Contacts of the helix formed by residues 581 - 599 (chain B) in PDB entry 6VW1
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 VAL 581 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B THR* 3.0 26.1 + - - +
232B GLU* 3.8 29.4 - - + +
233B ILE* 3.6 30.5 - - + -
520B LEU* 4.0 8.7 - - + +
580B ASN* 1.3 77.2 + - - +
582B ARG* 1.3 69.5 + - - +
583B PRO* 3.3 3.1 - - - -
584B LEU* 3.1 10.5 + - + +
585B LEU* 3.0 46.2 + - + +
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Residues in contact with ARG 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLU* 5.3 0.6 + - - -
580B ASN* 3.5 19.5 + - - +
581B VAL* 1.3 83.6 - - + +
583B PRO* 1.3 68.8 - - + +
585B LEU* 4.4 7.0 - - + -
586B ASN* 2.9 48.7 + - - +
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Residues in contact with PRO 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B PHE* 3.5 31.0 - - + +
524B GLN* 3.8 24.9 - - + +
527B GLU* 4.1 29.6 - - + +
539B LEU* 3.9 6.4 - - + +
580B ASN* 3.8 21.3 - - + +
581B VAL 3.5 3.6 - - - -
582B ARG* 1.3 93.3 - - + +
584B LEU* 1.3 56.1 + - - +
586B ASN* 3.3 3.5 + - + +
587B TYR* 2.9 28.2 + - - +
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Residues in contact with LEU 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ILE* 5.1 4.0 - - + -
236B LEU* 4.7 7.2 - - + -
446B ILE* 4.7 2.5 - - + -
447B VAL* 5.2 2.2 - - + -
450B LEU* 4.1 19.1 - - + -
519B THR* 3.7 24.0 - - + +
520B LEU* 4.7 11.2 - - + -
523B PHE* 3.6 43.4 - - + +
580B ASN 5.2 1.5 + - - +
581B VAL* 3.1 17.5 + - + +
583B PRO* 1.3 78.3 - - - +
585B LEU* 1.3 82.9 + - + +
587B TYR* 3.1 5.6 + - - +
588B PHE* 3.0 41.3 + - + -
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Residues in contact with LEU 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU* 4.0 29.6 - - + +
233B ILE* 4.8 6.5 - - - -
236B LEU* 4.4 17.3 - - + -
581B VAL* 3.0 43.0 + - + +
582B ARG* 4.0 6.5 - - + +
584B LEU* 1.3 95.5 - - + +
586B ASN* 1.3 62.0 + - - +
588B PHE* 3.3 3.4 + - - +
589B GLU* 2.9 36.4 + - - +
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Residues in contact with ASN 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLU* 4.7 9.2 + - - +
539B LEU* 5.3 10.1 + - + +
540B HIS* 5.8 0.3 + - - -
582B ARG* 2.9 41.7 + - - +
583B PRO* 3.7 5.2 - - + +
585B LEU* 1.3 77.3 - - - +
587B TYR* 1.3 66.7 + - - +
588B PHE 3.4 0.3 + - - -
589B GLU* 3.5 20.9 + - - +
590B PRO* 4.2 3.5 - - - +
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Residues in contact with TYR 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 3.8 13.1 + - + +
414B THR* 5.7 0.5 - - - +
438B PHE* 3.6 13.3 - - - -
439B LEU* 3.6 26.5 - - + +
442B GLN* 3.0 30.9 + - + -
446B ILE* 5.3 0.2 - - + -
523B PHE* 3.3 38.4 - + + -
526B GLN* 5.5 5.2 - - + -
539B LEU* 4.1 21.0 - - + +
540B HIS* 3.5 39.3 + - + +
583B PRO 2.9 14.0 + - - +
584B LEU 3.1 9.4 + - - +
586B ASN* 1.3 79.7 - - - +
588B PHE* 1.3 86.2 + + - +
589B GLU 3.8 0.2 + - - -
590B PRO* 3.9 6.2 - - - +
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Residues in contact with PHE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 3.9 19.9 - - + +
439B LEU* 3.5 31.9 - - + -
442B GLN* 3.9 13.0 - - + -
443B ALA* 3.5 24.5 - - + -
446B ILE* 4.2 9.6 - - + -
447B VAL* 3.6 26.9 - - + -
523B PHE* 3.9 14.8 - + - -
584B LEU* 3.0 34.5 + - + +
585B LEU 3.3 2.7 + - - +
587B TYR* 1.3 100.6 - + - +
589B GLU* 1.3 64.7 + - - +
590B PRO* 3.4 3.8 - - - -
591B LEU* 3.3 12.7 + - + +
592B PHE* 2.9 21.3 + - - +
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Residues in contact with GLU 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B LEU* 2.9 21.9 + - - +
586B ASN* 3.8 14.9 - - - +
587B TYR 3.5 0.4 - - - -
588B PHE* 1.3 76.5 - - - +
590B PRO* 1.3 69.7 - - + +
592B PHE* 3.0 36.7 + - - +
593B THR* 3.0 26.8 + - + +
596B LYS* 5.3 1.2 + - - -
