   L         +----13             +5hod_A    
                                                 !     !  
  RT------------------IA--QTNA----KT   L         !     !               +4rdu_A    
                                                 !     !             +-4 
  RA------------RT----IT--QCNA------   L         !     !           +-6 +5eea_B    
                                                 !     !           ! ! 
  RT------------------IA--QTNAMC----   L         !     +-----------7 +2h1k_B    
                                           +----16                 ! 
  RA------------------IA--QCNAMC----   L   !     !                 +-4cyc_A    
                                           !     !  
  --------------------IA----NA------       !     !                  +4qtr_D    
                                           !     !               +--5 
  RA------------------IA----NA------       !     !  +-----------10  +4xrs_G    
                                           !     !  !            !  
  --NGRGTGLC----LCRG----------------     -17     +-15            +---4ofa_A    
                                           !        !  
  --------------------TA--QCNAMC----       !        !             +--4rbo_D    
                                           !        +-------------8 
  ----------SG--AT--YTRG------------   L   !                      +--4rb3_D    
                                           !  
  ------------------RTNAQAIASCRTVA--   L   !         +---------------5b7j_A    
                                           +--------14  
  ------------RGKG--SGSA--QAVCRT----   L             +---------------5gzb_A    
                                         


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

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


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

  
  ----EA--KG--RTRTRT------                    +-2han_B    
                                    +---------8 
  ----EC--KG----RA------PA   L      !         +-5krb_G    
                                    !  
  ----EC--KGAG--RG--------   L   +-12           +4ond_A    
                                 !  !     +-----3 
  --------KGVG--RG--------   L   !  !     !     +4tnt_B    
                                 !  +----10  
  --------KGVT--RG--------       !        !     +5emc_A    
                                 !        !   +-4 
  ----EC--KGAGKGRG--------   L   !        +---7 +1hcq_E    
                                 !            ! 
  --YGEC--KGAGKGRG--------   L -13            +-4oln_B    
                                 !  
  HG--ECAGKGAAKGRT------RT   L   !             +1lo1_A    
                                 !           +-2 
  ----EC--KG--KGRA--RT----   L   !           ! +5l0m_A    
                                 !     +-----9 
  --------KAVA--RA--------   L   !     !     ! +5e69_A    
                                 !     !     +-1 
  --------KGVT--RG--------   L   +----11       +5cbz_E    
                                       !  
  ----EA--KG--KTRG--------   L         !        +4cn3_D    
                                       !      +-5 
  --------KGVG--RG----RA--   L         +------6 +3g6t_A    
                                              ! 
  --------KGVT--RG--------   L                +2c7a_B    
                               


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

  
  LCNGKGYGMGRC--FCECEG------SGHGVC----------------------------------------------                                    +-1kln_A    
                                                                                                                  +-1 
  --------------------KT--YG------RGNGNGRC----YG--YAIGSCYC--NGRC--FG--------QAHG                                +-2 +-4yfu_D    
                                                                                                                ! ! 
  --------------------NAKA--------RG--NT----QC----YCMC------QC--NGPTYGATRT--QC--                              +-3 +---4x0q_B    
                                                                                                              ! ! 
  --------------------KC----------RGNGNG----TGFG--YGMG----RG------KASAEARANGQGHG   L                +---------4 +----4bwj_A    
                                                                                                    !         ! 
  --------------------KT----------RG------EGKGYGACYCAC----RC--------QTATRTNGQGHC   L            +---5         +----4xvk_A    
                                                                                                !   ! 
  ----------------------KT--------RTNG------------YA------------------------QA--       +--------6   +--------------1x9m_A    
                                                                                       !        ! 
  --------------------------------RTTT------IGYG--YG----------------------NGQT--     --7        +------------------4ztu_A    
                                                                                       ! 
  ----------RASA----------------------------------------------------------------       +---------------------------5m1s_D    
                                                                                     


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

  
  ------------RT----                    +-----------4jjn_F    
                                        !  
  ----------AT------                    !             +4g92_B    
                                        !           +-3 
  RG------IT--------                +--15  +--------4 +5b0z_D    
                                    !   !  !        ! 
  --------IT--------                !   !  !        +5b1m_D    
                                    !   !  !  
  --------------RART                !   !  !          +3x1t_G    
                                    !   +-13        +-2 
  --------------RT--                !      !      +-8 +5gt0_C    
                                    !      !      ! ! 
  --------------RG--                !      !      ! +4jjn_G    
                                    !      +-----11  
  --------------RG--                !             !   +5t5k_E    
                                 +-16             ! +-1 
  --------------RT--             !  !             +-9 +5b0z_C    
                                 !  !               ! 
  ----------------RT             !  !               +5b31_G    
                                 !  !  
  ------RA--ET------             !  !                +4ne1_p    
                                 !  !              +-7 
  --------------RT--             !  !              ! +4x23_O    
                                 !  !     +-------10  
  ----LT--------RA--       +----17  !     !        ! +5ay8_E    
                           !     !  !     !        +-6 
  --LT----------RC--       !     !  +----14          +5av9_A    
                           !     !        !  
  ----LT------------       !     !        !         +4z5t_A    
                           !     !        !       +-5 
  ----------LC--RG--     -18     !        +------12 +4jjn_A    
                           !     !                !  
  --LT--------------       !     !                +-3wtp_A    
                           !     !  
  --------IT--------       !     +-----------------3wkj_D    
                           !  
  RC----------------       +-----------------------4jjn_D    
                         


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

  
  RG--IT------                           +5b0z_D    
                             +-----------1 
  ----IT------               !           +5b1m_D    
                        +---14  
  RG----------          !    !   +-------4xzq_D    
                        !    +--13  
  ------RT----          !        +-------4jjn_F    
                     +-15  
  RG----------       !  !         +------3x1t_H    
                     !  !         !  
  --------RART       !  !         !        +3x1t_G    
                     !  +--------12      +-2 
  --------RT--       !            !    +-6 +5gt0_C    
                     !            !    ! ! 
  --------RG--       !            !    ! +4jjn_G    
                     !            +----9 
  --------RG--       !                 !   +5t5k_E    
                   -16                 ! +-3 
  --------RT--       !                 +-7 +5b0z_C    
                     !                   ! 
  ----------RT       !                   +5b31_G    
                     !  
  --------RT--       !                +4x23_O    
                     !            +---8 
  --LC----RG--       !            !   ! +4jjn_A    
                     !            !   +-4 
  --LT----RC--       !            !     +5av9_A    
                     +-----------11  
  --LT--------                    !    +4z5t_A    
                                  !  +-5 
  --LT----RA--                    +-10 +5ay8_E    
                                     !  
  --LT--------                       +--3wtp_A    
                   


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

  
  HARAYT----LT----RC--                  +------1kx5_E    
                                        !  
  --RAYT----LT----RC--                  !         +5av9_A    
                                        !       +-3 
  HGRG------LC----RG--             +---12       ! +4jjn_A    
                                   !    !     +-7 
  --RA------LT--------             !    !     ! ! +4z5t_A    
                                   !    !   +-9 +-4 
  HGRA------LT----RA--             !    !   ! !   +5ay8_E    
                                   !    +--10 ! 
  ------PG--------RT--          +-13        ! +4x23_O    
                                !  !        !  
  --------KTLT--------          !  !        +--3wtp_A    
                                !  !  
  ------------RT------          !  !    +------4jjn_F    
                             +-14  +---11  
  ----------------RG--       !  !       !      +5t5k_E    
                             !  !       +------1 
  --------------IT----       !  !              +5b1m_D    
                             !  !  
  --------------IT----     -15  +------------5b0z_D    
                             !  
  ------------------RT       !               +5b31_G    
                             !             +-6 
  ----------------RT--       !             ! +5b0z_C    
                             +-------------8 
  ----------------RG--                     ! +4jjn_G    
                                           +-5 
  ----------------RART                       ! +3x1t_G    
                                             +-2 
  ----------------RT--                         +5gt0_C    
                           


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

  
  ------RT--                      +5b0z_C    
                             +----8 
  --------RT                 !    +5b31_G    
                      +------9 
  ------RART          !      !       +3x1t_G    
                      !      !     +-1 
  ------RT--          !      +-----6 +5gt0_C    
                      !            ! 
  ------RG--       +-12            +4jjn_G    
                   !  !  
  --IT------       !  !            +5b1m_D    
                   !  !    +-------2 
  --IT------       !  +---10       +5b0z_D    
                   !       !  
  ----RT----     -13       +-------4jjn_F    
                   !  
  ------RG--       !                +5t5k_E    
                   !              +-3 
  --LT------       !    +---------5 +4z5t_A    
                   !    !         ! 
  --LT--RA--       !    !         +5ay8_E    
                   +---11  
  ------RT--            !         +4x23_O    
                        +---------7 
  LC----RG--                      ! +4jjn_A    
                                  +-4 
  --LT--RC--                        +5av9_A    
                 


> 1lat_A:GLUCOCORTICOID RECEPTOR MUTANT/DNA COMPLEX

  
  ----KGVG--RG   L                 +4tnt_B    
                                 +-1 
  --ECKG--KGRA   L   +-----------6 +5l0m_A    
                     !           ! 
  ----KAVA--RA   L   !           +5e69_A    
                     !  
  ----KGVT--RG   L   !              +5cbz_E    
                     !            +-3 
  --ECKA--RGRG   L   !     +------5 +4nqa_I    
                   -10     !      ! 
  --ECKGAG--RG   L   !     !      +4ond_A    
                     !  +--8 
  --EAKG--KTRG   L   !  !  !      +4cn3_D    
                     !  !  !  +---2 
  --ECKG--RGRG   L   !  !  !  !   +2nll_B    
                     +--9  +--7 
  ----KGVT--RG          !     !   +5emc_A    
                        !     +---4 
  --ECKG----RA   L      !         +5krb_G    
                        ! 
  YGECKGAGKGRG   L      +---------4oln_B    
                   


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

  
  --------------IA--QCNAMG--   L                              +2r5z_A    
                                                            +-3 
  --------------VA--QTNA----   L                          +-6 +5hod_A    
                                                          ! ! 
  --------------IA--QTNA----   L                       +--8 +4rdu_A    
                                                       !  ! 
  --------------IA----NA----                           !  ! +4qtr_D    
                                                 +----12  +-4 
  --------------IA--QTNA----   L                 !     !    +5lux_L    
                                                 !     !  
  --------RT----IA--QCNA----   L                 !     !    +5jlw_D    
                                        +-------13     +----1 
  --------------IA--QCNAMC--   L        !        !          +4cyc_A    
                                        !        !  
  --------------NC--ICNARGRG   L        !        !       +--4xrm_B    
                                        !        +------10  
  --------RT----IT--QCNA----   L        !                !  +5eea_B    
                                   +---14                +--2 
  --------------IA--QTNA----   L   !    !                   +5lty_K    
                                   !    !  
  --------------IA--QTNAMC--   L   !    !                  +-2h1k_B    
                                   !    !                +-9 
  --------------IA----NA----       !    !                ! +-4xrs_G    
                                 -15    +---------------11  
  --------------TA--QCNAMC--       !                     !   +4rbo_D    
                                   !                     ! +-5 
  RT------------NT----NAIARG   L   !                     +-7 +4cyc_B    
                                   !                       ! 
  --RGTGLCLCRG--------------       !                       +-4ofa_A    
                                   !  
  ------------RTNAQAIASCRTVA   L   +------------------------5b7j_A    
                                 


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

  
  RT------------------NT--NAIARG------   L                                     +1puf_B    
                                                                             +-7 
  RA------------------IAQTNA----------   L                                   ! +5lux_L    
                                                                             ! 
  RT----------RT------IAQCNA----------   L                             +-----8     +5jlw_D    
                                                                       !     !   +-1 
  RA----------RT------ITQCNA----------   L                             !     ! +-2 +5eea_B    
                                                                       !     ! ! ! 
  RT------------------IAQTNA----KT----   L                          +-12     +-4 +4rdu_A    
                                                                    !  !       ! 
  RT------------------IAQTNA----------   L                          !  !       +5lty_K    
                                                                    !  !  
  --RT----------------NT--NAIARG------   L                      +--13  !     +4cyc_B    
                                                                !   !  +----10  
  --------------------NCICNA------RGRG   L                      !   !        +4xrm_B    
                                                                !   !  
  --------------------IA--NA----------                    +----15   !       +4qtr_D    
                                                          !     !   +-------9 
  RA------------------IA--NA----------                    !     !           +4xrs_G    
                                                          !     !  
  RT------------------VTKGNAKA--------   L                !     !            +2lkx_A    
                                                    +----17     +------------3 
  RT------------------VAQTNA----------   L          !     !                  +5hod_A    
                                                    !     !  
  RT----------------KTIAQCNA----RT----   L          !     !       +----------1ig7_A    
                                                    !     !       !  
  --------------------TAQCNAMC--------           +-19     +------14          +4rbo_D    
                                                 !  !             !        +-5 
  RT----------------YANC--NAKG--------   L       !  !             +-------11 +4j19_B    
                                                 !  !                      !  
  RA------------------IAQCNA----------   L       !  !                      +-4cyc_A    
                                             +--20  !  
  --------------------ITKGNA------RGRA   L   !   !  +------------------------1zq3_P    
                                             !   !  
  RC------------------IAQCNAYC--------   L   !   !   +--------------------3rkq_B    
                                             !   !   !  
  --NGRGTGLG--LCRG--------------------     -21   +--18                    +4ew0_A    
                                             !       !     +--------------6 
  --NGRGTGLC--LCRG--------------------       !       +----16              +4ofa_A    
                                             !             !  
  --NGRGTG--LG--LCRG------------------       !             +--------------4e9f_A    
                                             !  
  --------------------RG--YG----------       +----------------------------1qbj_C    
                                           


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

  
  ----------RGSTDCHGTTTTRG--DAEC--RG   L                    +----------1llm_D    
                                                      +-----7 
  --------RGST--YGYC----QC--TGSTRGYT   L              !     !          +4is1_C    
                                                      !     +----------1 
  ----------DG--YCKG--RGQA----TC----   L              !                +5kkq_D    
                                           +----------8 
  ----------RG--DCEC--RGRG--DCHG----   L   !          !              +-1f2i_J    
                                           !          !           +--5 
  PCYC------RG--DA----RGRG--DCHG----   L   !          !           !  +-2prt_A    
                                           !          !           ! 
  ----------QA--SGNA--KGQASTSCDC--KG   L   !          +-----------6      +1mey_C    
                                         --9                      !    +-2 
  ----------RGSTDTEG--RGRGSGDCHG--TT   L   !                      !    ! +4x9j_A    
                                           !                      +----4 
  ----------RGSTDAHA--RGRGSTDCHG--TT   L   !                           ! +5kl3_A    
                                           !                           +-3 
  ----------RA----NC------ATSGDC--KG   L   !                             +2gli_A    
                                           ! 
  ----NTEC----RCRG------------------   L   +---------------------------1nkp_A    
                                         


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

  
  ETDTRGTCYTST--RG   L                      +3s8q_A    
                                        +---1 
  AT--QAAT--SA----       +--------------2   +4z5h_A    
                         !              ! 
  ----QASTCTSARTET   L   !              +---5j2y_A    
                       --5 
  ----KGSGTTSTQCQG   L   !              +----3zhm_A    
                         !            +-3 
  ----SCATRTNCQTHT   L   +------------4 +----4jcy_A    
                                      ! 
  --TT--RGQTITRGST   L                +-----5jub_B    
                       


