Contacts of the helix formed by residues 71 - 82 (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 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.9 15.6 - - + +
19B ALA* 3.2 36.5 - - + +
22B SER* 5.1 2.1 + - - -
28B LEU* 4.2 4.9 - - - +
32B ALA* 5.6 0.9 - - - +
67B VAL 3.1 9.7 + - - +
68B ALA 3.4 3.7 + - - +
70B LEU* 1.3 78.8 - - - +
72B GLY* 1.3 67.0 + - - +
73B ALA* 3.7 13.6 + - - +
74B SER* 2.6 36.5 + - - +
75B GLY 3.0 18.5 + - - -
351B ARG* 4.8 6.2 + - - -
352B PHE* 4.4 3.8 - - - -
355B ASP* 5.3 1.0 - - - +
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Residues in contact with GLY 72 (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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68B ALA* 3.5 5.0 + - - -
71B ASP* 1.3 73.8 + - - +
73B ALA* 1.3 56.8 + - - +
75B GLY* 3.3 1.0 + - - -
76B TRP* 2.8 31.4 + - - +
183B LEU* 3.9 7.8 - - - +
244B ILE* 3.6 30.2 - - - +
352B PHE* 4.1 6.6 - - - -
355B ASP* 3.7 16.7 + - - -
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Residues in contact with ALA 73 (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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22B SER* 5.4 1.1 - - - -
28B LEU* 4.0 7.6 - - + -
71B ASP* 3.3 14.6 + - - +
72B GLY* 1.3 75.5 - - - +
74B SER* 1.3 56.9 + - - +
76B TRP* 3.3 2.4 + - - +
77B VAL* 2.9 34.1 + - - +
183B LEU* 4.2 5.8 - - + +
185B GLY* 3.6 40.8 - - - +
186B THR* 3.7 12.7 - - + +
355B ASP* 4.2 3.4 + - - -
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Residues in contact with SER 74 (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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15B ILE* 4.5 8.8 + - - +
28B LEU* 3.9 13.3 - - - +
32B ALA* 4.8 8.3 + - - +
36B LEU* 3.6 22.9 - - - +
67B VAL* 3.7 14.1 - - - -
71B ASP* 2.6 34.1 + - - +
73B ALA* 1.3 75.0 - - - +
75B GLY* 1.3 52.9 + - - +
77B VAL* 3.5 0.8 + - - -
78B THR* 2.7 38.4 + - - -
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 3.6 11.2 - - - +
67B VAL* 3.6 8.7 - - - +
68B ALA* 3.6 30.7 - - - -
71B ASP 3.0 11.1 + - - -
72B GLY 3.7 0.2 - - - -
74B SER* 1.3 77.5 - - - +
76B TRP* 1.3 57.5 + - - +
78B THR* 3.3 4.1 + - - -
79B GLY 2.9 23.2 + - - -
240B ALA* 3.7 7.3 - - - +
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Residues in contact with TRP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY 2.8 18.3 + - - +
73B ALA 3.5 4.0 - - - +
75B GLY* 1.3 72.7 - - - +
77B VAL* 1.3 64.9 + - - +
79B GLY* 3.1 2.1 + - - -
80B ILE* 3.0 38.4 + - + +
133B PHE* 3.6 25.7 - + - -
135B SER* 3.0 32.0 + - - -
183B LEU* 3.6 19.7 - - + -
186B THR* 3.5 24.5 - - + -
237B ILE* 3.4 32.3 - - + -
240B ALA* 3.8 22.4 - - + +
241B VAL* 3.9 12.3 - - + -
244B ILE* 4.9 2.9 - - + -
359B GLY* 3.6 33.0 - - - -
362B HIS* 3.8 14.8 - + + -
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Residues in contact with VAL 77 (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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28B LEU* 4.0 22.0 - - + -
36B LEU* 4.0 17.3 - - + -
42B ILE* 4.7 1.6 - - + -
73B ALA 2.9 19.7 + - - +
74B SER 3.8 2.9 - - - +
76B TRP* 1.3 76.2 - - - +
78B THR* 1.3 60.5 + - - +
80B ILE* 3.2 2.6 + - - +
81B VAL* 2.8 50.4 + - + +
107B TRP* 4.6 12.3 - - + -
135B SER* 4.7 2.0 - - - -
136B GLY* 4.1 26.2 - - - +
186B THR* 4.3 16.8 - - + -
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Residues in contact with THR 78 (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 LEU* 3.4 22.9 - - - +
41B ALA* 4.0 31.0 - - + +
42B ILE* 3.9 9.8 - - + +
44B LEU* 5.0 4.3 - - + -
60B PHE* 4.1 3.5 - - + -
63B THR 5.5 0.2 - - - -
64B VAL* 4.0 21.8 - - + +
67B VAL* 3.9 9.0 - - + +
74B SER 2.7 23.0 + - - -
75B GLY* 3.5 8.5 - - - -
77B VAL* 1.3 77.8 - - - +
79B GLY* 1.3 55.3 + - - +
82B GLY* 3.0 29.5 + - - -
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Residues in contact with GLY 79 (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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60B PHE* 4.2 1.6 - - - -
64B VAL* 3.9 9.4 - - - -
75B GLY 2.9 13.1 + - - -
76B TRP 3.1 3.7 + - - -
78B THR* 1.3 77.0 - - - +
80B ILE* 1.3 60.5 + - - +
82B GLY 4.4 0.2 - - - -
83B VAL* 3.6 16.1 - - - +
233B PHE 4.8 1.9 - - - +
236B GLY* 3.4 43.9 - - - -
237B ILE* 4.1 1.4 + - - +
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Residues in contact with ILE 80 (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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76B TRP* 3.0 53.3 + - + +
77B VAL* 4.0 1.1 - - - +
79B GLY* 1.3 76.5 - - - +
81B VAL* 1.3 70.4 + - + +
82B GLY 3.1 1.1 - - - -
83B VAL* 3.1 18.1 + - - +
84B HIS* 3.5 30.8 + - + +
110B SER* 5.0 7.4 - - - +
133B PHE* 5.1 2.5 - - + +
135B SER* 3.6 25.1 - - - +
233B PHE* 6.0 5.6 - - + -
237B ILE* 3.7 29.4 - - + -
362B HIS* 4.8 6.7 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.8 24.8 - - + +
77B VAL* 2.8 29.7 + - + +
80B ILE* 1.3 78.4 - - + +
82B GLY* 1.3 55.3 - - - +
84B HIS* 3.4 13.4 + - + +
85B PRO* 3.2 21.3 - - - +
107B TRP* 3.8 27.8 - - + -
108B MSE 3.6 20.8 + - - +
135B SER 3.6 25.1 - - - +
136B GLY* 4.6 0.9 - - - -
140B CYS* 4.0 8.5 - - - -
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 5.0 1.3 - - - -
42B ILE* 4.0 25.9 - - - +
44B LEU* 5.7 0.5 + - - +
45B LEU* 3.6 20.4 + - - +
60B PHE* 3.9 10.8 - - - -
77B VAL 3.7 0.6 + - - -
78B THR 3.0 22.6 + - - -
81B VAL* 1.3 78.5 - - - +
83B VAL* 1.3 55.8 + - - +
85B PRO* 3.5 11.2 - - - +
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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