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Residues in contact with PRO 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ILE* 4.9 12.1 - - + +
439B LEU* 3.8 18.2 - - + -
538B PRO* 5.7 3.1 - - + -
540B HIS* 4.4 15.0 - - + +
586B ASN 4.2 3.6 - - - +
587B TYR 3.9 10.8 - - - +
588B PHE 3.5 4.0 - - - -
589B GLU* 1.3 93.9 - - + +
591B LEU* 1.3 61.2 + - - +
593B THR* 2.9 22.8 + - - +
594B TRP* 3.0 12.7 + - - +
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Residues in contact with LEU 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 5.1 5.4 - - + -
240B LEU* 4.8 0.4 - - + -
436B ILE* 4.0 11.2 - - + +
439B LEU* 3.5 38.0 - - + +
440B LEU* 3.8 32.1 - - + +
443B ALA* 3.5 20.6 - - + -
588B PHE* 3.3 14.9 + - + +
590B PRO* 1.3 80.0 - - - +
592B PHE* 1.3 57.5 + - - +
594B TRP* 3.7 23.4 - - + +
595B LEU* 2.8 54.0 + - + +
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Residues in contact with PHE 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PRO* 4.2 14.1 - - + -
236B LEU* 3.5 49.3 - - + +
239B HIS* 3.6 26.5 - + + -
588B PHE 2.9 14.0 + - - +
589B GLU* 3.0 31.6 + - - +
591B LEU* 1.3 76.8 - - - +
593B THR* 1.3 56.9 + - - +
595B LEU* 3.3 4.7 + - - +
596B LYS* 3.0 57.7 + - + +
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Residues in contact with THR 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B GLU* 3.0 29.5 + - + +
590B PRO* 2.9 19.8 + - + +
592B PHE* 1.3 75.1 - - - +
594B TRP* 1.3 62.3 + - - +
596B LYS* 3.2 22.0 + - - +
597B ASP* 3.0 22.7 + - - +
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Residues in contact with TRP 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B TYR* 3.6 22.4 - + - -
284B PRO* 3.5 38.1 - - + -
285B PHE* 4.0 20.6 - + - -
436B ILE* 3.8 31.4 - - + -
590B PRO 3.0 17.6 + - - +
591B LEU* 3.7 15.5 - - + +
593B THR* 1.3 78.0 + - - +
595B LEU* 1.3 82.3 + - + +
597B ASP* 3.3 9.2 + - + +
598B GLN* 2.9 58.0 + - + +
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Residues in contact with LEU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 4.4 10.8 - - + -
239B HIS* 4.0 14.1 - - + +
240B LEU* 3.8 33.4 - - + +
243B TYR* 3.6 35.4 - - + -
440B LEU* 5.0 0.7 - - + -
591B LEU* 2.8 48.1 + - + +
592B PHE* 3.6 4.3 - - - +
594B TRP* 1.3 95.7 - - + +
596B LYS* 1.3 65.5 + - - +
598B GLN* 3.1 1.5 + - - +
599B ASN* 2.9 32.2 + - - +
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Residues in contact with LYS 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B HIS* 3.4 37.4 - - + +
589B GLU* 5.3 1.2 + - - -
592B PHE* 3.0 49.1 + - + +
593B THR* 3.2 21.4 + - - +
595B LEU* 1.3 76.5 - - - +
597B ASP* 1.3 63.5 + - - +
599B ASN* 3.7 6.8 + - - +
600B LYS* 4.0 7.3 + - - +
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Residues in contact with ASP 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B THR 3.0 13.7 + - - +
594B TRP* 3.6 11.9 - - + +
595B LEU 3.1 0.4 - - - -
596B LYS* 1.3 78.2 - - - +
598B GLN* 1.3 64.1 + - + +
599B ASN 3.2 1.0 + - - -
600B LYS* 3.3 38.9 + - - +
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Residues in contact with GLN 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B TYR* 4.3 15.4 - - + -
247B LYS* 6.0 0.2 - - - -
285B PHE* 6.1 1.0 - - - -
594B TRP* 2.9 59.1 + - + +
595B LEU* 3.1 8.5 + - - +
597B ASP* 1.3 79.1 + - - +
599B ASN* 1.3 64.2 + - - +
600B LYS* 3.3 17.5 + - - +
601B ASN* 4.6 1.9 + - - +
602B SER* 4.6 4.9 + - - -
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Residues in contact with ASN 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B HIS* 3.1 44.3 + - + +
242B ALA* 3.7 14.0 - - - +
243B TYR* 3.8 22.9 + - - +
595B LEU* 2.9 21.1 + - - +
596B LYS 3.7 4.7 + - - +
597B ASP 3.2 0.8 - - - -
598B GLN* 1.3 80.1 - - - +
600B LYS* 1.3 63.9 + - - +
601B ASN 3.2 2.7 - - - -
602B SER* 3.0 31.5 + - - +
604B VAL* 4.0 16.2 - - + +
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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