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

  
  --ECKG--KGRARTRC   L                          +5l0m_A    
                                       +--------5 
  --ECKG----RAPARC   L                 !        +5krb_G    
                                       ! 
  --EAKG--KTRG----   L          +------8         +4cn3_D    
                                !      !      +--1 
  --ECKG--RGRG----   L          !      !      !  +2nll_B    
                                !      +------7 
  ----KGVT--RG----   L          !             ! +5cbz_E    
                                !             +-3 
  ----KAVA--RA----   L   +------9               +5e69_A    
                         !      ! 
  --ECKGAG--RG----   L   !      !                  +4ond_A    
                         !      !                +-2 
  ----KGVG--RG----   L   !      !              +-4 +4tnt_B    
                       -10      !              ! ! 
  ----KGVT--RG----       !      +--------------6 +5emc_A    
                         !                     ! 
  YGECKGAGKGRG----   L   !                     +-4oln_B    
                         !  
  --ECKA--RGRG----   L   +-----------------------4nqa_I    
                       


> 1lq1_D:DNA COMPLEXED STRUCTURE OF THE KEY TRANSCRIPTION FACTOR INITIATING DEVELOPMENT IN SPORULATION BACTERIA

  
  --YAKTPTPG--YTRG----   L                                   +4mte_D    
                               +-----------------------------1 
  KA--SG--AT--YTRG----   L   +-2                             +4rb3_D    
                             ! ! 
  ----TT--SGLTYART----   L --3 +-----------------------------2nra_C    
                             ! 
  --------RTTTDAVTRGRG   L   +-----------------------------1gxp_A    
                           


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

  
  CA--QG--VTRTDCYA----RT----FA----RG--RGNTDTMCEA----KA   L         +---5a77_B    
                                                             +----11  
  SANCSC--KGLT--------DAECNATG--RCKGST------------DA--   L   !     +---2ex5_A    
                                                             !  
  ST--NA--VTHGTCNA--ATLCYCECAT--YG--NA--SADCTCKTKGSA--   L   !                +4lq0_A    
                                                             !              +-1 
  SGMGRG--RG--KTYA--LTVT----TT----KT--SC--------RGEC--   L   !            +-7 +4lox_A    
                                                             !            ! ! 
  --MTHT--EC--------RGRG--QGKG------NT------ET--KTRG--   L   !            ! +4z1x_A    
                                                             !            ! 
  STIGRG--RG----MC--LTEC--STKG----TT--NA------MGRTSC--   L   !            !       +5t2n_A    
                                                           -13          +-8     +-2 
  --------RARG----RTRGSTRTQGTA--------SC----ATMCRGTC--   L   !          ! !   +-3 +5t2h_A    
                                                             !          ! !   ! ! 
  SCMCRG--RG--------YTST--ECTT--------RG----TTRG------   L   !          ! ! +-5 +5thg_A    
                                                             !        +-9 ! ! ! 
  STST--YC----------ECRG----------TA--AA----VAQTRT----   L   !        ! ! +-6 +5t2o_A    
                                                             !        ! !   ! 
  SC--YT--------------RGKGTTTCIG--AC--NA----AT--IC----   L   !     +-10 !   +5t8d_A    
                                                             !     !  ! ! 
  SA--RG--RGNTKTST--STEC--QGTA--------ST----AT--KG----   L   !     !  ! +-4yhx_A    
                                                             +----12  !  
  CGRGST----------KARGQTFAQGNG----HC--SC----LAQGRGQA--   L         !  +--4yit_A    
                                                                   !  
  STMG--------KGYC--RT--RGVTSA----FC--MC----STQTRGEC--   L         !   +5esp_A    
                                                                   +---4 
  SGSTLG--QG--KTYA--RGKGVT--------HC--HG------QTRTDC--   L             +4yis_A    
                                                           


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

  
  --RT--NT--RGEC----RCQT--                            +2ypa_A    
                                                   +--1 
  ------ST------AT----RTRG             +-----------5  +4zpk_B    
                                       !           ! 
  RT--STRT----AT----RGRG--       +-----7           +--4zpr_B    
                                 !     ! 
  ------NT----ET----RCMT--       !     !              +2ql2_D    
                                 !     +--------------3 
  --------------RTRG------       !                    +5sy7_B    
                               --9 
  KT--HGNT----EC----RCRG--   L   !                    +1nkp_A    
                                 !        +-----------2 
  ------HGNT--LGEC----RCRC   L   !   +----6           +5i50_B    
                                 !   !    ! 
  ------HG----ITEC----RCRG   L   +---8    +-----------5nj8_D    
                                     ! 
  ------RTNT----EC----RCRG   L       !             +--4h10_B    
                                     +-------------4 
  ------HG------ET----RCRG   L                     +--5gnj_I    
                               


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

  
  ----KG--WTKA----------HCHGRGTA--ACNA--KGRG   L   +----------------------1tf6_A    
                                                   !  
  ----RGSTDTEG--RG--RGSGDCHGTTRG--DAEG--RG--   L   !                        +4x9j_A    
                                                   !                      +-1 
  ----ECVASCKG--RG--DG--YCKGRGQA----TC------   L   !                +-----3 +5kkq_D    
                                                   !                !     ! 
  ----DA--SCHG--RGRGDC--SCNA--NCKTSAHG--RG--   L   !        +-------5     +5ei9_F    
                                                 -11        !       ! 
  PCYCRG--DA----RG--RG--DCHG--RG--DCEC--RG--   L   !        !       +-----2prt_A    
                                                   !  +-----8 
  ----QA--SGNA--KG--QASTSCDCKGRG--DCHA--RG--   L   !  !     !             +1mey_C    
                                                   !  !     !     +-------4 
  ----DC--YCKG--RG--QA----TC--RC--SCDC--VT--   L   !  !     !     !       +5k5i_A    
                                                   !  !     +-----7 
  ----RGSTDAHA--RG--RGSTDCHGTTRG--DAEG--RG--   L   !  !           !       +5kl3_A    
                                                   +-10           +-------2 
  ----AT--YC--------RA----NC----ATSGDC--KG--   L      !                   +2gli_A    
                                                      !  
  ------------------RG--DCECRGRG--DCHG------   L      !             +------1f2i_J    
                                                      ! +-----------6 
  ----------------RGST--YGYC--QC--TGSTRGYT--   L      +-9           +------4is1_C    
                                                        ! 
  ----RGSTDCHGTTTT--RG--DAECRG--------------   L        +------------------1llm_D    
                                                 


> 1mow_A:E-DREI

  
  --YTLT--YC----RGSGECRG----TG----QG--VG--DCTARTEARGSCSAIAQAKG--NT--SCYAQA----QA--TGYCRG--RG----VA--------------TC   L                    +-------1mow_A    
                                                                                                                                          !  
  SGMGRG--------LT--VT------TT------KT--SC--------RGECSAKGIGKT------SGITQAIA--QA--TC--DT--RG----WT--YC----TC------   L                    !           +4lox_A    
                                                                                                                                          !           ! 
  STIGRG--------LT--EC--ST--KG------TT--NA------MGRTSCHT--NCWC--RG--------QG------STLAKG--RG----WC----RG--TG------   L                    !           !     +5t2n_A    
                                                                                                                                          !         +-7   +-3 
  SC--YT------------RGKGTT--TC--IG--AC--NA----AT--IC--HT--ECIT--------RCHTRGRGET--AAYTQA--YT----WC--RGST--ST------   L                    !         ! !   ! ! +5t8d_A    
                                                                                                                                          !         ! ! +-4 +-1 
  ------RA------------------------------SC----ATMCRGTCHC--NAKT----------YA--RG----SARTKG--KG----WT--ECET--TT------   L                    !         ! ! ! !   +5t2h_A    
                                                                                                                         +---------------12         ! +-5 ! 
  SCMC----------------------------------RG----TTRG----TTYTHG------------YCRGRGIT------QC--------MC--HT----TGKT----   L   !                !         !   ! +5thg_A    
                                                                                                                         !                !       +-8   ! 
  STST------------------------------TA--AA----VAQTRT--YC----AT----------QARTRGEC----YAKG--KG----WC----------------   L   !                !       ! !   +5t2o_A    
                                                                                                                         !                !       ! ! 
  CGRG--ST--TTKARG--QTFA--QG--NG----HC--SC----LAQGRGQACCMT--AC--ST--AT--QAYA--IC--TART----KGRT--VA--EC--QT--------   L   !                !       ! !   +4yit_A    
                                                                                                                         !                !     +-9 ! +-2 
  STMG----------RT----RGVT--SA----FC----MC----STQTRGECCTSTVAFT--ST--TCSCATKA--IT--TC--STDA--RG--TC----KT--TG------   L   !                !     ! ! +-6 +5esp_A    
                                                                                                                       -14                !     ! !   ! 
  --MT--EC----------------------------NT------ET--KTRGSG--YA------------YTST--RG--ST--NT--------AT----VT--RG------   L   !                +----10 !   +4z1x_A    
                                                                                                                         !                      ! ! 
  SA------------ST--EC----QG--TA--------ST----AT--KG--CAFCSC--IT--ST--STQAQA------TA--KG--KG----WC--EA----TA------   L   !                      ! +4yhx_A    
                                                                                                                         !                      !  
  SGSTLG--------RG--KGVT------------HC--HG------QTRTDCSANAKGSC--ST--TASARGQGRG--------YC------------RTEA--VG------   L   !                      +-4yis_A    
                                                                                                                         !  
  --YTLT--YC----RGSGECRGVT--TG----QG--VG----TARTEARGSC--------------------------WC----DCDC--RGHA--VC--------------   L   !     +------------------2vs7_A    
                                                                                                                         +----13  
  ----------------------------------------------------CA--QGVT--RT--DCYA--RT------FA--RGRGNTDT--MC--EA----------KA   L         !                +-5a77_B    
                                                                                                                               +---------------11  
  ----------------------------------------------------SAIAQAKG------ST--RG----QA--TAYCRT--ST----VA----IT------KTTT   L                          +-2vbo_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    
                                                                                               +-----------4 
  --------------------------SC--EG------------QG--TGYGVGYT----QG------WGEGRG------------   L   !           +-------------4boc_A    
                                                                                               ! 
  ----------------------------KT--YG------------YG--YAIGSC------------------------QA--HG       !                       +---4yfu_D    
                                                                                             --6                     +-1 
  ----------------------------KC----------------FG--YGMG----------------------NG--QG--HG   L   !                   +-2 +---4bwj_A    
                                                                                               !                   ! ! 
  ----------------------NA--KA--------RG------QC----YCMC------------------------QC------       !         +---------3 +----4x0q_B    
                                                                                               !         !         ! 
  ----------------------------KT------RG--EG----YGACYCAC--------------------RTNG--QG--HC   L   +---------5         +-----4xvk_A    
                                                                                                         ! 
  ------------------------------------------------------------------------------QA------                 +---------------1x9m_A    
                                                                                             


> 1mwi_A:CRYSTAL STRUCTURE OF A MUG-DNA PRODUCT COMPLEX

  
  ----RA--NTQG--RC   L              +--------2dp6_A    
                         +----------2 
  SGKT------AARG--   L   !          !        +5hf7_A    
                       --3          +--------1 
  --KT------AARG--       !                   +4z47_A    
                         ! 
  ------TT------RA       +-------------------4yig_E    
                       


> 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 --6       +------------2 +2i9t_A    
                                   !                    ! 
  RGRGYTCTECRG------KT------   L   !                    +3do7_A    
                                   ! 
  RGRG----EGRG--------------   L   +--------------------1bvo_A    
                                 


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

  
  ------RA------RT--ITQCNA------   L                          +5eea_B    
                                                            +-1 
  RA----RT----------IAQTNA----KT   L                  +-----2 +4rdu_A    
                                                      !     ! 
  ----YART----------IAQTNA------   L   +-------------11     +5lty_K    
                                       !              !  
  ------RT----------VAQTNA------   L   !              !     +5hod_A    
                                       !              +-----4 
  ----YARA----------IAQTNA------   L   !                    +5lux_L    
                                       !  
  KT----RT----------IAQTNAMC----   L   !                      +2h1k_B    
                                       !                    +-3 
  --RT--RA----------IAQCNAMG----   L   !                  +-7 +2r5z_A    
                                     -14                  ! ! 
  ------RA----------IAQCNAMC----   L   !            +----10 +-4cyc_A    
                                       !            !     !  
  ------RT------RT--IAQCNA------   L   !            !     ! +5jlw_D    
                                       !            !     +-5 
  ------------------IA--NA------       !  +--------12       +4qtr_D    
                                       !  !         !  
  ------RA----------IA--NA------       !  !         !       +-4xrs_G    
                                       !  !         !     +-6 
  ------------------NCICNARGRG--   L   +-13         +-----9 +-4xrm_B    
                                          !               ! 
  --------RT--------NT--NAIARG--   L      !               +--4cyc_B    
                                          !  
  ------------------TAQCNAMC----          !                +-4rbo_D    
                                          +----------------8 
  ----------KASGATYTRG----------   L                       +-4rb3_D    
                                     


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

  
  KT--HGNT----ECRCRG   L                          +1nkp_A    
                                        +---------1 
  ----HGNT--LGECRCRC   L                !         +5i50_B    
                                 +------6 
  ----HGNT----ECRCRG   L         !      !      +--1nkp_E    
                                 !      +------4 
  ----HG------ETRCRG   L         !             +--5gnj_I    
                           +-----8 
  --RT--NT--RGECRCQT       !     !                +2ypa_A    
                           !     !           +----2 
  ----ST------ATRTRG       !     !    +------5    +4zpk_B    
                           !     !    !      ! 
  ----ST------ATRTRG     --9     +----7      +----5sy7_B    
                           !          ! 
  --------NG--SCHTRC       !          +-----------5nj8_C    
                           ! 
  ----HG----ITECRCRG   L   !                      +5nj8_D    
                           +----------------------3 
  ----HG------ETRTRG   L                          +5v0l_A    
                         


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

  
  HGNTLGECRCRC   L                         +-5i50_B    
                           +---------------4 
  HG----ETRCRG   L         !               +-5gnj_I    
                           ! 
  HGNT--ECRCRG   L         !   +--------------1nkp_A    
                     +-----7   ! 
  RTNT--ECRCRG   L   !     ! +-5                +4h10_B    
                     !     ! ! !              +-1 
  --NTRGECRCQT       !     ! ! +--------------2 +2ypa_A    
                     !     +-6                ! 
  ST----ATRTRG     --8       !                +4zpk_B    
                     !       ! 
  --NT--ETRCMT       !       !                +2ql2_D    
                     !       +----------------3 
  ST----ATRTRG       !                        +5sy7_B    
                     ! 
  HGKT--EARCRC   L   +-----------------------1a0a_B    
                   


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

  
  --HGNT--LGECRCRC   L                      +-5i50_B    
                         +------------------2 
  --HG------ETRCRG   L   !                  +-5gnj_I    
                         ! 
  RT--NT--RGECRCQT     --5                    +2ypa_A    
                         !               +----1 
  --ST------ATRTRG       !        +------3    +4zpk_B    
                         !        !      ! 
  --ST------ATRTRG       +--------4      +----5sy7_B    
                                  ! 
  ------NG--SCHTRC                +-----------5nj8_C    
                       


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

  
  ----------RG----NC----YGAT--CTRG   L                         +3a5t_B    
                                                             +-1 
  ------NT--ATAT----RG------------   L              +--------3 +5t01_B    
                                                    !        ! 
  ------RA--NA--AAVT----STRG------   L     +--------6        +1nwq_C    
                                           !        ! 
  RGQGNARTAGQT--FTRG--------------   L   +-7        +---------1gd2_G    
                                         ! ! 
  ------RA--NA--ATAT----STRG------   L   ! !                  +2e42_A    
                                         ! +------------------2 
  ----RG----NC--YGAT----CTRG------   L --8                    +2wt7_B    
                                         ! 
  --------------NT----ATAT--STRG--   L   !                 +--1dh3_C    
                                         !               +-4 
  ----NG--AT----STRG--------------       +---------------5 +--5szx_B    
                                                         ! 
  ----------NCTT--AT------RG------   L                   +----2dgc_A    
                                       


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

  
  VGRG------PG----NG               +---------------1oe4_B    
                           +-------3 
  ------KT--AARGPG--       !       !              +4z47_A    
                           !       +--------------1 
  ----SGKT--AARGPG--   L --4                      +5hf7_A    
                           ! 
  KT------TT--------       !                    +--4yig_E    
                           +--------------------2 
  ----------PALA----                            +--4uqm_A    
                         


> 1omh_A:CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL- FREE STRUCTURE.

