Contacts of the strand formed by residues 5 - 17 (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 ILE 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 1.3 73.5 - - - +
6B THR* 1.3 61.1 + - - +
7B ASP 3.5 22.9 - - - +
8B VAL* 3.9 12.6 - - + -
38B VAL* 3.5 27.4 - - + -
39B ARG 3.4 6.1 - - - +
40B THR* 4.1 2.2 - - + +
67B LEU* 3.4 40.4 - - + +
68B ILE* 3.5 6.5 - - + +
69B GLY* 2.8 28.1 + - - -
70B THR* 2.8 24.2 + - - +
71B SER 4.9 0.2 - - - +
72B PRO* 4.2 16.8 - - + -
104B CYS* 4.4 12.1 - - - -
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Residues in contact with THR 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LYS* 4.8 0.9 - - + -
5B ILE* 1.3 76.3 - - - +
7B ASP* 1.3 77.6 + - - +
39B ARG* 2.7 30.4 + - - +
40B THR 3.7 1.3 + - - +
41B ASP* 3.4 37.7 - - + +
68B ILE* 3.4 21.8 - - - +
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Residues in contact with ASP 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.5 4.0 - - - +
6B THR* 1.3 104.2 + - - +
8B VAL* 1.3 68.8 + - - +
9B ASP* 3.7 20.3 - - - +
37B ARG 4.3 0.4 - - - -
38B VAL* 3.6 0.7 - - - -
39B ARG* 2.9 54.9 + - + -
68B ILE* 3.9 3.1 - - - -
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.9 9.2 - - + -
7B ASP* 1.3 81.0 - - - +
9B ASP* 1.3 65.2 + - - +
10B VAL* 4.3 4.1 + - + +
36B VAL* 4.2 20.6 - - + -
37B ARG 3.5 4.3 - - - +
38B VAL* 4.9 6.7 - - + -
60B VAL* 4.6 10.8 - - + -
61B ARG* 6.0 0.5 - - - +
64B ALA* 3.9 29.5 - - + +
67B LEU* 3.9 41.5 - - + -
68B ILE* 4.0 10.5 - - + +
100B VAL* 5.4 0.2 - - + -
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Residues in contact with ASP 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP* 3.7 22.7 - - - +
8B VAL* 1.3 79.2 + - - +
10B VAL* 1.3 64.5 + - - +
11B TRP* 3.6 25.7 - - + -
36B VAL* 3.4 4.3 - - - +
37B ARG* 2.8 66.5 + - - +
39B ARG* 4.8 0.9 + - - +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.8 5.8 - - + +
9B ASP* 1.3 81.5 - - - +
11B TRP* 1.3 74.1 + - - +
34B THR* 3.4 28.9 - - + -
35B VAL 3.3 4.7 - - - +
36B VAL* 4.3 4.5 - - + -
57B ALA* 3.8 21.3 - - + -
60B VAL* 3.5 28.5 - - + -
61B ARG* 2.9 48.1 + - + +
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Residues in contact with TRP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 3.6 19.3 - - + -
10B VAL* 1.3 80.0 + - - +
12B VAL* 1.3 63.6 + - - +
13B VAL* 4.1 4.3 - - + -
34B THR* 3.2 8.7 - - - +
35B VAL* 2.8 53.4 + - + +
37B ARG* 3.4 48.9 - - + -
47B TRP* 3.4 26.7 - + - -
61B ARG* 4.6 1.8 - - - +
359B GLU* 6.0 0.7 - - + -
362B LEU* 3.6 41.5 - - + +
363B ARG* 3.2 36.3 - - - +
366B ALA* 4.3 16.2 - - + -
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 1.3 78.3 - - - +
13B VAL* 1.3 60.8 + - - +
32B THR* 3.5 26.9 - - + -
33B ARG 3.5 3.1 - - - +
34B THR* 4.3 1.6 - - - +
53B GLY* 3.5 21.3 - - - -
54B ALA* 4.2 3.4 - - - +
57B ALA* 3.6 28.0 - - + -
61B ARG* 5.2 6.7 - - - +
366B ALA* 3.3 21.6 - - - +
369B ASN* 3.3 29.3 - - - +
374B ASP* 3.6 4.0 - - - +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 4.4 1.3 - - + -
12B VAL* 1.3 83.4 - - - +
14B ASN* 1.3 64.7 + - - +
15B LEU* 3.7 27.8 - - + -
31B GLU 3.6 0.5 - - - +
32B THR* 3.0 6.5 - - - +
33B ARG* 2.9 47.9 + - + +
35B VAL* 4.3 10.8 - - + -
334B ILE* 5.5 2.7 - - + -
362B LEU* 3.8 29.4 - - + +
365B TYR* 3.4 16.4 - - + +
366B ALA* 3.8 17.9 - - + +
369B ASN* 4.0 0.9 - - - -
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Residues in contact with ASN 14 (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* 1.3 71.9 - - - +
15B LEU* 1.3 59.8 + - - +
16B PRO* 4.4 0.2 - - - +
31B GLU 3.4 3.8 - - - -
32B THR* 2.6 26.9 + - - -
365B TYR* 3.1 32.2 + - - +
368B VAL* 3.8 19.6 + - + +
369B ASN* 2.8 31.3 + - - +
372B ASP* 3.8 15.0 + - - +
373B GLY 3.0 21.0 + - - -
375B LEU* 3.7 20.9 - - + +
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Residues in contact with LEU 15 (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* 3.7 25.3 - - + -
14B ASN* 1.3 76.2 - - - +
16B PRO* 1.3 66.4 - - + +
17B LEU* 5.2 0.2 - - - -
30B GLY* 3.0 3.1 - - - -
31B GLU* 2.8 37.1 + - - +
33B ARG* 4.6 5.6 - - + -
35B VAL* 6.1 0.4 - - + -
49B GLU* 6.0 0.4 - - - +
302B LEU* 3.4 35.4 - - + -
332B ASP 3.9 15.5 - - - +
333B ASP* 4.2 17.5 - - - +
334B ILE* 4.7 10.1 - - + -
365B TYR* 3.5 38.4 - - + -
375B LEU* 6.0 0.2 - - - -
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Residues in contact with PRO 16 (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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14B ASN 4.4 0.4 - - - +
15B LEU* 1.3 94.8 - - + +
17B LEU* 1.3 66.1 + - - +
18B VAL* 5.2 3.1 - - + -
28B LYS* 6.1 5.4 - - + -
29B THR 3.8 8.5 - - - +
30B GLY* 4.1 0.9 - - - -
302B LEU* 5.4 1.6 - - - +
330B HIS* 4.4 0.5 - - - -
331B ALA* 3.6 38.8 + - + -
332B ASP* 3.9 21.7 - - + +
365B TYR* 4.1 15.7 - - + +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU 4.9 0.4 - - - +
16B PRO* 1.3 80.1 - - - +
18B VAL* 1.3 66.6 + - - +
26B GLU* 4.9 2.1 - - - +
29B THR* 3.0 40.5 + - + +
30B GLY* 4.1 14.8 - - - +
31B GLU* 3.4 46.7 - - + +
302B LEU* 4.2 13.7 - - + -
326B MSE 5.4 1.6 - - + +
329B LEU* 3.3 33.0 - - + +
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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