Contacts of the strand formed by residues 49 - 58 (chain F) 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 LYS 49 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B GLN* 5.7 7.2 - - - +
45F MET* 3.4 5.3 - - - -
46F VAL* 2.8 33.9 + - + +
47F ASP* 3.6 23.6 - - + +
48F GLY* 1.3 78.7 - - - +
50F PRO* 1.3 72.1 - - + +
51F VAL* 3.8 5.1 + - + +
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Residues in contact with PRO 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 4.4 25.8 - - + +
2F GLN* 4.1 14.9 + - - +
43F ASN* 6.1 5.6 - - + +
44F VAL 3.7 4.9 - - - +
45F MET* 3.2 24.4 - - + -
48F GLY 4.4 0.7 - - - +
49F LYS* 1.3 89.3 - - + +
51F VAL* 1.3 63.9 + - - +
38J GLN* 3.9 18.6 - - + -
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F GLN* 3.6 19.1 - - + +
4F ILE* 3.7 35.2 - - + -
43F ASN* 3.6 7.4 - - - +
44F VAL* 2.9 36.9 + - + +
46F VAL* 3.4 30.7 - - + -
49F LYS* 4.0 7.0 - - + +
50F PRO* 1.3 81.2 - - - +
52F ASN* 1.3 67.7 + - - +
53F LEU* 3.5 5.0 + - + +
173F ILE* 5.3 1.8 - - + -
177F LEU* 4.0 13.0 - - + -
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Residues in contact with ASN 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F GLN 3.0 15.5 + - - +
3F ALA* 3.3 13.3 - - + +
4F ILE 3.0 25.9 + - - +
41F SER* 4.1 15.2 - - - -
42F ALA 3.3 12.6 + - - -
43F ASN* 3.8 12.2 + - - +
51F VAL* 1.3 71.2 - - - +
53F LEU* 1.3 71.5 + - - +
54F GLY* 3.6 1.6 + - - -
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ILE* 3.9 27.1 - - + +
6F CYS* 4.7 7.0 - - + -
23F TYR* 3.8 34.3 - - + +
40F TYR 4.0 0.2 - - - +
41F SER* 3.3 5.2 - - - -
42F ALA* 3.0 42.6 + - + +
44F VAL* 4.1 16.4 - - + -
51F VAL* 3.5 6.8 + - + +
52F ASN* 1.3 74.4 + - - +
54F GLY* 1.3 59.7 + - - +
55F LEU* 4.0 25.3 + - + +
169F PHE* 4.9 5.4 - - + -
172F ALA* 6.1 2.9 - - + -
173F ILE* 4.3 21.5 - - + -
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Residues in contact with GLY 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ILE 2.9 16.3 + - - +
5F LYS* 3.8 0.6 - - - -
6F CYS* 2.9 31.9 + - - +
39F ASN* 4.9 1.3 - - - -
40F TYR 3.6 5.4 - - - -
41F SER* 4.7 2.7 - - - -
52F ASN* 3.6 3.6 + - - -
53F LEU* 1.3 73.0 - - - +
55F LEU* 1.3 61.3 + - - -
56F TRP* 3.6 14.0 - - - -
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F CYS* 3.4 18.4 - - + -
8F VAL* 5.6 0.2 - - + -
20F LEU* 3.9 22.7 - - + -
23F TYR* 4.9 3.6 - - + -
24F THR* 3.5 32.1 - - + -
39F ASN* 3.3 5.0 + - - +
40F TYR* 2.7 59.8 + - + +
41F SER 5.3 0.4 - - - +
42F ALA* 5.4 3.6 - - + -
53F LEU* 4.0 27.8 - - + +
54F GLY* 1.3 71.7 - - - -
56F TRP* 1.3 62.9 + - - +
57F ASP 3.8 1.9 + - - -
169F PHE* 3.8 28.5 - - + -
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Residues in contact with TRP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LYS* 3.5 51.6 - - + +
6F CYS 2.9 13.5 + - - +
7F VAL* 3.6 12.7 - - + -
8F VAL* 3.0 29.1 + - - +
37F PHE* 3.5 26.5 - + + -
38F ASP 3.8 4.9 - - - -
39F ASN* 3.3 20.7 - - + +
54F GLY* 3.6 19.5 + - - -
55F LEU* 1.3 75.3 - - - +
57F ASP* 1.3 61.3 + - - +
58F THR* 3.6 4.1 + - - +
70F LEU 5.1 0.2 - - - -
71F SER* 3.9 13.5 - - - +
36N PRO* 5.5 4.0 - - + -
39N TRP* 4.1 24.0 - + - -
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Residues in contact with ASP 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL 4.5 2.4 - - - +
16F LYS* 3.9 13.9 - - - +
17F THR* 2.5 39.3 + - - +
20F LEU* 3.4 29.0 - - + +
35F THR* 3.3 14.9 + - - +
37F PHE* 3.5 3.1 - - - -
38F ASP* 2.8 38.8 + - + +
40F TYR* 3.7 18.3 + - + -
55F LEU 3.8 0.8 + - - -
56F TRP* 1.3 69.5 - - - +
58F THR* 1.3 67.4 + - - +
202F MG 4.2 0.2 - - - -
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Residues in contact with THR 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 4.0 15.5 - - + -
8F VAL 2.9 24.5 + - - +
9F VAL* 3.6 14.9 - - + +
10F GLY 5.0 0.2 + - - -
16F LYS* 3.5 17.0 - - - -
35F THR* 3.9 11.8 - - - +
36F VAL 4.6 0.4 - - - -
37F PHE* 4.5 6.5 - - + -
56F TRP 4.0 8.7 - - - +
57F ASP* 1.3 79.7 + - - +
59F ALA* 1.3 64.5 + - - +
60F GLY 3.7 0.2 + - - -
68F ARG* 3.7 27.4 - - + +
71F SER* 3.9 22.4 - - - +
200F GCP 4.1 0.5 + - - -
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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