Contacts of the strand formed by residues 2 - 10 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D HIS* 5.6 5.8 + - + -
1G MET* 1.3 74.8 - - - +
3G ALA* 1.3 76.2 + - - +
50G PRO 4.3 3.5 + - - +
51G VAL* 3.4 18.1 - - + +
52G ASN 2.8 23.4 + - - -
177G LEU* 3.6 35.9 - - + +
16K ASN* 2.9 37.0 + - - +
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Residues in contact with ALA 3 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET 3.3 7.2 + - - +
2G GLN* 1.3 90.3 + - - +
4G ILE* 1.3 67.3 + - - +
52G ASN* 3.2 20.6 - - + +
76G ASP* 4.0 7.0 - - - +
176G VAL* 5.5 0.2 - - - +
16K ASN* 5.2 0.5 + - - -
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Residues in contact with ILE 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G GLN* 4.9 0.4 - - + -
3G ALA* 1.3 81.5 - - - +
5G LYS* 1.3 64.5 + - - +
6G CYS 3.9 0.2 - - - -
51G VAL* 3.8 24.0 - - + -
52G ASN 2.8 7.4 + - - +
53G LEU* 3.9 19.3 - - + -
54G GLY* 2.8 27.7 + - - -
76G ASP* 3.6 5.6 - - + -
77G VAL* 4.1 14.1 - - + -
172G ALA 5.3 1.1 - - - +
173G ILE* 3.9 39.0 - - + +
176G VAL* 4.0 29.6 - - + -
177G LEU* 4.1 17.5 - - + -
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Residues in contact with LYS 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 1.3 73.8 - - - +
6G CYS* 1.3 58.7 + - - +
7G VAL* 3.7 4.5 - - + -
54G GLY* 3.9 2.2 - - - -
56G TRP* 3.4 53.2 - - + +
70G LEU 5.2 0.8 + - - -
71G SER 2.7 29.2 + - - -
73G PRO* 2.6 27.0 + - - +
74G GLN* 3.6 17.3 - - + +
75G THR* 3.7 11.9 - - - +
76G ASP* 2.8 46.2 + - - +
77G VAL 3.1 8.5 + - - +
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Residues in contact with CYS 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LYS* 1.3 73.3 - - - +
7G VAL* 1.3 62.2 + - - +
8G VAL* 4.2 7.8 + - - +
53G LEU* 4.2 9.6 - - + -
54G GLY 3.0 16.5 + - - +
55G LEU* 3.5 16.5 - - + -
56G TRP* 2.9 25.8 + - - -
77G VAL* 3.2 26.0 - - + -
79G LEU* 3.8 35.4 - - - -
169G PHE* 4.9 2.7 - - - -
172G ALA* 4.8 6.5 - - + -
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Residues in contact with VAL 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 3.7 11.9 - - - -
6G CYS* 1.3 76.6 - - - +
8G VAL* 1.3 63.3 + - - +
9G VAL* 3.9 13.9 - - + -
56G TRP* 3.6 11.7 - - + +
58G THR* 4.0 15.5 - - + -
71G SER* 3.6 16.2 - - - +
72G TYR* 4.1 9.0 - - + -
75G THR* 3.3 27.4 - - + +
77G VAL 3.0 6.3 + - - -
78G PHE* 3.3 31.9 - - + -
79G LEU 3.0 23.7 + - - +
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Residues in contact with VAL 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G CYS* 4.2 10.1 - - - +
7G VAL* 1.3 75.0 - - - +
9G VAL* 1.3 58.6 + - - +
16G LYS* 4.0 21.5 - - + +
19G LEU* 4.4 9.0 - - + -
20G LEU* 3.9 32.1 - - + -
55G LEU* 5.5 0.4 - - + -
56G TRP 2.9 12.7 + - - +
57G ASP* 4.8 1.6 - - - -
58G THR* 2.6 36.2 + - - -
79G LEU* 3.5 24.0 - - + +
81G CYS* 3.6 28.0 - - - -
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Residues in contact with VAL 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 3.9 19.5 - - + -
8G VAL* 1.3 79.7 - - - +
10G GLY* 1.3 53.7 + - - +
16G LYS* 3.5 6.5 - - - -
58G THR* 3.5 12.8 - - - +
68G ARG* 4.5 0.4 - - - -
72G TYR* 3.8 22.7 - - + +
78G PHE* 4.5 7.0 - - + -
79G LEU 2.9 8.9 + - - +
80G ILE* 3.9 25.1 - - + -
81G CYS* 2.8 34.5 + - - +
97G TRP* 3.9 26.9 - - + -
101G VAL* 4.0 11.4 - - + -
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Residues in contact with GLY 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 1.3 77.9 - - - +
11G ASP* 1.3 70.2 + - - +
14G VAL* 4.3 0.9 - - - -
16G LYS* 2.9 17.9 + - - +
58G THR* 4.8 0.6 + - - -
60G GLY* 3.1 13.3 - - - -
81G CYS 3.6 14.1 - - - -
97G TRP* 3.3 25.2 - - - -
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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