Contacts of the helix formed by residues 474 - 506 (chain A) in PDB entry 3I5G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 474 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLN* 4.2 1.3 - - - -
472A PHE* 3.9 22.7 + - - -
473A ASN* 1.3 73.3 - - - +
475A PHE* 1.3 73.5 + - - +
476A GLU* 2.9 19.0 + - - -
477A GLN* 2.7 19.9 + - - +
478A LEU* 3.1 9.5 + - - +
591A TYR* 4.0 2.9 - - - -
592A SER* 4.1 3.5 + - - -
594A ALA 4.3 4.0 + - - -
596A TRP* 3.2 23.4 + - - +
599A LYS* 2.9 21.5 + - - -
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Residues in contact with PHE 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A SER* 5.3 4.3 - - - -
474A SER* 1.3 81.9 + - - +
476A GLU* 1.3 62.0 + - + +
478A LEU* 4.0 3.1 - - + -
479A CYS* 3.2 38.6 + - - -
533A LEU* 3.9 18.6 - - + -
536A LEU* 3.8 15.0 - - + -
596A TRP* 3.1 50.5 - + + +
599A LYS* 4.3 26.5 - - + -
600A ASN* 3.3 33.4 - - + -
647A ILE* 3.8 19.1 - - + -
648A SER* 3.9 11.4 - - - -
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Residues in contact with GLU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 4.9 2.2 - - - +
273A GLU* 3.7 29.8 - - + +
275A SER* 5.0 12.8 - - - -
276A ARG* 5.3 4.5 - - - +
279A TYR* 3.7 13.6 - - - -
281A GLN* 3.6 12.0 - - - +
474A SER* 3.3 12.0 - - - -
475A PHE* 1.3 75.1 - - + +
477A GLN* 1.3 78.8 + - - +
479A CYS* 3.3 7.8 + - - +
480A ILE* 3.1 26.1 + - - +
599A LYS* 2.7 44.8 + - - +
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Residues in contact with GLN 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 4.7 2.6 - - - +
281A GLN* 4.1 7.2 + - - +
284A GLU* 5.1 1.0 + - - -
468A GLU* 3.0 36.8 + - + +
470A PHE* 3.1 29.2 - - + -
472A PHE 3.8 3.1 - - - +
473A ASN* 3.4 35.2 - - + +
474A SER* 2.7 32.6 + - - +
476A GLU* 1.3 88.3 - - - +
478A LEU* 1.3 60.4 + - - +
480A ILE* 3.1 3.0 + - - +
481A ASN* 2.8 37.9 + - - +
591A TYR* 3.8 5.6 - - + -
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Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A SER 3.1 9.6 + - - +
475A PHE* 4.1 6.7 - - + +
476A GLU 3.3 0.2 - - - -
477A GLN* 1.3 79.7 - - - +
479A CYS* 1.3 58.7 + - - +
481A ASN* 3.4 0.3 + - - -
482A TYR* 2.8 29.8 + - + +
526A ILE* 4.3 14.4 - - + -
532A ILE* 4.2 13.0 - - + -
533A LEU* 4.1 24.2 - - + -
580A PHE* 4.9 1.1 - - + -
582A LEU* 3.5 31.4 - - + -
584A HIS* 4.7 1.1 - - - +
591A TYR* 3.5 27.9 - - + +
596A TRP* 3.8 31.6 - - + -
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Residues in contact with CYS 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A PHE* 3.2 46.8 + - - -
476A GLU* 3.3 11.1 + - - +
477A GLN 3.2 0.4 - - - -
478A LEU* 1.3 80.0 - - - +
480A ILE* 1.3 58.9 + - + +
482A TYR* 3.4 7.7 + - - +
483A THR* 3.0 20.1 + - - -
533A LEU* 5.4 7.0 - - - -
647A ILE* 5.2 4.0 - - - -
648A SER* 5.6 0.9 - - - -
651A HIS* 3.0 50.1 + - + +
