Contacts of the helix formed by residues 485 - 506 (chain A) in PDB entry 2VL7
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 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A SER* 3.9 2.9 - - - -
483A GLY 4.3 0.2 + - - -
484A LYS* 1.3 75.6 - - - +
486A GLU* 1.3 64.2 + - - +
487A ASP* 3.2 12.7 + - - +
488A SER* 2.7 48.5 + - - -
489A ILE* 3.1 10.2 + - - +
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Residues in contact with GLU 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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472A ARG* 5.2 8.1 + - - +
475A ILE* 3.8 21.0 - - + +
476A GLU* 3.1 36.5 - - - +
479A SER* 3.6 21.4 + - - +
485A ASP* 1.3 71.5 - - - +
487A ASP* 1.3 60.5 + - - +
489A ILE* 3.2 4.5 + - - +
490A ILE* 2.9 40.6 + - + +
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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
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463A TYR* 5.0 4.2 + - - -
485A ASP* 3.2 11.8 + - - +
486A GLU* 1.3 78.6 - - - +
488A SER* 1.3 56.7 + - - +
490A ILE* 3.7 15.5 - - - +
491A HIS* 2.9 28.8 + - - +
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Residues in contact with SER 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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484A LYS* 3.2 33.7 + - - +
485A ASP* 2.7 29.4 + - - -
487A ASP* 1.3 71.7 - - - +
489A ILE* 1.3 65.4 + - - +
491A HIS* 3.4 8.6 - - - +
492A ASP* 3.1 22.0 + - - +
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Residues in contact with ILE 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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332A SER* 3.3 24.2 - - - +
475A ILE* 4.0 16.2 - - + +
478A LEU* 3.9 35.0 - - + +
479A SER* 3.7 19.5 - - - +
482A THR* 3.5 14.6 - - - +
484A LYS* 3.5 23.6 - - + -
485A ASP 3.1 11.5 + - - +
486A GLU* 3.2 6.0 + - - +
488A SER* 1.3 76.6 + - - +
490A ILE* 1.3 68.5 + - - +
492A ASP* 3.1 4.2 + - - +
493A LEU* 2.9 32.9 + - + +
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Residues in contact with ILE 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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463A TYR* 3.3 46.2 - - + +
464A PRO* 3.6 15.7 - - + -
466A VAL* 4.1 13.7 - - + -
475A ILE* 3.8 27.8 - - + -
486A GLU* 2.9 29.1 + - + +
487A ASP* 3.7 15.3 - - - +
489A ILE* 1.3 74.1 - - - +
491A HIS* 1.3 62.5 + - - +
493A LEU* 3.3 8.5 + - - +
494A THR* 2.8 29.6 + - - +
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Residues in contact with HIS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ASP 2.9 14.3 + - - +
488A SER* 3.4 13.2 - - - +
490A ILE* 1.3 77.7 - - - +
492A ASP* 1.3 58.9 + - - +
494A THR 3.3 0.2 + - - -
495A ALA* 2.9 30.5 + - - +
524A GLU* 3.0 31.3 + - + +
525A TYR* 3.5 34.6 - + - -
528A ASP* 3.2 37.9 + - - -
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Residues in contact with ASP 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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188A LEU* 4.1 2.9 - - - +
330A PRO* 3.0 28.6 - - - +
331A GLU* 3.0 32.2 + - + +
332A SER* 3.0 30.3 + - - +
484A LYS* 4.4 2.2 - - - +
488A SER 3.1 11.4 + - - +
489A ILE 3.1 7.8 + - - +
491A HIS* 1.3 77.0 + - - +
493A LEU* 1.3 63.2 + - + +
495A ALA* 3.2 7.2 + - - +
496A ILE* 3.0 28.6 + - - +
