Contacts of the helix formed by residues 143 - 150 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G SER* 3.7 15.1 + - - -
44G GLU* 2.8 17.9 + - - -
118G ARG* 3.4 17.8 - - - +
122G GLN* 4.1 7.4 - - - -
140G PHE* 5.6 0.2 - - - -
142G ARG* 1.3 76.1 - - - +
144G VAL* 1.3 64.5 + - - +
145G TYR* 3.0 20.7 + - - +
146G SER* 2.8 16.5 + - - -
147G ASP 3.2 17.2 + - - -
186G LEU* 4.0 14.8 - - - -
189G PHE* 4.1 2.1 - - - -
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Residues in contact with VAL 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G PHE* 3.7 18.8 - - + -
118G ARG* 3.9 7.8 - - + +
119G LEU* 3.6 43.5 - - + +
122G GLN* 3.4 20.5 + - - +
143G SER* 1.3 76.3 - - - +
145G TYR* 1.3 72.2 + - + +
147G ASP* 3.6 13.0 - - - +
173G HIS* 3.0 23.4 + - - +
177G LEU* 3.4 36.1 - - + -
184G ILE* 4.6 2.9 - - + -
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Residues in contact with TYR 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G GLN* 4.5 7.4 - - - -
143G SER* 3.0 6.8 + - - +
144G VAL* 1.3 79.7 - - + +
146G SER* 1.3 60.5 + - - +
147G ASP 3.2 1.6 - - - -
148G ARG* 3.3 1.7 + - - -
149G TYR* 2.9 36.3 + + - +
173G HIS* 4.7 2.2 - + - -
177G LEU* 4.0 21.5 - - + -
184G ILE* 3.8 26.7 + - + +
185G THR* 5.1 3.3 - - - -
186G LEU* 3.9 37.3 + - + -
189G PHE* 4.2 1.1 - + - -
229G TRP* 4.1 17.5 - - + -
239G PHE* 4.3 14.7 - + + +
241G ALA* 4.8 13.2 - - - +
242G LEU* 3.2 49.4 - - + -
245G ILE* 5.4 2.3 - - + +
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Residues in contact with SER 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 2.7 34.1 + - - -
118G ARG* 5.2 0.4 + - - -
142G ARG* 3.7 11.4 - - - +
143G SER* 2.8 28.4 + - - -
145G TYR* 1.3 71.4 - - - +
147G ASP* 1.3 66.5 + - - +
148G ARG 3.0 2.0 - - - -
150G ILE* 2.8 48.4 + - - +
151G PHE* 3.3 5.0 + - - -
229G TRP* 3.9 5.5 - - - -
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Residues in contact with ASP 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G GLN* 3.4 10.7 - - - +
114G SER* 2.5 27.1 + - - -
115G PHE* 3.2 24.9 + - + +
118G ARG* 2.8 28.2 + - - +
143G SER 3.2 10.3 + - - +
144G VAL* 3.6 14.6 - - - +
145G TYR 3.2 0.4 - - - -
146G SER* 1.3 76.4 - - - +
148G ARG* 1.3 58.9 + - - +
151G PHE 3.9 0.7 + - - -
152G ALA* 3.0 25.6 + - - +
169G TYR* 2.5 28.9 + - - +
301G DTP 4.3 2.2 - - - -
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Residues in contact with ARG 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G TYR 3.3 4.9 + - - +
147G ASP* 1.3 79.7 - - - +
149G TYR* 1.3 83.3 + - + +
150G ILE 3.3 0.6 + - - -
152G ALA* 3.9 2.7 - - - -
153G LYS* 2.9 32.1 + - - +
166G TRP* 4.5 7.5 - - + -
169G TYR* 3.3 17.3 - - + +
170G GLN* 2.7 43.3 + - - +
173G HIS* 3.1 48.9 + - + +
174G SER* 2.7 28.3 + - - +
238G HIS* 3.3 30.3 + - - -
239G PHE* 3.6 9.1 - - - -
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Residues in contact with TYR 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G TYR* 2.9 30.9 + + + +
148G ARG* 1.3 95.1 + - + +
150G ILE* 1.3 61.6 + - - +
153G LYS* 3.8 14.6 - - + +
166G TRP* 6.3 0.4 - + - -
173G HIS* 4.9 0.4 - + - -
225G GLN* 3.8 22.0 - - - +
229G TRP* 4.5 20.9 - + + +
235G THR* 3.8 23.0 + - + +
236G LYS 3.5 17.9 - - - -
237G LEU* 3.8 12.3 - - + -
238G HIS* 2.7 41.9 + + - -
239G PHE* 3.3 15.9 - + - -
242G LEU* 3.6 30.5 - - + -
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Residues in contact with ILE 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G ARG* 6.3 0.2 - - - -
146G SER* 2.8 37.3 + - - +
149G TYR* 1.3 77.8 - - - +
151G PHE* 1.3 83.1 + - + +
154G ASN* 3.1 28.1 + - - +
222G LEU* 4.0 13.4 - - + +
225G GLN* 3.7 12.6 - - + +
226G HIS* 3.5 69.1 - - + +
229G TRP* 3.9 14.6 - - + -
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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