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Residues in contact with ILE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 3.3 43.5 - - - +
273A GLU* 4.2 8.1 - - + +
465A ALA* 4.0 17.3 - - + +
466A GLY 3.4 24.9 - - - +
468A GLU* 3.8 16.8 - - + +
476A GLU 3.1 9.0 + - - +
477A GLN 3.1 6.8 + - - +
479A CYS* 1.3 78.2 - - + +
481A ASN* 1.3 64.7 + - - +
483A THR* 3.1 8.4 + - - -
484A ASN* 2.9 32.0 + - - +
651A HIS* 4.9 2.2 - - + -
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Residues in contact with ASN 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A PHE* 3.2 37.4 - - + -
468A GLU* 3.1 43.2 + - - +
477A GLN* 2.8 22.6 + - - +
478A LEU 3.9 0.7 - - - +
480A ILE* 1.3 70.5 - - - +
482A TYR* 1.3 60.0 + - - +
484A ASN* 3.3 0.9 + - - +
485A GLU* 2.8 32.1 + - - +
584A HIS* 3.8 7.4 - - + -
589A VAL* 4.0 5.3 - - - +
591A TYR* 2.8 33.7 + - - +
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Residues in contact with TYR 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A LEU* 2.8 19.7 + - + +
479A CYS* 3.4 6.1 - - - +
481A ASN* 1.3 75.5 - - - +
483A THR* 1.3 63.1 + - - +
485A GLU* 3.4 4.1 + - - +
486A ARG* 3.2 43.3 + - + +
523A ILE* 4.2 11.7 - - + -
526A ILE* 3.7 42.8 - - + -
527A GLU* 2.8 38.9 + - + +
533A LEU* 4.0 20.9 - - + -
584A HIS* 4.6 0.4 - - - -
651A HIS* 4.1 17.5 - + - -
652A LYS* 4.0 19.2 - - + +
655A LEU* 3.9 19.1 - - + -
656A ASN* 5.0 0.5 + - - -
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Residues in contact with THR 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 3.9 18.9 - - + +
464A ILE* 4.2 12.3 - - + -
465A ALA 5.5 0.4 - - - +
479A CYS 3.0 7.9 + - - -
480A ILE* 3.1 11.9 + - + +
482A TYR* 1.3 74.3 - - - +
484A ASN* 1.3 70.1 + - - +
486A ARG* 3.2 6.8 + - - +
487A LEU* 3.1 36.4 + - + +
651A HIS* 2.9 29.8 + - - -
655A LEU* 3.5 24.9 - - + +
658A LEU* 5.0 0.4 - - + -
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Residues in contact with ASN 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A THR* 5.6 5.5 - - - +
464A ILE* 4.5 3.0 - - - +
465A ALA 2.8 28.7 + - - +
466A GLY* 3.1 18.3 + - - -
467A PHE* 3.1 30.0 + - + +
480A ILE* 2.9 21.6 + - - +
483A THR* 1.3 77.0 - - - +
485A GLU* 1.3 53.3 + - - +
487A LEU* 2.7 23.4 + - - +
488A GLN* 2.6 35.0 + - - +
585A TYR* 3.9 11.7 + - - +
695A CYS 5.1 1.6 - - - +
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Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A PHE* 4.6 0.2 - - - -
481A ASN 2.8 20.5 + - - +
482A TYR* 3.5 9.9 - - + +
483A THR 3.2 0.2 - - - -
484A ASN* 1.3 72.9 - - - +
486A ARG* 1.3 57.5 + - - +
488A GLN 3.4 0.2 + - - -
489A GLN* 3.0 26.9 + - - +
519A LEU* 3.2 34.3 - - - +
522A CYS* 3.9 19.3 - - - +
523A ILE* 3.4 26.5 - - + +
526A ILE* 5.6 0.9 - - + -
583A HIS 5.0 0.2 - - - +
584A HIS* 2.5 41.2 + - + +
585A TYR* 3.6 22.1 + - - -
