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Examples of RESULT (c)


In the figures below,
  • Red spheres indicate the position of ANGL_CORE residues, orange spheres the position of ANGL residues, and yellow spheres the position of ANGL_SUPP residues, respectively.
  • Large spheres indicate the position of FLEX/D2/PB/DSSP variable residue positions.
  • Structural superpositions of Ca traces were carried out with the DaliLite server.
  • Backbone structures are obtained using ProteinViewer, where N-terminal is colored red and C-terminal blue.

    • (1) Domain-swapped Dimers


    (a) Monomeric / Homo-multimeric: PpL (Cluster 29, PDBID: 1k50 A and 1k50 B)
    Superposition of the Ca traces
    (and D2 variable residues)    		 Amino acid code and
    Variable residue positions (w.r.t five codes)
    jpg image Amino Acid:   EEVTIKANLIFANGSTQTAEFKGTFEKATSEAYAYADTLKKDNGEWTADVADKGYTLNIKFAG

    FLEX var.:                                                      xxxxxxxxxxxxx
    ANGL var.:      x                                             xxxxxxx      x

    D2 var.:      --                                      xx       xxxxxxx     --
    PB var.:      --x                                        x     xxxxxxxx   x--
    DSSP var.:                                                 xxxxxxxxxxxxxxxx  




    (b) Conformations of the hinge regions

    Cluster 6 (PDBID: 1bmb A and 1fyr B)
    Superposition of the Ca traces
    (and D2 variable residues)    		 Amino acid code and
    Variable residue positions
    jpg image Amino Acid: "GKYFLWVVKF"

    FLEX var.:  "    xxxxx "
    ANGL var.:  "     xxxx "

    D2 var.:    "          "
    PB var.:    "    xxxxx "
    DSSP var.:  "x    xx xx"


    Cluster 23 (PDBID: 1huf A and 1k46 A)
    Superposition of the Ca traces
    (and D2 variable residues)    		 Amino acid code and
    Variable residue positions
    jpg image Amino Acid: "TGKLRGNVAA"

    FLEX var.:  "   xxxxx  "
    ANGL var.:  "    xx   x"

    D2 var.:    "    x     "
    PB var.:    "   xxxxx  "
    DSSP var.:  "xxxxxxxxxx"


    Cluster 53 (PDBID: 1y50 A and 1y51 A)
    Superposition of the Ca traces
    (and D2 variable residues)    		 Amino acid code and
    Variable residue positions
    jpg image Amino Acid: "MGVMSLGIPK"

    FLEX var.:  " xxxxxxxx "
    ANGL var.:  "   xx x   "

    D2 var.:    "     xx   "
    PB var.:    "        x "
    DSSP var.:  "   xxx    "


    Cluster 8 (PDBID: 1c0b A and 1f0v A)
    Superposition of the Ca traces
    (and D2 variable residues)    		 Amino acid code and
    Variable residue positions
    jpg image Amino Acid: "VACEGNPYVP"

    FLEX var.:  "     xxxx "
    ANGL var.:  "   xxx  x "

    D2 var.:    "    xxx   "
    PB var.:    "   xxxxxx "
    DSSP var.:  "  xxxxxxxx"


    Cluster 4 (PDBID: 1aoj A and 1i0c A)
    Superposition of the Ca traces
    (and D2 variable residues)    		 Amino acid code and
    Variable residue positions
    jpg image Amino Acid: "ILDDRRQWWK"

    FLEX var.:  "  xxxxxxx "
    ANGL var.:  " xxxxxxxx "

    D2 var.:    " xx   xx  "
    PB var.:    "xxxxxxx x "
    DSSP var.:  " xxxxxx   "


    Cluster 29 (PDBID: 1k50 A and 1k50 B)
    Superposition of the Ca traces
    (and D2 variable residues)    		 Amino acid code and
    Variable residue positions
    jpg image Amino Acid: "ADVADKGYTL"

    FLEX var.:  "   xxxxxxx"
    ANGL var.:  " xxxxxxx  "

    D2 var.:    "  xxxxxxx "
    PB var.:    "  xxxxxxxx"
    DSSP var.:  "xxxxxxxxxx"



    (2) Other examples


    (a) Member of a dimer:  The V domain of Bence-Jones protein Mcg (Cluster 11, PDBID: 1dcl A and 1dcl B)
    Superposition of the Ca traces
    (and D2 variable residues)    		 Amino acid code and
    Variable residue positions
    jpg image                                         CDR1                    CDR2                                     CDR3          
                                         <------->                 <----->                                <-------->       
    Amino Acid: PSALTQPPSASGSLGQSVTISCTGTSSNVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVT

    FLEX var.:  xxxx                    xxxxxxxxx                                                            xxxx          
    ANGL var.:   xxx      x   xxxxx    xxxxxx xxxx     xx               xxxx x      x        x              xxxxxx    xx    

    D2 var.:    --     x                 xxxxxx x               x        x x                        xx       xxx x    x    
    PB var.:    --xx    xxxxxxxxxx    xxxxxxxx xxx                     xxx  x                      xxxxx  xxx  xxx  xxxxx  
    DSSP var.:    x x   xxx x   x      xxxxxxxxx             x                               x   xxx        x  xx x  x  x  x