Contacts of the helix formed by residues 143 - 150 (chain C) in PDB entry 2OCP
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 SER 143 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C SER* 3.7 14.8 + - - -
44C GLU* 2.8 18.2 + - - -
118C ARG* 3.4 17.7 - - - +
122C GLN* 4.1 7.6 - - - -
142C ARG* 1.3 77.6 - - - +
144C VAL* 1.3 66.1 + - - +
145C TYR* 3.0 20.1 + - - +
146C SER* 2.8 17.6 + - - -
147C ASP 3.2 16.6 + - - -
186C LEU* 4.0 14.8 - - - -
189C PHE* 4.1 1.4 - - - -
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PHE* 3.7 19.7 - - + -
118C ARG* 3.9 7.8 - - + +
119C LEU* 3.6 42.8 - - + +
122C GLN* 3.4 20.8 + - + +
143C SER* 1.3 74.6 - - - +
145C TYR* 1.3 72.6 + - + +
147C ASP* 3.6 12.2 - - - +
173C HIS* 3.0 22.8 + - - +
177C LEU* 3.4 35.9 - - + -
184C ILE* 4.6 3.4 - - + -
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Residues in contact with TYR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLN* 4.5 7.6 - - - -
143C SER* 3.0 7.1 + - - +
144C VAL* 1.3 78.2 - - + +
146C SER* 1.3 60.4 + - - +
147C ASP 3.2 1.6 - - - -
148C ARG* 3.3 2.4 + - - +
149C TYR* 2.9 35.9 + + - +
173C HIS* 4.7 1.6 - - - -
177C LEU* 4.0 20.6 - - + -
184C ILE* 3.8 26.8 + - + +
185C THR* 5.1 3.3 - - - -
186C LEU* 3.9 37.1 + - + -
189C PHE* 4.2 1.3 - + - -
229C TRP* 4.1 17.3 - - + -
239C PHE* 4.3 15.5 - + + +
241C ALA* 4.8 13.3 - - - +
242C LEU* 3.2 47.8 - - + -
245C ILE* 5.4 2.3 - - + +
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Residues in contact with SER 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 2.7 33.7 + - - -
118C ARG* 5.2 0.6 + - - -
142C ARG* 3.7 11.6 - - - +
143C SER* 2.8 28.2 + - - -
145C TYR* 1.3 72.3 - - - +
147C ASP* 1.3 66.7 + - - +
148C ARG 3.0 2.0 - - - -
150C ILE* 2.8 48.2 + - - +
151C PHE* 3.3 5.2 + - - -
229C TRP* 3.9 5.8 - - - -
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Residues in contact with ASP 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLN* 3.4 11.2 - - - +
114C SER* 2.5 28.5 + - - -
115C PHE* 3.2 23.8 + - + +
118C ARG* 2.8 27.0 + - - +
143C SER 3.2 10.1 + - - +
144C VAL* 3.6 14.8 - - - +
145C TYR 3.2 0.6 - - - -
146C SER* 1.3 77.1 - - - +
148C ARG* 1.3 57.8 + - - +
151C PHE 3.9 0.5 + - - -
152C ALA* 3.0 26.2 + - - +
169C TYR* 2.5 28.8 + - - +
301C DTP 4.3 2.5 - - - -
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Residues in contact with ARG 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C VAL 3.9 0.2 + - - -
145C TYR 3.3 4.0 + - - +
146C SER 3.0 0.2 - - - -
147C ASP* 1.3 79.1 - - - +
149C TYR* 1.3 85.8 + - + +
150C ILE 3.3 0.8 + - - -
152C ALA* 3.9 2.5 - - - -
153C LYS* 2.9 31.5 + - - +
166C TRP* 4.5 7.2 - - + -
169C TYR* 3.3 18.6 - - + +
170C GLN* 2.7 44.4 + - - +
173C HIS* 3.1 49.1 + - + +
174C SER* 2.7 29.1 + - - +
238C HIS* 3.3 29.7 + - - -
239C PHE* 3.6 8.9 - - - -
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Residues in contact with TYR 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C TYR* 2.9 30.9 + + + +
148C ARG* 1.3 94.7 + - + +
150C ILE* 1.3 63.1 + - - +
153C LYS* 3.8 14.5 - - + +
166C TRP* 6.3 0.7 - + - -
173C HIS* 4.9 0.4 - + - -
225C GLN* 3.8 22.3 - - - +
229C TRP* 4.5 20.1 - + + +
235C THR* 3.8 22.8 - - + +
236C LYS 3.5 19.1 - - - -
237C LEU* 3.8 12.8 - - + -
238C HIS* 2.7 41.8 + + - -
239C PHE* 3.3 15.5 - + - -
242C LEU* 3.6 30.5 - - + -
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ARG* 6.3 0.2 - - - -
146C SER* 2.8 37.5 + - - +
149C TYR* 1.3 77.3 - - - +
151C PHE* 1.3 82.5 + - + +
154C ASN* 3.1 28.8 + - - +
222C LEU* 4.0 13.1 - - + +
225C GLN* 3.7 12.1 - - + +
226C HIS* 3.5 69.1 - - + +
229C TRP* 3.9 14.8 - - + -
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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