Contacts of the helix formed by residues 89 - 106 (chain B) in PDB entry 2V76
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 GLN 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.7 36.3 - - + +
8B TRP 4.6 6.1 + - - +
87B THR* 2.8 14.9 + - - +
88B ALA* 1.3 84.5 - - + +
90B GLY* 1.3 64.2 + - - +
91B ASN 3.2 3.1 - - - -
92B ASP* 3.0 26.0 + - - +
93B ILE* 2.9 23.0 + - + +
1107B PGE 5.8 2.2 - - - +
15C GLU* 6.2 2.5 - - + +
19C ARG* 3.8 48.2 - - + +
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Residues in contact with GLY 90 (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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63B ARG* 3.5 11.6 - - - +
64B ASP 4.3 5.8 + - - -
67B MET 4.0 16.2 - - - -
68B PHE* 3.9 6.5 - - - -
87B THR* 3.7 18.7 + - - +
88B ALA 3.4 4.4 + - - -
89B GLN* 1.3 76.9 - - - +
91B ASN* 1.3 57.2 + - - +
93B ILE* 3.4 3.4 + - - +
94B PHE* 2.8 30.1 + - - +
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Residues in contact with ASN 91 (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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63B ARG* 2.9 42.0 + - + +
64B ASP 4.8 2.0 + - - -
88B ALA 5.2 0.4 + - - -
89B GLN 3.2 1.0 - - - -
90B GLY* 1.3 77.5 - - - +
92B ASP* 1.3 61.4 + - - +
94B PHE* 3.6 0.8 - - - +
95B GLN* 2.9 51.7 + - - +
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Residues in contact with ASP 92 (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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7B PHE* 3.8 20.9 - - + -
89B GLN* 3.0 31.8 + - - +
91B ASN* 1.3 82.0 + - - +
93B ILE* 1.3 58.4 + - - +
95B GLN* 3.4 4.9 + - - +
96B ALA* 2.9 30.1 + - - +
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Residues in contact with ILE 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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7B PHE* 3.6 42.4 - - + -
9B VAL* 4.2 10.1 - - + -
28B LEU* 4.0 12.3 - - + -
30B VAL* 4.5 8.3 - - + -
68B PHE* 3.7 38.8 - - + -
87B THR* 3.9 27.6 - - + +
89B GLN 2.9 19.1 + - - +
90B GLY 3.7 4.7 - - - +
92B ASP* 1.3 73.7 - - - +
94B PHE* 1.3 58.9 + - - +
96B ALA* 3.2 3.1 + - - +
97B VAL* 2.9 36.0 + - + +
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Residues in contact with PHE 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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61B TYR* 3.4 45.0 - + - -
62B GLY* 4.0 8.7 - - - -
63B ARG* 3.4 55.0 - - + +
68B PHE* 3.8 9.6 - + + -
90B GLY 2.8 18.7 + - - +
91B ASN 3.6 3.8 - - - +
93B ILE* 1.3 77.0 - - - +
95B GLN* 1.3 67.6 + - - +
97B VAL* 3.3 3.0 + - - +
98B GLU* 2.8 62.4 + - - +
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Residues in contact with GLN 95 (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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63B ARG* 3.9 6.9 - - - +
91B ASN* 2.9 43.5 + - - +
92B ASP* 3.9 5.6 - - - +
94B PHE* 1.3 90.9 - - - +
96B ALA* 1.3 57.5 + - - +
98B GLU* 3.3 17.5 + - - +
99B THR* 2.9 38.5 + - - +
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Residues in contact with ALA 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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5B SER* 5.5 3.8 - - - -
7B PHE* 4.5 10.3 - - + -
30B VAL* 3.7 24.2 - - + +
92B ASP 2.9 18.3 + - - +
93B ILE* 3.6 5.4 - - - +
95B GLN* 1.3 76.3 - - - +
97B VAL* 1.3 57.5 + - - +
99B THR* 3.5 6.0 + - - -
100B ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 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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30B VAL* 4.0 13.5 - - + -
35B LEU* 3.6 30.3 - - + -
55B TYR* 3.9 11.9 - - + -
