Contacts of the strand formed by residues 36 - 41 (chain B) in PDB entry 2OHW
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 VAL 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B PHE* 3.9 29.4 - - + -
31B SER* 3.8 9.0 - - - +
32B LEU 3.4 16.8 - - - +
33B ARG* 3.1 16.2 + - - +
35B ARG* 1.3 78.6 - - - +
37B VAL* 1.3 62.4 + - - +
38B LEU 3.7 21.8 - - - +
39B ALA* 4.5 0.7 - - + -
106B VAL* 4.1 13.9 - - + -
107B ILE 3.7 3.8 - - - -
108B ALA* 4.5 0.7 - - - +
113B VAL* 3.9 3.1 - - - +
115B ARG* 3.7 11.8 + - - +
118B ILE* 3.5 40.7 - - + +
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Residues in contact with VAL 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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35B ARG 4.0 9.0 - - - +
36B VAL* 1.3 75.4 - - - +
38B LEU* 1.3 64.7 + - - +
57B GLU* 3.3 37.2 - - + +
61B SER* 3.7 11.9 - - - +
64B VAL* 4.0 22.7 - - + -
107B ILE* 2.8 19.5 + - + +
109B ALA* 4.1 9.0 - - + +
113B VAL* 4.3 9.4 - - + -
115B ARG* 3.6 26.8 + - - +
117B LEU 4.3 1.7 - - - +
118B ILE* 3.8 16.9 - - - +
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Residues in contact with LEU 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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36B VAL* 3.7 5.1 - - - +
37B VAL* 1.3 83.3 - - - +
39B ALA* 1.3 62.1 + - - +
40B LEU* 3.7 21.3 - - + -
53B GLU* 3.8 11.7 - - + +
54B ALA* 3.5 34.3 - - + +
57B GLU* 4.1 17.7 - - + +
105B ILE* 5.4 0.2 - - - +
106B VAL* 3.4 1.9 - - - -
107B ILE* 2.8 42.0 + - + +
117B LEU 5.5 1.1 - - - +
118B ILE* 3.5 23.8 - - - +
119B TYR* 4.4 3.4 - - - +
120B ILE* 4.4 17.3 - - + -
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Residues in contact with ALA 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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14B MET* 4.1 14.2 - - + +
28B PHE* 4.5 8.3 - - + -
36B VAL* 4.5 4.0 - - + -
38B LEU* 1.3 75.6 - - - +
40B LEU* 1.3 69.5 + - - +
44B GLN* 4.4 2.6 - - - +
103B LEU* 4.0 25.1 - - + -
105B ILE 3.3 10.3 - - - +
106B VAL* 4.2 6.1 - - + -
118B ILE* 2.9 18.0 + - + +
119B TYR* 4.0 13.0 - - - +
120B ILE* 4.6 1.7 + - - +
125B TYR* 5.4 1.0 - - - -
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Residues in contact with LEU 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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38B LEU* 3.7 27.6 - - + -
39B ALA* 1.3 81.3 - - - +
41B THR* 1.3 55.1 + - - +
44B GLN* 3.4 15.0 - - + +
45B VAL* 4.0 19.5 - - + +
51B TYR* 3.9 16.2 - - + -
54B ALA* 4.4 4.7 - - + -
80B TYR* 3.6 37.7 - - + +
103B LEU* 3.5 6.8 - - - +
104B GLY 2.7 28.9 + - - -
105B ILE* 2.9 24.8 + - + +
107B ILE* 5.9 0.2 - - + -
120B ILE* 4.0 13.7 - - + -
125B TYR* 6.0 0.2 - - - -
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Residues in contact with THR 41 (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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40B LEU* 1.3 77.0 - - - +
42B LYS* 1.3 64.0 + - - +
43B GLY 3.4 1.7 + - - -
44B GLN* 3.0 23.8 + - - +
45B VAL* 2.9 20.8 + - - +
102B PRO 3.4 11.2 - - - +
103B LEU* 4.1 7.0 - - + +
104B GLY 3.6 0.7 - - - -
125B TYR* 3.7 29.6 - - + -
128B SER* 2.7 29.7 + - - +
129B VAL* 3.8 26.0 - - + -
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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