  
  LTSTHAVT--AGRARG----TTSTPT----RGKGIG--QT--RAKGNTDG--VTKG--RT------NTTCKCRT   L            +------------------1omh_A    
                                                                                   +--------2 
  FAQGNTFA------QART--------NGEG------EGNGPG--------NAKT--HA----RA----------   L   !        !     +------------4ht4_A    
                                                                                 --3        +-----1 
  --RGMTKARA--RA----WAIGTG--------------------------------------LTQA--------   L   !              +------------4lvi_A    
                                                                                   ! 
  ------------------------------------------------------MG----RT------------   L   +---------------------------5byg_D    
                                                                                 


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

  
  ----QGCGTALC------------------------                                +-1orn_A    
                                                     +----------------2 
  ------------YG--------------------RG   L        +--4                +-5kn8_A    
                                                  !  ! 
  ----NG--RG----FGRC------------------       +----5  +------------------4ejy_A    
                                             !    ! 
  LTNGRGTG--LC----LCRG--------YTNTKT--       !    +---------------------4ofa_A    
                                           --6 
  --------------------IAQTNAMC--------   L   !                          +2h1k_B    
                                             !         +----------------1 
  --------------------IAQCNAMG--------   L   +---------3                +2r5z_A    
                                                       ! 
  --------------------TAQCNAMC--------                 +----------------4rbo_D    
                                           


> 1owf_A:CRYSTAL STRUCTURE OF A MUTANT IHF (BETAE44A) COMPLEXED WITH THE NATIVE H' SITE

  
  ------RTRTNAPTKTIC   L     +1owf_A    
                           +-1 
  --RTRT--RTNTPAQT--   L   ! +2np2_A    
                         --3 
  --RT--RARANAPAKT--   L   ! +1owf_B    
                           +-2 
  QTIT--RTRT--PT----         +4qju_B    
                         


> 1owf_B:CRYSTAL STRUCTURE OF A MUTANT IHF (BETAE44A) COMPLEXED WITH THE NATIVE H' SITE

  
  --RT--RARANAPAKT--   L       +1owf_B    
                             +-1 
  --RTRT--RTNTPAQT--   L   +-2 +2np2_A    
                           ! ! 
  ------RTRTNAPTKTIC   L --3 +1owf_A    
                           ! 
  QTIT--RTRT--PT----       +-4qju_B    
                         


> 1p71_B:ANABAENA HU-DNA CORCRYSTAL STRUCTURE (TR3)

  
  --RT--RARANAPAKT--   L       +1owf_B    
                             +-1 
  --RTRT--RTNTPAQT--   L   +-2 +2np2_A    
                           ! ! 
  ------RTRTNAPTKTIC   L --3 +1owf_A    
                           ! 
  QTIT--RTRT--PT----       +4qju_B    
                         


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

  
  RG--YTTTEC----RG--RC--QA----KARC   L             +----------1p7h_L    
                                               +---3 
  RGRGYT--EC----RAKTRTTTQA--------   L         !   +----------1a66_A    
                                         +-----4 
  RGRGYT------SG--------RT--------   L   !     !              +2i9t_A    
                                         !     +--------------1 
  RGRGYTEC--------------RT--------   L --5                    +1gji_A    
                                         ! 
  RGRG--EG--RG--------------------   L   !                  +-1bvo_A    
                                         +------------------2 
  ------------------------PTRG----   L                      +-1nfk_A    
                                       


> 1pdn_C:CRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS RESOLUTION REVEALS STRUCTURAL BASIS FOR PAX DEVELOPMENTAL MUTATIONS

  
  NG----STHG--CTSTKG----ITSA   L                +------------1pdn_C    
                                     +----------2 
  NG----SCHG----SGKT----IASA   L   +-3          +------------1k78_A    
                                   ! ! 
  RT--HGSGRGHG--RT----------   L --4 +-----------------------1tc3_C    
                                   ! 
  --KT------VT--KGDCRGTA----   L   !                         +3sjm_A    
                                   +-------------------------1 
  --RT------RT----IAQCNA----   L                             +5jlw_D    
                                 


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

  
  ----------ST--RTQT--KG                                    +5d5w_B    
                                                  +---------3 
  KTHG------------------                          !         ! +5hdn_C    
                                         +--------4         +-1 
  ----------ST--RTQT--MT   L             !        !           +5d8k_B    
                                         !        ! 
  ----------STVTRGQTNTMT   L          +--6        +----------5d5v_B    
                                      !  ! 
  --------DCKT--RGYC----   L          !  !                   +4uno_A    
                               +------7  +-------------------2 
  --------DCKT--RCYA----   L   !      !                      +5e8i_D    
                               !      ! 
  ----------KT--RGYA----   L --8      !       +--------------4iri_A    
                               !      +-------5 
  ------YAQTTC----------   L   !              +--------------5k5q_D    
                               ! 
  ----ST--VT------------   L   +-----------------------------4aik_A    
                             


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

  
  ------DCKT--RG----RGYA--------   L                  +--------------1dux_F    
                                                      ! 
  ------DCKT--RGAT--RCYA--------   L                  !               +5e8i_D    
                                                      !        +------1 
  --------KT--RGAT--RGYA--------   L                  !        !      +4iri_A    
                                             +--------9        ! 
  --------STVT------RGQTNT--MT--   L         !        !      +-7       +5d5v_B    
                                             !        !      ! !     +-4 
  --KTHG------------------------             !        !      ! !     ! ! +5hdn_C    
                                             !        !      ! +-----5 +-3 
  --------ST--------RTQT--MT----   L         !        +------8       !   +5d8k_B    
                                             !               !       ! 
  --------ST--------RTQT--KG----       +----10               !       +5d5w_B    
                                       !     !               ! 
  ------DCKT--RGST--RGYA--------   L   !     !               !       +4bnc_A    
                                       !     !               +-------2 
  ------DCKT--RGST--RGYC--------   L   !     !                       +4uno_A    
                                     -11     !  
  RC------QG------------------SG       !     !                   +---4qlc_U    
                                       !     +-------------------6 
  ----------NAST--RGHT--STFT----   L   !                         +---5x07_F    
                                       !  
  ------------------YG----------       +-----------------------------3irr_C    
                                     


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

  
  HT--RT--RA----IAQCNAMG----   L                                +2r5z_A    
                                                              +-2 
  --------RT----VAQTNA------   L                            +-3 +5hod_A    
                                                            ! ! 
  ------YARA----IAQTNA------   L              +-------------4 +5lux_L    
                                              !             ! 
  --RA----RT----IAQTNA----KT   L              !             ! +4rdu_A    
                                              !             +-1 
  --------RA--RTITQCNA------   L              !               +5eea_B    
                                              !  
  --KT----RT----IAQTNAMC----   L          +--11            +-2h1k_B    
                                          !   !          +-7 
  --------RT--RTIAQCNA------   L          !   !          ! ! +5jlw_D    
                                          !   !    +-----9 +-5 
  --------------IA--NA------              !   !    !     !   +4qtr_D    
                                          !   !    !     ! 
  --------RA----IAQCNAMC----   L          !   !    !     +---4cyc_A    
                                   +-----12   +---10  
  --------RA----IA--NA------       !      !        !        +-4xrs_G    
                                   !      !        !      +-6 
  --------------NCICNARGRG--   L   !      !        +------8 +-4xrm_B    
                                 -13      !               ! 
  ----------RT--NT--NAIARG--   L   !      !               +--4cyc_B    
                                   !      !  
  --------------TAQCNAMC----       !      +------------------4rbo_D    
                                   !  
  ------YART----IAQTNA------   L   +-------------------------5lty_K    
                                 


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

  
  KT----RT----------------IAQTNAMC----------   L                                  +2h1k_B    
                                                                                +-3 
  --RT--RA----------------IAQCNAMG----------   L                                ! +2r5z_A    
                                                                        +-------8 
  ------RT------------RT--IAQCNA------------   L                        !       ! +5jlw_D    
                                                                        !       +-4 
  ------RA----------------IAQCNA------MC----   L                   +---11         +4cyc_A    
                                                                   !    !  
  --------RT--------------NT--NAIARG--------   L                   !    !       +4cyc_B    
                                                                   !    +-------6 
  ------------------------NCICNA--------RGRG   L             +----13            +4xrm_B    
                                                             !     !  
  ------RA----------------IA--NA------------                 !     !            +4xrs_G    
                                                             !     !   +--------9 
  ------------------------IA--NA------------                 !     !   !        +4qtr_D    
                                                             !     +--12  
  ------------------------TAQCNAMC----------                 !         !        +4rbo_D    
                                                             !         +--------7 
  --------NGRGTGLC----LCRG------------------       +--------14                  +4ofa_A    
                                                   !         !  
  RA----RT----------------IAQTNA----KT------   L   !         !                       +4rdu_A    
                                                   !         !                     +-1 
  ------RA------------RT--ITQCNA------------   L   !         !                   +-2 +5eea_B    
                                                   !         !                   ! ! 
  ----YART----------------IAQTNA------------   L -15         !           +-------5 +5lty_K    
                                                   !         !           !       ! 
  ----YARA----------------IAQTNA------------   L   !         +----------10       +5lux_L    
                                                   !                     !  
  ------RT----------------VAQTNA------------   L   !                     +-------5hod_A    
                                                   !  
  ----------------TGKG----------------------   L   +-----------------------------4pxi_B    
                                                 


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

  
  --------------ST--SAYT--ECQT--------------RT--PT----   L                               +---------------4hf1_A    
                                                                                  +-----13  
  ----------RG--TTRGTTTT--RTET--------------HA--------   L                     +-18      +---------------4p9u_B    
                                                                               !  !  
  --------ST----STQAQGST--SART------------------KT----   L                     !  +----------------------5trd_B    
                                                                               !  
  ----------RG--STRGMCTT--RT--------------------------   L                     !                          +4u0y_B    
                                                                               !                  +-------1 
  --------ETNT--SCRGHC----RT----------------QA--------   L                  +-21                  !       +5d4s_B    
                                                                            !  !         +-------10  
  --------------ITRGECSC--SGKG------------------------   L                  !  !         !        !      +5i2d_R    
                                                                            !  !  +-----14        +------3 
  --------------HT--STAT--STRG------------------------   L                  !  !  !      !               +5lej_A    
                                                                            !  +-19      !  
  ----------------KGEA--------------------RG--LGNC----   L                  !     !      +----------------5kbj_B    
                                                                            !     !  
  --------------EGRTRGRG--YT--------------------------   L                  !     +-----------------------4yo2_A    
                                                                         +-22  
  ----------------YAQTTC----QC------------------------   L               !  !                    +-------5k5q_D    
                                                                         !  !     +-------------11  
  ------------------AT--------------------------------                   !  !  +-17              +-------5fyw_R    
                                                                         !  !  !  !  
  ------------------------------------------------ITHG   L               !  !  !  +----------------------5iyc_T    
                                                                         !  !  !  
  ------RC------------QG------------------------SG----                   !  !  !                     +---4qlc_U    
                                                                         !  !  !     +---------------9 
  --------------------------NASTHT--STFT--------------   L               !  +-20     !               +---5x07_F    
                                                                         !     !     !  
  ------------------------------YGRG------------------                +-23     !  +-15                   +4wcg_B    
                                                                      !  !     !  !  !                 +-6 
  ----------YA--KTPTPG----YTRG------------------------   L            !  !     !  !  !                 ! +4mte_D    
                                                                      !  !     !  !  +-----------------7 
  ------------------------------YG--------------------                !  !     +-16                    ! +4lb5_B    
                                                                      !  !        !                    +-2 
  --------------SG--AT----YTRG------------------------   L            !  !        !                      +4rb3_D    
                                                                      !  !        !  
  ------------------NTVC--ECSTYTSTYC--------RA--------   L         +-24  !        +----------------------5ed4_A    
                                                                   !  !  !  
  ----------------RGSTRT--STHG------------------RA----   L         !  !  !             +------------3zpl_B    
                                                                   !  !  +------------12  
  ----YA--------PTATPARA--YA--------------------------   L         !  !                !           +5bpd_A    
                                                                +-25  !                +-----------5 
  --------NT----KTPTQTSC----KA------------------RT----   L      !  !  !                            +5bmz_D    
                                                                !  !  !  
  KC--------------MGSGTT--TTYC------------------------   L   +-26  !  +----------------------------5f7q_C    
                                                             !  !  !  
  MTPT--------RT--------------------------------------   L   !  !  +----------------------------5fmf_V    
                                                             !  !  
  --------------NATT--ECVT----HT------------RT--------   L -27  +----------------------------4s04_B    
                                                             !  
  --------------------------NT----NA--IARG------------   L   !                            +4cyc_B    
                                                             !                          +-4 
  --------------------------NC--ICNA--RGRG------------   L   +--------------------------8 +4xrm_B    
                                                                                        ! 
  ------------------RT------IA--QCNA------------------   L                              +--5jlw_D    
                                                           


> 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.

