Contacts of the helix formed by residues 583 - 592 (chain B) in PDB entry 5VR6
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 ASN 583 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535B TYR* 4.6 1.3 - - - -
582B GLN* 1.3 77.5 - - - +
584B SER* 1.3 59.0 + - - +
585B LYS* 3.2 12.4 + - - +
586B ASP* 2.7 50.4 + - - +
587B PHE* 2.9 25.1 + - - +
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Residues in contact with SER 584 (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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491B TRP* 4.2 12.2 - - - -
535B TYR* 3.6 38.4 - - - -
582B GLN 3.9 0.6 + - - -
583B ASN* 1.3 74.3 - - - +
585B LYS* 1.3 58.9 + - - +
587B PHE* 3.4 7.9 - - - +
588B VAL* 2.9 34.8 + - - +
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Residues in contact with LYS 585 (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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583B ASN* 3.2 9.9 + - - +
584B SER* 1.3 80.4 + - - +
586B ASP* 1.3 67.6 + - - +
588B VAL* 3.4 4.7 + - - +
589B GLN* 3.2 22.2 + - - +
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Residues in contact with ASP 586 (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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582B GLN* 3.5 20.7 - - + +
583B ASN* 2.7 37.9 + - - +
585B LYS* 1.3 74.9 - - - +
587B PHE* 1.3 66.1 + - - +
589B GLN* 3.4 7.3 + - - +
590B MET* 3.0 24.1 + - - +
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Residues in contact with PHE 587 (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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491B TRP* 5.0 2.0 - + - -
494B TRP* 4.1 9.4 - + - -
535B TYR* 3.5 36.6 - + + +
538B TYR* 4.1 15.0 - + - -
539B ILE* 4.1 13.5 - - + -
567B SER* 3.6 35.4 - - - -
570B GLU* 3.5 29.6 - - + -
571B ALA 4.5 0.7 - - - -
582B GLN* 4.1 9.5 + - + +
583B ASN 2.9 18.5 + - - +
584B SER 3.4 5.8 - - - +
586B ASP* 1.3 75.9 - - - +
588B VAL* 1.3 63.3 + - + +
590B MET* 3.2 19.2 + - + +
591B VAL* 2.9 46.4 + - + +
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Residues in contact with VAL 588 (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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491B TRP* 4.0 25.4 - - + -
494B TRP* 4.2 24.0 - - + +
584B SER 2.9 20.9 + - - +
585B LYS* 3.9 5.8 - - - +
586B ASP 3.4 0.4 - - - -
587B PHE* 1.3 77.1 - - + +
589B GLN* 1.3 64.0 + - - +
591B VAL* 3.4 8.4 + - - +
592B ARG* 3.2 29.3 + - + +
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Residues in contact with GLN 589 (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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585B LYS 3.2 13.4 + - - +
586B ASP* 3.7 11.0 - - - +
587B PHE 3.3 0.2 - - - -
588B VAL* 1.3 76.5 - - - +
590B MET* 1.3 62.4 + - - +
592B ARG* 3.2 31.0 + - - +
593B LYS* 4.1 16.6 + - - +
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Residues in contact with MET 590 (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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634A THR* 3.4 29.8 - - - +
635A LEU* 4.3 10.1 - - - -
566B ALA 5.4 1.1 - - - +
570B GLU* 3.4 37.0 - - + +
582B GLN* 3.7 10.8 - - - +
586B ASP 3.0 16.8 + - - +
587B PHE* 3.5 13.2 - - + +
589B GLN* 1.3 77.5 - - - +
591B VAL* 1.3 82.5 + - + +
593B LYS* 2.9 38.3 + - + +
594B ILE* 4.1 19.1 + - - +
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Residues in contact with VAL 591 (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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494B TRP* 4.1 7.4 - - + -
566B ALA* 3.5 25.7 - - + +
567B SER* 3.7 16.8 - - - +
587B PHE* 2.9 43.3 + - + +
588B VAL* 3.8 7.4 - - - +
589B GLN 3.3 0.4 - - - -
590B MET* 1.3 96.3 - - + +
592B ARG* 1.3 60.7 + - - +
593B LYS 3.1 1.2 + - - -
594B ILE* 3.3 13.1 + - - +
704B SO4 3.2 30.4 + - - +
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Residues in contact with ARG 592 (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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588B VAL* 3.2 25.3 + - + +
589B GLN* 3.5 18.6 + - - +
590B MET 3.1 0.6 - - - -
591B VAL* 1.3 75.1 - - - +
593B LYS* 1.3 60.9 + - + +
594B ILE 3.4 2.0 - - - +
704B SO4 3.3 14.4 - - - +
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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
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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