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A TYR* 3.2 25.1 + - + +
483A THR 3.2 9.1 + - - +
485A GLU* 1.3 76.5 - - - +
487A LEU* 1.3 58.0 + - - +
489A GLN* 3.6 11.6 + - - +
490A PHE* 3.1 22.9 + - - +
523A ILE* 3.7 31.3 - - + +
527A GLU* 3.9 14.2 + - - -
655A LEU* 3.7 30.2 - - + +
656A ASN* 2.7 32.5 + - - +
659A MET* 3.8 41.7 - - + +
663A TYR* 4.5 4.1 + - - -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 4.3 14.7 - - + +
462A LEU* 4.4 6.5 - - + -
464A ILE* 3.7 32.8 - - + -
483A THR* 3.1 27.5 + - + +
484A ASN* 2.7 20.3 + - - +
486A ARG* 1.3 75.1 - - - +
488A GLN* 1.3 66.9 + - - +
489A GLN 3.1 1.1 - - - -
490A PHE* 3.2 9.0 + - + +
491A PHE* 3.1 19.8 + - - +
658A LEU* 4.5 0.9 - - + -
659A MET* 3.2 27.4 - - + -
662A LEU* 3.4 21.3 - - + -
669A PHE* 5.4 1.0 - - - -
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Residues in contact with GLN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 5.1 0.5 - - - -
484A ASN 2.6 17.5 + - - +
487A LEU* 1.3 72.6 - - - +
489A GLN* 1.3 59.0 + - - +
491A PHE* 3.0 28.6 + - - +
492A ASN* 2.8 50.1 + - - +
519A LEU* 3.7 13.0 - - + -
585A TYR* 3.7 39.1 + - + +
671A ARG* 5.2 1.4 + - - -
696A ASN 3.8 5.4 - - - +
697A GLY* 3.0 29.7 + - - -
700A GLU* 3.5 13.7 - - + +
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Residues in contact with GLN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A GLU 3.0 17.3 + - - +
486A ARG* 3.6 13.4 + - - +
488A GLN* 1.3 74.8 - - - +
490A PHE* 1.3 66.4 + - - +
492A ASN* 3.1 9.0 + - - +
493A HIS* 2.8 23.2 + - + +
516A GLY* 3.3 33.5 + - - +
517A LEU* 4.9 1.2 - - - +
519A LEU* 3.9 8.9 - - + +
520A GLN* 3.1 29.3 + - - +
523A ILE* 3.7 21.1 - - + +
663A TYR* 3.9 14.3 + - - +
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A SER* 4.8 0.2 - - - -
173A LEU* 4.2 23.6 - - + -
486A ARG 3.1 12.6 + - - +
487A LEU* 3.2 15.0 - - + +
488A GLN 3.2 0.2 - - - -
489A GLN* 1.3 79.0 - - - +
491A PHE* 1.3 58.0 + - - +
493A HIS* 3.3 4.4 + + - +
494A HIS* 3.0 26.3 + - + +
659A MET* 4.8 3.4 - - - -
662A LEU* 3.5 48.5 - - + -
663A TYR* 3.2 47.0 + + + +
665A THR 4.9 0.7 - - - -
667A PRO* 3.4 44.0 - - + -
669A PHE* 4.1 8.1 - + - -
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Residues in contact with PHE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.9 31.4 - - + -
119A PHE* 3.4 41.3 - + + -
487A LEU 3.1 7.4 + - - +
488A GLN* 3.0 33.1 + - - +
490A PHE* 1.3 77.2 - - - +
492A ASN* 1.3 71.2 + - - +
494A HIS* 2.9 4.5 + - - +
495A MET* 2.9 45.1 + - + +
669A PHE* 3.5 50.3 - + + -
701A GLY* 4.2 8.1 - - - -
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Residues in contact with ASN 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A GLN* 2.8 43.5 + - - +
489A GLN* 3.4 9.4 - - - +
491A PHE* 1.3 77.5 - - - +
493A HIS* 1.3 57.7 + - - +
495A MET* 3.3 5.8 + - - +
