Contacts of the strand formed by residues 36 - 41 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.8 32.8 - - + -
31A SER* 4.0 8.5 - - - +
32A LEU 3.5 15.9 - - - +
33A ARG* 3.1 16.1 + - - +
35A ARG* 1.3 78.1 - - - +
37A VAL* 1.3 61.4 + - - +
38A LEU 3.7 23.1 - - - +
39A ALA* 4.5 0.9 - - + +
106A VAL* 4.1 9.9 - - + -
107A ILE 3.8 5.2 - - - +
108A ALA* 4.5 0.7 - - - +
113A VAL* 3.9 9.7 - - - +
115A ARG* 4.0 5.4 + - - +
118A ILE* 3.5 40.5 - - + +
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Residues in contact with VAL 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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35A ARG 4.0 8.3 - - - +
36A VAL* 1.3 75.5 - - - +
38A LEU* 1.3 64.5 + - - +
57A GLU* 3.2 39.9 - - + +
61A SER* 6.5 0.2 - - - -
64A VAL* 4.2 16.4 - - + -
107A ILE* 2.8 22.6 + - + +
109A ALA* 4.2 11.2 - - + +
113A VAL* 4.2 14.8 - - + -
115A ARG* 3.5 29.4 + - - +
117A LEU 4.2 2.6 - - - +
118A ILE* 3.7 16.2 - - - +
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Residues in contact with LEU 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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36A VAL* 3.7 5.3 - - - +
37A VAL* 1.3 83.4 - - - +
39A ALA* 1.3 67.8 + - - +
40A LEU* 5.0 4.7 - - + -
53A GLU* 3.9 9.9 - - + +
54A ALA* 3.6 38.1 - - + +
57A GLU* 4.0 19.3 - - + +
105A ILE* 5.3 0.6 - - + +
106A VAL* 3.5 1.9 - - - -
107A ILE* 2.8 41.4 + - + +
117A LEU 5.4 1.3 - - - +
118A ILE* 3.4 22.9 - - - +
119A TYR 4.4 2.9 - - - +
120A ILE* 4.4 24.2 - - + -
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Residues in contact with ALA 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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14A MET* 4.1 14.7 - - + +
28A PHE* 4.5 7.6 - - + -
36A VAL* 4.5 3.8 - - + -
38A LEU* 1.3 77.3 - - - +
40A LEU* 1.3 69.9 + - - +
44A GLN* 4.4 2.1 - - - +
103A LEU* 4.0 26.5 - - + -
105A ILE* 3.4 9.9 - - - +
106A VAL* 4.3 6.1 - - + -
118A ILE 2.8 17.7 + - - +
119A TYR* 4.0 13.0 - - - +
120A ILE 4.6 0.2 + - - -
125A TYR* 5.4 1.0 - - - -
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Residues in contact with LEU 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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38A LEU* 5.0 6.7 - - + -
39A ALA* 1.3 78.9 - - - +
41A THR* 1.3 60.8 + - - +
44A GLN* 3.4 20.4 - - + +
45A VAL* 3.9 20.2 - - + -
51A TYR* 4.4 8.3 - - + -
54A ALA* 4.5 8.5 - - + -
80A TYR* 3.8 37.0 - - + +
103A LEU* 3.5 7.2 - - - +
104A GLY 2.8 22.5 + - - -
105A ILE* 2.9 23.4 + - + +
120A ILE* 3.3 35.2 - - + -
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Residues in contact with THR 41 (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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40A LEU* 1.3 76.1 - - - +
42A LYS* 1.3 65.9 + - - +
43A GLY 3.3 1.4 + - - -
44A GLN* 3.0 25.3 + - - +
45A VAL* 2.9 21.1 + - - +
102A PRO 3.4 12.1 - - - +
103A LEU* 4.2 5.8 - - + +
104A GLY 3.7 0.9 - - - -
125A TYR* 3.7 34.3 - - + -
128A SER* 2.7 29.7 + - - +
129A VAL* 3.8 22.0 - - + -
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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