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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
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188A LEU* 3.5 35.4 - - + -
189A GLU* 5.3 7.9 - - - +
462A PRO 4.9 0.8 - - - +
464A PRO* 4.1 22.2 - - + -
471A VAL* 5.7 1.8 - - + -
474A ARG* 5.0 12.6 - - - -
475A ILE* 3.8 29.2 - - + -
478A LEU* 4.5 9.0 - - + -
489A ILE* 2.9 29.1 + - + +
490A ILE 3.7 6.1 - - - +
492A ASP* 1.3 72.6 - - + +
494A THR* 1.3 61.6 + - - +
496A ILE* 3.6 12.3 - - + +
497A VAL* 3.3 23.4 - - - +
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Residues in contact with THR 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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461A LEU* 3.6 34.3 - - + -
462A PRO* 3.7 18.6 - - + +
463A TYR* 3.8 4.2 - - - -
464A PRO* 3.3 19.6 - - - +
490A ILE 2.8 15.6 + - - -
491A HIS 3.6 0.4 - - - -
493A LEU* 1.3 75.0 - - - +
495A ALA* 1.3 64.4 + - - +
497A VAL* 3.2 6.1 + - - +
498A ILE* 3.0 27.3 + - + +
525A TYR* 3.3 29.3 + - + +
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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
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491A HIS 2.9 20.2 + - - +
492A ASP* 3.7 8.5 - - - +
494A THR* 1.3 72.4 - - - +
496A ILE* 1.3 63.4 + - - +
498A ILE* 3.4 12.0 + - - +
499A LYS* 2.9 36.0 + - + +
525A TYR* 3.9 10.2 - - + -
528A ASP* 4.0 26.7 - - + +
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Residues in contact with ILE 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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185A HIS* 4.2 18.6 - - + +
188A LEU* 3.6 32.1 - - + -
328A THR* 3.6 28.6 - - - +
330A PRO* 3.9 22.0 - - + -
492A ASP* 3.0 21.8 + - - +
493A LEU* 3.6 15.9 - - + +
494A THR 3.3 0.2 - - - -
495A ALA* 1.3 76.4 - - - +
497A VAL* 1.3 60.1 + - + +
499A LYS* 3.3 2.5 + - - +
500A GLN* 2.8 42.2 + - + +
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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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436A MET* 3.9 27.1 - - + +
462A PRO* 3.6 31.6 - - + +
493A LEU 3.3 18.2 - - - +
494A THR 3.2 5.5 + - - +
496A ILE* 1.3 80.6 - - + +
498A ILE* 1.3 63.1 + - - +
500A GLN* 4.1 4.8 - - + +
501A THR* 2.6 37.0 + - - +
504A ARG* 5.3 1.8 - - - +
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Residues in contact with ILE 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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436A MET* 4.5 7.0 - - - -
458A LEU* 3.9 11.6 - - + +
461A LEU* 4.0 1.3 - - + -
462A PRO* 3.9 12.6 - - + -
494A THR* 3.0 27.9 + - + +
495A ALA* 3.7 6.5 - - - +
497A VAL* 1.3 75.7 - - - +
499A LYS* 1.3 59.0 + - + +
501A THR* 3.6 1.9 - - - -
502A ILE* 3.0 48.1 + - + +
522A TYR* 3.6 27.4 - - + +
525A TYR* 3.6 36.6 - - + -
529A LEU* 4.0 16.4 - - + -
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Residues in contact with LYS 499 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASN* 5.9 2.4 + - - +
35A PRO* 5.9 1.6 - - - +
327A GLY 5.4 2.0 + - - +
328A THR* 3.4 30.0 - - + +
495A ALA* 2.9 27.1 + - + +
496A ILE* 5.2 0.2 - - - -
498A ILE* 1.3 76.4 - - + +
500A GLN* 1.3 59.8 + - - +
502A ILE* 3.5 6.1 + - - +
503A GLY* 2.8 26.7 + - - -
528A ASP* 3.1 36.5 + - + +
529A LEU* 4.3 16.8 - - + +
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Residues in contact with GLN 500 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO* 5.2 12.2 - - - +
