Contacts of the helix formed by residues 475 - 504 (chain A) in PDB entry 2O8C
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 ASP 475 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A LYS 4.1 2.6 + - - -
472A PRO 3.6 2.1 - - - +
474A PHE* 1.3 89.6 - - + +
476A PRO* 1.3 73.2 - - - +
477A ASN* 3.4 24.2 + - - +
478A LEU* 3.1 35.1 + - + +
479A SER* 2.9 29.0 + - - -
573A ALA* 5.6 1.2 - - - +
577A ILE* 4.3 13.6 - - + +
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Residues in contact with PRO 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PHE 3.5 9.4 - - - +
475A ASP* 1.3 92.2 - - - +
477A ASN* 1.3 60.5 + - + +
479A SER* 2.8 23.0 + - - +
480A GLU* 3.5 14.2 + - - +
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Residues in contact with ASN 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ASP* 3.1 18.4 + - - +
476A PRO* 1.3 82.7 - - + +
478A LEU* 1.3 59.6 + - - +
480A GLU* 3.6 5.2 + - - +
481A LEU* 3.1 32.2 + - - +
573A ALA* 4.8 15.0 - - - +
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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
----------------------------------------------------------
470A VAL* 4.8 5.8 - - + -
471A LYS 4.3 13.0 - - - +
472A PRO* 4.0 8.1 - - + +
475A ASP* 3.1 32.3 + - + +
477A ASN* 1.3 78.3 - - - +
479A SER* 1.3 60.2 + - - +
481A LEU* 3.7 8.4 - - + +
482A ARG* 3.0 31.2 + - - +
570A TYR* 3.7 42.6 + - + +
573A ALA* 3.9 27.4 - - + -
574A GLN* 4.6 13.9 - - + +
577A ILE* 4.3 15.3 - - + -
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Residues in contact with SER 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PRO 3.4 19.7 + - - -
473A SER* 4.9 5.4 - - - -
475A ASP 2.9 9.3 + - - -
476A PRO* 2.8 28.5 + - - +
478A LEU* 1.3 77.7 - - - +
480A GLU* 1.3 58.9 + - - +
482A ARG* 3.4 16.6 + - - +
483A GLU* 3.3 22.0 - - - +
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Residues in contact with GLU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A PRO 3.5 13.5 + - - +
477A ASN* 4.1 4.1 - - - +
478A LEU 3.3 0.2 - - - -
479A SER* 1.3 79.2 + - - +
481A LEU* 1.3 64.9 + - - +
482A ARG 3.3 0.4 - - - -
483A GLU* 3.3 30.3 + - - +
484A ILE* 3.4 18.0 - - + +
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ASN* 3.1 27.4 + - - +
478A LEU* 3.9 11.2 - - + +
479A SER 3.4 0.2 - - - -
480A GLU* 1.3 78.5 - - - +
482A ARG* 1.3 61.2 + - - +
484A ILE* 3.4 21.0 + - + +
485A MET* 3.2 24.1 + - + +
566A ASN* 4.1 30.3 - - + +
569A GLU* 4.5 16.2 - - + +
570A TYR* 3.6 43.5 - - + +
573A ALA* 5.8 0.4 - - + -
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Residues in contact with ARG 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PRO* 3.8 28.1 + - + +
478A LEU 3.0 15.7 + - - +
479A SER* 3.4 17.8 + - - +
481A LEU* 1.3 74.1 - - - +
483A GLU* 1.3 66.6 + - - +
484A ILE 3.3 0.2 - - - -
485A MET* 3.2 13.1 + - + +
486A ASN* 2.8 55.4 + - - +
570A TYR* 4.6 12.5 - - + +
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Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A SER 3.3 18.4 - - - +
480A GLU* 3.3 20.6 + - - +
481A LEU 3.2 0.4 - - - -
482A ARG* 1.3 87.3 + - + +
484A ILE* 1.3 56.9 + - + +
486A ASN* 3.6 6.7 - - - +
487A ASP* 2.6 49.0 + - - +
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Residues in contact with ILE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A GLU* 3.4 22.9 - - + +
481A LEU* 3.6 23.3 - - + +
482A ARG 3.3 0.4 - - - -
483A GLU* 1.3 75.4 - - + +
485A MET* 1.3 62.9 + - - +
487A ASP* 4.4 4.4 - - - +
488A LEU* 3.1 43.4 + - + +
566A ASN* 3.4 24.5 - - - +