  
  NTVTFTLTFAVATTNAVTFTPALTFAVATA   L         +1qna_B    
                                             ! 
  NTVAFTLTFAVATTNAVTFAPALAFTVATA   L         !     +1cdw_A    
                                       +-----4   +-1 
  NAVTFTLTFAVATANTVTFAPALAFTVATA   L   !     ! +-2 +1ytb_A    
                                       !     ! ! ! 
  NTVAFTLTFAVATTNAVAFAPALTFTVATA   L --5     +-3 +1rm1_A    
                                       !       ! 
  NTVAFCLTFAVATTNAVTFTPALTFTVATA   L   !       +4wzs_D    
                                       ! 
  NTVTFALAFTVATTNAVTFTPALTFAVTTA   L   +-----5n9g_G    
                                     


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

  
  --RC----PTTC--WC   L      +--------------1qpi_A    
                         +--8 
  TTHTRTQAATSCYTYT   L   !  !     +--------5dy0_D    
                         !  +-----6 
  ----TGKG----YCFA   L   !        +--------4pxi_B    
                         !  
  --EC--KGQCTGYGRC   L   !              +--4jl3_B    
                         !              ! 
  TA----ECAC--YCRA       !          +---3    +5haw_A    
                       -10          !   !  +-1 
  TA--STECAGATYTRG   L   !          !   +--2 +4gck_A    
                         !    +-----5      ! 
  VT--AGDT--TTYTLA   L   !    !     !      +5gpc_B    
                         !    !     ! 
  TA--AT----LCFGHA       ! +--7     !   +--4i6z_B    
                         ! !  !     +---4 
  ----TCKGAG--YTHA       ! !  !         +--5k7z_A    
                         +-9  ! 
  MTRGAAVT--TTYT--   L     !  +------------5fmp_B    
                           ! 
  LG----KG--STYTHT   L     +---------------4l62_M    
                       


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

  
  ----SG--TC------RG------LCKA   L                          +1qpz_A    
                                                            ! 
  ITYTSGMTAA--STRG--NT--AGLCAT   L   +----------------------3   +3oqm_C    
                                     !                      ! +-1 
  IT--ST--ATTTSTRG----VTAGLCAC   L   !                      +-2 +1rzr_C    
                                   --4                        ! 
  LTYCSGYGQC--STRG--HT--AGLGAC   L   !                        +1efa_B    
                                     ! 
  LCYCSGVTAT--ST----HT--AGLCAC   L   +-----------------------2bjc_A    
                                   


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

  
  RT--SAYCMT------FT--------   L              +-----1j5n_A    
                                   +----------4 
  RTTASTYAFALT----PTAT--STRA   L   !          +-----5jh0_D    
                                   ! 
  ----------VT----FG--FCSA--     --6                  +4qr9_A    
                                   !                +-1 
  RT--NGFTIA--RA--NASG--ST--   L   !      +---------3 +1j47_A    
                                   !      !         ! 
  RT--NTFTMA--RT--NG----SA--   L   +------5         +4y60_C    
                                          ! 
  RT--NTFTMA--RA--NGAC--ST--   L          !         +4s2q_D    
                                          +---------2 
  RC--NTFTMA--RAHTNTAT--SA--   L                    +3u2b_C    
                                 


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

  
  ------------------STTTDT----------QC--HC--FA--KT------------TGRAYC--QC--LG--KGDGQG   L                          +------1qzh_E    
                                                                                                  +---------------1 
  ------DG--TGFGYGKT------YT----KG------------------FG--IGHG----RGYG--QG------------   L       +--2               +------2i0q_A    
                                                                                               !  ! 
  --------------------------YTFT------NT--SG--WG----------------KGFG--EGKG--KG------         +-3  +----------------------3u58_C    
                                                                                             ! ! 
  ------------KC--------------------------------------------------------------------       +-4 +-------------------------3rn5_C    
                                                                                           ! ! 
  EGTGYG------------------------------KG----------------------KT--YG----------------   L --5 +--------------------------1s40_A    
                                                                                           ! 
  --------DC--EC--LCRC--ACAC------RCFC--RC--------RC--ECEC--RC------QC--------------   L   +---------------------------3a5u_B    
                                                                                         


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

  
  ----KGVT--RG--   L                     +5cbz_E    
                             +-----------1 
  --ECKA--RGRG--   L         !           +4nqa_I    
                       +-----9 
  ----KAVA--RA--   L   !     !           +5e69_A    
                       !     +-----------2 
  --ECKG--KGRA--   L   !                 +5l0m_A    
                       !  
  --ECKG--RGRG--   L -10          +------2nll_B    
                       !     +----7 
  --EAKG--KTRG--   L   !     !    !     +4cn3_D    
                       !     !    +-----4 
  --ECKG----RA--   L   !     !          +5krb_G    
                       +-----8 
  ----KGVG--RG--   L         !             +4tnt_B    
                             !           +-3 
  --ECKGAG--RG--   L         !         +-5 +4ond_A    
                             !         ! ! 
  ----KGVT--RG--             +---------6 +5emc_A    
                                       ! 
  YGECKGAG--KGRG   L                   +-4oln_B    
                     


> 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 
  STSTRGKGIT--RG----RG--------   L   !            +---3mky_B    
                                     +------------1 
  --SGRAAT--TTRG--------------   L                +---3vwb_A    
                                   


> 1r8d_B:CRYSTAL STRUCTURE OF MTAN BOUND TO DNA

  
  RG--HTHC------YG   L                      +-------1r8d_B    
                                          +-4 
  RA--HT----------                        ! +-------2vz4_A    
                                       +--6 
  YT--RTFC--KG----   L                 !  !     +---5d8c_A    
                                       !  +-----3 
  KG--RTFC------YG   L                 !        +---4wls_B    
                         +-------------7 
  KG--RT----------   L   !             !            +5i44_I    
                         !             !   +--------1 
  RA--RT----------       !             !   !        +4r24_B    
                       --8             +---5 
  RG--RTYT------RT   L   !                 !        +4r4e_B    
                         !                 +--------2 
  EC--QT--RGRT--HT   L   !                          +5c8e_C    
                         ! 
  ECTGRGRT--RARC--   L   +--------------------------1rh6_B    
                       


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

  
  KCRT----YC--               +--------------------1r8e_A    
                             ! 
  RAHT--------               !             +------2vz4_A    
                     +-------7       +-----4 
  RGRTYT--RT--   L   !       !       !     !   +--4r4e_B    
                     !       !       !     +---3 
  ST--FC------   L   !       !       !         +--2zhg_A    
                     !       +-------6 
  YTRTFCKG----   L   !               !         +--5d8c_A    
                   --8               !   +-----2 
  KGRTFC--YG--   L   !               !   !     +--4wls_B    
                     !               +---5 
  KGQGRT------   L   !                   !        +5i44_I    
                     !                   +--------1 
  RART--------       !                            +4r24_B    
                     ! 
  ----------RG   L   +----------------------------1nlw_D    
                   


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

  
  ----TT--SGLTYART----YTPCITRGDCKT   L     +-----------------------------2nra_C    
                                         +-3 
  ----TT--PTTCSTNT--RT------------   L   ! !        +--------------------4lln_I    
                                         ! +--------2 
  ------YAQTTC--QC----------------   L --4          !              +-----5k5q_D    
                                         !          +--------------1 
  --------------RGYG--------------       !                         +-----1qbj_C    
                                         ! 
  LTETTTRAECRCRCQC----------------   L   +-----------------------------3n97_A    
                                       


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

  
  QTTTKTQAQASTQALT----TT   L                                 +3cro_R    
                                                        +----1 
  --AT--QAAT--SA--------                    +-----------3    +4z5h_A    
                                            !           ! 
  ------QASTCTSART----ET   L   +------------4           +----5j2y_A    
                               !            ! 
  QT--STNTVTATSTQTRTETTT   L   !            !              +-2r1j_L    
                             --5            +--------------2 
  ----TT--RGQTITRG----ST   L   !                           +-5jub_B    
                               ! 
  QT--SGQTTTTGSTRG----LT   L   +-----------------------------3l1p_A    
                             


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

  
  ----LG--TTRGECRC--RTQT------   L                                   +------5vi8_F    
                                              +----------------------5 
  ----LGET--RGECRT--RT--------   L            !                      +------4yln_L    
                                              !  
  ----LTETTTRAECRC--RCQC------   L            !                             +3n97_A    
                                              !              +--------------3 
  ------------RTTT--DAVT--RGRG   L            !            +-6              +1gxp_A    
                                              !            ! ! 
  --------TT--PTTC--STNT------   L         +-10      +-----7 +---------------4lln_I    
                                           !  !      !     ! 
  ----------QAPCST--VT--------   L         !  !      !     !                +4aik_A    
                                           !  ! +----8     +----------------2 
  ----------RGSTRT--STHG------   L         !  ! !    !                      +3zpl_B    
                                           !  ! !    ! 
  --------------------------YG             !  ! !    !                +-----3eyi_B    
                                        +-11  +-9    +----------------4 
  ----------------RGAC--LG----          !  !    !                     +-----4wx9_A    
                                        !  !    ! 
  ------YAKTPTPG----YTRG------   L      !  !    !                           +4mte_D    
                                     +-12  !    +---------------------------1 
  KA------SG--AT----YTRG------   L   !  !  !                                +4rb3_D    
                                     !  !  !  
  --------TT--SGLT--YART------   L -13  !  +-----------------------------2nra_C    
                                     !  !  
  --------TTRG--AT--STQC----RG   L   !  +-----------------------------2w7n_B    
                                     !  
  --RC------------------------   L   +-----------------------------4roc_A    
                                   


> 1rm1_A:STRUCTURE OF A YEAST TFIIA/TBP/TATA-BOX DNA COMPLEX

  
  NAVTFTLTFAVATANTVTFAPALAFTVATA   L                           +1ytb_A    
                                                             +-1 
  NTVAFTLTFAVATTNAVAFAPALTFTVATA   L                       +-2 +1rm1_A    
                                                           ! ! 
  NTVAFTLTFAVATTNAVTFAPALAFTVATA   L                     +-3 +1cdw_A    
                                                         ! ! 
  NTVAFCLTFAVATTNAVTFTPALTFTVATA   L   +-----------------4 +4wzs_D    
                                       !                 ! 
  NTVTFALAFTVATTNAVTFTPALTFAVTTA   L --5                 +5n9g_G    
                                       ! 
  NTVTFTLTFAVATTNAVTFTPALTFAVATA   L   +-----------------1qna_B    
                                     


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

  
  ----TT--RGQTITRG----ST   L   +-----------------------------5jub_B    
                               ! 
  --AT--QAAT--SA--------       !                        +----4z5h_A    
                               !                    +---1 
  ------QASTCTSART--ET--   L --5           +--------2   +----5j2y_A    
                               !           !        ! 
  ----TTQA--LTSAET------   L   !     +-----3        +--------2o4a_A    
                               !     !     ! 
  QT----VTNT--STRG------   L   +-----4     +-----------------3o9x_A    
                                     ! 
  ----TT----ATYTQTQT----   L         +-----------------------3qws_B    
                             


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

  
  ----------ICIC--QG--TGLGKG----SG------------------------RC                                 +1rxw_A    
                                                                                      +------1 
  --------IA--AGVG--QC--LCQC----MG--------------KCKA------RC                        +-2      +5k97_A    
                                                                                    ! ! 
  ITYTQT--KTAA----------------------------------------------             +----------3 +-------4q0w_A    
                                                                         !          ! 
  --------------------VG----PGRC--NG------------------------       +-----4          +-------5t9j_B    
                                                                   !     ! 
  ------FCRT------------------------LT--TGEGEG--------FTRT--   L --5     +------------------5hp4_A    
                                                                   ! 
  CTHTKA------------------------------RT------RC----RG------       +------------------------5v07_Z    
                                                                 


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

  
  ITYTSGMTAA--STRG--NT--AGLCAT   L                              +3oqm_C    
                                                              +-1 
  IT--ST--ATTTSTRG----VTAGLCAC   L                          +-2 +1rzr_C    
                                                            ! ! 
  LTYCSGYGQC--STRG--HT--AGLGAC   L   +----------------------3 +1efa_B    
                                     !                      ! 
  ----SG--TC------RG------LCKA   L --4                      +1qpz_A    
                                     ! 
  LCYCSGVTAT--ST----HT--AGLCAC   L   +-----------------------2bjc_A    
                                   


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

  
  EGTGYG--SG--DGKGATFTSGVGNGYTLGYGYG--KG----YT--RGDGNG--KT--YG--NGAG--RT--   L            +-----------------1s40_A    
                                                                                   +------1 
  ----QT----------------------------------RT----------LTTTKTFTQT----ST--HT       +-2      +-----------------4gnx_B    
                                                                                 ! ! 
  ------KG--WGYT--------YCFA--MA--RG--RT--IGWGDG--------------------------   L --3 +------------------------4hja_A    
                                                                                 ! 
  ----------------------------------QC--HC--------------TGRAYC------------   L   +--------------------------1qzh_E    
                                                                               


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

  
  --------------SANCTGTTPT----------------RT--   L                             +----5hlg_E    
                                                                          +----6 
  ------------DCLT--AGTTRG----RG--------RA----   L                        !    +----5h3r_A    
                                                           +--------------9 
  --YA--------PTATPARAYA----------------------   L         !              !        +5bpd_A    
                                                           !              +--------3 
  ------NT----KTPTQTSC--KA------------------RT   L         !                       +5bmz_D    
                                                           !  
  --------------------------YG----------------             !                        +4lb5_B    
                                                           !                +-------1 
  KA----------SG--AT--YTRG--------------------   L      +-12                !       +4rb3_D    
                                                        !  !       +--------8 
  ----RC------------QG--------------------SG--          !  !       !        !   +---4qlc_U    
                                                        !  !       !        +---5 
  --------------------NASTRGHT--STFT----------   L      !  !   +--10            +---5x07_F    
                                                        !  !   !   !  
  --------------------------YGRG--------------          !  !   !   !               +4wcg_B    
                                                     +-13  +--11   +---------------4 
  --------YA--KTPTPG--YTRG--------------------   L   !  !      !                   +4mte_D    
                                                     !  !      !  
  --------------YAQTTC--QC--------------------   L   !  !      !                   +5k5q_D    
                                                     !  !      +-------------------2 
  ------ST----STQAQGSTSART------------KT------   L -14  !                          +5trd_B    
                                                     !  !  
  ----------RGSTRGMCTTRT----------------------   L   !  !                     +-----4u0y_B    
                                                     !  +---------------------7 
  ------------ST--SAYTECQT----------RT--PT----   L   !                        +-----4hf1_A    
                                                     !  
  ----------------------ST--RTQT--KG----------       +-----------------------------5d5w_B    
                                                   


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

  
  ----------------ST--SAYTECQT----------------RT--PT------   L                                     +---------------4hf1_A    
                                                                                            +-----12  
  ------------RG--TTRGTTTTRTET----------------HA----------   L                           +-16      +---------------4p9u_B    
                                                                                         !  !  
  ----------ST----STQAQGSTSART--------------------KT------   L                           !  +----------------------5trd_B    
                                                                                         !  
  ------------------RGSTRTSTHG--------------------RA------   L                           !             +------------3zpl_B    
                                                                                         !  +---------10  
  ------YA--------PTATPARAYA------------------------------   L                           !  !          !           +5bpd_A    
                                                                                      +-18  !          +-----------4 
  ----------NT----KTPTQTSC--KA----------------------RT----   L                        !  !  !                      +5bmz_D    
                                                                                      !  !  !  
  --------------------------------YG----------------------                            !  !  !                           +4lb5_B    
                                                                                      !  !  !                +----------2 
  ----------------SG--AT--YTRG----------------------------   L                        !  !  !        +-------9          +4rb3_D    
                                                                                      !  !  !        !       ! 
  ------------------KGEA--------------------RG--LGNC------   L                        !  +-17     +-13       +----------5kbj_B    
                                                                                      !     !     !  !  
  --------------------------------YGRG--------------------                            !     !     !  !                 +4wcg_B    
                                                                                      !     !     !  +-----------------5 
  ------------YA--KTPTPG--YTRG----------------------------   L                        !     !  +-14                    +4mte_D    
                                                                                   +-19     !  !  !  
  --------RC------------QG------------------------------SG                         !  !     !  !  !               +---4qlc_U    
                                                                                   !  !     !  !  !            +--6 
  --------------------------NAST--HT--STFT----------------   L                     !  !     !  !  +------------8  +---5x07_F    
                                                                                   !  !     +-15               ! 
  ------------------YAQTTC--QC----------------------------   L                     !  !        !               +------5k5q_D    
                                                                                   !  !        !  
  ------------RG--STRGMCTTRT------------------------------   L                     !  !        !                     +4u0y_B    
                                                                                +-20  !        !              +------1 
  ----------ETNT--SCRGHC--RT------------------QA----------   L                  !  !  !        +--------------7      +5d4s_B    
                                                                                !  !  !                       ! 
  ----------------ITRGECSCSGKG----------------------------   L                  !  !  !                       +------5i2d_R    
                                                                                !  !  !  
  --RC------------EGRTRGRGYT------------------------------   L               +-21  !  +-------------------------4yo2_A    
                                                                             !  !  !  
  ----------------------------------------------------HG--   L               !  !  !           +---------------5iyc_T    
                                                                             !  !  +----------11  
  --------------------AT----------------------------------                +-22  !              +---------------5fyw_R    
                                                                          !  !  !  
  ----KC------------MGSGTTTTYC----------------------------   L            !  !  +----------------------------5f7q_C    
                                                                       +-23  !  
  IT--PT--------RT----------------------------------------   L         !  !  +----------------------------5fmf_V    
                                                                    +-24  !  
  ----------------------AA--ET--------------------RG------   L      !  !  +----------------------------5eix_A    
                                                                 +-25  !  
  --------------------SC--------RGKC----------------------       !  !  +-----------------------------5fur_G    
                                                                 !  !  
  RC------------------------------------------------------   L -26  +-----------------------------4roc_A    
                                                                 !  
  --------------------------NT------NA--IARG--------------   L   !                            +4cyc_B    
                                                                 +----------------------------3 
  --------------------------NC----ICNA--RGRG--------------   L                                +4xrm_B    
                                                               


