Contacts of the strand formed by residues 181 - 186 (chain F) in PDB entry 6CP3
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 PHE 181 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89F ARG* 3.3 34.1 - - - -
92F LEU* 3.7 33.0 - - + -
178F HIS* 3.8 5.6 - - - -
179F GLY 5.8 0.2 - - - -
180F GLY* 1.3 82.5 - - - -
182F SER* 1.3 70.8 + - - +
183F VAL* 5.8 1.8 - - + -
212F GLU* 4.9 2.5 - - - -
213F SER 4.5 5.2 - - - -
214F LYS* 3.4 24.0 - - + +
243F PHE* 3.9 37.0 - + + -
247F GLU* 5.4 0.2 - - + -
249F GLN* 3.8 33.9 - - + -
250F ASP 3.1 8.3 + - - +
251F VAL* 4.8 4.9 - - + -
252F LEU* 3.2 20.8 + - - +
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Residues in contact with SER 182 (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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92F LEU* 5.2 0.5 - - - +
175F ALA* 4.0 15.3 + - - +
178F HIS* 5.0 0.7 - - - -
181F PHE* 1.3 82.2 + - - +
183F VAL* 1.3 67.0 + - - +
206F VAL* 5.9 1.6 - - - -
214F LYS* 2.7 10.0 + - - +
215F VAL* 2.9 23.4 - - - -
216F ALA* 2.9 22.5 + - - +
252F LEU* 3.3 30.3 - - - +
254F PHE* 4.5 11.2 - - - -
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Residues in contact with VAL 183 (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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92F LEU* 6.3 0.2 - - + -
181F PHE* 5.8 1.8 - - + -
182F SER* 1.3 79.0 - - - +
184F PHE* 1.3 61.4 + - - +
185F THR* 4.0 11.4 - - - +
216F ALA* 3.4 16.2 - - + +
218F VAL* 4.5 2.9 - - + -
236F GLY* 3.8 24.2 - - - +
239F ILE* 3.9 29.8 - - + +
240F ALA* 4.3 13.9 - - + -
243F PHE* 4.8 7.6 - - + -
251F VAL* 4.7 6.5 - - + -
252F LEU 2.9 10.3 + - - +
253F LEU* 3.4 16.6 - - + +
254F PHE* 3.3 20.6 + - - -
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Residues in contact with PHE 184 (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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164F THR* 6.2 2.7 - - + -
167F ILE* 4.3 16.6 - - + -
168F GLN* 6.4 0.7 - - + -
171F ILE* 4.4 4.7 - - + -
182F SER 4.0 1.6 - - - -
183F VAL* 1.3 71.2 - - - +
185F THR* 1.3 75.1 + - - +
186F GLY* 3.9 11.7 - - - -
189F GLU* 6.5 0.2 - - + -
197F LEU* 3.6 31.6 - - + -
201F MET* 5.3 1.6 - - + -
215F VAL* 4.2 8.1 - - + +
216F ALA 3.0 8.4 + - - +
217F LEU* 3.7 16.6 - - + -
218F VAL* 2.9 25.3 + - - +
219F PHE* 3.6 37.5 - + - -
254F PHE* 3.5 33.6 - + + -
256F ASP* 4.3 23.3 - - + -
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Residues in contact with THR 185 (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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183F VAL* 4.0 7.4 + - - +
184F PHE* 1.3 83.3 + - - +
186F GLY* 1.3 58.2 + - - +
187F VAL* 3.3 23.8 + - + +
218F VAL* 2.9 13.1 - - + +
232F VAL* 3.9 20.6 - - + +
233F ALA* 4.2 6.3 - - - -
236F GLY* 3.5 23.0 - - - -
253F LEU* 4.3 3.3 - - - +
254F PHE 3.0 12.0 + - - -
255F ILE* 3.8 11.1 - - + -
256F ASP 3.1 25.8 + - - +
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Residues in contact with GLY 186 (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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184F PHE* 3.9 6.5 - - - -
185F THR* 1.3 70.6 - - - +
187F VAL* 1.3 60.6 + - - +
188F GLY 3.8 0.7 - - - -
189F GLU* 4.7 7.0 - - - -
218F VAL 2.9 10.0 + - - -
219F PHE* 3.5 27.6 - - - -
220F GLY 2.8 31.7 + - - +
221F GLN* 3.4 3.4 - - - +
232F VAL* 4.3 1.0 - - - +
256F ASP 3.3 7.0 - - - -
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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