Contacts of the helix formed by residues 143 - 150 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F SER* 3.7 14.4 + - - -
44F GLU* 2.8 17.9 + - - -
118F ARG* 3.4 17.2 - - - +
122F GLN* 4.1 7.6 - - - -
142F ARG* 1.3 76.6 - - - +
144F VAL* 1.3 65.6 + - - +
145F TYR* 3.0 20.5 + - - +
146F SER* 2.8 17.6 + - - -
147F ASP 3.2 17.2 + - - -
186F LEU* 4.0 15.5 - - - -
189F PHE* 4.1 1.7 - - - -
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Residues in contact with VAL 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F PHE* 3.7 18.2 - - + -
118F ARG* 3.9 8.0 - - + +
119F LEU* 3.6 44.2 - - + +
122F GLN* 3.4 20.2 + - + +
143F SER* 1.3 77.2 - - - +
145F TYR* 1.3 71.9 + - + +
147F ASP* 3.6 11.8 - - - +
148F ARG 3.9 0.2 + - - -
173F HIS* 3.0 23.0 + - - +
177F LEU* 3.4 36.6 - - + -
184F ILE* 4.6 3.1 - - + -
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Residues in contact with TYR 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F GLN* 4.5 7.2 - - - -
143F SER* 3.0 7.3 + - - +
144F VAL* 1.3 79.4 - - + +
146F SER* 1.3 59.2 + - - +
147F ASP 3.2 1.8 - - - -
148F ARG* 3.2 2.3 + - - +
149F TYR* 2.9 36.0 + + - +
173F HIS* 4.7 2.0 - - - -
177F LEU* 4.0 21.5 - - + -
184F ILE* 3.8 26.4 + - + +
185F THR* 5.1 3.1 - - - -
186F LEU* 3.9 37.8 + - + -
189F PHE* 4.2 1.3 - + - -
229F TRP* 4.1 17.9 - - + -
239F PHE* 4.3 14.8 - + + +
241F ALA* 4.8 13.5 - - - +
242F LEU* 3.2 48.5 - - + -
245F ILE* 5.4 2.7 - - + +
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Residues in contact with SER 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F GLU* 2.7 34.1 + - - -
118F ARG* 5.2 0.4 + - - -
142F ARG* 3.7 11.1 - - - +
143F SER* 2.8 27.8 + - - -
145F TYR* 1.3 72.5 - - - +
147F ASP* 1.3 67.5 + - - +
148F ARG 3.0 2.2 - - - -
150F ILE* 2.8 48.2 + - - +
151F PHE* 3.3 4.6 + - - -
229F TRP* 3.9 6.0 - - - -
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Residues in contact with ASP 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F GLN* 3.4 11.4 - - - +
114F SER* 2.5 27.9 + - - -
115F PHE* 3.2 25.7 + - + +
118F ARG* 2.8 27.8 + - - +
143F SER 3.2 9.7 + - - +
144F VAL* 3.6 14.4 - - - +
145F TYR 3.2 0.6 - - - -
146F SER* 1.3 76.4 - - - +
148F ARG* 1.3 57.5 + - - +
151F PHE 3.9 0.7 + - - -
152F ALA* 3.0 25.8 + - - +
169F TYR* 2.5 29.0 + - - +
301F DTP 4.3 2.2 - - - -
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Residues in contact with ARG 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F VAL 3.9 0.2 + - - -
145F TYR 3.2 4.7 + - - +
146F SER 3.0 0.2 - - - -
147F ASP* 1.3 81.2 - - - +
149F TYR* 1.3 86.0 + - + +
150F ILE 3.4 0.3 + - - -
152F ALA* 3.9 2.9 - - - -
153F LYS* 2.9 31.4 + - - +
166F TRP* 4.5 7.0 - - + -
169F TYR* 3.3 16.6 - - + +
170F GLN* 2.7 43.9 + - - +
173F HIS* 3.1 50.1 + - + +
174F SER* 2.7 28.9 + - - +
238F HIS* 3.3 29.4 + - - -
239F PHE* 3.6 9.3 - - - -
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Residues in contact with TYR 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F TYR* 2.9 31.2 + + + +
148F ARG* 1.3 94.5 + - + +
150F ILE* 1.3 62.5 + - - +
153F LYS* 3.8 13.8 - - + +
166F TRP* 6.3 0.2 - + - -
173F HIS* 4.9 0.4 - + - -
225F GLN* 3.8 22.5 - - - +
229F TRP* 4.5 19.7 - + + +
235F THR* 3.8 23.1 + - + +
236F LYS 3.5 17.9 - - - -
237F LEU* 3.8 12.6 - - + -
238F HIS* 2.7 41.2 + + - -
239F PHE* 3.3 16.5 - + - -
242F LEU* 3.6 30.5 - - + -
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Residues in contact with ILE 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F SER* 2.8 37.1 + - - +
149F TYR* 1.3 76.9 - - - +
151F PHE* 1.3 83.0 + - + +
154F ASN* 3.1 28.6 + - - +
222F LEU* 4.0 13.1 - - + +
225F GLN* 3.7 12.4 - - + +
226F HIS* 3.5 69.8 - - + +
229F TRP* 3.9 14.1 - - + -
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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