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

  
  RG------NC--YGAT--CTRG   L                +3a5t_B    
                                     +------1 
  --NT----ATAT----RG----   L   +-----2      +5t01_B    
                               !     ! 
  NG----AT----STRG------     --3     +------5szx_B    
                               ! 
  --NCRT--ATAT--STRG----   L   +------------1t2k_D    
                             


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

  
  RGAC--                                +1t38_A    
                                     +--1 
  RAAC--              +--------------2  +1yfh_A    
                      !              ! 
  RGACLG         +----4              +--4wx9_A    
                 !    ! 
  RCQC--         !    !    +------------3gx4_X    
               +-5    +----3 
  ----YG       ! !         +------------1sfu_A    
             --6 ! 
  ----YG       ! +----------------------3irr_C    
               ! 
  --RGYG       +------------------------1qbj_C    
             


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

  
  SAIAQGKT--NTSCYA----QA----QATCYARG--RG--SAVA------KGTC   L                +1t9i_B    
                                                                          +-1 
  STITQANG----ST------RGRG--YCTCYCRG--------VCQT----KGTC   L         +---10 +3mxb_R    
                                                                     !    !  
  CA--QGVT--RTDCYA------RT----FA--RGRGNTDT--MCEA------KA   L      +-15    +5a77_B    
                                                                  !  !  
  SAIAQA------SC------RGKG--QATAYC----ST----VA------KTTT   L      !  !     +2vbl_B    
                                                                  !  +-----2 
  SAIAQAKG----ST------RG----QATAYCRT--ST----VA--IT--KTTT   L      !        +2vbo_A    
                                                                  !  
  SGSTLGQG----KTYA----RGKGVT------HCHG--------QTRTDC----   L      !           +4yis_A    
                                                                  !         +-8 
  STMG--------KGYC----RT--RGVTSA--FCMC------STQTRGEC----   L      !         ! +5esp_A    
                                                                  !         !  
  ------RA--RG------RTRGSTRTQGTA----SC------ATMCRGTC----   L      !         !          +5t2h_A    
                                                               +-16         !        +-4 
  SCMCRG--RG----------YTST--ECTT----RG------TTRG--------   L   !  !         !      +-5 +5thg_A    
                                                               !  !      +-12      ! ! 
  STST----------------ECRG--------TAAA------VAQTRT------   L   !  !      !  !    +-6 +5t2o_A    
                                                               !  !      !  !    ! ! 
  SC--YT----------------RGKGTTTCIG--NA------AT--IC------   L   !  !      !  !  +-9 +5t8d_A    
                                                               !  !      !  !  ! ! 
  STIGRGRG------MC----LTEC--STKG--TTNA--------MGRTSC----   L   !  !  +--13  !  ! ! +5t2n_A    
                                                               !  !  !   !  +-11 +-3 
  SGMGRGRG----KTYA----LTVT----TT--KTSC----------RGEC----   L -17  !  !   !     !   +4lox_A    
                                                               !  !  !   !     !  
  --MTHTEC------------RGRG--QGKG--NT--------ET--KTRG----   L   !  +-14   !     +-4z1x_A    
                                                               !     !   !  
  SA--RGRG--NTKTST----STEC--QGTA----ST------AT--KG------   L   !     !   +-4yhx_A    
                                                               !     !  
  CGRGST----------TTKARGQTFAQGNG--HCSC------LAQGRGQA----   L   !     +-----4yit_A    
                                                               !  
  STITQAKG--RGSTNT----QGST--ATTC--YT--SC----VCDTRGSTKGTG   L   !       +2xe0_B    
                                                               +-------7 
  SAIAQAKG--NTSCYA----QA----QATGYCRG--RG----VA--------TC   L           +1mow_A    
                                                             


> 1tc3_C:TRANSPOSASE TC3A1-65 FROM CAENORHABDITIS ELEGANS

  
  --RGHCRGRGQAQGKG--   L       +-----------------------------2glo_A    
                             +-2 
  --------NG----NA--   L     ! !                            +2kdz_A    
                           +-3 +----------------------------1 
  --------NC--RGDC--   L   ! !                              +5eyb_B    
                         --4 ! 
  NG--STHG--CTSTKG--   L   ! +-----------------------------1pdn_C    
                           ! 
  ------YTVC--KGDCKC   L   +-----------------------------2qhb_A    
                         


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

  
  --KG--WTKA--------HCHG--RG--TAACNAKGRGLTSTRGRG   L         +-------------1tf6_A    
                                                         +---4 
  --RGSTDAHARG--RGSTDCHG--TT--RGDAEGRG----------   L     !   +-------------5kl3_A    
                                                       +-5 
  RGST--YGYC----QC--TGSTRGYT--------------------   L   ! !                 +4is1_C    
                                                       ! +-----------------2 
  --------------DC--YCKG--RG--QA--TC------------   L --6                   +5k5i_A    
                                                       ! 
  --RGSTDTEGRG--RGSGDCHG--TT--RGDAEGRG----------   L   !                   +4x9j_A    
                                                       !                 +-1 
  --TT----ECRGYGECVASCKG--RG--DGYCKGRG----------   L   +-----------------3 +5kkq_D    
                                                                         ! 
  --NG--SGHGRG--DA--SCHG--RGRGDCSCNA------------   L                     +5ei9_F    
                                                     


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

  
  ------YAQTTC--QC----------   L                              +5k5q_D    
                                               +--------------2 
  ST--STQAQGSTSART----------   L         +-----7              +5trd_B    
                                         !     ! 
  ----------------YGRG------             !     +--------------4wcg_B    
                                         ! 
  ----DCLT--AGTTRG--RG------   L   +-----8                   +5h3r_A    
                                   !     !                 +-3 
  ------RGSTRTSTHG----------   L   !     !     +-----------4 +3zpl_B    
                                   !     !     !           ! 
  NT--KTPTQTSC--KA--------RT   L   !     +-----6           +--5bmz_D    
                                 --9           ! 
  --------QC----------------       !           +--------------5hso_A    
                                   ! 
  ETNTSCRGHC--RT--------QA--   L   !                          +5d4s_B    
                                   !                    +-----1 
  --RGSTRGMCTTRT------------   L   +--------------------5     +4u0y_B    
                                                        ! 
  ----ST--SAYTECQT----RTPT--   L                        +-----4hf1_A    
                                 


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

  
  ----HTDTKTRTATFTLTDTQTFT----WTRTRT----HTHTSTST--------   L   +---------1uaa_B    
                                                               ! 
  ----HT----------------FT----FTRTRTNTATHTST----ET----ET     --3       +-4c2u_D    
                                                               !    +--1 
  FT--HT------------ST--FT----WGRTRT----HGSTMT----RTEGEG       +----2  +-2is6_B    
                                                                    ! 
  FTTTHT----------------FTDTYTWTRTRT--------------------   L        +----2pjr_A    
                                                             


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

  
  TT----ECRGYG--ECVASCKGRG--DGYCKG--RGQA----TC--   L                            +5kkq_D    
                                                          +---------------------1 
  NG--SGHGRG----DA--SCHGRGRGDCSCNA----NCKTSAHGRG   L   +--4                     +5ei9_F    
                                                       !  ! 
  ------------RGST--YGYC----QCTGSTRGYT----------   L   !  +---------------------4is1_C    
                                                     --5 
  RGSTDAHARG----RGSTDCHGTT--RGDAEG--RG----------   L   !        +---------------5kl3_A    
                                                       +--------3 
  RGSTDTEGRG----RGSGDCHGTT--RGDAEG--RG----------   L            !              +4x9j_A    
                                                                +--------------2 
  DC--YCKGRG----QA----TC----RCSCDC--VT----------   L                           +5k5i_A    
                                                     


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

  
  --------------NAST--RGHT--STFT----   L                         +--------5x07_F    
                                                   +-------------3 
  ------RGSTRT--STHG------------RA--   L           !             +--------3zpl_B    
                                               +---7 
  ----------QG------------------SG--           !   !                 +----4qlc_U    
                                               !   !    +------------2 
  ------------ST------------------RA           !   +----5            +----5bs8_A    
                                               !        ! 
  ----------KT----RGAT--RCYA--------   L     +-8        +-----------------5e8i_D    
                                             ! ! 
  ----YAQTTC----QC------------------   L     ! !    +---------------------5k5q_D    
                                             ! !    ! 
  ----------------------YG----------         ! +----6                     +4lb5_B    
                                           +-9      !    +----------------1 
  ----SG--AT----YTRG----------------   L   ! !      +----4                +4rb3_D    
                                           ! !           ! 
  RT--------------------------------   L -10 !           +----------------5fmf_V    
                                           ! ! 
  --------SGTT--TTYC----------------   L   ! +----------------------------5f7q_C    
                                           !  
  --DCKGRGNA--RT--------KT------KGRA   L   +-----------------------------5ddg_A    
                                         


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

  
  RART--IT--QCNA--   L                                     +5eea_B    
                                                         +-1 
  RT----IA--QTNA--   L                             +-----4 +4rdu_A    
                                                   !     ! 
  RT----IA--QTNA--   L                         +---7     +5lty_K    
                                               !   ! 
  RA----IA--QCNAMG   L                         !   !     +2r5z_A    
                                               !   +-----3 
  RT----VA--QTNA--   L                         !         +5hod_A    
                                     +---------8 
  RTRT--IA--QCNA--   L               !         !          +5jlw_D    
                                     !         !        +-2 
  RT----IA--QTNAMC   L               !         !      +-5 +2h1k_B    
                                   +-9         !      ! ! 
  RA----IA--QCNAMC   L             ! !         +------6 +4cyc_A    
                                   ! !                ! 
  ------IA----NA--              +-10 !                +--4qtr_D    
                                !  ! ! 
  RA----IA--QTNA--   L          !  ! +-------------------5lux_L    
                         +-----11  !  
  ------TA--QCNAMC       !      !  +---------------------4rbo_D    
                       -12      !  
  ----RTNAQAIASCRT   L   !      +----------------------5b7j_A    
                         !  
  --NCRGDC--RGDC--   L   +-----------------------------5eyb_B    
                       


> 1w36_B:RECBCD:DNA COMPLEX

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


> 1w36_C:RECBCD:DNA COMPLEX

  
  RT----NT--NAIARG   L            +4cyc_B    
                         +--------1 
  ------NT--NAIARG   L   !        +1puf_B    
                       --3 
  HTRT--NCSTNARG--   L   !       +1k61_B    
                         +-------2 
  ----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--NGRC--------QAHG              !            +-4yfu_D    
                                                                                  !          +-1 
  LCMGRCEG--------SGHGVC--------------------------------------------       +------5        +-2 +-1kln_A    
                                                                           !      !        ! ! 
  --------KC------------RGNG--NG----TGFG--YGMG----RG------------QGHG   L   !      !      +-3 +---4bwj_A    
                                                                           !      !      ! ! 
  ----------KA----------RG--NT------QC------MC------QC--------------     --6      +------4 +---4x0q_B    
                                                                           !             ! 
  ----------------------RG--------EG--YGAC--AC----RC--------------HC   L   !             +----4xvk_A    
                                                                           ! 
  ------------NG--------RT----------IGYG----------------EGMCTCNGQT--       +------------------4ztu_A    
                                                                         


> 1xbr_B:T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA

  
  ------RG----TTATFTFG                              +1xbr_B    
                                                  +-1 
  ------RG----TTATFTFG   L   +--------------------2 +1h6f_B    
                             !                    ! 
  ------RG----TT--FGFT     --3                    +-5t1j_B    
                             ! 
  RGRGYT--TTQA--------   L   +----------------------1a66_A    
                           


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

  
  HTTTKGMTSTKATT--QT----QT--KARARTKTST--RG----EA----RA----------   L                                +1xo0_B    
                                                                            +-----------------------1 
  HTTAECMASTKTTTQTQT--CTRAMTKARARTRCSA--YA----QG----RA----------   L     +--2                       +5u91_B    
                                                                         !  ! 
  ----------------------------------TTQAATYG--YAKT--------------   L   +-3  +-----------------------5jk0_B    
                                                                       ! ! 
  ----------TATAITSAYCTT--------------------RTLT--RT------------   L --4 +--------------------------4e0p_A    
                                                                       ! 
  ----------------------------------------------------NGRGTTRGKT   L   +----------------------------5ds9_A    
                                                                     


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

  
  --IAQTNA------   L   +---------------------------5lty_K    
                       !  
  --NCICNARGRG--   L   !                      +----4xrm_B    
                       !                      !  
  --TAQCNAMC----       !                      !        +4rbo_D    
                       !                 +---10      +-2 
  RTIAQCNA------   L   !                 !    !    +-3 +5jlw_D    
                       !                 !    !    ! ! 
  --VAQTNA------   L   !                 !    +----6 +5hod_A    
                       !                 !         ! 
  --IA--NA------     -14            +---11         ! +4qtr_D    
                       !            !    !         +-4 
  --IAQTNA------   L   !            !    !           +5lux_L    
                       !            !    !  
  --IAQTNA----KT   L   !            !    !         +4rdu_A    
                       !            !    !       +-1 
  RTITQCNA------   L   !         +-12    +-------8 +5eea_B    
                       !         !  !            ! 
  --IAQCNAMC----   L   !         !  !            +-4cyc_A    
                       !         !  !  
  --NT--NAIARG--   L   !         !  !            +-4cyc_B    
                       +--------13  +------------9 
  --IAQTNAMC----   L             !               ! +2h1k_B    
                                 !               +-5 
  --IAQCNAMG----   L             !                 +2r5z_A    
                                 !  
  --VASGNA------   L             !               +-3cmy_A    
                                 +---------------7 
  --IA--NA------                                 +-4xrs_G    
                     


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

  
  ------NT------KTPTQTSC--KA------------------RT   L                            +-5bmz_D    
                                                                              +-5 
  --------------DCLT--AGTTRG----RG----------RA--   L                        +-8 +-5h3r_A    
                                                                            ! ! 
  ----------------SANCTGTTPT----------------RT--   L      +-----------------9 +---5hlg_E    
                                                          !                 ! 
  ----------------RGSTRTSTHG----------------RA--   L      !                 +----3zpl_B    
                                                       +-14  
  ----------------YAQTTC--QC--------------------   L   !  !                     +5k5q_D    
                                                       !  !       +-------------3 
  ------ST------STQAQGSTSART------------KT------   L   !  +------10             +5trd_B    
                                                       !          !  
  --------------ST--SAYTECQT----------RT--PT----   L   !          +--------------4hf1_A    
                                                       !  
  ----------------------------YG----------------       !                         +4lb5_B    
                                                       !                     +---1 
  KA------------SG--AT--YTRG--------------------   L -15          +----------7   +4rb3_D    
                                                       !          !          ! 
  --YA----------PTATPARAYA----------------------   L   !      +--11          +---5bpd_A    
                                                       !      !   !  
  ----RC--------------QG------------------------       !      !   !           +--4qlc_U    
                                                       !  +--12   +-----------6 
  ----------------------NASTRGHT--STFT----------   L   !  !   !               +--5x07_F    
                                                       !  !   !  
  ----------------------------YGRG--------------       !  !   !                 +4wcg_B    
                                                       +-13   +-----------------4 
  --------YA----KTPTPG--YTRG--------------------   L      !                     +4mte_D    
                                                          !  
  ------------RGSTRGMCTTRT----------------------   L      !                      +4u0y_B    
                                                          +----------------------2 
  ----------ETNTSCRGHC--RT----------------------   L                             +5d4s_B    
                                                     


