Contacts of the strand formed by residues 6 - 9 (chain J) in PDB entry 2OHI
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 LYS 6 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B GLU 5.1 4.9 + - - -
227B GLN* 3.9 25.8 - - - +
4J ALA 4.1 0.8 + - - -
5J ALA* 1.3 74.2 - - - +
7J ARG* 1.3 79.6 + - - +
8J ILE* 3.4 11.1 + - + +
13J TYR* 3.4 3.1 - - - -
14J TRP* 2.9 44.5 + - + +
181J ARG* 3.8 39.5 - - + +
182J LEU* 4.8 9.2 - - - -
185J GLU* 5.0 8.2 + - - -
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Residues in contact with ARG 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ASP* 2.8 44.4 + - - -
162B GLU* 3.4 37.9 + - - +
164B GLY 5.8 0.7 - - - +
225B ARG* 6.1 1.4 - - - +
227B GLN* 4.3 10.8 - - - +
5J ALA 4.1 1.4 + - - -
6J LYS* 1.3 87.7 + - - +
8J ILE* 1.3 61.7 + - - +
9J SER* 3.5 19.3 + - - +
11J GLY 4.9 4.6 - - - +
12J VAL 3.5 1.1 - - - +
13J TYR* 3.5 44.6 + - + -
70J GLN* 5.0 14.3 + - - +
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Residues in contact with ILE 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B GLN* 4.5 13.5 - - - +
6J LYS* 3.4 17.9 + - + +
7J ARG* 1.3 76.9 - - - +
9J SER* 1.3 65.3 + - - +
12J VAL* 2.8 35.4 + - + +
13J TYR* 4.4 2.5 - - - +
14J TRP* 4.8 3.8 - - + +
38J TYR* 4.1 30.3 - - + -
165J ILE* 4.6 3.8 - - + -
167J PHE* 5.2 1.3 - - + -
182J LEU* 4.3 16.8 - - + -
228J MET* 4.0 37.0 - - + +
230J ALA* 5.0 4.7 - - + -
236J ILE* 4.0 22.2 - - + -
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Residues in contact with SER 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 6.0 3.1 - - - -
162B GLU 3.9 6.7 - - - -
163B ASP* 5.4 4.9 - - - +
7J ARG* 3.5 10.9 - - - +
8J ILE* 1.3 77.6 - - - +
10J ASP* 1.3 68.0 + - - +
11J GLY 3.0 1.4 + - - -
12J VAL* 2.8 24.7 + - - +
163J ASP* 3.3 17.4 + - - -
165J ILE* 3.2 29.7 - - - +
228J MET* 5.7 1.3 - - - -
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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