Contacts of the helix formed by residues 8 - 19 (chain A) in PDB entry 2OX6
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 ASN 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLY 3.8 1.9 + - - +
7A LEU* 1.3 73.7 - - - +
9A ALA* 1.3 56.6 + - - +
10A ILE* 3.2 8.8 + - - +
11A GLU* 3.0 47.0 + - - +
12A MET* 2.8 35.3 + - - +
133B SER* 4.4 8.3 - - - -
134B LEU 2.9 27.4 + - - +
135B ILE* 4.7 4.8 - - - +
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Residues in contact with ALA 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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8A ASN* 1.3 77.1 - - - +
10A ILE* 1.3 68.1 + - + +
12A MET* 3.4 1.9 + - - +
13A SER* 3.1 23.0 + - - -
40A TRP 3.2 27.1 - - - +
41A GLU* 3.6 15.7 - - - +
42A ASN 4.3 0.2 - - - -
43A ALA* 3.4 32.1 - - + +
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Residues in contact with ILE 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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8A ASN* 3.2 5.9 + - - +
9A ALA* 1.3 79.9 - - + +
11A GLU* 1.3 59.2 + - - +
13A SER* 3.2 5.3 + - - -
14A TYR* 2.9 49.6 + - + +
41A GLU 5.2 1.6 - - - +
89B VAL* 3.8 14.4 - - + -
114B ASN* 4.9 5.4 - - + +
134B LEU* 3.5 43.3 - - + +
136B ASN* 3.5 46.9 - - + +
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Residues in contact with GLU 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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6A GLY 4.0 3.5 - - - +
7A LEU* 3.5 15.9 - - + -
8A ASN* 3.0 41.0 + - - +
10A ILE* 1.3 73.2 - - - +
12A MET* 1.3 60.4 + - - +
14A TYR 3.3 0.2 + - - -
15A LEU* 2.8 33.5 + - - +
118B TRP* 3.9 18.8 - - + -
121B LYS* 3.3 32.1 + - + +
133B SER* 3.2 13.7 + - - -
134B LEU* 2.8 39.7 + - + -
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Residues in contact with MET 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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7A LEU* 3.8 33.0 - - + +
8A ASN 2.8 24.0 + - - +
9A ALA 3.9 2.7 - - - +
11A GLU* 1.3 74.3 - - - +
13A SER* 1.3 55.4 + - - +
15A LEU* 3.9 4.7 - - - +
16A ARG* 3.0 29.3 + - - +
40A TRP* 3.4 45.7 + - + +
41A GLU* 4.0 3.3 - - - +
47A ALA* 4.1 20.2 - - + -
51A ALA 4.2 12.6 - - - +
52A GLN* 3.9 16.2 - - - -
55A LEU* 3.7 33.0 - - + +
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Residues in contact with SER 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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9A ALA 3.1 14.1 + - - -
10A ILE* 3.2 10.1 + - - -
12A MET* 1.3 76.0 - - - +
14A TYR* 1.3 66.2 + - - +
16A ARG* 3.4 4.7 + - - +
17A GLN* 2.9 57.3 + - - +
41A GLU* 3.2 36.8 + - - +
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Residues in contact with TYR 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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10A ILE* 2.9 38.2 + - + +
11A GLU* 4.4 1.1 - - - +
13A SER* 1.3 81.7 - - - +
15A LEU* 1.3 60.8 + - - +
17A GLN* 3.8 17.2 + - - +
18A SER* 2.9 29.1 + - - -
20B SER* 3.4 36.9 + - - -
111B GLU* 3.6 22.9 - - - +
114B ASN* 2.9 49.9 + - + +
115B THR* 4.2 8.1 - - - -
118B TRP* 3.8 27.7 - - + -
134B LEU* 5.5 0.4 - - + -
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Residues in contact with LEU 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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7A LEU* 3.7 27.4 - - + -
11A GLU 2.8 17.6 + - - +
12A MET* 3.9 4.9 - - - +
14A TYR* 1.3 73.1 - - - +
16A ARG* 1.3 66.8 + - - +
18A SER* 2.8 23.6 + - - +
19A LEU* 3.3 13.5 + - + +
55A LEU* 3.5 35.2 - - + +
56A LEU* 4.0 15.7 - - + +
59A ASP* 3.9 32.8 - - + +
118B TRP* 3.6 27.4 - - + -
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Residues in contact with ARG 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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12A MET 3.0 18.5 + - - +
13A SER* 3.4 11.3 + - - +
15A LEU* 1.3 77.0 - - - +
17A GLN* 1.3 82.8 + - - +
19A LEU* 3.0 17.9 + - - +
20A SER 3.4 7.3 + - - -
21A LEU* 2.9 43.6 + - + +
22A SER* 3.6 10.5 - - - +
23A ALA* 3.6 20.0 - - - +
26A VAL* 3.4 32.5 - - + -
38A LEU* 5.6 2.4 - - - +
41A GLU* 2.6 41.4 + - - +
55A LEU* 4.4 9.8 - - + +
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Residues in contact with GLN 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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13A SER* 2.9 43.6 + - - +
14A TYR* 3.5 22.8 + - - +
15A LEU 3.3 0.2 - - - -
16A ARG* 1.3 99.2 - - - +
18A SER* 1.3 60.3 + - - +
20A SER* 3.1 14.6 + - - +
21A LEU 4.9 3.1 - - - +
17B GLN* 3.5 17.9 - - - +
20B SER* 3.4 43.8 - - - +
111B GLU* 5.6 0.9 - - - +
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Residues in contact with SER 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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14A TYR 2.9 16.5 + - - -
15A LEU* 2.8 21.0 + - - +
17A GLN* 1.3 75.8 - - - +
19A LEU* 1.3 61.1 + - - +
20A SER* 3.4 1.5 + - - -
59A ASP* 4.3 1.2 + - - -
115A THR* 3.4 11.4 - - - +
119A ARG* 3.0 32.2 + - - -
17B GLN 5.1 2.2 - - - -
18B SER* 5.5 9.8 - - - +
20B SER* 5.3 0.9 + - - -
118B TRP* 4.1 19.5 + - - -
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Residues in contact with LEU 19 (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 LEU* 3.4 20.6 - - + +
16A ARG* 3.0 9.2 + - - +
18A SER* 1.3 78.2 - - - +
20A SER* 1.3 70.9 + - - +
21A LEU* 3.2 24.2 + - + +
55A LEU* 3.9 26.2 - - + +
58A ILE* 3.9 19.1 - - + -
59A ASP* 3.6 30.3 - - + +
62A ILE* 3.7 25.6 - - + -
111A GLU 4.1 1.9 - - - +
112A LEU* 3.6 17.4 - - + +
115A THR* 3.3 10.4 + - - -
119A ARG* 3.9 4.7 - - - +
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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