> 1yfh_A:WT HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAINING AN ALKYLATED CYTOSINE

  
  RGAC--                           +---1t38_A    
                    +--------------1 
  RGACLG            !              +---4wx9_A    
               +----3 
  RCQC--       !    !     +------------3gx4_X    
             --4    +-----2 
  ----YG       !          +------------1sfu_A    
               ! 
  ----YG       +-----------------------3irr_C    
             


> 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

  
  ------DCKT--RGAT--RCYA------   L                           +5e8i_D    
                                                          +--1 
  --------KT--RGAT--RGYA------   L                     +--5  +4iri_A    
                                                       !  ! 
  ------DCKT--RG----RGYA------   L                   +-6  +--1dux_F    
                                                     ! ! 
  --------ST--------RTQT--KG--                +------7 +-----5d5w_B    
                                              !      ! 
  --------STVT------RGQTNTMT--   L            !      !      +5d5v_B    
                                              !      +------4 
  --KTHG----------------------                !             ! +5hdn_C    
                                     +--------9             +-3 
  --------ST--------RTQT--MT--   L   !        !               +5d8k_B    
                                     !        ! 
  ------DCKT--RGST--RGYA------   L   !        !              +4bnc_A    
                                   -10        !   +----------2 
  ------DCKT--RGST--RGYC------   L   !        +---8          +4uno_A    
                                     !            ! 
  RC------QG----------------SG       !            +----------4qlc_U    
                                     !  
  ----------NA----RAHT--STLT--   L   +-----------------------2a07_K    
                                   


> 1ytb_A:CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX

  
  NTVAFTLTFAVATTNAVAFAPALTFTVATA   L         +1rm1_A    
                                           +-1 
  NAVTFTLTFAVATANTVTFAPALAFTVATA   L     +-2 +1ytb_A    
                                         ! ! 
  NTVAFTLTFAVATTNAVTFAPALAFTVATA   L   +-3 +1cdw_A    
                                       ! ! 
  NTVAFCLTFAVATTNAVTFTPALTFTVATA   L --4 +4wzs_D    
                                       ! 
  NTVTFALAFTVATTNAVTFTPALTFAVTTA   L   +5n9g_G    
                                     


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

  
  KGTA--NAYASGATST--LT----------KT--RCST----TTSTRGYCTT--QT   L                   +---------1z19_B    
                                                                      +----------1 
  HTTAECMA--ST----KTTTQTQTCTRAKA------SA--YA--QG----------   L   +----2          +---------5u91_B    
                                                                 !    ! 
  ------------AATAKGNA--IT------------TTQAATYGYAKT----TT--   L --3    +--------------------5jk0_B    
                                                                 ! 
  --------------------------------KA--------RT----RT------   L   +-------------------------4e0p_A    
                                                               


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

  
  ----NTKTPTQTSC--KA------------RT   L                             +---5bmz_D    
                                                                 +-5 
  ------DCLT--AGTTRG------RG--RA--   L                           ! !  +5h3r_A    
                                                    +------------6 +--2 
  --------RGSTRTSTHG----------RA--   L              !            !    +3zpl_B    
                                                    !            ! 
  --------SANCTGTTPT----------RT--   L           +--8            +---5hlg_E    
                                                 !  ! 
  SAEA----KC------RCRA----KG------   L           !  !        +-------4kdp_B    
                                                 !  +--------7 
  ----------QC--------------------               !           +-------5hso_A    
                                         +------10  
  --------YAQTTC--QC--------------   L   !       !                 +--5k5q_D    
                                         !       ! +---------------4 
  ----------------------YG--------       !       ! !               ! +4lb5_B    
                                         !       ! !               +-1 
  ----STSTQAQGSTSART--------KT----   L -11       +-9                 +5trd_B    
                                         !         ! 
  --YA--PTATPARAYA----------------   L   !         !                +-5bpd_A    
                                         !         +----------------3 
  ----------------------YGRG------       !                          +-4wcg_B    
                                         !  
  ----------KGTGKANGYAST----------   L   +---------------------------1zlk_A    
                                       


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

  
  ------SCTA--KTVCHTKG--   L                         +1je8_F    
                                                   +-1 
  ------KGTC--KGTCHT----   L   +-------------------2 +4wuh_B    
                               !                   ! 
  ------KGTG--KANGYAST--   L   !                   +1zlk_A    
                             --5 
  ----SANCTG----TTPT----   L   !               +---5hlg_E    
                               +---------------4 
  --DCLT--AG----TTRG--RG   L                   ! +-5h3r_A    
                                               +-3 
  NTKTPTQT--SC----KA----   L                     +-5bmz_D    
                             


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

  
  ------YART--------IA--QTNA------   L                +---------------5lty_K    
                                            +--------12  
  --------RT--------VA--QTNA------   L      !         !               +5hod_A    
                                            !         +---------------3 
  ------YARA--------IA--QTNA------   L      !                         +5lux_L    
                                            !  
  --RA----RT--------IA--QTNA----KT   L      !                           +4rdu_A    
                                            !                         +-1 
  --------RA----RT--IT--QCNA------   L      !                    +----5 +5eea_B    
                                            !                    !    ! 
  --------RA--------IA--QCNAMC----   L      !                    !    +4cyc_A    
                                            !              +-----9 
  --------RA--------IA----NA------          !              !     !     +4xrs_G    
                                         +-15              !     !   +-6 
  ------------------NC--ICNARGRG--   L   !  !              !     +---8 +4xrm_B    
                                         !  !              !         ! 
  ----------RT------NT----NAIARG--   L   !  !          +--10         +-4cyc_B    
                                         !  !          !   !  
  --KT----RT--------IA--QTNAMC----   L   !  !          !   !           +2h1k_B    
                                         !  !          !   !         +-2 
  HT--RT--RA--------IA--QCNAMG----   L   !  !          !   !         ! +2r5z_A    
                                         !  !  +------13   +---------7 
  --------RT----RT--IA--QCNA------   L -16  !  !       !             ! +5jlw_D    
                                         !  !  !       !             +-4 
  ------------------IA----NA------       !  !  !       !               +4qtr_D    
                                         !  +-14       !  
  ------------------TA--QCNAMC----       !     !       +---------------4rbo_D    
                                         !     !  
  ----------------RTNAQAIASCRTVA--   L   !     !       +---------------5b7j_A    
                                         !     +------11  
  ------------RGKGSGSA--QAVCRT----   L   !             +---------------5gzb_A    
                                         !  
  --NC--YG------------------------       +---------------------------5n9g_C    
                                       


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

  
  --QTSTRGEC----RG----   L                           +1zrf_A    
                                                   +-2 
  ----HT--STATSTRG----   L              +----------3 +5lej_A    
                                        !          ! 
  ----STRGECTANGKG----   L   +----------4          +-3mzh_A    
                             !          ! 
  ----ITRGECSCSGKG----   L   !          +------------5i2d_R    
                           --6 
  --RGSTRGMCTTRT------   L   !                       +4u0y_B    
                             !    +------------------1 
  ETNTSCRGHC--RT----QA   L   +----5                  +5d4s_B    
                                  ! 
  ----------------YG--            +------------------4lb5_B    
                           


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

  
  ------------------NAST--RGHT--STFT----   L                              +--------5x07_F    
                                                           +--------------8 
  --------RGSTRT--STHG----------------RA   L               !              +--------3zpl_B    
                                                           !  
  --------YAQTTC----QC------------------   L            +-12                      +5k5q_D    
                                                        !  !  +-------------------4 
  --ST----STQAQGST--SART----------------   L            !  !  !                   +5trd_B    
                                                        !  +-10  
  --------------------------YG----------                !     !                    +4lb5_B    
                                                     +-13     !           +--------3 
  --------SG--AT----YTRG----------------   L         !  !     +-----------9        +4rb3_D    
                                                     !  !                 ! 
  YA------PT----RA--YA------------------   L         !  !                 +--------5bpd_A    
                                                  +-14  !  
  ----RT--------------------------------   L      !  !  +-------------------------5fmf_V    
                                                  !  !  
  ------STRGMCTT--RT--------------------   L      !  !                    +-----4u0y_B    
                                                  !  +--------------------6 
  --------ST--SAYT--ECQT------------RT--   L   +-15                       +-----4hf1_A    
                                               !  !  
  --------------QG----------------------       !  !                     +-----4qlc_U    
                                               !  !     +---------------7 
  --------------KT----RGAT--RGYA--------   L   !  !     !               !     +1bc8_C    
                                               !  !     !               +-----1 
  --------------KT----RGAT--RCYA--------   L   !  +----11                     +5e8i_D    
                                             -16        !  
  ------------AA----ET----------------RG   L   !        !                +----5eix_A    
                                               !        +----------------5 
  ------------SG------------------------       !                         !    +5iwi_C    
                                               !                         +----2 
  ------------SA------------------------   L   !                              +5npk_d    
                                               !  
  ------DCKGRGNA--RT--------KT----------   L   +-----------------------------5ddg_A    
                                             


> 2a3v_C:STRUCTURAL BASIS FOR BROAD DNA-SPECIFICITY IN INTEGRON RECOMBINATION

  
  KATT--AAYT--WTTTKATTQTSTLTLTNT--ST--LTLTITFTRTSTKA----------------QA--DCKCTCIC   L                 +----------2a3v_C    
                                                                                          +----------1 
  HTTAECMA--ST----KTTT--QTQT--CTRA--MT--------------RARTRCSA--YA----QG----------   L      !          +----------5u91_B    
                                                                                       +--3 
  HTTTKGMT--------KATT----QT----QT------------------RARTKTST--RG----EA----------   L   !  !    +----------------1xo0_B    
                                                                                     --4  +----2 
  ----------------AATA--KGNA--IT--------------------------TTQAATYG--YAKT----TT--   L   !       +----------------5jk0_B    
                                                                                       ! 
  --------------------------------------------------------RTLT----RT------------   L   +------------------------4e0p_A    
                                                                                     


> 2aq4_A:TERNARY COMPLEX OF THE CATALYTIC CORE OF REV1 WITH DNA AND DCTP.

  
  IASAYAHALGLGSG----HA------------WG----------------DTWA------KGYTMG----------               +---2aq4_A    
                                                                                          +--4 
  --NA--HALGIGSG--------EG--------FG----------------ETYG----TGKGFTHG----------            !  +---3gqc_A    
                                                                                          ! 
  ----------------------VASA----AAPT--MT------------EG----RT--------FT--RT----       +----5       +5c5j_A    
                                                                                     !    !     +-1 
  ----------------------AG--------PCIAKA--------KC--YC--------------LCST--RC--       !    !   +-2 +4f4y_B    
                                                                                     !    !   ! ! 
  --------------------MAMG------AGPTFAIT------------ET------------------------     --6    +---3 +-4u6p_B    
                                                                                     !        ! 
  --------------FCYC--------TTAT--------SCICDCEC--ST------------------SG--RCRT       !        +--4tqr_A    
                                                                                     ! 
  ------------------QT----IT--RTST----------------------TA--------------------       +-----------5kfz_A    
                                                                                   


> 2ayg_A:CRYSTAL STRUCTURE OF HPV6A E2 DNA BINDING DOMAIN BOUND TO AN 18 BASE PAIR DNA TARGET

  
  --NCKGCA--YGRA--------------------------   L                    +----------2ayg_A    
                                                     +------------2 
  KTTGYCNG--RT----------------------------   L       !            !          +1b3t_A    
                                                   +-3            +----------1 
  KGTAYCNG--RT----------------------------   L     ! !                       +5t7x_B    
                                                 +-4 ! 
  --------IC----RCKCIC--EC--RC------------   L   ! ! +-----------------------1zzi_A    
                                               --5 ! 
  ------------------------------RC--------   L   ! +-------------------------2itl_B    
                                                 ! 
  --------------------VG--MG--FG--RTETKTAG   L   +--------------------------2up1_A    
                                               


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

  
  KANT--RGMGYAMCKTNC--KTDA----TT--   L                              +-2b9s_A    
                                              +---------------------1 
  ----ECRA--YAMCKTNT--KT----------       +----2                     +-1k4t_A    
                                         !    ! 
  ------------------KA----QG------   L --3    +-----------------------5u91_B    
                                         ! 
  ------------------------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    
                                       ! 
  ----------KC----KA--VARA------       !      +------------4p4m_A    
                                       +------4 
  ----------KT--HCVGLCIGRG------              +------------5hrb_A    
                                     


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

  
  ------NT--NAIARG--   L                                  +4cyc_B    
                                                     +----6 
  ------NCRGRG------   L                             !    +4xrm_B    
                                                     ! 
  ----RTIAQCNA------   L                          +--8        +5jlw_D    
                                                  !  !      +-1 
  ------IAQTNA----KT   L                          !  !    +-4 +4rdu_A    
                                                  !  !    ! ! 
  ----RTITQCNA------   L                   +------9  +----7 +5eea_B    
                                           !      !       ! 
  ------IAQCNAMC----   L                   !      !       +4cyc_A    
                                           !      ! 
  ------IAQTNAMC----   L                +-10      !        +2h1k_B    
                                        !  !      +--------5 
  ------IAQCNAMG----   L                !  !               +2r5z_A    
                                        !  !  
  ------IA--NA------       +-----------11  !               +4qtr_D    
                           !            !  +---------------2 
  RA----IAQTNA------   L   !            !                  +5lux_L    
                           !            !  
  ------TAQCNAMC----     -12            !                +4rbo_D    
                           !            +----------------3 
  ------VAQTNA------   L   !                             +5hod_A    
                           !  
  --RT--------------       +-----------------------------5vi8_T    
                         


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

  
  ----------NASTRGHTSTFT------   L                         +--------5x07_F    
                                              +------------5 
  --RGSTRT--STHG----------RA--   L            !            +--------3zpl_B    
                                       +------8 
  ------QG------------------SG         !      !              +------4qlc_U    
                                       !      +--------------4 
  ------SA----------------RG--   L     !                     !  +---5npk_d    
                                       !                     +--3 
  ------SG----------------RT--       +-9                        !  +5iwi_C    
                                     ! !                        +--1 
  ------AA----ET----------RG--   L   ! !                           +5eix_A    
                                     ! ! 
  --YAQTTC----QC--------------   L   ! !      +---------------------5k5q_D    
                                     ! !      ! 
  ----------------YG----------     -10 +------7                  +--4lb5_B    
                                     !        !   +--------------2 
  RT--------------------------   L   !        +---6              +--5fmf_V    
                                     !            ! 
  STRGMCTT--RT----------------   L   !            +-----------------4u0y_B    
                                     !  
  ------DCKGRGNARTKT----KGRA--   L   +-----------------------------5ddg_A    
                                   


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

  
  --ECKA--RGRG--   L   +----------------------4nqa_I    
                       !  
  ----KGVT--RG--   L   !                       +5cbz_E    
                       !                     +-3 
  --EAKG--KTRG--   L   !                     ! ! +4cn3_D    
                       !                +----4 +-1 
  --ECKG--KGRA--   L   !                !    !   +5l0m_A    
                     -10              +-7    ! 
  ----KAVA--RA--   L   !              ! !    +5e69_A    
                       !       +------8 ! 
  --ECKG--RGRG--   L   !       !      ! +-----2nll_B    
                       !       !      ! 
  --ECKG----RA--   L   !       !      +-------5krb_G    
                       !       ! 
  ----KGVG--RG--   L   +-------9                +4tnt_B    
                               !              +-2 
  --ECKGAG--RG--   L           !            +-5 +4ond_A    
                               !            ! ! 
  ----KGVT--RG--               +------------6 +5emc_A    
                                            ! 
  YGECKGAG--KGRG   L                        +-4oln_B    
                     


