Contacts of the helix formed by residues 592 - 598 (chain A) in PDB entry 5WRV
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 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A PHE* 3.9 3.0 + - - -
591A PHE* 1.3 67.3 - - - +
593A LEU* 1.3 59.0 + - - +
594A ALA* 3.3 4.3 + - - +
595A LEU* 3.1 22.7 + - + +
702A GOL 2.8 30.2 + - - +
86B TYR* 2.5 30.1 + - - -
89B TYR* 4.4 8.0 - - - +
90B ARG* 3.8 13.0 + - - -
117B GLN* 2.9 23.4 - - - +
207B GOL 5.6 6.7 + - - -
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Residues in contact with LEU 593 (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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591A PHE* 3.0 19.2 + - + +
592A ASP* 1.3 69.1 - - - +
594A ALA* 1.3 65.0 + - - +
595A LEU 3.1 2.2 - - - -
596A ASN* 3.0 39.1 + - - +
597A HIS* 3.5 9.5 + - - +
702A GOL 3.7 16.2 - - - -
113B GLU* 3.7 16.6 - - - +
117B GLN* 3.1 2.4 - - - +
143B TYR* 4.1 15.7 - - + +
146B GLU* 3.7 20.6 - - + -
147B ARG* 3.5 47.6 - - + +
150B ASN* 4.5 2.9 - - - +
203B NA 3.6 13.0 - - - -
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Residues in contact with ALA 594 (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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592A ASP* 3.3 6.0 - - - +
593A LEU* 1.3 77.3 - - - +
595A LEU* 1.3 58.0 + - - +
597A HIS* 2.9 34.6 + - - +
598A VAL* 3.6 1.0 + - - +
82B PHE* 3.5 15.7 - - + -
86B TYR* 3.9 19.1 - - + -
113B GLU* 3.8 1.7 - - - +
114B LEU* 4.0 22.7 - - + +
117B GLN* 2.9 24.3 - - - +
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Residues in contact with LEU 595 (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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592A ASP* 3.1 21.0 + - + +
593A LEU 3.1 0.4 - - - -
594A ALA* 1.3 75.5 - - - +
596A ASN* 1.3 61.8 + - - +
598A VAL* 3.2 25.9 + - + +
702A GOL 4.1 8.1 - - - +
56B ILE* 4.5 12.3 - - + +
57B GLN* 4.1 14.0 + - - +
86B TYR* 3.3 33.1 - - + +
90B ARG* 4.3 11.0 - - - +
204B ACT 3.7 40.0 - - + +
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Residues in contact with ASN 596 (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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593A LEU* 3.0 21.6 + - - +
595A LEU* 1.3 76.5 - - - +
597A HIS* 1.3 61.1 + - - +
598A VAL 3.4 2.6 + - - +
599A ALA* 5.3 2.8 - - - +
702A GOL 3.0 46.0 - - - -
143B TYR* 3.5 41.7 + - + +
204B ACT 4.4 15.2 - - - +
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Residues in contact with HIS 597 (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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593A LEU* 3.5 18.7 + - - +
594A ALA* 2.9 12.9 + - - +
596A ASN* 1.3 80.1 + - - +
598A VAL* 1.3 60.0 + - - +
599A ALA* 3.1 8.4 + - - +
82B PHE* 3.9 4.0 - - + -
109B ASP* 5.2 1.7 + - + +
110B LYS* 2.8 63.1 + - + +
113B GLU* 2.9 44.7 + - + +
141B ASP* 4.2 17.0 - - + -
143B TYR* 4.7 12.5 - + - -
147B ARG* 4.4 1.6 - - - -
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Residues in contact with VAL 598 (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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594A ALA 3.7 10.5 - - - +
595A LEU* 3.2 24.3 + - + +
596A ASN 3.4 1.8 - - - +
597A HIS* 1.3 73.1 - - - +
599A ALA* 1.3 59.6 + - - +
53B VAL* 3.9 22.5 - - + +
56B ILE* 3.7 45.8 - - + -
57B GLN* 2.9 33.6 + - - +
82B PHE* 3.8 19.1 - - + -
83B GLU* 5.2 2.7 - - + -
86B TYR* 4.3 9.9 - - + -
206B GOL 4.6 2.1 + - - -
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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