Contacts of the strand formed by residues 2 - 10 (chain A) in PDB entry 2OV2
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 GLN 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 79.4 - - - +
3A ALA* 1.3 61.4 + - - +
49A LYS* 4.6 15.9 - - - +
50A PRO 4.1 3.5 + - - +
51A VAL* 4.0 25.4 - - + +
52A ASN* 2.8 24.2 + - - +
177A LEU* 3.5 36.9 + - + +
133D LYS* 6.4 0.7 - - + -
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Residues in contact with ALA 3 (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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1A MET 3.5 5.3 + - - +
2A GLN* 1.3 76.8 - - - +
4A ILE* 1.3 60.9 + - - +
51A VAL* 4.7 0.4 - - - -
52A ASN* 3.3 26.5 - - + +
177A LEU* 5.5 0.7 - - - +
133D LYS* 2.6 38.2 + - - +
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Residues in contact with ILE 4 (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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3A ALA* 1.3 78.5 - - - +
5A LYS* 1.3 70.3 + - - +
6A CYS* 4.5 0.2 - - + -
51A VAL* 4.0 13.7 - - + -
52A ASN 3.0 7.7 + - - +
53A LEU* 4.2 17.2 - - + +
54A GLY* 2.9 29.5 + - - +
76A ASP* 3.5 4.5 - - + -
77A VAL* 4.2 7.9 - - + -
172A ALA* 5.3 0.9 - - + +
173A ILE* 3.9 37.7 - - + -
176A VAL* 4.0 30.7 - - + -
177A LEU* 3.9 26.9 - - + -
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Residues in contact with LYS 5 (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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4A ILE* 1.3 71.6 - - - +
6A CYS* 1.3 58.4 + - - +
7A VAL* 3.9 4.3 - - + -
54A GLY* 3.8 3.4 - - - -
56A TRP* 3.5 53.1 - - + +
70A LEU 5.1 0.8 + - - -
71A SER 2.8 29.8 + - - -
73A PRO* 2.6 26.3 + - - +
74A GLN* 3.9 17.4 - - + +
75A THR* 3.6 12.5 - - - +
76A ASP* 2.9 43.3 + - - +
77A VAL* 3.2 8.0 + - - +
133D LYS* 5.0 0.2 - - - +
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Residues in contact with CYS 6 (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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4A ILE* 4.5 0.9 - - + -
5A LYS* 1.3 74.3 - - - +
7A VAL* 1.3 60.4 + - - +
8A VAL* 4.5 3.5 - - - +
53A LEU* 4.2 12.1 - - + -
54A GLY 2.9 13.9 + - - +
55A LEU* 3.5 22.3 - - + +
56A TRP* 3.0 24.6 + - - +
77A VAL* 3.3 24.5 - - + -
79A LEU* 3.8 34.3 - - - -
169A PHE* 4.9 2.5 - - - -
172A ALA* 4.8 7.0 - - + -
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Residues in contact with VAL 7 (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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5A LYS* 3.9 8.1 - - + -
6A CYS* 1.3 74.8 - - - +
8A VAL* 1.3 63.0 - - - +
9A VAL* 4.1 5.4 - - + -
56A TRP* 3.7 20.2 - - + +
58A THR* 4.0 22.7 - - + -
71A SER* 3.7 12.1 - - - +
72A TYR* 4.1 8.5 - - + -
75A THR* 3.3 27.1 - - + +
77A VAL 2.9 6.5 + - - -
78A PHE* 3.3 33.2 - - + -
79A LEU 3.0 24.6 + - - +
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Residues in contact with VAL 8 (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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6A CYS* 4.5 7.2 - - - +
7A VAL* 1.3 76.5 - - - +
9A VAL* 1.3 57.7 + - - +
16A LYS* 3.8 25.4 - - + +
19A LEU* 4.7 3.6 - - + -
20A LEU* 3.8 37.0 - - + -
55A LEU* 5.0 0.9 - - + -
56A TRP 2.8 15.2 + - - +
57A ASP* 4.8 1.3 - - - -
58A THR* 2.6 35.0 + - - -
79A LEU* 3.6 22.0 - - + +
81A CYS* 3.8 26.2 - - - -
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Residues in contact with VAL 9 (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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7A VAL* 4.1 17.7 - - + -
8A VAL* 1.3 78.0 - - - +
10A GLY* 1.3 59.8 + - - +
16A LYS* 3.4 11.7 - - - +
58A THR* 3.3 17.0 - - - +
68A ARG* 4.3 1.3 - - - -
72A TYR* 3.9 23.1 - - + +
78A PHE* 4.6 4.5 - - + -
79A LEU 3.0 9.5 + - - +
80A ILE* 3.9 18.8 - - + -
81A CYS* 3.0 26.0 + - - +
97A TRP* 3.9 19.3 - - + -
101A VAL* 3.9 23.3 - - + -
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Residues in contact with GLY 10 (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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9A VAL* 1.3 78.9 - - - +
11A ASP* 1.3 69.8 + - - +
14A VAL* 4.3 0.9 - - - -
16A LYS* 3.0 15.4 + - - +
59A ALA 4.8 0.2 - - - -
60A GLY* 3.2 13.3 - - - -
81A CYS 3.5 14.6 - - - -
97A TRP* 3.3 27.3 - - - -
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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