• Backbone structures are obtained using ProteinViewer, where N-terminal is colored red and C-terminal blue.
• Click the images to view larger image.
• Click PDB IDs to view the corresponding PDB file
• See the bottom for explanation of the DSSP codes and the 5-tile codes. 
• "<" and ">" denote the N-terminal and the C-terminal of the sequence respectively.
  

(1) KH Domain of Ribosomal Protein S3 (1j5e chain C) and KH Domain of hnRNP K (1cbs)

			"Analysis of spacial structures of KH domains in hnRNP K and S3 reveals that they are topologically dissimilar and thus belong to different protein folds. ... The two distinct topologies might have arisen from an ancestral KH-motif protein by N- and C-terminal extensions, or one of the existing topologies may have evolved from the other by extension, displacement, and deletion." (Grishin, 2001)
1j5e (ResC62-107)	1khm (ResA11-72)

1j5e VAVTVHVAKPGVV   IGR GGERIRVLREELAKL T         G K NVALNVQE code 0000000Q0QAAA   B00 RRQAAAAAAAAAAAB 0         R R 00000000 LCS  0000000 0QAAA   B0  R QAAAAAAAA   B 0         R R 00000000 code 0000000 0QAAAAAAB0QBR QAAAAAAAA   BR0000000000RGRG00000000QAAA 1khm ITTQVTI PKDLARSIIGKGG QRIKQIRHE   SGASIKIDEPLEGSEDRIITITGTQDQI *RATIO :  lcs/trimmed_seq_a = 0.857 (=   36/   42), lcs/trimmed_seq_b = 0.632 (=   36/   57)

Structural alignment by ComSubstruct

DSSP .LLLL.leeeelLHHHHHLLLLLHHHHHHHHHHlllllllLLEEEELL................... 1j5e .DNVA.vtvhvaKPGVVIGRGGERIRVLREELAkltgknvALNVQEVQ...................                       || || ||   | |              | 1khm pIITTqvtipkdLARSIIGKGGQRIKQIRHESG......aSIKIDEPLegsedriititgtqdqiqn DSSP lLEEEeeeeehhHHHHHHLLLLHHHHHHHHHHL......lEEEELLLLlllleeeeeeeelhhhhhl *Z-score 1.1  AR 33  RMSD 3.3A  SI 27%

Structural alignment by DaliLite

(2) RecA ATPase domain (2reb) and Adenylate Kinase (2ak3)

			"P-loop ATPases are probably the most diversified and abundant protein superfamily. These enzymes are characterized by Walker A (P-loop) [(shown in purple below)] and B [(shown in green below)] motifs. The detection of proteins with these motifs by sequence analysis tools is relatively straightforward and a monophyletic origin of the P-loop ATPases has been proposed. Representative structures for the most of the distinct families of P-loop ATPases have been determined. All these structures display a certain resemblance: they have alpha-beta-alpha sandwich architecture with the central mainly parallel beta-sheet and are composed of beta-alpha units. However, connectivity between these beta-alpha units is not the same in different ATPase families. The notable difference is in relative location of Walker A and B motifs." (Grishin, 2001)
2reb (Res42-232)	2ak3 (ResA4-215)

