Contacts of the helix formed by residues 488 - 512 (chain A) in PDB entry 2H3W
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 PRO 488 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A THR 3.9 6.5 - - - +
487A VAL* 1.3 90.9 - - + +
489A GLU* 1.3 58.6 + - - +
490A GLN* 4.4 4.9 - - + +
491A GLN* 2.7 45.0 + - + +
492A LYS* 3.1 5.9 + - - +
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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
----------------------------------------------------------
487A VAL 3.3 3.3 + - - -
488A PRO* 1.3 70.9 - - - +
490A GLN* 1.3 61.6 + - - +
492A LYS* 3.1 23.3 + - + +
493A VAL 3.4 1.2 + - - -
616A THR* 6.0 0.3 - - - +
617A LEU* 3.1 43.1 - - + +
620A ASN* 3.5 24.7 - - - +
621A HIS* 2.7 29.8 + - + +
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Residues in contact with GLN 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A PRO* 3.1 4.9 - - + +
489A GLU* 1.3 78.7 - - - +
491A GLN* 1.3 64.3 + - - +
493A VAL* 3.3 24.6 - - + +
494A GLU* 3.2 32.0 + - - +
497A ARG* 5.8 2.0 - - - +
621A HIS* 3.8 29.2 + - + +
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Residues in contact with GLN 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A VAL* 3.6 20.2 - - + -
488A PRO* 2.7 30.3 + - + +
490A GLN* 1.3 80.3 + - - +
492A LYS* 1.3 61.6 + - - +
493A VAL 3.3 0.3 + - - -
494A GLU* 2.9 39.8 + - - +
495A LEU* 3.4 26.9 + - + +
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Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A PHE* 3.9 3.7 - - + -
481A GLY 2.9 23.2 + - - +
482A MET* 3.7 33.9 - - - +
484A ASP 2.7 24.9 + - - -
485A SER* 5.9 0.4 - - - +
487A VAL* 2.6 34.1 + - + +
488A PRO 3.1 7.8 + - - +
489A GLU* 3.1 21.7 + - + +
491A GLN* 1.3 75.1 - - - +
493A VAL* 1.3 60.3 + - - +
495A LEU* 3.4 12.2 + - - +
496A LEU* 2.9 28.9 + - - +
617A LEU* 3.7 17.0 - - + +
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Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLU 3.6 14.4 - - - +
490A GLN* 3.3 15.7 - - + +
491A GLN 3.1 0.2 - - - -
492A LYS* 1.3 78.2 - - - +
494A GLU* 1.3 63.1 + - - +
496A LEU* 3.1 5.1 + - - +
497A ARG* 3.0 63.6 + - - +
617A LEU* 3.7 34.1 - - + +
618A LEU* 4.0 9.9 - - + -
621A HIS* 4.0 19.1 - - + +
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Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A GLN* 3.2 34.8 + - - +
491A GLN* 2.9 35.4 + - - +
493A VAL* 1.3 77.7 - - + +
495A LEU* 1.3 58.6 + - + +
496A LEU 3.3 0.2 + - - -
497A ARG* 3.3 12.0 + - - +
498A LYS* 2.9 32.0 + - - +
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ASP 4.5 2.0 - - - +
477A ALA* 3.6 36.8 - - + +
478A PHE* 3.7 17.5 - - + +
481A GLY* 4.2 17.5 - - - -
487A VAL* 5.1 3.8 - - + -
491A GLN* 3.4 30.7 + - + +
492A LYS* 3.4 12.5 + - - +
493A VAL 3.3 0.4 - - - -
494A GLU* 1.3 79.2 - - + +
496A LEU* 1.3 61.6 + - - +
498A LYS* 3.5 13.0 + - + +
499A ALA* 3.0 24.4 + - - +
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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
----------------------------------------------------------
427A LEU* 4.2 7.2 - - + -
432A PHE* 5.0 0.2 - - + -
435A VAL* 5.0 0.2 - - - +
478A PHE* 3.5 22.9 - - + -
492A LYS 2.9 13.4 + - - +
493A VAL* 3.1 9.1 + - - +
495A LEU* 1.3 73.8 - - - +
497A ARG* 1.3 67.2 + - - +
499A ALA* 3.2 4.2 + - - +
500A VAL* 3.0 42.1 + - + +
614A MET* 3.7 47.3 - - + +
617A LEU* 3.7 23.8 - - + -
618A LEU* 4.1 26.7 - - + -
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Residues in contact with ARG 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU* 4.5 10.1 + - - -
