Contacts of the strand formed by residues 7 - 18 (chain A) in PDB entry 3OV6
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 HIS 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLU* 1.3 92.0 - - + +
8A VAL* 1.3 73.3 + - - +
9A SER* 4.6 7.0 + - - -
33A ASP* 4.3 7.3 - - - +
103A GLU* 2.8 33.8 + - + -
104A LEU 3.0 21.1 - - - +
105A HIS* 3.5 23.8 - + + +
106A SER 4.9 0.4 - - - +
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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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7A HIS* 1.3 81.0 - - - +
9A SER* 1.3 72.1 + - - +
32A LEU* 3.5 30.3 - - + -
33A ASP* 3.8 17.0 - - - +
103A GLU* 3.4 2.8 - - - -
104A LEU* 2.8 36.3 + - + +
171A LEU* 3.6 13.9 - - + +
175A LEU* 3.8 26.7 - - + -
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Residues in contact with SER 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 HIS* 4.6 6.7 + - - -
8A VAL* 1.3 79.3 - - - +
10A PHE* 1.3 61.0 + - - +
11A HIS* 4.1 18.6 - - - -
31A TRP 4.2 0.2 - - - -
32A LEU* 3.4 10.4 - - - +
33A ASP* 2.8 45.8 + - - -
102A CYS 3.5 11.0 - - - -
103A GLU* 4.3 15.5 - - - -
113A PHE* 5.2 1.1 - - - -
171A LEU* 3.8 4.9 - - - -
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Residues in contact with PHE 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 SER* 1.3 73.9 - - - +
11A HIS* 1.3 63.6 + - - +
12A VAL* 4.1 8.5 - - + -
30A GLY* 4.1 11.2 - - - -
31A TRP 3.0 28.0 - - - -
32A LEU* 4.0 2.2 - - - -
37A THR* 3.5 22.2 - - - -
38A HIS* 3.9 10.8 - - - -
101A GLY* 3.5 2.1 - - - -
102A CYS 3.0 32.4 + - - +
113A PHE* 4.3 0.2 - - - -
167A CYS* 3.6 8.1 - - - -
170A PHE* 3.7 30.1 - + - -
171A LEU* 3.6 25.6 - - + +
174A LEU* 3.7 21.1 - - + -
1105A MK0 3.9 39.9 - - + -
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Residues in contact with HIS 11 (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 SER* 4.1 19.7 + - - -
10A PHE* 1.3 80.9 - - - +
12A VAL* 1.3 66.8 - - - +
13A ILE* 4.0 22.6 + - + +
29A SER 3.9 0.3 - - - +
30A GLY* 3.6 2.3 - - - -
31A TRP* 2.9 51.8 + - + +
33A ASP 4.5 11.7 + - - -
99A LYS* 4.4 20.6 - - + -
100A ALA 3.3 12.6 - - - +
101A GLY* 4.3 0.4 - - - -
113A PHE* 3.9 28.1 - + + -
1063A TYR* 5.9 1.0 + - - -
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Residues in contact with VAL 12 (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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10A PHE* 4.1 18.6 - - + -
11A HIS* 1.3 76.4 - - - +
13A ILE* 1.3 66.0 + - - +
14A GLN* 3.6 22.4 + - - +
29A SER 3.3 4.3 - - - +
70A PHE* 5.0 0.4 - - + -
98A VAL 3.8 0.9 - - - +
99A LYS* 3.6 3.6 - - - -
100A ALA 2.7 34.5 + - - +
1105A MK0 3.6 80.1 - - + -
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Residues in contact with ILE 13 (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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11A HIS* 4.0 21.5 - - + +
12A VAL* 1.3 79.3 - - - +
14A GLN* 1.3 66.4 + - - +
15A ILE* 3.4 27.1 - - + -
28A GLY* 2.9 25.8 - - - -
29A SER* 2.9 21.6 + - - +
31A TRP* 3.7 17.5 - - + +
98A VAL 3.6 1.8 - - - +
99A LYS* 4.8 3.6 - - + -
1054A LEU 3.9 9.4 - - - +
1055A SER* 2.9 30.7 - - - +
1056A PHE* 3.6 31.0 - - + +
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Residues in contact with GLN 14 (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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12A VAL* 3.6 8.1 - - - +
13A ILE* 1.3 78.1 - - - +
15A ILE* 1.3 66.5 + - - +
16A PHE* 3.5 27.8 - - + -
27A GLN 3.3 4.5 - - - +
73A TYR* 2.9 37.4 + - - -
96A VAL 4.5 0.2 - - - -
97A GLN* 3.3 5.9 - - - -
98A VAL* 2.9 48.8 + - + +
1056A PHE* 3.7 1.7 - - - -
1105A MK0 3.0 58.5 - - + +
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Residues in contact with ILE 15 (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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13A ILE* 3.4 30.5 - - + -
14A GLN* 1.3 77.1 - - - +
16A PHE* 1.3 64.7 + - - +
17A SER* 4.2 15.6 + - - +
25A ARG* 4.6 0.8 - - - +
26A GLY* 3.4 3.8 - - - -
27A GLN* 2.8 53.5 + - + +
28A GLY* 5.5 0.2 - - - -
95A GLU* 4.8 2.5 - - - +
96A VAL 3.5 6.5 - - - +
97A GLN* 4.6 1.6 - - + -
1033A SER* 4.2 10.1 - - - +
1054A LEU* 3.7 25.1 - - + +
1056A PHE* 3.9 6.7 - - + -
1062A PHE* 3.7 36.6 - - + -
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Residues in contact with PHE 16 (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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14A GLN* 3.5 44.9 - - + -
15A ILE* 1.3 77.9 - - - +
17A SER* 1.3 62.4 + - - +
18A PHE* 3.6 29.8 + + + -
25A ARG 3.5 4.7 - - - +
26A GLY* 4.4 8.7 - - - -
74A LEU* 3.8 26.7 - - + -
77A LEU* 4.9 22.2 - - + -
78A THR* 5.3 9.9 - - + -
95A GLU* 3.5 5.9 - - - +
96A VAL* 2.8 56.0 + - + +
98A VAL* 4.5 8.1 - - + -
1105A MK0 4.2 9.2 - - + -
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Residues in contact with SER 17 (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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15A ILE* 4.2 5.9 - - - +
16A PHE* 1.3 73.3 - - - +
18A PHE* 1.3 62.5 + - - +
19A VAL* 3.7 8.7 + - - +
23A TRP* 5.1 0.2 - - - -
24A ALA* 3.0 4.5 - - - -
25A ARG* 2.8 63.1 + - - +
94A PHE 4.0 4.5 - - - -
95A GLU* 3.2 25.6 + - - +
1033A SER* 3.5 9.2 + - - -
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Residues in contact with PHE 18 (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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16A PHE* 3.6 35.7 - + + -
17A SER* 1.3 69.8 - - - +
19A VAL* 1.3 64.4 + - - +
20A ASN* 3.3 13.6 - - - +
21A GLN* 5.2 3.8 - - - -
23A TRP 3.7 2.7 - - - -
24A ALA* 3.3 27.1 - - + -
77A LEU* 5.9 0.4 - - + -
78A THR* 5.0 15.3 - - + -
81A ILE* 3.7 33.0 - - + -
82A GLN* 5.1 14.4 - - + -
92A TYR 4.0 1.7 - - - +
93A PRO* 3.4 2.0 - - - +
94A PHE* 3.1 73.6 + + + +
96A VAL* 4.9 4.5 - - + -
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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