Contacts of the strand formed by residues 3 - 10 (chain E) 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 ALA 3 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E GLN* 1.3 75.4 - - - +
4E ILE* 1.3 68.4 + - - +
52E ASN* 3.3 17.5 - - + +
76E ASP* 4.2 5.8 - - - +
176E VAL* 5.5 0.5 - - - +
177E LEU* 5.6 2.3 - - - +
16I ASN* 4.9 7.6 - - - +
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Residues in contact with ILE 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ALA* 1.3 79.8 - - - +
5E LYS* 1.3 67.8 + - - +
51E VAL* 3.8 22.0 - - + -
52E ASN 2.9 9.7 + - - +
53E LEU* 3.8 20.4 - - + -
54E GLY* 2.8 32.7 + - - +
76E ASP* 3.6 3.6 - - + -
77E VAL* 4.2 8.1 - - + -
172E ALA* 5.4 1.1 - - + +
173E ILE* 3.9 32.3 - - + +
176E VAL* 4.1 29.4 - - + -
177E LEU* 3.9 24.7 - - + -
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Residues in contact with LYS 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ALA 4.3 0.2 - - - -
4E ILE* 1.3 70.6 - - - +
6E CYS* 1.3 58.2 + - - +
7E VAL* 3.8 4.3 - - + -
54E GLY* 3.9 3.1 - - - -
56E TRP* 3.5 52.9 - - + +
70E LEU 5.0 1.2 + - - -
71E SER 2.6 31.8 + - - -
73E PRO* 2.8 19.2 + - - +
74E GLN* 3.7 21.3 - - + +
75E THR* 3.7 13.6 - - - +
76E ASP* 2.7 44.0 + - - +
77E VAL 3.1 8.7 + - - +
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Residues in contact with CYS 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 3.7 0.6 + - + -
5E LYS* 1.3 73.1 - - - +
7E VAL* 1.3 62.7 + - - +
8E VAL* 4.3 6.0 - - - +
53E LEU* 4.2 10.8 - - + -
54E GLY 3.0 14.7 + - - +
55E LEU* 3.4 20.4 - - + +
56E TRP* 2.9 25.8 + - - +
77E VAL* 3.2 25.6 - - + -
79E LEU* 3.9 35.0 - - - -
169E PHE* 5.0 1.6 - - - -
172E ALA* 4.9 6.1 - - + -
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Residues in contact with VAL 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 3.8 8.1 - - - -
6E CYS* 1.3 76.0 - - - +
8E VAL* 1.3 63.2 + - - +
9E VAL* 4.0 14.6 - - + -
56E TRP* 3.7 18.4 - - + +
58E THR* 4.0 16.4 - - + -
71E SER* 3.8 14.8 - - - +
72E TYR* 4.1 9.0 - - + -
75E THR* 3.4 24.7 - - + +
77E VAL 3.0 6.1 + - - -
78E PHE* 3.3 31.5 - - + -
79E LEU 2.9 24.8 + - - +
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Residues in contact with VAL 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E CYS* 4.3 8.5 - - - +
7E VAL* 1.3 76.3 - - - +
9E VAL* 1.3 59.6 + - - +
16E LYS* 3.8 25.2 - - + +
19E LEU* 5.0 2.9 - - + -
20E LEU* 4.0 33.0 - - + -
55E LEU* 5.4 0.2 - - + -
56E TRP 2.9 15.0 + - - +
57E ASP* 4.8 1.3 - - - -
58E THR* 2.5 35.3 + - - +
79E LEU* 3.5 24.5 - - + +
81E CYS* 3.7 26.7 - - - -
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Residues in contact with VAL 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E VAL* 4.0 18.6 - - + -
8E VAL* 1.3 78.6 - - - +
10E GLY* 1.3 58.6 + - - +
16E LYS* 3.5 6.3 - - - -
58E THR* 3.6 13.5 - - + +
68E ARG* 4.4 1.3 - - - -
72E TYR* 3.9 22.9 - - + +
78E PHE* 4.6 5.8 - - + -
79E LEU 2.9 9.2 + - - +
80E ILE* 3.5 26.0 - - + -
81E CYS* 2.9 28.2 + - - +
97E TRP* 4.1 23.8 - - + -
101E VAL* 4.1 10.5 - - + -
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Residues in contact with GLY 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 1.3 78.4 - - - +
11E ASP* 1.3 69.5 + - - +
14E VAL* 4.4 0.9 - - - -
16E LYS* 3.1 17.2 + - - +
58E THR* 4.9 0.4 + - - -
59E ALA 4.7 0.2 - - - +
60E GLY* 3.1 13.0 - - - -
81E CYS 3.5 15.9 - - - -
97E TRP* 3.2 24.9 - - - -
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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