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Residues in contact with MET 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU* 3.2 19.7 - - + +
482A ARG* 3.2 14.3 + - + +
484A ILE* 1.3 78.9 - - - +
486A ASN* 1.3 59.4 + - - +
489A GLU* 3.6 16.5 + - - +
563A TYR* 3.6 54.9 + - + +
566A ASN* 3.7 35.0 - - - +
567A LYS* 3.9 22.7 - - + +
570A TYR* 5.2 9.6 - - + -
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Residues in contact with ASN 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 ARG* 2.8 33.8 + - - +
483A GLU* 3.2 8.1 + - - +
485A MET* 1.3 75.8 - - - +
487A ASP* 1.3 66.1 + - - +
489A GLU* 3.2 17.3 + - - +
490A LYS* 3.2 38.6 + - - +
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Residues in contact with ASP 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLU* 2.6 32.9 + - - +
484A ILE* 4.4 4.0 - - - +
486A ASN* 1.3 73.2 + - - +
488A LEU* 1.3 66.6 + - + +
490A LYS* 3.3 33.7 + - + +
491A LYS* 3.2 29.9 + - - +
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE* 3.1 39.0 + - + +
485A MET 4.3 0.7 - - - +
486A ASN 3.3 0.2 - - - -
487A ASP* 1.3 78.1 - - + +
489A GLU* 1.3 56.8 + - - +
491A LYS* 3.1 18.6 + - + +
492A MET* 2.9 34.8 + - + +
559A LEU* 3.8 34.2 - - + +
562A GLU* 5.1 9.4 - - + +
563A TYR* 3.6 45.3 - - + +
566A ASN* 4.6 4.9 - - - +
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Residues in contact with GLU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A MET 3.6 11.4 + - - +
486A ASN* 3.2 14.7 + - - +
488A LEU* 1.3 75.1 - - - +
490A LYS* 1.3 63.7 + - - +
492A MET* 3.4 18.1 + - - +
493A GLN* 3.4 23.6 + - - +
521A TYR* 5.8 7.2 - - + +
563A TYR* 5.2 5.7 - - + +
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Residues in contact with LYS 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASN* 3.2 37.6 + - - +
487A ASP* 3.4 29.4 + - - +
488A LEU 3.2 0.4 - - - -
489A GLU* 1.3 77.6 - - - +
491A LYS* 1.3 61.3 + - + +
492A MET 3.3 0.2 - - - -
493A GLN* 3.7 10.9 + - - +
494A SER* 3.6 17.0 + - - -
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Residues in contact with LYS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ASP* 3.2 17.9 + - - +
488A LEU* 3.1 22.7 + - + +
490A LYS* 1.3 78.7 - - + +
492A MET* 1.3 62.3 + - - +
494A SER* 2.7 26.1 + - - +
495A THR* 3.2 17.3 + - + +
559A LEU* 5.1 12.1 - - + +
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Residues in contact with MET 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LEU* 2.9 24.4 + - + +
489A GLU* 3.5 15.9 - - - +
490A LYS 3.3 0.4 - - - -
491A LYS* 1.3 78.8 - - - +
493A GLN* 1.3 61.7 + - + +
495A THR* 2.6 23.0 + - - +
496A LEU* 3.3 14.9 + - - +
513A LEU* 3.6 29.3 - - + +
521A TYR* 3.8 40.4 - - + -
523A PHE* 5.8 0.2 - - + -
556A LEU* 3.8 25.8 - - + -
559A LEU* 3.8 31.4 - - - +
560A ASN* 6.4 1.3 - - - -
563A TYR* 6.2 2.9 - - + -
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Residues in contact with GLN 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 GLU* 3.4 16.8 + - - +
490A LYS* 4.0 11.0 - - - +
491A LYS 3.3 0.2 - - - -
492A MET* 1.3 77.4 - - + +
494A SER* 1.3 61.4 + - - +
495A THR 3.3 0.2 - - - -
496A LEU* 3.4 26.8 + - + +
497A ILE* 3.4 25.4 - - + +
513A LEU* 5.6 2.9 - - + -
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Residues in contact with SER 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A LYS 3.6 10.0 + - - -
491A LYS* 2.7 31.2 + - - +
493A GLN* 1.3 79.1 - - - +
495A THR* 1.3 60.7 + - - +
496A LEU 3.2 0.4 - - - -
497A ILE* 3.7 7.5 + - - +
498A SER* 3.2 25.5 + - - -
