Statistical analysis of representative 60 pairs: RESULT (a) Examples

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 of the compact and the extended forms		Amino acid code (Upper row) Variable residue positions (Lower row)
FLEX variable residue positions				EEVTIKANLIFANGSTQTAEFKGTFEKATSEAYAYADTLKKDNGEWTADVADKGYTLNIKFAG                                                   xxxxxxxxxxxxx
D2 variable residue positions				EEVTIKANLIFANGSTQTAEFKGTFEKATSEAYAYADTLKKDNGEWTADVADKGYTLNIKFAG --                                      xx       xxxxxxx     --
PB variable residue positions				EEVTIKANLIFANGSTQTAEFKGTFEKATSEAYAYADTLKKDNGEWTADVADKGYTLNIKFAG --x                                        x     xxxxxxxx   x--
DSSP variable residue positions				EEVTIKANLIFANGSTQTAEFKGTFEKATSEAYAYADTLKKDNGEWTADVADKGYTLNIKFAG                                              xxxxxxxxxxxxxxxx

(b) Conformations of the hinge regions

Cluster 6 (PDBID: 1bmb A and 1fyr B)

		FLEX var. positions		D2 var. positions		PB var. positions		DSSP var. positions
Superposition of the Ca traces
AA code Var. posi.		"GKYFLWVVKF" "    xxxxx "		"GKYFLWVVKF" "          "		"GKYFLWVVKF" "    xxxxx "		"GKYFLWVVKF" "x    xx xx"

Cluster 23 (PDBID: 1huf A and 1k46 A)

		FLEX var. positions		D2 var. positions		PB var. positions		DSSP var. positions
Superposition of the Ca traces
AA code Var. posi.		"TGKLRGNVAA" "   xxxxx  "		"TGKLRGNVAA" "    x     "		"TGKLRGNVAA" "   xxxxx  "		"TGKLRGNVAA" "xxxxxxxxxx"

Cluster 53 (PDBID: 1y50 A and 1y51 A)

		FLEX var. positions		D2 var. positions		PB var. positions		DSSP var. positions
Superposition of the Ca traces
AA code Var. posi.		"MGVMSLGIPK" " xxxxxxxx "		"MGVMSLGIPK" "     xx   "		"MGVMSLGIPK" "        x "		"MGVMSLGIPK" "   xxx    "

Cluster 8 (PDBID: 1c0b A and 1f0v A)

		FLEX var. positions		D2 var. positions		PB var. positions		DSSP var. positions
Superposition of the Ca traces
AA code Var. posi.		"VACEGNPYVP" "     xxxx "		"VACEGNPYVP" "    xxx   "		"VACEGNPYVP" "   xxxxxx "		"VACEGNPYVP" "  xxxxxxxx"

Cluster 4 (PDBID: 1aoj A and 1i0c A)

		FLEX var. positions		D2 var. positions		PB var. positions		DSSP var. positions
Superposition of the Ca traces
AA code Var. posi.		"ILDDRRQWWK" "  xxxxxxx "		"ILDDRRQWWK" " xx   xx  "		"ILDDRRQWWK" "xxxxxxx x "		"ILDDRRQWWK" " xxxxxx   "

Cluster 29 (PDBID: 1k50 A and 1k50 B)

		FLEX var. positions		D2 var. positions		PB var. positions		DSSP var. positions
Superposition of the Ca traces
AA code Var. posi.		"ADVADKGYTL" "   xxxxxxx"		"ADVADKGYTL" "  xxxxxxx "		"ADVADKGYTL" "  xxxxxxxx"		"ADVADKGYTL" "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		Amino acid code Variable positions
FLEX variable positions				CDR1                    CDR2                                     CDR3                                    <------->                 <----->                                <-------->        PSALTQPPSASGSLGQSVTISCTGTSSNVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVT xxxx                    xxxxxxxxx                                                            xxxx
D2 variable positions				CDR1                    CDR2                                     CDR3                                    <------->                 <----->                                <-------->        PSALTQPPSASGSLGQSVTISCTGTSSNVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVT --     x                 xxxxxx x               x        x x                        xx       xxx x    x
PB variable positions				CDR1                    CDR2                                     CDR3                                    <------->                 <----->                                <-------->        PSALTQPPSASGSLGQSVTISCTGTSSNVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVT --xx    xxxxxxxxxx    xxxxxxxx xxx                     xxx  x                      xxxxx  xxx  xxx  xxxxx
DSSP variable positions				CDR1                    CDR2                                     CDR3                                    <------->                 <----->                                <-------->        PSALTQPPSASGSLGQSVTISCTGTSSNVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVT   x x   xxx x   x      xxxxxxxxx             x                               x   xxx        x  xx x  x  x  x