Contacts of the strand formed by residues 3 - 10 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H MET 3.4 7.0 + - - +
2H GLN* 1.3 90.2 + - - +
4H ILE* 1.3 65.6 + - - +
51H VAL* 4.7 0.2 - - - -
52H ASN* 3.2 20.6 - - + +
76H ASP* 3.7 9.4 - - - +
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Residues in contact with ILE 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H ALA* 1.3 78.0 - - - +
5H LYS* 1.3 66.7 + - - +
6H CYS 4.3 0.2 - - - +
51H VAL* 3.8 17.0 - - + -
52H ASN 2.8 9.8 + - - +
53H LEU* 3.7 19.2 - - + +
54H GLY* 2.8 32.9 + - - +
76H ASP* 3.6 4.3 - - + -
77H VAL* 4.1 9.4 - - + -
172H ALA 5.2 0.4 - - - +
173H ILE* 3.8 37.5 - - + -
176H VAL* 4.0 31.0 - - + -
177H LEU* 3.9 24.5 - - + -
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Residues in contact with LYS 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ALA 4.2 0.2 - - - -
4H ILE* 1.3 72.7 - - - +
6H CYS* 1.3 59.0 + - - +
7H VAL* 3.8 4.7 - - + -
54H GLY* 3.8 4.3 - - - -
56H TRP* 3.6 54.1 - - + +
70H LEU 5.1 1.0 + - - -
71H SER 2.9 27.9 + - - -
73H PRO* 2.8 24.9 + - - +
74H GLN* 3.7 21.5 - - + +
75H THR* 3.7 11.6 - - - +
76H ASP* 2.8 42.9 + - - +
77H VAL 3.2 7.8 + - - +
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Residues in contact with CYS 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ILE* 3.8 0.6 + - + -
5H LYS* 1.3 73.5 - - - +
7H VAL* 1.3 61.2 + - - +
8H VAL* 4.2 5.8 + - - +
53H LEU* 4.4 9.2 - - + -
54H GLY 2.9 15.3 + - - +
55H LEU* 3.5 21.2 - - + -
56H TRP* 2.9 26.0 + - - -
77H VAL* 3.3 24.9 - - + -
79H LEU* 3.8 35.0 - - - -
169H PHE* 4.8 3.6 - - - -
172H ALA* 4.9 5.2 - - + -
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Residues in contact with VAL 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LYS* 3.8 12.1 - - + -
6H CYS* 1.3 78.0 - - - +
8H VAL* 1.3 64.0 + - - +
9H VAL* 4.2 4.3 - - + -
56H TRP* 3.7 11.4 - - + +
58H THR* 4.1 22.7 - - + -
71H SER* 3.7 17.0 - - - +
72H TYR* 4.1 12.6 - - + -
75H THR* 3.2 26.2 - - + +
77H VAL 3.0 6.7 + - - -
78H PHE* 3.4 29.8 - - + -
79H LEU 3.0 24.3 + - - +
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Residues in contact with VAL 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H CYS* 4.4 7.4 - - - +
7H VAL* 1.3 75.2 - - - +
9H VAL* 1.3 57.6 + - - +
16H LYS* 3.7 26.8 - - + +
19H LEU* 4.7 2.9 - - + -
20H LEU* 3.9 31.6 - - + -
56H TRP 3.0 12.8 + - - +
57H ASP* 4.9 1.8 - - - +
58H THR* 2.5 35.2 + - - -
79H LEU* 3.5 26.2 - - + +
81H CYS* 3.6 27.6 - - - -
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Residues in contact with VAL 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H VAL* 4.0 8.5 + - + -
8H VAL* 1.3 78.6 - - - +
10H GLY* 1.3 54.5 + - - +
16H LYS* 3.4 7.5 - - - +
58H THR* 3.7 12.6 - - - +
68H ARG* 4.4 1.6 - - - -
72H TYR* 3.7 33.4 - - + +
78H PHE* 4.7 4.3 - - + -
79H LEU 2.9 9.3 + - - +
80H ILE* 3.5 29.4 - - + -
81H CYS* 2.8 35.3 + - - +
97H TRP* 4.0 20.4 - - + -
101H VAL* 4.0 15.5 - - + -
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Residues in contact with GLY 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 1.3 78.6 - - - +
11H ASP* 1.3 70.1 + - - +
14H VAL* 4.5 0.7 - - - -
16H LYS* 3.0 15.0 + - - +
60H GLY* 3.2 11.4 - - - -
81H CYS 3.5 13.7 - - - -
97H TRP* 3.2 28.0 - - - -
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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