Contacts of the strand formed by residues 31 - 40 (chain A) in PDB entry 2OQH
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 GLU 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A VAL 3.7 0.5 - - - +
14A ASN* 3.1 5.1 - - - +
15A LEU* 2.8 40.8 + - + +
17A LEU* 3.5 27.4 - - + +
30A GLY* 1.3 75.2 - - - +
32A THR* 1.3 73.4 + - - +
33A ARG* 3.5 15.3 + - + +
300A GLY* 2.6 43.3 - - - +
302A LEU* 3.5 19.5 - - + +
326A MSE 6.0 0.2 - - - +
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Residues in contact with THR 32 (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* 3.7 16.2 - - + -
13A VAL 3.2 9.9 - - - +
14A ASN* 2.7 23.1 + - - +
31A GLU* 1.3 76.6 - - - +
33A ARG* 1.3 75.9 + - - +
52A TRP* 3.6 16.0 + - - -
53A GLY* 3.7 22.9 - - - +
369A ASN* 4.0 4.1 + - - +
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Residues in contact with ARG 33 (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* 3.5 2.5 - - - +
13A VAL* 2.8 46.1 + - + +
15A LEU* 5.5 0.2 - - + -
31A GLU* 3.5 26.4 - - + +
32A THR* 1.3 88.1 - - - +
34A THR* 1.3 58.7 + - - +
35A VAL* 4.1 0.4 - - + -
49A GLU* 2.7 37.7 + - + +
50A THR* 3.1 32.2 + - - +
51A MSE 3.6 13.5 - - - +
52A TRP 3.4 7.6 - - - +
272A TYR* 4.9 3.2 - - - +
299A GLY 3.0 27.7 + - - -
300A GLY 3.3 12.2 + - - -
301A GLU* 3.5 18.8 + - - +
302A LEU* 3.8 14.4 - - + -
305A ALA* 3.9 8.3 - - - +
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Residues in contact with THR 34 (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 VAL* 3.4 29.8 - - + -
11A TRP 3.4 4.7 - - - +
12A VAL* 4.0 2.8 - - - +
33A ARG* 1.3 72.6 - - - +
35A VAL* 1.3 63.8 + - - +
36A VAL* 4.3 9.0 - - + +
48A GLY 4.0 0.2 - - - +
49A GLU* 3.3 2.9 - - - +
50A THR* 2.9 50.2 + - + +
51A MSE 4.3 0.2 - - - -
52A TRP 2.7 19.6 + - - -
53A GLY* 3.4 19.1 + - - -
56A VAL* 3.9 4.2 - - + +
57A ALA* 3.8 12.3 + - - +
60A VAL* 4.8 2.0 - - + -
99A ALA* 5.1 0.2 - - - +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP 3.8 0.3 - - - +
10A VAL* 3.4 4.2 - - - +
11A TRP* 2.8 39.6 + - + +
13A VAL* 4.2 18.2 - - + -
33A ARG* 5.2 0.2 - - + -
34A THR* 1.3 77.5 - - - +
36A VAL* 1.3 65.4 + - - +
47A TRP* 3.7 31.9 - - + -
48A GLY 3.3 11.7 - - - +
49A GLU* 4.6 12.3 - - + -
304A ILE* 4.4 4.5 - - + -
334A ILE* 3.8 28.9 - - + -
362A LEU* 4.1 15.5 - - + -
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Residues in contact with VAL 36 (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 VAL* 4.1 22.4 - - + -
9A ASP 3.3 8.7 - - - +
10A VAL* 4.1 9.6 - - + -
11A TRP* 4.8 0.2 - - - -
34A THR* 4.3 5.2 - - + -
35A VAL* 1.3 79.0 - - - +
37A ARG* 1.3 67.3 + - - +
38A VAL* 4.3 10.1 - - + -
46A GLY 3.7 0.2 - - - +
47A TRP* 3.3 10.4 - - - -
48A GLY 2.8 34.0 + - - +
60A VAL* 4.0 22.9 - - + -
99A ALA* 3.9 30.1 - - + +
100A VAL* 4.7 7.6 - - + -
103A ALA* 4.3 3.1 - - + +
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Residues in contact with ARG 37 (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 ASP 3.5 1.6 - - - +
8A VAL* 3.4 5.7 - - - -
9A ASP* 2.9 59.4 + - + +
11A TRP* 3.6 37.3 - - + -
36A VAL* 1.3 75.9 - - - +
38A VAL* 1.3 70.5 + - - +
39A ARG* 3.3 29.9 + - - +
45A GLU* 3.5 22.5 + - + +
46A GLY 3.2 8.5 - - - +
47A TRP* 3.4 28.6 - - + +
359A GLU* 3.9 26.9 + - - -
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Residues in contact with VAL 38 (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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5A ILE* 3.7 40.4 - - + -
7A ASP 3.5 2.5 - - - -
8A VAL* 4.9 9.4 - - + -
36A VAL* 4.4 8.3 - - + -
37A ARG* 1.3 77.9 - - - +
39A ARG* 1.3 62.9 + - - +
40A THR* 4.6 6.6 - - + +
44A VAL 3.8 0.9 - - - +
45A GLU* 3.2 5.2 - - - -
46A GLY 2.7 39.5 + - - +
67A LEU* 5.8 0.2 - - + -
72A PRO* 5.1 3.4 - - + -
100A VAL* 4.7 7.6 - - + +
103A ALA* 3.5 30.5 - - + +
104A CYS* 4.7 12.8 - - - -
107A ALA* 5.0 3.0 - - + +
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Residues in contact with ARG 39 (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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5A ILE* 3.3 5.5 - - - +
6A THR* 2.6 41.5 + - - +
7A ASP* 2.7 48.0 + - + +
9A ASP* 5.1 0.2 + - - -
37A ARG* 3.3 39.9 + - - +
38A VAL* 1.3 72.5 - - - +
40A THR* 1.3 63.5 + - - +
43A GLY* 5.4 5.0 + - - +
44A VAL 3.9 2.5 - - - +
45A GLU* 2.4 35.1 + - + +
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Residues in contact with THR 40 (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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3A LEU* 3.4 19.8 - - + +
4A LYS 3.1 12.8 - - - +
5A ILE* 4.6 2.9 - - - -
6A THR* 3.8 4.5 - - - -
38A VAL* 4.6 11.2 - - + +
39A ARG* 1.3 82.9 - - - +
41A ASP* 1.3 53.5 + - - +
42A SER* 2.6 34.4 + - - -
43A GLY* 2.8 16.6 + - - -
44A VAL* 2.8 30.4 + - + +
72A PRO* 4.3 20.2 - - + -
107A ALA* 4.7 7.2 - - + -
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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