Contacts of the strand formed by residues 29 - 40 (chain B) 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 THR 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B PRO* 3.8 6.3 - - - +
17B LEU* 3.0 46.8 + - + +
26B GLU* 5.8 2.7 - - - +
27B THR* 3.4 10.0 + - - +
28B LYS* 1.3 84.2 - - - +
30B GLY* 1.3 69.9 + - - +
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU 3.0 15.3 - - - -
16B PRO* 4.1 1.6 - - - -
17B LEU* 3.8 14.3 - - - +
29B THR* 1.3 83.8 + - - +
31B GLU* 1.3 61.9 + - - +
375B LEU* 3.8 24.0 - - - +
376B THR* 5.0 0.3 + - - -
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL 3.6 0.5 - - - +
14B ASN* 3.4 0.9 - - - -
15B LEU* 2.8 35.5 + - - +
17B LEU* 3.4 29.4 - - + +
30B GLY* 1.3 74.8 - - - +
32B THR* 1.3 62.6 + - - +
33B ARG* 3.6 21.2 + - + +
299B GLY 4.7 0.7 - - - +
300B GLY* 2.9 40.4 - - - +
302B LEU* 3.4 21.0 - - + +
375B LEU* 3.9 5.5 - - - +
376B THR* 3.6 13.6 - - + +
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.5 28.3 - - + -
13B VAL 3.0 11.7 - - - +
14B ASN* 2.6 20.4 + - - +
31B GLU* 1.3 70.8 - - - +
33B ARG* 1.3 76.3 + - - +
52B TRP* 3.7 16.8 + - - -
53B GLY* 3.8 14.1 - - - -
369B ASN* 3.7 3.1 - - - +
374B ASP* 3.5 4.4 - - - +
375B LEU* 2.8 28.0 + - - +
376B THR* 3.1 19.7 + - - +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.5 3.7 - - - +
13B VAL* 2.9 39.7 + - + +
15B LEU* 4.6 7.2 - - + -
31B GLU* 3.6 28.9 + - + +
32B THR* 1.3 93.2 + - - +
34B THR* 1.3 62.6 + - - +
35B VAL* 5.1 2.9 - - + -
49B GLU* 2.4 37.6 + - - +
50B THR* 3.3 30.2 + - - +
51B MSE 3.9 7.1 - - - +
52B TRP 3.3 8.1 - - - -
272B TYR* 5.8 1.4 - - - -
299B GLY 4.8 4.6 + - - -
300B GLY 3.1 12.5 + - - -
301B GLU* 3.6 18.6 + - - +
302B LEU* 3.1 33.5 - - + +
305B ALA* 4.3 4.0 - - - +
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Residues in contact with THR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.4 28.0 - - + -
11B TRP 3.2 5.6 - - - +
12B VAL* 4.3 0.9 - - - +
33B ARG* 1.3 73.6 - - - +
35B VAL* 1.3 64.2 + - - +
36B VAL* 4.3 10.2 + - + +
49B GLU* 3.1 5.2 - - - +
50B THR* 2.8 49.5 + - + +
51B MSE 3.7 1.2 + - - -
52B TRP 2.8 21.0 + - - -
53B GLY* 3.4 18.7 + - - -
56B VAL* 3.9 4.6 - - + +
57B ALA* 4.0 13.4 - - + +
60B VAL* 4.9 1.6 - - + -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.3 4.3 - - - +
11B TRP* 2.8 47.7 + - + +
13B VAL* 4.3 17.9 - - + -
15B LEU* 6.1 0.4 - - + -
33B ARG* 4.9 2.0 - - + -
34B THR* 1.3 77.6 - - - +
36B VAL* 1.3 66.1 + - - +
47B TRP* 3.8 30.3 - - + -
48B GLY 3.5 9.2 - - - +
49B GLU* 4.2 10.8 - - + -
304B ILE* 4.5 3.8 - - + -
334B ILE* 3.9 28.5 - - + -
362B LEU* 4.2 15.3 - - + -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.2 21.5 - - + -
9B ASP 3.4 7.9 - - - +
10B VAL* 4.3 7.0 - - + -
11B TRP* 4.5 0.2 - - - -
34B THR* 4.4 3.8 - - + -
35B VAL* 1.3 80.1 - - - +
37B ARG* 1.3 67.9 - - - +
38B VAL* 4.5 9.4 - - + -
46B GLY 3.7 0.5 - - - +
47B TRP* 3.4 9.9 - - - -
48B GLY 2.7 35.9 + - - +
60B VAL* 3.8 28.7 - - + -
99B ALA* 3.9 28.9 - - + +
100B VAL* 4.7 7.4 - - + -
103B ALA* 4.2 3.6 - - + +
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP 3.8 0.7 - - - +
8B VAL* 3.5 4.5 - - - -
9B ASP* 2.8 65.8 + - + +
11B TRP* 3.4 37.3 - - + -
36B VAL* 1.3 74.0 - - - +
38B VAL* 1.3 72.2 + - - +
39B ARG* 3.0 36.4 + - - +
45B GLU* 4.1 19.5 + - + -
46B GLY 3.3 8.1 - - - +
47B TRP* 3.4 28.5 - - + -
359B GLU* 3.5 23.8 + - - -
363B ARG* 4.7 8.3 - - - +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.5 42.0 - - + -
7B ASP 3.6 2.7 - - - -
8B VAL* 4.9 9.4 - - + -
36B VAL* 4.5 9.2 - - + -
37B ARG* 1.3 77.9 - - - +
39B ARG* 1.3 61.6 + - - +
40B THR* 4.8 5.4 - - + +
44B VAL 3.9 0.9 - - - +
45B GLU* 3.2 4.0 - - - -
46B GLY* 2.8 41.5 + - - +
72B PRO* 5.3 3.1 - - + -
100B VAL* 4.7 9.6 - - + +
103B ALA* 3.6 26.0 - - + +
104B CYS* 4.7 13.7 - - - -
107B ALA* 5.3 2.5 - - + -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.4 5.4 - - - +
6B THR* 2.7 39.1 + - - +
7B ASP* 2.9 41.4 + - + +
9B ASP* 4.8 1.5 + - - +
37B ARG* 3.0 47.2 + - - +
38B VAL* 1.3 75.2 - - - +
40B THR* 1.3 64.3 + - - +
43B GLY* 5.4 2.9 - - - +
44B VAL 3.8 2.7 - - - +
45B GLU* 3.2 27.7 + - + +
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 3.5 23.2 - - + +
4B LYS 3.0 15.0 - - - +
5B ILE* 4.5 4.9 - - + -
6B THR* 3.7 8.5 + - - +
38B VAL* 4.8 3.6 - - + +
39B ARG* 1.3 85.2 - - - +
41B ASP* 1.3 60.1 + - - +
42B SER* 3.0 25.3 + - - -
43B GLY* 3.2 10.9 + - - -
44B VAL* 2.8 28.9 + - + +
72B PRO* 4.2 18.2 - - + -
107B ALA* 4.8 9.9 - - + -
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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