58B LEU* 5.3 2.5 - - + -
61B TYR* 3.7 24.0 - - + -
68B PHE* 4.2 13.9 - - + -
93B ILE* 2.9 20.5 + - + +
94B PHE 3.7 3.6 - - - +
96B ALA* 1.3 73.6 - - - +
98B GLU* 1.3 67.5 + - - +
100B ALA* 3.2 2.5 + - - +
101B ILE* 2.9 45.1 + - + +
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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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61B TYR* 3.6 17.7 + - - +
94B PHE* 2.8 48.5 + - + +
95B GLN* 3.6 22.4 + - - +
97B VAL* 1.3 77.7 - - - +
99B THR* 1.3 57.6 + - - +
101B ILE* 3.5 2.8 + - - +
102B HIS* 2.9 31.2 + - + +
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Residues in contact with THR 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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95B GLN* 2.9 23.8 + - - +
96B ALA* 3.7 6.3 - - - -
98B GLU* 1.3 74.3 - - - +
100B ALA* 1.3 66.6 + - - +
102B HIS* 3.3 6.4 + - + +
103B ARG* 3.0 64.8 + - - +
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Residues in contact with ALA 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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30B VAL* 4.2 3.8 - - + -
31B GLU 3.7 11.4 - - - +
32B ALA* 4.1 10.0 - - - +
55B TYR* 3.6 28.3 - - + +
96B ALA 3.0 18.2 + - - +
97B VAL 3.2 3.6 + - - +
99B THR* 1.3 76.5 - - - +
101B ILE* 1.3 58.6 + - - +
103B ARG* 3.4 7.2 + - - +
104B GLN* 3.0 27.1 + - - +
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Residues in contact with ILE 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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55B TYR* 3.6 38.4 - - + +
58B LEU* 5.5 1.3 - - + -
61B TYR* 3.6 25.6 - - + +
97B VAL* 2.9 37.4 + - + +
98B GLU* 3.9 3.8 - - - +
100B ALA* 1.3 74.1 - - - +
102B HIS* 1.3 65.9 + - - +
104B GLN* 3.2 10.6 + - - +
105B LYS* 2.9 52.6 + - + +
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Residues in contact with HIS 102 (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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98B GLU* 2.9 21.1 + - + +
99B THR* 3.3 7.6 + - - +
101B ILE* 1.3 78.4 - - - +
103B ARG* 1.3 68.8 + - - +
105B LYS* 3.4 10.1 + - + +
106B ALA* 3.3 21.0 + - + +
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Residues in contact with ARG 103 (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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99B THR* 3.0 45.6 + - + +
100B ALA* 3.7 6.7 - - - +
102B HIS* 1.3 81.0 - - + +
104B GLN* 1.3 63.8 + - - +
106B ALA* 3.2 21.6 - - - +
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Residues in contact with GLN 104 (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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32B ALA 4.4 8.5 - - - +
33B GLU* 4.1 37.2 + - - +
55B TYR* 3.6 31.6 - - - +
56B THR* 4.0 23.4 - - - +
100B ALA 3.0 13.4 + - - +
101B ILE* 3.2 12.5 + - - +
103B ARG* 1.3 74.2 - - - +
105B LYS* 1.3 67.8 + - + +
106B ALA 3.2 5.5 + - - -
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Residues in contact with LYS 105 (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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101B ILE* 2.9 42.3 + - + +
102B HIS* 3.8 10.3 - - + +
103B ARG 3.3 0.2 - - - -
104B GLN* 1.3 78.4 - - + +
106B ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 106 (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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102B HIS* 3.3 13.4 + - + +
103B ARG* 3.2 19.9 + - - +
104B GLN 3.1 6.7 - - - -
105B LYS* 1.3 83.6 - - - +
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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