2reb   <SLSLDIALGAGG    LP MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID A         EHALDPIY code   <GQAAAAABQBR0    00 0RG00000000RRRQAAAAAAAAAAAAABR0000000 Q         BRG00QAA LCS       AAAAAB   0    00 0  000000  RRRQ     AAAAAAAAB 0000000 Q         BR 0 QAA code  AAAAAAAAABG  0P><J0030  000000  RRRQ     AAAAAAAAB 00000000QAAAAAAAAABR 0 QAA 2ak3  WPHVYAFLQTK  LP><RLLRA  AIMGAP  GSGK     GTVSSRITK HFELKHLSSGDLLRDNMLRG T EIG 2reb ARK     L GVD I            D  NLLCSQP D   TGEQALE                 ICDALARSGAVDV   I VVDS code AAA     B 00R Q            A  BG000R0 R   0QAAAAA                 AAAAAAABRBG00   0 0030 LCS  AAA     B 00  Q            A  BG000 0 R   0QAAAAA                 AAAAAAABR G00   0 00 0 code AAAAAAAABR0000QAAAAAAAAAAAAAHQBG000 00RGOR0QAAAAAAAB0000000000000QAAAAAAABR G00RQB0R00 00 2ak3 VLAKTFIDQGKLIPDDVMTRLVLHELKNLTQYNWL LDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTA RWIHPGSGRV YN 2reb VAA    L             TPKAEIEGLAARMMSQAMRKLA GNLKQSNTLLIFINQTGGNALKFYAS  VRLDIRRIGA> code QAB    R             00QAABO3QAAAAAAAAAAAAA AAAAABR0000000OH00QAAAABGR  0000000R00> LCS  Q B    R             00QA B  QAAAAAAAAAAAAA AAAAA              AAAAB R  00000  R code Q B0000R00RG0Q00R000000QA BG QAAAAAAAAAAAAA9AAAAA              AAAAB RRG00000  RG 2ak3 I EFNPPKTMGIDDLTGEPLVQRED DR PETVVKRLKAYEAQTEPVLE              YYRKK GVLETFSG  TE *RATIO :  lcs/trimmed_seq_a = 0.732 (=  120/  164), lcs/trimmed_seq_b = 0.577 (=  120/  208)

Structural alignment by ComSubstruct

DSSP <llLHHHHHHlllLLLL.  LLLEEEEELLLLLLHHHHHHHHHHHHHhllllEEEEELLL.......lllhhh 2reb <tgSLSLDIAlgaGGLP.  MGRIVEIYGPESSGKTTLTLQVIAAAQregktCAFIDAEH.......aldpiy                                | |   ||| | 2ak3  kiWPHVYAF..lQTKLp><RLLRAAIMGAPGSGKGTVSSRITKHFE.....LKHLSSGDllrdnmlrgteig DSSP  llHHHHHHH..hHLLLl><LLLEEEEELLLLLLHHHHHHHHHHHLL.....LEEEEHHHhhhhhhhlllhhh DSSP hhhllllhhhleeelllLHHHHHHHHHHHHhhllLLEEEEEL 2reb arklgvdidnllcsqpdTGEQALEICDALArsgaVDVIVVDS                            |     |           | 2ak3 vlaktfidqgklipddvMTRLVLHELKNLT....QYNWLLDG DSSP hhhhhhhhllllllhhhHHHHHHHHHHHHL....LLLEEEEL DSSP HHhlllhhhhllhHHHHHHHHHHHHH.......................................... 2reb VAaltpkaeieglAARMMSQAMRKLA..........................................                            | 2ak3 FP..........rTLPQAEALDRAYQidtvinlnvpfevikqrltarwihpgsgrvyniefnppktmg DSSP LL..........lLHHHHHHHHLLLLlleeeeeellhhhhhhhhlleeeelllleeeellllllllll DSSP .................hhhhhhlleeeeeellLLHHHHHHlLEEEELLLLllll> 2reb .................gnlkqsntllifinqtGGNALKFYaSVRLDIRRIgavk>       2ak3 iddltgeplvqreddrpetvvkrlkayeaqtepVLEYYRKKgVLETFSGTE..tn DSSP llllllllllllhhhlhhhhhhhhhhhhhhhhhHHHHHHHHlLEEEEELLL..ll *Z-score 3.3  AR 99  RMSD 3.2A  SI 10%

Structural alignment by DaliLite

[The DSSP code]

• H = alpha helix
• B = residue in isolated beta-bridge
• E = extended strand, participates in beta ladder
• G = 3-helix (3/10 helix)
• I = 5 helix (pi helix)
• T = hydrogen bonded turn
• S = bend
• L = no assigned structure

[The 5-tile code]

• 0 = DDDDD    (extended strand, small blue spheres)
• 1 = DDDDU
• 2 = DDDUD
• 3 = DDDUU
• 8 = DUDDD
• 9 = DUDDU
• A = DUDUD    (helix, large red spheres)
• B = DUDUU    (turn, large yellow spheres)
• G = UDDDD
• H = UDDDU
• I = UDDUD
• J = UDDUU
• O = UUDDD
• P = UUDDU
• Q = UUDUD    (turn, large yellow spheres)
• R = UUDUU    (turn, large yellow spheres)