427A LEU* 4.2 25.4 - - + +
490A GLN* 5.8 1.8 - - - +
493A VAL* 3.0 44.6 + - + +
494A GLU* 3.8 10.8 - - - +
496A LEU* 1.3 77.9 - - - +
498A LYS* 1.3 57.5 + - - +
500A VAL* 3.3 2.4 + - - +
501A GLN* 2.8 38.4 + - + +
618A LEU* 4.2 17.6 + - + +
621A HIS 4.0 11.9 + - - -
623A ARG* 3.0 48.9 - - - +
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Residues in contact with LYS 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ASP* 3.7 28.3 - - + +
494A GLU 2.9 18.4 + - - +
495A LEU* 3.7 15.3 - - + +
496A LEU 3.2 0.2 - - - -
497A ARG* 1.3 78.9 - - - +
499A ALA* 1.3 56.7 + - - +
501A GLN* 3.5 6.3 + - + +
502A ALA* 2.9 30.1 + - - +
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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
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435A VAL* 3.9 16.6 - - + +
472A SER* 5.5 0.5 + - - -
474A ASP* 3.7 26.8 - - - +
475A SER* 3.9 15.7 + - - +
478A PHE* 4.1 7.9 - - + -
495A LEU 3.0 17.8 + - - +
496A LEU 3.2 4.5 + - - +
498A LYS* 1.3 75.8 - - - +
500A VAL* 1.3 59.3 + - - +
502A ALA* 3.2 3.1 + - - +
503A HIS* 2.9 29.8 + - - +
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Residues in contact with VAL 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 3.9 26.2 - - + -
428A SER* 4.1 16.8 - - - +
431A ALA* 3.6 19.8 - - + +
432A PHE* 4.2 9.9 - - + +
435A VAL* 3.8 23.3 - - + +
496A LEU* 3.0 33.3 + - + +
497A ARG* 3.6 7.4 - - - +
499A ALA* 1.3 75.7 - - - +
501A GLN* 1.3 60.3 + - - +
503A HIS* 3.2 3.8 + - - +
504A ARG* 2.9 27.1 + - + +
614A MET* 4.8 0.4 - - + -
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Residues in contact with GLN 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LYS 4.3 8.9 + - - -
427A LEU* 4.0 24.2 - - - +
428A SER 5.3 1.0 - - - +
497A ARG* 2.8 26.6 + - + +
498A LYS* 3.8 7.0 - - - +
500A VAL* 1.3 76.2 - - - +
502A ALA* 1.3 58.4 + - - +
504A ARG* 3.2 15.6 + - - +
505A ALA* 2.9 29.9 + - - +
1601A COA 5.2 4.0 + - - -
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Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A SER* 4.8 7.9 - - - +
474A ASP* 3.2 33.7 - - + +
498A LYS 2.9 15.4 + - - +
499A ALA 3.4 5.2 - - - +
501A GLN* 1.3 75.0 - - - +
503A HIS* 1.3 58.1 + - - +
505A ALA* 3.2 8.6 + - - +
506A TYR* 3.0 27.3 + - - +
509A ARG* 5.0 1.6 + - - -
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Residues in contact with HIS 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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430A ASP* 3.9 7.9 - - - -
431A ALA* 3.5 21.3 - - + +
434A GLN* 3.3 28.0 - - + +
435A VAL* 4.6 5.6 - - + -
453A GLU* 2.9 29.9 + - - -
468A ILE* 3.7 8.9 - - + +
469A ARG 5.0 1.8 - - - -
470A SER* 3.5 28.4 + - - -
499A ALA 2.9 16.4 + - - +
500A VAL* 3.5 6.1 - - - +
502A ALA* 1.3 74.3 - - - +
504A ARG* 1.3 55.4 + - - +
506A TYR* 3.3 6.3 + - - +
507A THR* 2.7 52.3 + - - -
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Residues in contact with ARG 504 (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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163A LEU* 6.2 0.2 - - - +
428A SER* 3.9 25.3 + - - -
430A ASP* 5.9 0.2 - - - +
431A ALA* 4.7 1.8 - - - -
500A VAL 2.9 13.9 + - - +
501A GLN* 3.5 22.2 - - - +
503A HIS* 1.3 78.3 + - - +
505A ALA* 1.3 58.1 + - - +
507A THR* 3.4 31.6 + - - +
508A ASP* 2.7 68.8 + - - +
511A ILE* 4.3 8.7 - - - +
1601A COA 2.8 49.3 + - - -
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Residues in contact with ALA 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A GLN 2.9 12.6 + - - +
502A ALA* 3.2 12.5 + - - +
