Contacts of the helix formed by residues 491 - 514 (chain A) in PDB entry 5HJP
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 LEU 491 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A ALA* 2.7 41.0 + - + +
488A LYS* 4.1 11.0 - - + +
489A LEU 3.3 0.6 - - - -
490A LEU* 1.4 69.8 - - - +
492A ARG* 1.3 79.0 + - - +
493A LEU 3.3 0.2 - - - -
494A PRO* 3.3 21.1 - - + +
495A ALA* 4.4 4.2 + - - +
376B ILE* 4.4 11.4 - - + -
382B ASP* 5.6 0.7 - - - +
396B GLN* 3.6 39.7 - - - +
397B GLN* 4.3 8.1 - - - +
400B VAL* 4.2 11.9 - - + -
422B LEU* 4.4 17.0 - - + -
425B LEU* 4.7 7.9 - - + -
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Residues in contact with ARG 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 2.8 48.9 + - - +
424A LEU* 4.6 9.5 - - + +
427A LYS* 3.2 44.7 - - - +
428A MET* 5.6 5.4 - - + +
431A MET* 5.4 4.9 - - - -
433A MET* 4.8 13.2 - - + -
441A LEU* 4.9 6.3 - - + -
488A LYS 3.4 18.2 + - - +
489A LEU* 3.7 12.6 - - - +
490A LEU 3.1 1.2 - - - -
491A LEU* 1.3 95.7 + - - +
493A LEU* 1.3 55.6 + - + +
494A PRO 3.6 0.2 - - - -
495A ALA* 3.3 17.5 + - - +
496A LEU* 2.8 37.4 + - + +
381B ALA* 6.2 1.0 - - - +
382B ASP* 5.2 4.2 + - - -
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 4.7 2.6 - - - +
441A LEU* 4.5 18.8 - - + -
444A ILE* 3.8 21.3 - - + -
445A ILE* 3.7 34.8 - - + -
464A ARG* 6.0 0.4 - - - +
489A LEU 4.4 6.3 - - - +
490A LEU* 3.3 20.0 - - + +
492A ARG* 1.3 73.9 - - + +
494A PRO* 1.4 60.3 - - + +
496A LEU* 3.3 12.2 + - + +
497A ARG* 2.9 29.3 + - - +
423B MET* 3.5 30.7 - - + -
426B VAL* 3.8 16.2 - - + +
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Residues in contact with PRO 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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490A LEU 3.4 11.4 - - - +
491A LEU* 3.3 23.8 - - + +
493A LEU* 1.4 88.3 - - + +
495A ALA* 1.3 61.4 + - - +
497A ARG* 3.2 4.5 + - - +
498A SER 3.1 17.8 + - - -
382B ASP* 5.7 0.2 - - - +
422B LEU 4.9 2.0 - - - +
425B LEU* 4.0 26.5 - - + +
426B VAL* 3.6 19.7 - - + -
429B ARG* 3.5 41.0 + - + +
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Residues in contact with ALA 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 4.6 9.2 - - + +
424A LEU* 4.7 1.1 - - + -
491A LEU 4.4 3.8 + - - +
492A ARG* 3.3 30.3 + - - +
493A LEU 3.3 0.2 - - - -
494A PRO* 1.3 77.8 - - - +
496A LEU* 1.3 57.0 + - - +
498A SER* 3.4 3.9 + - - -
499A ILE* 2.9 36.5 + - + +
382B ASP* 4.1 25.5 + - + +
429B ARG* 4.1 10.0 - - - +
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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
----------------------------------------------------------
378A GLU* 3.8 26.8 - - + +
381A ILE* 3.9 17.3 - - + -
382A ALA* 4.1 14.6 - - + +
424A LEU* 3.7 32.0 - - + +
428A MET* 6.0 2.7 - - + -
441A LEU* 6.4 1.1 - - + -
445A ILE* 3.6 30.3 - - + -
492A ARG* 2.8 19.5 + - + +
493A LEU* 3.3 15.2 + - + +
495A ALA* 1.3 72.8 - - - +
497A ARG* 1.3 55.1 + - - +
499A ILE* 3.7 4.2 - - + -
500A GLY* 2.8 32.7 + - - -
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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
----------------------------------------------------------
378A GLU* 2.9 35.1 + - - +
445A ILE* 5.7 2.8 + - - +
448A ASN* 4.1 27.8 + - - +
450A ASP* 5.8 4.6 + - - +
464A ARG* 4.4 8.7 - - - +
493A LEU 2.9 13.8 + - - +
494A PRO 3.2 8.5 + - - +
496A LEU* 1.3 77.0 - - - +
498A SER* 1.4 62.0 + - - +
500A GLY* 3.4 1.0 + - - -
501A LEU* 3.1 38.9 + - + +
426B VAL* 3.6 45.8 + - + +
427B SER* 4.6 3.4 - - - +
429B ARG* 3.8 10.1 - - + -
430B THR* 2.7 37.0 + - - +