183A GLU* 4.1 13.0 + - - +
185A HIS* 3.4 26.6 + - + +
326A SER* 3.9 1.0 + - - -
327A GLY* 4.4 4.8 - - - +
328A THR* 3.0 38.0 + - + +
496A ILE* 2.8 31.5 + - + +
497A VAL* 4.1 5.6 - - + +
499A LYS* 1.3 72.7 - - - +
501A THR* 1.3 58.7 + - - +
503A GLY* 3.5 2.2 + - - -
504A ARG* 3.1 44.0 + - - +
507A ARG* 5.4 4.3 + - - -
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Residues in contact with THR 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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390A PHE* 3.5 43.9 - - + -
436A MET* 3.5 17.3 - - + +
456A LEU* 3.8 6.2 - - + +
458A LEU* 3.5 18.2 - - + -
497A VAL* 2.6 24.4 + - - +
498A ILE 3.6 3.8 - - - -
500A GLN* 1.3 74.3 - - - +
502A ILE* 1.3 64.8 + - - +
504A ARG* 3.0 37.7 + - - +
505A ALA 3.7 3.1 + - - -
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Residues in contact with ILE 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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34A LYS* 5.7 2.2 - - - -
352A TYR* 4.5 7.4 - - - +
456A LEU* 4.0 10.8 - - + -
458A LEU* 4.3 16.2 - - + -
498A ILE* 3.0 28.0 + - + +
499A LYS* 3.9 4.5 - - - +
501A THR* 1.3 75.6 - - - +
503A GLY* 1.3 57.5 + - - +
505A ALA* 3.1 22.9 + - - +
506A PHE* 3.0 44.3 + - + -
515A ILE* 4.5 20.2 - - + -
517A LEU* 4.8 0.2 - - + -
529A LEU* 3.4 37.2 - - + -
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Residues in contact with GLY 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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34A LYS* 4.8 10.7 - - - +
35A PRO* 4.4 16.3 - - - +
499A LYS 2.8 17.9 + - - -
500A GLN 3.7 3.4 - - - -
501A THR 3.2 0.4 - - - -
502A ILE* 1.3 73.1 - - - +
504A ARG* 1.3 62.3 + - - +
505A ALA 3.1 2.5 + - - -
506A PHE 4.0 7.5 - - - +
507A ARG* 3.1 33.6 + - - +
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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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388A LEU* 5.8 2.2 - - + +
390A PHE* 3.9 26.4 - - + -
435A VAL 4.7 2.1 + - - -
436A MET* 4.2 21.8 + - - +
453A PHE* 5.3 0.9 - - - -
497A VAL* 4.8 2.6 + - - +
500A GLN* 3.1 27.3 + - - +
501A THR* 3.0 42.3 + - - +
503A GLY* 1.3 74.2 - - - +
505A ALA* 1.3 62.5 + - - +
507A ARG* 4.6 15.8 + - - +
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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
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388A LEU* 5.3 2.9 - - + -
453A PHE* 3.8 36.0 - - + -
456A LEU* 3.2 29.2 - - + -
501A THR 3.7 1.0 + - - -
502A ILE 3.1 12.8 + - - +
504A ARG* 1.3 81.1 - - - +
506A PHE* 1.3 73.1 + - + +
507A ARG* 4.1 1.9 + - - +
511A ASP* 4.6 1.4 - - - +
513A VAL* 4.5 2.2 - - + +
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Residues in contact with PHE 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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34A LYS* 3.1 39.9 + - - -
348A GLY* 4.4 15.7 - - - -
349A ARG 6.0 0.4 - - - -
350A GLY* 5.4 6.5 - - - -
352A TYR* 4.2 13.2 - + - -
502A ILE* 3.0 41.1 + - + +
503A GLY 4.0 2.6 - - - +
505A ALA* 1.3 77.5 - - + +
507A ARG* 1.3 64.5 + - - +
508A ASP 3.5 2.7 - - - +
511A ASP* 3.1 34.1 - - + +
513A VAL* 3.4 28.0 - - + -
515A ILE* 3.5 23.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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