504A ARG* 1.3 76.4 - - - +
506A TYR* 1.3 64.1 + - - +
508A ASP* 3.3 8.9 + - - +
509A ARG* 3.0 44.4 + - - +
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Residues in contact with TYR 506 (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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49A TYR* 5.8 3.4 - - + -
53A ALA* 4.9 7.0 - - + -
467A THR 3.5 21.2 + - - -
468A ILE* 4.0 15.9 - - + -
469A ARG* 3.5 46.7 + - + +
472A SER* 5.8 6.7 - - - -
502A ALA 3.0 13.9 + - - +
503A HIS* 3.6 11.7 - - + +
504A ARG 3.3 0.2 - - - -
505A ALA* 1.3 76.0 - - - +
507A THR* 1.3 58.2 + - - +
509A ARG* 3.2 27.6 + - + +
510A ALA* 2.8 26.9 + - + +
515A ALA* 4.6 14.1 - - + -
516A PHE* 3.2 34.3 + + - -
517A ASP* 4.3 0.9 + - - -
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Residues in contact with THR 507 (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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430A ASP* 5.0 0.8 + - - +
468A ILE* 3.6 15.6 - - + +
503A HIS* 2.7 42.8 + - - -
504A ARG* 3.5 30.6 - - - +
506A TYR* 1.3 78.3 - - - +
508A ASP* 1.3 60.3 + - - +
510A ALA* 3.3 2.1 + - - +
511A ILE* 3.1 24.2 + - + +
1601A COA 3.4 38.4 - - + +
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Residues in contact with ASP 508 (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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504A ARG* 2.7 58.6 + - - +
505A ALA* 3.7 7.5 - - - +
506A TYR 3.3 0.2 - - - -
507A THR* 1.3 75.0 - - - +
509A ARG* 1.3 63.9 + - + +
511A ILE* 3.1 10.8 - - - +
512A ARG* 2.9 49.7 + - - +
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Residues in contact with ARG 509 (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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49A TYR* 3.2 53.6 + - - -
502A ALA 5.0 1.4 + - - -
505A ALA* 3.0 36.8 + - - +
506A TYR* 3.6 39.8 - - + +
508A ASP* 1.3 75.0 - - + +
510A ALA* 1.3 61.4 + - - +
512A ARG* 3.2 8.8 + - - +
514A GLU* 2.7 63.9 + - + +
515A ALA* 4.1 1.3 - - - -
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Residues in contact with ALA 510 (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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455A ALA* 3.8 10.1 - - + -
457A LEU* 3.3 18.5 - - - +
466A ASP* 4.3 4.2 - - + +
467A THR 4.6 2.2 - - - +
468A ILE* 3.5 27.4 - - + -
506A TYR* 2.8 18.1 + - + +
507A THR 3.6 2.7 - - - +
509A ARG* 1.3 77.0 - - - +
511A ILE* 1.3 62.6 + - - +
513A GLY* 3.1 12.3 + - - -
515A ALA* 3.9 23.1 - - + +
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Residues in contact with ILE 511 (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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163A LEU* 3.8 24.5 - - + -
164A GLY* 4.9 5.6 - - - -
455A ALA* 4.6 4.3 - - + -
456A SER 3.5 28.0 - - - +
457A LEU* 4.2 1.5 - - - +
459A MET* 3.2 33.8 - - + +
460A PHE* 3.7 2.8 - - - -
504A ARG* 4.3 7.4 - - - +
507A THR* 3.1 14.1 + - + +
508A ASP* 3.1 24.7 - - - +
510A ALA* 1.3 76.5 - - - +
512A ARG* 1.3 78.0 + - + +
513A GLY 3.3 1.1 - - - -
1601A COA 3.5 28.3 - - - +
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Residues in contact with ARG 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 4.4 4.0 - - - +
164A GLY* 4.2 21.2 + - - -
166A GLN* 5.9 1.9 - - - +
459A MET* 4.0 17.7 - - + +
460A PHE* 3.4 19.6 - - + -
508A ASP* 2.9 45.8 + - - +
509A ARG* 3.2 5.3 + - - +
510A ALA 3.1 1.0 - - - -
511A ILE* 1.3 99.2 - - - +
513A GLY* 1.3 62.4 + - - +
514A GLU* 3.3 23.8 + - - +
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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