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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
----------------------------------------------------------
419A ARG* 3.5 17.5 + - - -
494A PRO 3.1 4.2 + - - -
495A ALA* 3.7 5.4 - - - -
497A ARG* 1.4 75.3 - - - +
499A ILE* 1.4 62.0 + - - +
501A LEU* 3.3 12.8 + - - +
502A LYS* 3.2 19.1 + - - +
382B ASP* 5.4 0.2 - - - -
429B ARG* 3.1 45.2 + - - +
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Residues in contact with ILE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ILE* 4.1 13.7 - - + -
416A ILE* 3.7 5.6 - - + +
419A ARG* 3.6 51.4 - - + +
420A VAL* 3.7 26.0 - - + -
423A GLU* 3.8 12.6 - - + -
424A LEU* 3.7 26.5 - - + -
495A ALA* 2.9 21.4 + - + +
496A LEU* 3.7 4.5 - - - +
497A ARG 3.4 0.2 - - - -
498A SER* 1.4 73.0 - - - +
500A GLY* 1.3 54.1 + - - +
502A LYS* 3.2 2.3 + - - -
503A CYS* 2.8 41.8 + - - +
382B ASP* 6.1 0.7 - - + -
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Residues in contact with GLY 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 3.6 19.8 + - - +
378A GLU* 4.6 2.7 - - - -
381A ILE* 3.5 23.3 - - - -
496A LEU 2.8 19.5 + - - -
497A ARG 3.8 2.2 - - - -
499A ILE* 1.3 73.1 - - - +
501A LEU* 1.4 55.5 + - - +
503A CYS* 3.4 2.3 + - - +
504A LEU* 2.9 30.7 + - - +
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 5.3 1.8 - - - +
497A ARG* 3.1 40.4 + - + +
498A SER* 3.4 12.1 - - - +
500A GLY* 1.4 75.7 - - - +
502A LYS* 1.4 56.4 + - - +
504A LEU* 3.4 14.1 + - + +
505A GLU* 3.2 27.5 + - - +
429B ARG 4.3 9.0 - - - +
430B THR* 4.7 5.6 - - + +
433B SER* 3.8 35.9 - - - +
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Residues in contact with LYS 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 3.7 15.7 - - + -
419A ARG* 3.4 32.4 - - - +
498A SER 3.2 8.6 + - - +
499A ILE 3.2 3.1 + - - +
501A LEU* 1.4 71.5 - - - +
503A CYS* 1.4 62.4 + - - +
505A GLU* 3.2 44.1 - - - +
506A HIS* 3.1 40.6 + - + -
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Residues in contact with CYS 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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377A ASN* 5.9 0.9 - - + -
381A ILE* 3.7 28.7 - - + -
416A ILE* 3.8 20.6 - - - -
420A VAL* 4.5 7.9 - - - -
499A ILE* 2.8 27.9 + - - +
500A GLY 3.5 6.3 - - - +
502A LYS* 1.4 76.7 - - - +
504A LEU* 1.3 59.8 + - - +
506A HIS* 3.6 7.8 + - - +
507A LEU* 3.4 28.6 + - + +
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Residues in contact with LEU 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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376A TRP* 3.6 37.2 - - + -
377A ASN* 4.5 20.8 - - + +
500A GLY 2.9 17.3 + - - +
501A LEU* 3.7 14.1 - - + +
502A LYS 3.3 0.2 - - - -
503A CYS* 1.3 75.6 - - - +
505A GLU* 1.3 62.2 + - - +
507A LEU* 3.5 5.1 + - + +
508A PHE* 3.1 48.5 + - + -
526A LEU* 3.8 14.1 - - + -
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Residues in contact with GLU 505 (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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501A LEU 3.2 11.0 + - - +
502A LYS* 3.2 55.4 - - + +
504A LEU* 1.3 74.4 - - - +
506A HIS* 1.3 65.4 + - - +
508A PHE* 3.2 13.0 + - + +
509A PHE* 3.1 55.2 + - + -
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Residues in contact with HIS 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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412A GLY 3.9 18.3 + - - -
413A VAL* 3.6 25.6 - - + +
415A ALA* 6.6 0.2 - - + -
416A ILE* 3.6 28.0 - - + +
502A LYS* 3.1 34.4 + - + -
503A CYS* 3.8 9.4 - - - +
504A LEU 3.3 0.4 - - - -
505A GLU* 1.3 80.2 - - - +
