Contacts of the helix formed by residues 94 - 102 (chain B) in PDB entry 2OT7
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 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE* 3.5 26.5 - - + +
63B ASP* 4.3 2.7 - - - +
65B LEU* 2.8 31.3 + - + +
67B ILE* 4.3 5.8 - - + +
93B THR* 1.3 72.1 - - - +
95B ARG* 1.3 54.2 + - - +
97B PHE* 3.2 7.1 + - + +
98B ARG* 2.7 49.6 + - - +
178B PHE* 3.5 46.2 - - + -
202B PHE* 5.7 1.1 - - + -
283B PHE* 4.7 11.4 - - + -
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Residues in contact with ARG 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 ASP* 3.2 46.3 + - + +
64B ASP* 3.5 31.5 + - - -
93B THR* 3.2 9.6 + - - +
94B VAL* 1.3 76.6 - - - +
96B GLU* 1.3 64.9 + - + +
98B ARG* 3.2 20.8 + - - +
99B LYS* 3.0 31.2 + - + +
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Residues in contact with GLU 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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91B ALA 4.4 1.2 - - - +
92B MET* 3.2 23.3 - - + +
93B THR* 3.0 40.7 + - - +
95B ARG* 1.3 78.1 - - + +
97B PHE* 1.3 62.3 + - - +
99B LYS* 3.5 7.9 + - - +
100B ILE* 3.4 26.1 + - + +
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Residues in contact with PHE 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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67B ILE* 3.7 18.8 - - + -
70B PRO* 5.3 0.7 - - + -
92B MET* 3.8 23.1 - - - -
93B THR 2.9 17.3 + - - +
94B VAL 3.5 4.0 - - - +
96B GLU* 1.3 72.5 - - - +
98B ARG* 1.3 61.8 + - - +
99B LYS 3.1 1.6 - - - -
100B ILE* 3.1 7.2 + - + +
101B ALA* 3.0 27.7 + - + +
131B ILE* 3.4 33.9 - - + -
133B GLY* 3.6 13.5 - - - -
178B PHE* 3.1 34.8 - + + -
179B GLY 3.4 24.2 - - - -
180B MET* 3.9 12.1 - - + +
283B PHE* 3.9 16.2 - + - -
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ASP* 3.0 42.3 + - - -
94B VAL* 2.7 30.1 + - - +
95B ARG* 3.7 21.4 - - - +
97B PHE* 1.3 72.8 - - - +
99B LYS* 1.3 64.8 + - - +
101B ALA* 3.9 0.9 - - - -
102B ASN* 3.2 42.1 + - - +
283B PHE* 3.3 44.2 - - + -
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Residues in contact with LYS 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 ARG* 3.0 22.0 + - + +
96B GLU* 3.5 9.6 - - - +
97B PHE 3.1 0.2 - - - -
98B ARG* 1.3 80.0 - - + +
100B ILE* 1.3 65.4 + - + +
102B ASN* 4.1 1.7 - - - +
103B SER* 3.3 22.9 + - - -
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Residues in contact with ILE 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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92B MET* 4.6 17.9 - - + -
96B GLU 3.4 14.1 + - - +
97B PHE* 3.1 7.6 + - - +
99B LYS* 1.3 75.4 - - + +
101B ALA* 1.3 62.1 + - - +
103B SER* 2.8 23.5 + - - +
106B TYR* 3.4 35.0 - - + +
131B ILE* 4.5 18.2 - - + -
180B MET* 4.0 15.0 - - + -
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Residues in contact with ALA 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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97B PHE* 3.0 16.7 + - + +
98B ARG 3.9 4.7 - - - +
99B LYS 3.3 0.2 - - - -
100B ILE* 1.3 77.7 - - - +
102B ASN* 1.3 58.8 + - - +
103B SER 3.2 0.6 + - - -
106B TYR 3.4 4.2 - - - +
107B CYS* 3.3 28.2 + - - -
180B MET* 3.6 36.9 - - + +
181B TRP 5.6 0.3 + - - -
283B PHE* 4.0 26.8 + - + -
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Residues in contact with ASN 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 ARG* 3.2 39.3 + - - +
99B LYS* 4.1 1.3 - - - +
101B ALA* 1.3 75.9 - - - +
103B SER* 1.3 66.2 + - - +
104B ASP* 5.0 1.9 - - - +
107B CYS* 4.0 11.0 - - - +
283B PHE* 3.5 24.9 + - - +
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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