Contacts of the helix formed by residues 92 - 101 (chain B) in PDB entry 2OR0
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 ASP 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ALA* 1.3 75.6 - - - +
93B PRO* 1.3 76.7 - - - +
94B GLN* 2.9 36.2 + - - +
95B VAL* 2.9 23.2 + - + +
96B GLN* 3.4 4.5 + - - +
201B TYR* 3.3 41.3 + - + +
203B THR 5.7 1.0 + - - +
204B LEU* 5.0 3.6 - - - +
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Residues in contact with PRO 93 (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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50B TYR* 4.3 3.1 + - - -
91B ALA 3.3 5.6 - - - +
92B ASP* 1.3 91.9 - - - +
94B GLN* 1.3 61.1 + - - +
96B GLN* 3.3 18.7 + - + +
97B GLU* 3.1 23.4 + - - +
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Residues in contact with GLN 94 (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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92B ASP* 2.9 16.4 + - - +
93B PRO* 1.3 78.0 - - - +
95B VAL* 1.3 57.4 + - - +
97B GLU* 3.4 8.0 + - + +
98B GLU* 3.0 35.1 + - + +
201B TYR* 3.7 45.4 + - + +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.2 2.7 - - + -
91B ALA* 3.9 21.5 - - + -
92B ASP 2.9 18.1 + - - +
94B GLN* 1.3 76.4 - - - +
96B GLN* 1.3 65.3 + - - +
98B GLU* 3.2 21.2 + - - +
99B ILE* 3.0 32.5 + - + +
142B TRP* 4.5 1.1 - - + -
165B ILE* 3.8 31.0 - - + -
201B TYR* 3.8 18.7 - - + +
202B ARG* 3.8 22.9 - - + -
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Residues in contact with GLN 96 (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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47B PRO* 4.2 2.8 - - - +
50B TYR* 3.9 22.5 - - + +
88B LEU* 3.2 35.6 + - + +
89B ALA* 3.2 27.2 + - - +
91B ALA 3.1 22.6 + - - -
92B ASP 3.4 7.9 + - - +
93B PRO* 3.3 19.0 + - + +
95B VAL* 1.3 76.5 - - - +
97B GLU* 1.3 57.7 + - - +
99B ILE* 3.9 0.2 - - - -
100B TRP* 2.9 48.0 + - + +
220B ARG* 4.1 10.4 + - - +
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Residues in contact with GLU 97 (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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50B TYR* 2.9 35.5 + - - +
93B PRO 3.1 13.1 + - - +
94B GLN* 3.6 11.4 - - + +
96B GLN* 1.3 74.7 - - - +
98B GLU* 1.3 61.8 + - + +
101B GLY* 2.9 43.6 + - - +
102B GLU 4.5 0.7 + - - -
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Residues in contact with GLU 98 (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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94B GLN* 3.0 20.4 + - + +
95B VAL* 3.2 16.5 + - - +
97B GLU* 1.3 78.1 - - + +
99B ILE* 1.3 62.3 + - - +
101B GLY 4.8 0.3 + - - -
102B GLU* 5.6 1.9 + - - +
142B TRP* 4.0 21.7 + - + -
201B TYR* 2.5 39.3 + - - -
202B ARG* 3.0 35.2 + - - -
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Residues in contact with ILE 99 (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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88B LEU* 3.7 29.8 - - + -
95B VAL* 3.0 17.1 + - + +
96B GLN 4.1 0.2 - - - +
98B GLU* 1.3 80.5 - - - +
100B TRP* 1.3 78.5 + - + +
101B GLY 3.8 0.4 - - - -
102B GLU 5.5 0.2 - - - -
103B ASP 3.6 1.7 + - - +
106B THR* 3.2 42.9 + - + +
108B MSE 4.0 17.5 - - + -
142B TRP* 3.5 35.2 + - + +
165B ILE* 3.7 30.1 - - + -
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Residues in contact with TRP 100 (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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46B GLN* 3.5 20.4 + - + -
47B PRO* 3.6 22.0 - - + -
50B TYR* 3.6 35.4 - + + -
85B PRO* 3.5 48.3 - - + +
88B LEU* 3.5 31.6 - - + -
89B ALA 4.5 0.4 - - - -
96B GLN* 2.9 30.2 + - + +
99B ILE* 1.3 89.4 - - + +
101B GLY* 1.3 62.5 + - - +
102B GLU 3.3 2.7 - - - -
103B ASP 3.7 5.4 - - - -
104B ASN* 2.7 55.2 + - - +
106B THR 3.6 16.9 + - - -
108B MSE 3.8 5.7 - - + +
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Residues in contact with GLY 101 (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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50B TYR* 4.1 6.7 - - - -
96B GLN 4.0 0.8 + - - -
97B GLU* 2.9 45.3 + - - -
98B GLU 4.7 0.2 - - - -
99B ILE 3.8 0.4 - - - -
100B TRP* 1.3 79.0 - - - +
102B GLU* 1.3 58.0 + - - +
104B ASN* 4.5 3.8 + - - -
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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