496A PHE* 2.9 27.7 + - - +
515A PHE* 3.1 38.2 + - + +
516A GLY* 3.7 2.2 - - - +
518A ASP* 4.4 2.0 - - - +
519A LEU* 4.1 12.3 - - - +
700A GLU* 3.2 26.4 + - - +
704A ILE* 3.6 17.5 - - - +
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Residues in contact with HIS 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A GLN* 2.8 13.4 + - + +
490A PHE* 3.4 8.5 - + - +
492A ASN* 1.3 74.5 - - - +
494A HIS* 1.3 70.1 + - - +
496A PHE* 3.1 5.6 + + - +
497A VAL* 3.0 45.3 + - + +
514A ASP* 2.6 38.4 + - - +
516A GLY* 4.2 2.9 - - - +
663A TYR* 4.0 30.3 - + - +
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Residues in contact with HIS 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.5 29.5 - - + +
490A PHE* 3.0 12.9 + - + +
491A PHE* 2.9 11.5 + - - +
493A HIS* 1.3 81.9 - - + +
495A MET* 1.3 64.1 + - - +
497A VAL* 3.3 7.4 + - + +
498A LEU* 3.2 45.0 + - + +
666A HIS* 3.6 31.3 + + - -
667A PRO* 3.6 38.6 + - + +
669A PHE* 4.1 8.7 - + + -
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Residues in contact with MET 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 4.0 25.5 - - + +
491A PHE* 2.9 34.3 + - + +
492A ASN* 3.5 9.2 - - - +
494A HIS* 1.3 79.0 - - - +
496A PHE* 1.3 63.3 + - - +
498A LEU* 3.1 3.8 + - + +
499A GLU* 3.0 50.2 + - + +
515A PHE* 4.2 3.1 - - + -
701A GLY* 3.8 18.2 - - - +
704A ILE* 3.2 40.4 - - + -
705A CYS* 4.3 16.6 - - - +
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Residues in contact with PHE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A ASN 2.9 9.8 + - - +
493A HIS* 3.1 8.5 + + - +
495A MET* 1.3 77.0 - - - +
497A VAL* 1.3 70.5 + - + +
499A GLU* 3.9 1.2 - - - +
500A GLN* 3.0 52.8 + - - +
510A TRP* 3.3 33.6 - + - -
512A PHE* 3.6 17.9 - - + -
513A ILE* 3.6 4.7 - - - -
514A ASP* 3.5 49.6 - - + +
515A PHE* 3.3 31.4 - + + +
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Residues in contact with VAL 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A HIS* 3.0 43.8 + - + +
494A HIS* 3.8 9.4 - - - +
495A MET 3.3 0.2 - - - -
496A PHE* 1.3 82.5 - - + +
498A LEU* 1.3 61.8 + - + +
500A GLN* 3.8 8.6 - - - +
501A GLU* 3.4 27.9 + - - +
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.6 28.5 - - + -
494A HIS* 3.2 40.3 + - + +
495A MET* 3.1 8.3 + - + +
497A VAL* 1.3 78.8 - - + +
499A GLU* 1.3 66.3 + - - +
500A GLN 3.1 2.0 - - - -
501A GLU* 3.3 20.3 + - + +
502A GLU* 2.8 30.8 + - - +
666A HIS* 5.6 6.1 - - + +
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Residues in contact with GLU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 6.1 0.5 - - - +
495A MET* 3.0 44.2 + - + +
496A PHE 4.1 0.4 - - - +
498A LEU* 1.3 77.6 - - - +
500A GLN* 1.3 60.9 + - - +
502A GLU* 4.0 3.8 - - - +
503A TYR* 3.0 36.0 + - - +
510A TRP* 3.5 25.6 - - + -
515A PHE* 4.6 3.8 - - + -
705A CYS* 6.2 2.5 - - - -