507A LEU* 1.4 60.4 + - + +
509A PHE* 3.3 29.3 + + - +
510A PHE* 3.3 40.6 + + + -
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Residues in contact with LEU 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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339A ILE* 5.4 11.0 - - + -
340A CYS* 4.3 15.3 - - - -
343A ALA* 5.7 4.0 - - + -
376A TRP* 4.1 30.1 - - + -
377A ASN* 6.2 0.7 - - + -
503A CYS* 3.4 16.7 + - + +
504A LEU* 3.8 11.4 - - + +
505A GLU 3.3 0.4 - - - -
506A HIS* 1.4 73.6 - - + +
508A PHE* 1.3 64.8 + - - +
510A PHE* 3.5 27.6 + - + +
511A LYS 3.2 15.9 + - - -
518A ILE* 5.1 0.7 - - - +
522A LEU* 4.8 11.9 - - + -
526A LEU* 3.6 27.9 - - + +
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Residues in contact with PHE 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 LEU* 3.1 47.7 + - + -
505A GLU* 3.2 12.4 + - + +
507A LEU* 1.3 76.9 - - - +
509A PHE* 1.4 57.2 + - + +
511A LYS* 3.2 29.8 + - - +
512A LEU* 2.8 36.5 + - - +
526A LEU* 3.4 39.0 - - + -
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Residues in contact with PHE 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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505A GLU* 3.1 52.7 + - + -
506A HIS* 3.3 36.7 + + - +
508A PHE* 1.4 79.4 - - + +
510A PHE* 1.4 58.0 + + + +
512A LEU* 4.0 6.7 - - + +
513A ILE* 2.8 46.6 + - + +
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Residues in contact with PHE 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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336A VAL 5.3 6.3 - - - -
339A ILE* 6.4 3.8 - - + -
340A CYS* 4.0 15.9 - - - -
411A ALA 5.3 6.7 - - - -
413A VAL* 4.5 20.2 - - + -
506A HIS* 3.3 36.1 + + + -
507A LEU* 3.7 32.8 - - + +
508A PHE 3.3 0.2 - - - -
509A PHE* 1.4 80.0 - + + +
511A LYS* 1.3 57.2 + - - +
513A ILE* 4.7 5.2 - - + -
514A GLY* 2.9 27.2 + - - -
515A ASP 4.2 2.9 + - - +
516A THR 5.2 0.9 - - - +
518A ILE* 4.1 18.6 - - + +
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Residues in contact with LYS 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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507A LEU 3.2 13.2 + - - +
508A PHE* 3.2 30.8 + - - +
510A PHE* 1.3 76.1 - - - +
512A LEU* 1.3 66.0 + - + +
514A GLY* 4.2 6.0 + - - -
518A ILE* 4.2 9.8 - - + +
523A MET* 3.8 26.5 - - + -
526A LEU* 3.8 33.3 + - + -
527A GLU* 2.8 36.3 + - - +
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Residues in contact with LEU 512 (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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508A PHE 2.8 20.9 + - - +
509A PHE* 4.0 6.7 - - + +
511A LYS* 1.3 76.4 - - + +
513A ILE* 1.3 71.9 + - + +
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Residues in contact with ILE 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A PHE* 2.8 26.0 + - + +
510A PHE* 4.4 4.0 - - + +
512A LEU* 1.3 82.0 - - + +
514A GLY* 1.3 60.4 + - - +
515A ASP* 3.4 36.3 - - + +
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Residues in contact with GLY 514 (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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510A PHE 2.9 18.7 + - - -
511A LYS* 4.5 6.5 - - - -
512A LEU 3.5 1.0 - - - -
513A ILE* 1.3 77.4 - - - +
515A ASP* 1.3 65.8 + - - +
516A THR 3.6 5.6 - - - -
517A PRO* 5.3 3.9 - - - +
518A ILE* 6.1 0.4 - - - -
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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) + - + + + + + -
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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