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

  
  ------------RT--RTIAQCNA------   L                                 +5jlw_D    
                                                                  +--1 
  ------------RA----IAQCNAMC----   L                              !  +4cyc_A    
                                                                +-9 
  ------------------IA--NA------                                ! !  +4qtr_D    
                                                                ! +--2 
  ------------RT----VAQTNA------   L                            !    +5hod_A    
                                                     +---------10  
  ------------RA----IA--NA------                     !          !        +4xrs_G    
                                                     !          !      +-3 
  ------------RA--RTITQCNA------   L                 !          !    +-5 +5eea_B    
                                                     !          !    ! ! 
  ----------YART----IAQTNA------   L                 !          +----7 +5lty_K    
                                                     !               ! 
  ----------YARA----IAQTNA------   L                 !               +5lux_L    
                                       +------------13  
  ------------RT----IAQTNAMC----   L   !             !                 +2h1k_B    
                                       !             !     +-----------6 
  ------------RA----IAQCNAMG----   L   !             !     !           +2r5z_A    
                                       !             !  +-11  
  ------------------TAQCNAMC----       !             !  !  !           +4rbo_D    
                                     -14             !  !  !         +-4 
  --------------RT--NT--NAIARG--   L   !             +-12  +---------8 +4cyc_B    
                                       !                !            ! 
  ------------------NCICNARGRG--   L   !                !            +-4xrm_B    
                                       !                !  
  ------------RT----IAQTNA----KT   L   !                +------------4rdu_A    
                                       !  
  QASTCTSART--------------------   L   +-----------------------------5j2y_A    
                                     


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

  
  ------RG----NCYGATCTRG   L                        +3a5t_B    
                                    +---------------1 
  ------NT--ATAT--RG----   L        !               +5t01_B    
                                 +--6 
  --RA--NA--AAVTSTRG----   L     !  !               +1nwq_C    
                                 !  +---------------2 
  RG--QGNARTAGQTFTRG----   L   +-7                  +1gd2_G    
                               ! ! 
  --RA--NA--ATATSTRG----   L   ! !                  +2e42_A    
                             --8 +------------------3 
  RG----NC--YGATCTRG----   L   !                    +2wt7_B    
                               ! 
  ------NG--AT--STRG----       !             +------5szx_B    
                               +-------------5 
  ------NT--ATATSTRG----   L                 !  +---1dh3_C    
                                             +--4 
  ------NCTT--AT--RG----   L                    +---2dgc_A    
                             


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

  
  RC------RA------RCQTNT--QGTC--RC   L                    +--------2dp6_A    
                                               +----------2 
  ----SGKT--------AARGCGAC----PG--   L         !          !        +5hf7_A    
                                         +-----3          +--------1 
  ------KT----AARGCGACQT--PG------       !     !                   +4z47_A    
                                       --4     ! 
  --KT------TT--------------------       !     +-------------------4yig_E    
                                         ! 
  ----------------PALA------------       +-------------------------4uqm_A    
                                       


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

  
  --QA----TC----RA--SCDC--VT   L                                 +5kkq_D    
                                                      +----------2 
  RGDC--SCNA----NCKTSAHG--RG   L                      !          +5ei9_F    
                                                      ! 
  --QA--SGNA--KGQASTSCDC--KG   L               +------6            +1mey_C    
                                               !      !          +-1 
  --RGSGDCHG--TTRG--DAEG--RG   L               !      !   +------3 +4x9j_A    
                                               !      !   !      ! 
  --RG--DA----RGRG--DCHG----   L               !      +---5      +2prt_A    
                                             +-8          ! 
  --RG--DCEC--RGRG--DCHG----   L             ! !          !  +---1f2i_J    
                                             ! !          +--4 
  ----ATSGDC--KGDCPTSGSARTKG   L             ! !             +---2gli_A    
                                   +---------9 ! 
  --RGSTDCHGTTTTRG--DAEC--RG   L   !         ! !      +----------1llm_D    
                                   !         ! +------7 
  RGST--YGYC----QC--TGSTRGYT   L -10         !        +----------4is1_C    
                                   !         ! 
  --RGSTDCHG--TTRG--DAEG--RG   L   !         +-------------------5kl3_A    
                                   !  
  --QA----TC----RC--SCDC--VT   L   +-----------------------------5k5i_A    
                                 


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

  
  LTAGETSGTTHT--------------------------   L             +-----------------2e1c_A    
                                                       +-2 
  ----------------------NCKGCA----------   L           ! +-----------------2ayg_A    
                                               +-------3 
  --------------TAFCSG--------LATGSGVGFA   L   !       !         +--------5tkz_B    
                                             --4       +---------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------NC----YGATCTRG   L                     +--------2wt7_B    
                                         +-----------------2 
  ------NT----ATAT------RG--------   L   !                 +--------5t01_B    
                                       --4 
  --RA--NA----AAVT----STRG--------   L   !         +----------------1nwq_C    
                                         +---------3 
  ------NT----ATAT----STRG--------   L             !                +1dh3_C    
                                                   +----------------1 
  RC--NC--AAAT----CTRC------------   L                              +2wt7_A    
                                       


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

  
  SANCSCKG--LT--------DAECNATG----RC--KGST--------------DA--QA----QCNT   L      +---------2ex5_A    
                                                                             +-15  
  SAIAQAKG--NT--SCYAQA----QATGYC--RG--------RG--VA--------------TC----   L   !  +---------1mow_A    
                                                                             !  
  SAIAQAKG------ST--RG----QATAYC--RT--------ST--VA--IT--------KTTT----   L   !      +------2vbo_A    
                                                                             !      !  
  SG--YA------------YTST--RGST----NT--HTNC------AT--VT--RG------------   L   !      !            +4z1x_A    
                                                                             !      !          +-8 
  CTFTSTYA--ST--KTSTATQA--KTTGRA--ET----RG------ATDT----TA------------   L   !      !          ! ! +4lq0_A    
                                                                             !      !          ! +-3 
  SAKGIGKT------SGITQAIA--QATC----EC----DT--RG--WTYC----TC------------   L   !      !          !   +4lox_A    
                                                                           -16      !          ! 
  TTYTHG------------YCRGRGIT------QC------------MCHT----TGKT----------   L   !      !        +-9       +5thg_A    
                                                                             !   +-13        ! !     +-2 
  HC--NAKT----------YA--RG--SA--RT--KG--KG----FTWTECET--TT------------   L   !   !  !        ! !   +-4 +5t2h_A    
                                                                             !   !  !        ! !   ! ! 
  HT--ECIT--------RCHTRGRGETAA--YT--QA--YT----RTWCRGST--ST------------   L   !   !  !        ! ! +-5 +5t8d_A    
                                                                             !   !  !     +-10 ! ! ! 
  HT--NCWC--RG--------QG----STYG--LA--KG--RG--LTWC--RG--TG------------   L   !   !  !     !  ! +-7 +5t2n_A    
                                                                             !   !  !     !  !   ! 
  YC------------AT--QARTRGEC----YA--KG--KG----RTWC--------------------   L   !   !  !  +-11  !   +5t2o_A    
                                                                             !   !  !  !  !  !  
  CAFCSC--IT--ST--STQAQA----TAYA--KG--KG--KG--FTWCEA----TA------------   L   +--14  !  !  !  +-4yhx_A    
                                                                                 !  +-12  !  
  CCMT--AC--ST--AT--QAYA--ICTART------------KGRTVAEC--QT--------------   L       !     !  +--4yit_A    
                                                                                 !     !  
  CTSTVAFT--ST--TCSCATKA--ITTC----ST------DA--RGTC--KT--TG------------   L       !     !  +5esp_A    
                                                                                 !     +--6 
  SANAKGSC--ST--TASARGQGRG--------------YC--------RTEA--VG------------   L       !        +4yis_A    
                                                                                 !  
  SAYCKTIT--RGDCYA----------IG----RG------RG--DTIC------IA------------   L       !       +1m5x_B    
                                                                                 +-------1 
  CA--QGVT--RT--DCYA--RT----FA----RG------RGNTDTMCEA------------KA----   L               +5a77_B    
                                                                           


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

  
  ----RT--                      +5b0z_C    
                           +----7 
  ------RT                 !    +5b31_G    
                    +------9 
  ----RART          !      !       +3x1t_G    
                    !      !     +-1 
  ----RT--          !      +-----4 +5gt0_C    
                 +-12            ! 
  ----RG--       !  !            +4jjn_G    
                 !  !  
  --RT----       !  !    +-------4jjn_F    
                 !  +---10  
  IT------       !       +-------5b0z_D    
               -13  
  ----RT--       !             +4x23_O    
                 !    +--------6 
  LC--RG--       !    !        ! +4jjn_A    
                 !    !        +-3 
  LT--RC--       !    !          +5av9_A    
                 +---11  
  ----RG--            !         +5t5k_E    
                      !    +----2 
  IT------            !    !    +5b1m_D    
                      +----8 
  LT------                 !    +4z5t_A    
                           +----5 
  LT--RA--                      +5ay8_E    
               


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

  
  SGYGYGQCPC----YCFCMAFASAICECLCQAMGRG--FT--                                +--2fdc_B    
                                                   +------------------------1 
  ----YT--PT----YT--------------QTMGRTNAFALA   L   !                        +--3v4r_B    
                                                 --3 
  ------------------------------DA----QA----   L   !     +---------------------4qqw_A    
                                                   +-----2 
  ----------RTEG----------------------------             +---------------------4tmu_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----KGRA--RTRC   L                   +5l0m_A    
                                            +--6 
  --EC--KG------RA--PARC   L                !  +5krb_G    
                               +------------7 
  ------KAVA----RA------   L   !            !   +5e69_A    
                               !            +---1 
  ------KGVT----RG------   L   !                +5cbz_E    
                             -10  
  --EA--KG----KTRG------   L   !                +4cn3_D    
                               !     +----------3 
  --EC--KG----RGRG------   L   !     !          +2nll_B    
                               !     ! 
  ------KGVG----RG------   L   +-----9          +4tnt_B    
                                     !    +-----2 
  --EC--KGAG----RG------   L         !    !     +4ond_A    
                                     +----8 
  ------KGVT----RG------                  !      +5emc_A    
                                          !    +-4 
  --EC--KA----RGRG------   L              +----5 +4nqa_I    
                                               ! 
  YG--EC--KGAG--KGRG----   L                   +4oln_B    
                             


> 2fld_B:I-MSOI RE-DESIGNED FOR ALTERED DNA CLEAVAGE SPECIFICITY

  
  SAYCLC--ITRGDCYA----QG------IG--NA--RG----RG--DT--IC--RG--------   L              +2fld_B    
                                                                                  +-8 
  CA--QG--VTRT--DCYA----RT----FA--------RG--RGNTDT--MCEA--------KA   L      +----10 +5a77_B    
                                                                            !     !  
  SAIAQA--KG----ST----RG----QATAYC--------RT--ST----VA--IT--KTTT--   L      !     +-2vbo_A    
                                                                            !  
  SAIAQG--KTNT--SCYA--QA----QATCYA--RG--------RG--SAVA------------   L      !     +------1t9i_B    
                                                                            !  +-12  
  SGSTLG--QG----KTYA--RGKGVT------------HC--HG--------QTRTDC------   L      !  !  +------4yis_A    
                                                                         +-14  !  
  STIGRG--RG------MC--LTEC--STKG--------TT--NA--------MGRTSC------   L   !  !  !              +5t2n_A    
                                                                         !  !  !            +-3 
  SCMCRG--RG----------YTST--ECTT------------RG------TTRG----------   L   !  !  !            ! ! +5thg_A    
                                                                         !  !  !          +-4 +-2 
  --------RARG------RTRGSTRTQGTA------------SC------ATMCRGTC------   L   !  !  !          ! !   +5t2h_A    
                                                                         !  !  !        +-5 ! 
  STST--YC------------ECRG--------------TA--AA------VAQTRT--------   L   !  +-13        ! ! +5t2o_A    
                                                                         !     !        ! ! 
  SC--YT----------------RGKGTTTC----IG--AC--NA------AT--IC--------   L   !     !        ! +5t8d_A    
                                                                       -15     !      +-7 
  STMG----------KGYC--RT--RGVTSA--------FC--MC------STQTRGEC------   L   !     !      ! !   +5esp_A    
                                                                         !     !      ! ! +-1 
  SGMGRG--RG----KTYA--LTVT----TT--------KT--SC----------RGEC------   L   !     !    +-9 +-6 +4lox_A    
                                                                         !     !    ! !   ! 
  --MTHT--EC----------RGRG--QGKG----------NT--------ET--KTRG------   L   !     !    ! !   +4z1x_A    
                                                                         !     +---11 ! 
  SA--RG--RGNT--KTST--STEC--QGTA------------ST------AT--KG--------   L   !          ! +4yhx_A    
                                                                         !          !  
  CGRG--------------KARGQTFAQGNG--------HC--SC------LAQGRGQA------   L   !          +-4yit_A    
                                                                         !  
  SAIAQA--KGNT--SCYA--QA----QATGYC--RG--------RG----VA--------TC--   L   +---------1mow_A    
                                                                       


> 2gli_A:FIVE-FINGER GLI/DNA COMPLEX

  
  AT--YC----------RA----NC--------ATSGDC--KGDCPTSGSARTKG   L               +--------2gli_A    
                                                                       +---5 
  NG--SGHGRG------DA--SCHG--RGRGDC--SCNA----NCKTSAHG--RG   L           !   !        +5ei9_F    
                                                                       !   +--------1 
  ECVASCKGRG------DG--YCKG--RG--QA----TC----RA--SCDC--VT   L         +-7            +5kkq_D    
                                                                     ! ! 
  QA--SGNAKG------QASTSCDC--KG--RG--DCHA--RG------------   L         ! !            +1mey_C    
                                                                  +--8 +------------2 
  DC--YCKGRG------QA----TC------RC--SCDC--VT------------   L      !  !              +5k5i_A    
                                                                  !  ! 
  ----------------RGSTDTEG--RG--RGSGDCHG--TTRG--DAEG--RG   L      !  !              +4x9j_A    
                                                               +--9  +--------------3 
  ----------PCYC--RG--DA----RG--RG--DCHG----RG--DCEC--RG   L   !  !                 +2prt_A    
                                                               !  ! 
  ----------------RG--DCEC--RG--RG--DCHG----------------   L   !  !           +-----1f2i_J    
                                                             -10  +-----------4 
  --------------RGST--YGYC------QC--TGSTRGYT------------   L   !              +-----4is1_C    
                                                               !  
  ----------------RGSTDAHA--RG--RGSTDCHG--TTRG--DAEG--RG   L   !        +-----------5kl3_A    
                                                               +--------6 
  ----------------RGSTDCHGTTTT--RG--DAEC--RG------------   L            +-----------1llm_D    
                                                             


> 2glo_A:SOLUTION STRUCTURE OF THE BRINKER DNA BINDING DOMAIN IN COMPLEX WITH THE OMB ENHANCER

  
  --RALTPTDCHGTCTCLTHT   L       +-----------------------------1j1v_A    
                               +-1 
  RT----HGSGRGHG--RT--   L   +-2 +-----------------------------1tc3_C    
                             ! ! 
  --------TCKG--------     --3 +-----------------------------5k7z_A    
                             ! 
  ----LTETTTRAECRCRCQC   L   +-----------------------------3n97_A    
                           