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Residues in contact with THR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LYS* 3.2 12.9 + - + +
492A MET* 2.6 33.3 + - - +
494A SER* 1.3 80.3 + - - +
496A LEU* 1.3 59.1 + - - +
498A SER* 3.8 7.4 - - - -
499A ALA* 3.0 29.3 + - - +
523A PHE* 4.3 16.7 - - - -
553A ASN* 5.6 6.7 + - - +
555A LYS* 4.4 27.1 - - + -
556A LEU* 5.6 4.1 - - + +
559A LEU* 5.0 9.9 - - + -
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A MET 3.3 13.1 + - - +
493A GLN* 3.4 27.4 - - + +
494A SER 3.2 0.4 - - - -
495A THR* 1.3 76.9 - - - +
497A ILE* 1.3 61.3 + - + +
499A ALA* 3.3 4.4 + - - +
500A ALA* 2.9 26.9 + - - +
507A PRO* 5.2 8.6 - - + +
508A GLY* 5.8 4.7 - - - +
511A ILE* 4.2 24.3 - - + +
512A LYS* 4.3 4.0 - - - +
513A LEU* 3.8 35.7 - - + +
523A PHE* 3.7 31.2 - - + -
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Residues in contact with ILE 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLN* 3.4 18.5 + - + +
494A SER* 3.7 6.5 + - - +
495A THR 3.5 0.2 - - - -
496A LEU* 1.3 75.7 - - + +
498A SER* 1.3 64.4 + - - +
500A ALA* 3.2 15.9 + - + +
501A ARG* 3.4 27.3 + - + +
507A PRO* 4.5 23.6 - - + -
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Residues in contact with SER 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A SER 3.2 20.4 + - - -
495A THR* 3.9 8.5 - - - -
497A ILE* 1.3 76.9 - - - +
499A ALA* 1.3 60.5 + - - +
501A ARG* 3.6 16.4 + - - +
502A ASP* 3.7 20.3 + - - +
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Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A THR 3.0 18.9 + - - +
496A LEU* 3.6 4.5 - - - +
498A SER* 1.3 73.8 - - - +
500A ALA* 1.3 62.7 + - - +
501A ARG 3.2 2.2 - - - -
502A ASP* 4.0 6.9 - - - +
503A LEU* 3.3 39.4 + - + +
511A ILE* 4.5 4.8 - - + +
523A PHE* 4.6 19.3 - - + -
539A PHE* 5.1 13.9 - - + -
551A PHE* 6.3 0.7 - - + -
553A ASN* 5.7 4.0 - - - +
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Residues in contact with ALA 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LEU 2.9 15.9 + - - +
497A ILE* 3.2 15.6 + - + +
499A ALA* 1.3 79.0 - - - +
501A ARG* 1.3 57.1 - - - +
504A GLY* 3.1 24.4 + - - -
505A LEU 3.3 27.1 + - - +
507A PRO* 4.2 16.6 - - + -
511A ILE* 4.8 8.1 - - + -
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Residues in contact with ARG 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A ILE* 3.4 25.2 + - + +
498A SER* 3.8 12.1 - - - +
499A ALA 3.2 0.2 - - - -
500A ALA* 1.3 77.9 - - - +
502A ASP* 1.3 68.6 + - - +
503A LEU 3.2 2.4 + - - -
504A GLY* 3.8 7.3 + - - -
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Residues in contact with ASP 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A SER* 3.7 18.3 + - - +
499A ALA* 3.8 7.4 + - - +
501A ARG* 1.3 80.4 - - - +
503A LEU* 1.3 68.6 + - + +
537A LYS* 5.1 23.7 + - + +
539A PHE* 5.5 9.4 - - + -
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Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ALA* 3.3 21.8 + - + +
501A ARG 3.2 0.2 - - - -
502A ASP* 1.3 86.1 - - + +
504A GLY* 1.3 61.2 + - - +
505A LEU* 4.5 3.2 - - + +
511A ILE* 4.0 23.6 - - + -
525A VAL* 5.7 0.2 - - + -
531A LYS* 3.8 51.3 - - + +
532A VAL* 5.5 5.2 - - + -
539A PHE* 4.5 27.1 - - + -
551A PHE* 4.3 25.4 - - + -
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Residues in contact with GLY 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ALA 3.1 14.0 + - - -
501A ARG 3.8 7.1 + - - -
503A LEU* 1.3 79.5 - - - +
505A LEU* 1.3 69.9 + - - +
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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