712A ARG* 2.7 44.5 + - - -
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Residues in contact with GLN 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A PHE* 3.0 43.4 + - - +
497A VAL* 3.8 10.8 - - - +
498A LEU 3.1 0.2 - - - -
499A GLU* 1.3 79.8 - - - +
501A GLU* 1.3 62.1 + - - +
503A TYR* 3.5 1.7 + - - +
504A LYS* 3.2 24.7 + - - +
510A TRP* 3.1 46.6 - - + +
512A PHE 5.7 0.2 + - - -
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Residues in contact with GLU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A VAL* 3.4 18.1 + - - +
498A LEU* 3.3 22.8 + - + +
499A GLU 3.3 0.2 - - - -
500A GLN* 1.3 79.4 - - - +
502A GLU* 1.3 61.6 + - - +
504A LYS* 3.5 10.2 + - + +
505A LYS* 3.1 25.2 + - + +
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Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A LEU 2.8 17.8 + - - +
499A GLU* 3.6 11.0 - - - +
500A GLN 3.2 0.2 - - - -
501A GLU* 1.3 75.5 - - - +
503A TYR* 1.3 60.3 + - + +
505A LYS* 3.0 49.3 + - - +
506A GLU* 3.3 15.0 + - + +
712A ARG* 3.7 25.6 - - - +
761A LYS* 4.2 16.1 + - - -
763A PHE* 4.9 8.9 - - + -
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Residues in contact with TYR 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A GLU* 3.0 29.6 + - - +
500A GLN 4.0 2.5 - - - +
502A GLU* 1.3 77.8 - - + +
504A LYS* 1.3 56.6 + - - +
506A GLU* 3.5 1.6 + - - +
507A GLY 3.1 5.2 + - - -
508A ILE* 2.6 65.1 + - + +
509A VAL 4.2 9.0 - - - -
510A TRP* 3.3 41.7 - + + -
511A GLU* 6.2 0.9 - - + -
512A PHE* 5.5 3.6 - + - -
708A GLY* 3.7 7.4 - - - -
709A PHE* 2.8 54.9 + + + -
712A ARG* 3.1 28.5 + - - -
763A PHE* 4.0 12.8 - + - -
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Residues in contact with LYS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLN 3.2 18.1 + - - +
501A GLU* 3.8 10.3 - - + +
502A GLU 3.1 0.6 - - - -
503A TYR* 1.3 74.3 - - - +
505A LYS* 1.3 63.7 + - - +
506A GLU 3.2 2.5 - - - -
507A GLY* 3.4 12.3 + - - +
508A ILE 4.7 3.1 - - - -
510A TRP* 5.9 0.6 - - + +
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Residues in contact with LYS 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A GLU* 3.1 15.3 + - + +
502A GLU* 3.0 36.4 + - - +
504A LYS* 1.3 77.0 - - - +
506A GLU* 1.3 69.5 + - + +
507A GLY 3.4 0.2 - - - -
759A ASN* 3.7 13.4 + - - +
761A LYS* 5.6 4.0 - - - +
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Residues in contact with GLU 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GLU* 3.3 16.7 + - - +
503A TYR 3.5 2.9 + - - +
504A LYS 3.2 0.2 - - - -
505A LYS* 1.3 90.9 - - + +
507A GLY* 1.3 63.5 + - - +
508A ILE* 3.4 3.7 + - + +
757A LEU 4.6 0.2 - - - +
758A GLY* 3.3 12.1 - - - -
759A ASN* 3.1 30.9 + - - +
760A THR* 2.5 52.4 + - - +
761A LYS* 3.2 21.6 + - + +
763A PHE* 3.8 30.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il