> 2gzk_A:STRUCTURE OF A COMPLEX OF TANDEM HMG BOXES AND DNA

  
  RC--NAFTIA--RG--NC--SALT--YAKTEAKARC--FAFTCGICVGAG   L   +--------------2gzk_A    
                                                           ! 
  RT--NGFTIA--RA--NASGST----YAPGRG------------------   L --7  +-----------1j47_A    
                                                           !  ! 
  RT--NTFTMA--RA--NGACST----YA----------------------   L   !  !            +4s2q_D    
                                                           +--6          +-1 
  RC--NTFTMA--RAHTNTATSA----YA----------------------   L      !  +-------3 +3u2b_C    
                                                              !  !       ! 
  RT--NTFTMA--RT--NG--SA----YA----------------------   L      !  !       +4y60_C    
                                                              +--5 
  ------------------------------------------VTFGFCSA             !        +4qr9_A    
                                                                 !     +--2 
  ----------------------------------RTSAYCMT--FT----   L         +-----4  +1j5n_A    
                                                                       ! 
  RTTASTYAFALT----PTATST--RA------------------------   L               +--5jh0_D    
                                                         


> 2h1k_B:CRYSTAL STRUCTURE OF THE PDX1 HOMEODOMAIN IN COMPLEX WITH DNA

  
  KT----RT----------------------IA--QTNAMC----   L                                 +2h1k_B    
                                                                                 +-1 
  --RT--RA----------------------IA--QCNAMG----   L                          +----5 +2r5z_A    
                                                                            !    ! 
  ------RT----------------------VA--QTNA------   L                          !    +5hod_A    
                                                                            !  
  RA----RT----------------------IA--QTNA----KT   L                +--------10       +4rdu_A    
                                                                  !         !     +-2 
  ------RA----------------RT----IT--QCNA------   L                !         !   +-3 +5eea_B    
                                                                  !         !   ! ! 
  ----YART----------------------IA--QTNA------   L             +-13         +---8 +5lty_K    
                                                               !  !             ! 
  ----YARA----------------------IA--QTNA------   L             !  !             +-5lux_L    
                                                               !  !  
  ------RT----------------RT----IA--QCNA------   L             !  !               +5jlw_D    
                                                               !  +---------------4 
  ------RA----------------------IA--QCNAMC----   L             !                  +4cyc_A    
                                                               !  
  ------RA----------------------IA----NA------                 !                    +-4xrs_G    
                                                           +--15                  +-7 
  ------------------------------IA----NA------             !   !        +---------9 +-4qtr_D    
                                                           !   !        !         ! 
  ------------------------------NC--ICNARGRG--   L         !   !     +-11         +-4xrm_B    
                                                           !   !     !  !  
  --------RT--------------------NT----NAIARG--   L         !   !  +-12  +-----------4cyc_B    
                                                        +-16   !  !  !  
  ------------------------------TA--QCNAMC----          !  !   !  !  !            +4rbo_D    
                                                        !  !   +-14  +------------6 
  --------NGRGTG------LC--LCRG----------------          !  !      !               +4ofa_A    
                                                     +-17  !      !  
  ----------KA----------SGAT--YTRG------------   L   !  !  !      +----------------4rb3_D    
                                                     !  !  !  
  --------------IGYGFG------------------------     -18  !  +----------------------4ztu_A    
                                                     !  !  
  ----------------------------RTNAQAIASCRTVA--   L   !  +-------------------------5b7j_A    
                                                     !  
  ----------------------YG--------------------   L   +---------------------------5kn8_A    
                                                   


> 2h27_A:CRYSTAL STRUCTURE OF ESCHERICHIA COLI SIGMAE REGION 4 BOUND TO ITS-35 ELEMENT DNA

  
  LGET--RGECRTRT------   L                     +-------------4yln_L    
                               +---------------1 
  LG--TTRGECRCRTQT----   L   +-2               +-------------5vi8_F    
                             ! ! 
  ----TTRG--ATSTQC--RG   L --3 +-----------------------------2w7n_B    
                             ! 
  --------RTTTDAVTRGRG   L   +-----------------------------1gxp_A    
                           


> 2h7g_X:STRUCTURE OF VARIOLA TOPOISOMERASE NON-COVALENTLY BOUND TO DNA

  
  HTRA--QAYCYT----------RT------KGKGYGKT------ETRGYG   L                     +------------2h7g_X    
                                                                   +---------2 
  ----MG--YA------KT------------NC----KTDA------TT--   L           !         !          +-2b9s_A    
                                                                +--3         +----------1 
  --------YA------KT------------NT----KT------------            !  !                    +-1k4t_A    
                                                             +--4  ! 
  ------------KTTT--QT----------------------RA------   L     !  !  +----------------------5u91_B    
                                                           +-5  ! 
  ------------------------RG--------------RG--------   L   ! !  +-------------------------3m4a_A    
                                                         --6 ! 
  --------------TT----QT--------------------RA------   L   ! +----------------------------1xo0_B    
                                                           ! 
  --------------------------FCKC------KC--------NTRG   L   +----------------------------1flo_A    
                                                         


> 2h8r_B:HEPATOCYTE NUCLEAR FACTOR 1B BOUND TO DNA: MODY5 GENE PRODUCT

  
  ----------------KT--RT--IAQTNAMC   L                                  +2h1k_B    
                                                                      +-1 
  ------------------RTRA--IAQCNAMG   L            +-------------------2 +2r5z_A    
                                                  !                   ! 
  --------------------RTRTIAQCNA--   L   +--------4                   +5jlw_D    
                                         !        ! 
  --------------------RA--IA--NA--     --5        +--------------------4xrs_G    
                                         ! 
  ATQAAT--SA----------------------       !                        +----4z5h_A    
                                         +------------------------3 
  --QASTCT--SARTET----------------   L                            +----5j2y_A    
                                       


> 2han_A:STRUCTURAL BASIS OF HETERODIMERIC ECDYSTEROID RECEPTOR INTERACTION WITH NATURAL RESPONSE ELEMENT HSP27 GENE PROMOTER

  
  --ECKA--RGRG   L   +----------------------4nqa_I    
                     !  
  --ECKG--KGRA   L   !                     +5l0m_A    
                     !                  +--5 
  --ECKG----RA   L   !                  !  +5krb_G    
                     !               +--7 
  ----KGVT--RG   L -10               !  !  +5cbz_E    
                     !               !  +--3 
  ----KAVA--RA   L   !      +--------8     +5e69_A    
                     !      !        ! 
  --EAKG--KTRG   L   !      !        !      +4cn3_D    
                     !      !        +------1 
  --ECKG--RGRG   L   !      !               +2nll_B    
                     +------9 
  --ECKGAG--RG   L          !                 +4ond_A    
                            !               +-2 
  ----KGVG--RG   L          !             +-4 +4tnt_B    
                            !             ! ! 
  ----KGVT--RG              +-------------6 +5emc_A    
                                          ! 
  YGECKGAGKGRG   L                        +-4oln_B    
                   


> 2han_B:STRUCTURAL BASIS OF HETERODIMERIC ECDYSTEROID RECEPTOR INTERACTION WITH NATURAL RESPONSE ELEMENT HSP27 GENE PROMOTER

  
  --ECKG--RGRG----KA   L               +-----2nll_B    
                             +---------7 
  --ECKA--RGRG------   L     !         +-----4nqa_I    
                             ! 
  --ECKG----RA--PA--   L   +-9     +---------5krb_G    
                           ! !     ! 
  --EAKG--KTRG------   L   ! !     !           +4cn3_D    
                           ! +-----8         +-2 
  --ECKG--KGRART----   L   !       !       +-3 +5l0m_A    
                           !       !       ! ! 
  ----KAVA--RA------   L   !       +-------5 +5e69_A    
                         -10               ! 
  ----KGVT--RG------   L   !               +-5cbz_E    
                           !  
  ----KGVG--RG------   L   !                  +4tnt_B    
                           !                +-1 
  --ECKGAG--RG------   L   !              +-4 +4ond_A    
                           !              ! ! 
  ----KGVT--RG------       +--------------6 +5emc_A    
                                          ! 
  YGECKGAGKGRG------   L                  +-4oln_B    
                         


> 2hdc_A:STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX

  
  --------------NA----RA--HTSTLT----------   L                                  +2a07_K    
                                                                +---------------1 
  ----------------NAST--RGHTSTFT----------   L                +-5               +5x07_F    
                                                              ! ! 
  ----------------NAST--RGHTST------------   L                ! +---------------3g73_A    
                                                          +---7 
  RT--LANTHGTTET--YTRG--------------------   L            !   !     +----------1f4k_B    
                                                          !   +-----4 
  --------------NAST--RGHT------------RTRA   L          +-8         !      +---1vtn_C    
                                                        ! !         +------3 
  --------YAQTTC----QC--------------------   L          ! !                +---5k5q_D    
                                                        ! ! 
  --------DCKGRGNA--RT----KT----KGRA------   L       +--9 +--------------------5ddg_A    
                                                     !  ! 
  ------------------------YG--------------           !  !     +----------------1sfu_A    
                                                     !  +-----6 
  ------------------------YG--------------       +--10        !               +3irr_C    
                                                 !   !        +---------------2 
  --RC--------QG--------------------SG----       !   !                        +4qlc_U    
                                               -11   !  
  ------------------RG----YG--------------       !   +-------------------------1qbj_C    
                                                 !  
  --------RTTT--DAVT----RGRG--------------   L   +-----------------------------1gxp_A    
                                               


> 2hdd_A:ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX

  
  ----------------------IA----NA------                                         +4qtr_D    
                                                                             +-1 
  ----------------RT----IT--QCNA------   L                                 +-2 +5eea_B    
                                                                           ! ! 
  ----------------------IA--QTNA------   L                       +---------6 +5lty_K    
                                                                 !         ! 
  ----------------------VA--QTNA------   L                       !         +5hod_A    
                                                              +-12  
  ----------------------IA--QTNA----KT   L                    !  !         +4rdu_A    
                                                              !  !      +--9 
  ----------------------IA--QCNAMC----   L                    !  +-----10  +4cyc_A    
                                                              !         !  
  ----------------------IA----NA------                    +--13         +---4xrs_G    
                                                          !   !  
  ----------------------IA--QTNAMC----   L                !   !              +2h1k_B    
                                                          !   !            +-3 
  ----------------------IA--QCNAMG----   L                !   !            ! +2r5z_A    
                                                          !   +------------8 
  ----------------RT----IA--QCNA------   L                !                ! +5jlw_D    
                                                      +--14                +-4 
  ----------------------IA--QTNA------   L            !   !                  +5lux_L    
                                                      !   !  
  ----------------------TA--QCNAMC----                !   !                  +4rbo_D    
                                                      !   !                +-5 
  RT--------------------NT----NAIARG--   L         +-15   !      +---------7 +4cyc_B    
                                                   !  !   !      !         ! 
  ----------------------NC--RG--------   L         !  !   +-----11         +4xrm_B    
                                                   !  !          !  
  NGRGTG------LC--LCRG----------------          +-16  !          +----------4ofa_A    
                                                !  !  !  
  --KA----------SGAT--YTRG------------   L      !  !  +---------------------4rb3_D    
                                             +-17  !  
  ------IGYGFG------------------------       !  !  +----------------------4ztu_A    
                                           -18  !  
  --------------------RTNAQAIASCRTVA--   L   !  +-------------------------5b7j_A    
                                             !  
  ----------------NTVCECSTYTSTYC------   L   +-------------------------5ed4_A    
                                           


> 2heo_D:GENERAL STRUCTURE-BASED APPROACH TO THE DESIGN OF PROTEIN LIGANDS: APPLICATION TO THE DESIGN OF KV1.2 POTASSIUM CHANNEL BLOCKERS.

  
  --------------ST--SAYT--ECQT------RT--PT--   L                                    +---------------4hf1_A    
                                                                                +--13  
  ----------RG--TTRGTTTT--RTET--------HA----   L                                !   +---------------4p9u_B    
                                                                                !  
  ------------------------------YGRG--------                               +---16                  +4wcg_B    
                                                                           !    !            +-----9 
  ------------------------------YG----------                               !    !            !     +4lb5_B    
                                                                           !    +-----------10  
  ----------------YAQTTC----QC--------------   L                           !                 !     +5k5q_D    
                                                                        +-17                 +-----7 
  --------ST----STQAQGST--SART------------KT   L                        !  !                       +5trd_B    
                                                                        !  !  
  ----------RG--STRGMCTT--RT----------------   L                        !  !                        +4u0y_B    
                                                                        !  !             +----------3 
  --------ETNT--SCRGHC----RT----------QA----   L                        !  !             !          +5d4s_B    
                                                                        !  +------------11  
  --------------ITRGECSC--SGKG--------------   L                        !                !         +5i2d_R    
                                                                     +-19                +---------5 
  --------------HT--STAT--STRG--------------   L                     !  !                          +5lej_A    
                                                                     !  !  
  --YA----------PTATPARA--YA----------------   L                     !  !                        +5bpd_A    
                                                                     !  !              +---------6 
  --------NT----KTPTQTSC----KA----------RT--   L                     !  !              !         +5bmz_D    
                                                                     !  !        +----12  
  --------------DCLT--AG--TTRG----RG------RA   L                  +-20  !        !     !         +5h3r_A    
                                                                  !  !  +-------14     +---------8 
  ----------------RGSTRT--STHG------------RA   L                  !  !           !               +3zpl_B    
                                                                  !  !           !  
  SA--EA----------KC--------RCRA--KG--------   L                  !  !           +----------------4kdp_B    
                                                                  !  !  
  ----------YA--KTPTPG----YTRG--------------   L                  !  !                          +4mte_D    
                                                               +-21  +--------------------------2 
  --------------SG--AT----YTRG--------------   L               !  !                             +4rb3_D    
                                                               !  !  
  ------RC------------QG------------------SG                   !  !                           +4qlc_U    
                                                               !  !         +-----------------1 
  --------------EGRTRGRG--YT----------------   L               !  !         !                 +4yo2_A    
                                                            +-22  !  +-----15  
  --------------------ST--------------------                !  !  !  !      !                 +5bs8_A    
                                                            !  !  +-18      +-----------------4 
  ----------------------SA------------------   L            !  !     !                        +5npk_d    
                                                         +-23  !     !  
  ------------------NTVC--ECSTYTSTYC--RA----   L         !  !  !     +------------------------5ed4_A    
                                                         !  !  !  
  --------------NATT--ECVT----HT------RT----   L      +-24  !  +----------------------------4s04_B    
                                                      !  !  !  
  ----------------MGSGTT--TTYC--------------   L      !  !  +-----------------------------5f7q_C    
                                                   +-25  !  
  --------------------------------------ITHG   L   !  !  +-----------------------------5iyc_T    
                                                 -26  !  
  ------------RT----------------------------   L   !  +-----------------------------5fmf_V    
                                                   !  
  --------LT----AGETSGTT--HT----------------   L   +-----------------------------2e1c_A    
                                                 


> 2hos_A:PHAGE-SELECTED HOMEODOMAIN BOUND TO UNMODIFIED DNA

  
  ----------------------IA--QTNA------   L   +----------------------------5lty_K    
                                             !  
  ----------------------VA--QTNA------   L   !                           +----5hod_A    
                                             !     +--------------------10  
  --------------------RTNAQAIASCRTVA--   L   !     !                     +----5b7j_A    
                                             !     !  
  ----------------------IA--QTNA----KT   L   !     !                          +4rdu_A    
                                             !     !                       +--3 
  ----------------RT----IT--QCNA------   L   !     !                       !  +5eea_B    
                                             !     !                  +----9 
  ----------------------IA----NA------       !     !                  !    ! +4qtr_D    
                                             !     !                  !    +-5 
  ----------------------IA----NA------       !     !                  !      +4xrs_G    
                                           -18     !                  !  
  ----------------RT----IA--QCNA------   L   !     !             +---11          +