Contacts of the strand formed by residues 37 - 46 (chain B) in PDB entry 2OV2
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 PHE 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B THR* 3.8 0.7 - - - -
36B VAL* 1.3 83.6 - - - +
38B ASP* 1.3 86.8 + - - +
39B ASN* 3.9 14.8 - - + -
56B TRP* 3.4 37.2 - + + -
57B ASP 3.3 20.0 - - - -
58B THR* 4.6 4.3 - - + -
67B LEU* 4.1 12.8 - - + -
71B SER* 3.3 24.7 - - - -
21J VAL* 4.1 12.8 - - + -
23J THR* 2.8 52.8 + - - +
36J PRO* 4.1 6.1 - - + -
39J TRP* 3.8 20.0 - + + -
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Residues in contact with ASP 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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17B THR* 6.2 0.2 - - - +
35B THR* 3.7 17.4 + - + +
36B VAL 4.7 0.7 + - - -
37B PHE* 1.3 90.2 + - - +
39B ASN* 1.3 60.4 + - - +
40B TYR* 3.5 27.2 + - + +
57B ASP* 2.9 37.9 + - + +
19J HIS* 2.8 18.7 + - - +
21J VAL 3.2 4.3 - - - +
22J HIS* 2.4 39.8 + - - -
23J THR 4.8 0.5 - - - +
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Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.9 6.7 - - + -
38B ASP* 1.3 75.1 - - - +
40B TYR* 1.3 66.4 + - - +
41B SER* 5.5 0.3 - - - -
54B GLY* 5.4 0.7 - - - -
55B LEU 3.3 9.9 + - - +
56B TRP* 3.2 48.5 - - - +
19J HIS* 3.5 6.2 - - - -
20J ARG* 2.8 47.1 + - - +
21J VAL* 2.9 32.3 + - + +
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.7 13.9 - - - +
20B LEU* 3.9 28.0 - - + -
21B ILE* 4.0 17.7 - - + +
24B THR* 5.3 0.4 - - + -
38B ASP* 3.5 17.6 - - + +
39B ASN* 1.3 78.6 - - - +
41B SER* 1.3 61.0 + - - +
54B GLY* 3.7 1.2 - - - -
55B LEU* 2.8 57.5 + - + +
57B ASP* 2.8 37.2 + - + -
17J PHE* 3.8 26.9 - + + -
18J GLU 3.2 10.1 - - - +
19J HIS* 3.6 38.9 - + - -
20J ARG* 4.9 0.2 - - - -
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN* 5.5 0.4 - - - -
40B TYR* 1.3 77.8 - - - +
42B ALA* 1.3 61.0 + - - +
52B ASN* 4.3 11.2 - - - -
53B LEU 3.4 9.2 - - - -
54B GLY* 5.1 2.5 - - - -
55B LEU* 5.6 1.3 - - - -
16J ASN 3.5 1.6 - - - +
17J PHE* 3.3 7.3 - - - -
18J GLU* 2.8 59.3 + - - +
20J ARG* 3.7 20.4 - - - +
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Residues in contact with ALA 42 (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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24B THR* 4.3 17.3 - - + -
41B SER* 1.3 77.0 - - - +
43B ASN* 1.3 61.3 + - - +
52B ASN* 3.4 3.9 - - - +
53B LEU* 2.7 51.1 + - + +
55B LEU* 5.2 1.5 - - + +
14J PRO* 4.2 20.9 - - + -
15J SER 3.5 12.3 - - - +
16J ASN 4.1 2.9 - - - -
17J PHE* 4.8 3.4 - - + -
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Residues in contact with ASN 43 (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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1B MET* 4.3 9.3 - - - +
42B ALA* 1.3 74.4 - - - +
44B VAL* 1.3 64.6 + - - +
50B PRO* 5.9 4.5 - - + -
51B VAL 3.5 12.9 + - - +
52B ASN* 3.7 19.3 + - - +
13J ALA 4.3 0.5 - - - +
14J PRO* 3.4 5.2 - - - +
15J SER* 2.9 46.3 + - - +
16J ASN* 3.5 27.9 + - - +
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Residues in contact with VAL 44 (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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23B TYR* 3.6 21.8 - - - +
42B ALA 4.2 0.6 + - - -
43B ASN* 1.3 79.0 - - - +
45B MET* 1.3 64.7 + - - +
46B VAL* 3.4 29.2 - - + -
50B PRO* 3.4 3.6 - - - +
51B VAL* 2.7 40.5 + - + +
53B LEU* 4.4 11.7 - - + -
173B ILE* 4.0 9.9 - - + -
11J ILE* 3.8 10.1 - - + -
12J SER* 3.6 22.7 - - - +
14J PRO* 3.9 12.1 - - + -
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Residues in contact with MET 45 (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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44B VAL* 1.3 74.1 - - - +
46B VAL* 1.3 61.8 + - - +
47B ASP 4.1 0.7 - - - -
48B GLY* 3.3 39.3 - - - +
49B LYS 3.4 1.3 - - - +
50B PRO* 3.8 28.5 - - + -
10J GLU 3.6 1.4 - - - +
11J ILE* 3.3 4.9 - - - -
12J SER* 2.9 48.9 + - - +
38N GLN* 6.3 3.4 - - + -
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Residues in contact with VAL 46 (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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2B GLN* 6.4 0.2 - - - -
44B VAL* 3.4 26.7 - - + -
45B MET* 1.3 70.8 - - - +
47B ASP* 1.3 74.7 + - + +
48B GLY 3.1 0.4 - - - -
49B LYS* 2.7 29.6 + - + +
51B VAL* 3.8 19.7 - - + -
173B ILE* 3.8 25.1 - - + -
174B ARG* 4.0 20.9 - - - +
177B LEU* 4.3 17.7 - - + -
10J GLU 3.6 2.2 - - - -
11J ILE* 4.1 8.1 - - + +
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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