Contacts of the strand formed by residues 77 - 82 (chain A) in PDB entry 1WXV
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 CYS 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A THR 3.8 2.5 + - - +
10A VAL* 3.4 12.4 - - + +
11A THR* 3.1 22.2 + - - -
56A PHE* 4.4 17.5 - - + -
72A GLY 4.3 8.7 - - - -
73A ILE* 4.5 1.1 - - + -
74A GLN* 3.1 49.3 + - - +
76A GLY* 1.3 82.4 - - - +
78A ARG* 1.3 67.4 + - - +
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Residues in contact with ARG 78 (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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11A THR* 3.7 21.5 + - + +
13A THR* 5.9 1.6 - - - +
18A LYS* 4.0 32.7 - - + +
56A PHE* 3.9 14.5 - - - -
77A CYS* 1.3 79.1 - - - +
79A VAL* 1.3 64.3 + - - +
80A MET 4.2 0.5 + - - -
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Residues in contact with VAL 79 (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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10A VAL* 3.3 23.6 - - + -
11A THR* 2.8 13.1 + - - +
12A VAL* 3.4 10.8 - - + -
13A THR* 3.0 26.6 + - - -
37A LEU* 4.9 5.6 - - + -
54A LEU* 3.3 32.8 - - + -
55A ILE 3.7 15.0 - - - +
56A PHE* 4.0 16.8 - - + -
61A LEU* 4.5 8.3 - - + -
73A ILE* 4.1 16.4 - - + -
78A ARG* 1.3 76.3 - - - +
80A MET* 1.3 62.4 + - - +
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Residues in contact with MET 80 (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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13A THR* 4.1 12.8 - - + +
53A LYS 3.5 0.9 - - - +
54A LEU* 3.6 1.9 - - - -
55A ILE* 2.8 69.9 + - + +
78A ARG 4.2 0.8 + - - -
79A VAL* 1.3 73.6 - - - +
81A LEU* 1.3 64.5 + - - +
82A ILE* 4.0 23.1 - - + -
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Residues in contact with LEU 81 (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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12A VAL* 3.4 22.2 - - + -
13A THR* 2.6 33.2 + - - +
14A HIS* 3.4 32.6 - - + +
41A VAL* 3.5 30.7 - - + -
45A ILE* 3.6 8.3 - - + -
47A VAL* 5.5 0.7 - - + -
52A GLN* 3.1 28.3 - - + +
53A LYS 3.2 28.7 - - - +
54A LEU* 3.4 12.3 - - + +
79A VAL 3.9 0.2 + - - -
80A MET* 1.3 76.0 - - - +
82A ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 82 (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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14A HIS* 4.1 1.8 - - - -
51A PHE 3.4 1.6 - - - +
52A GLN 3.4 0.9 - - - -
53A LYS* 2.7 60.1 + - + +
55A ILE* 3.3 28.5 - - + -
80A MET* 4.0 22.7 - - + -
81A LEU* 1.3 77.1 - - - +
83A GLY* 1.3 61.7 + - - +
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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