Contacts of the strand formed by residues 202 - 207 (chain F) in PDB entry 6GL7
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 VAL 202 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F LEU* 4.3 17.7 - - + +
166F CYS* 3.5 20.6 - - - -
189F ARG* 3.7 31.4 + - - +
193F VAL* 5.0 1.6 - - + -
200F ILE* 3.7 13.3 + - + +
201F SER* 1.3 84.5 + - - +
203F ALA* 1.3 65.4 + - - +
204F TYR* 3.3 33.6 - - + +
221F LEU* 4.0 10.9 - - - +
243F CYS* 4.2 1.1 - - + -
244F THR 3.4 6.7 - - - +
245F VAL* 3.9 17.5 - - + -
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Residues in contact with ALA 203 (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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201F SER* 5.7 2.0 - - - +
202F VAL* 1.3 76.0 - - - +
204F TYR* 1.3 69.6 + - - +
205F ARG* 5.9 0.9 + - - -
219F ASP* 3.6 39.9 - - + +
220F SER 4.1 2.0 - - - -
221F LEU* 4.7 3.1 - - + -
243F CYS* 3.1 23.9 - - - +
244F THR* 3.1 14.8 + - - +
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Residues in contact with TYR 204 (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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165F LEU 3.6 1.9 + - - -
166F CYS* 2.7 53.6 + - + -
167F PHE* 3.9 12.1 - + - -
188F PHE* 3.3 38.8 - + + -
189F ARG* 3.3 42.6 - - + -
202F VAL* 3.3 21.8 - - + +
203F ALA* 1.3 77.2 - - - +
205F ARG* 1.3 69.4 + - - +
216F CYS* 3.9 1.7 - - - -
217F ALA 3.5 2.1 - - - +
219F ASP 3.4 5.3 + - - -
220F SER 2.8 40.8 + - - +
221F LEU* 3.9 6.1 - - + -
242F VAL 3.4 5.8 - - - +
243F CYS* 3.6 11.7 - - + -
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Residues in contact with ARG 205 (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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188F PHE* 5.0 1.4 - - - -
203F ALA 5.9 1.0 + - - -
204F TYR* 1.3 79.4 - - - +
206F LEU* 1.3 67.1 + - - +
207F LEU* 3.9 20.8 - - - +
216F CYS* 3.7 22.4 - - - +
217F ALA 4.4 2.9 - - - +
218F PRO* 4.5 16.2 - - + -
219F ASP* 4.9 11.4 + - - +
241F ALA* 3.7 3.5 - - - +
242F VAL* 2.8 60.8 + - + +
243F CYS* 5.6 1.2 - - - +
244F THR* 4.4 15.8 + - - +
253F VAL* 5.6 4.2 - - - +
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Residues in contact with LEU 206 (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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188F PHE* 3.9 25.1 - - + -
205F ARG* 1.3 80.8 - - - +
207F LEU* 1.3 69.8 + - - +
209F GLY* 5.0 5.0 + - - -
210F GLU* 5.5 2.3 - - - +
214F PHE* 3.9 16.2 - - + +
215F ARG* 3.7 35.7 - - - +
216F CYS* 3.7 17.0 + - + +
223F VAL* 4.0 10.3 - - + -
239F LEU* 4.1 15.3 - - + -
240F VAL 3.5 10.3 - - - +
241F ALA* 4.3 5.4 - - + -
258F PHE* 4.3 17.3 - - + -
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Residues in contact with LEU 207 (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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205F ARG* 3.9 24.9 - - - +
206F LEU* 1.3 80.9 - - - +
208F GLU* 1.3 76.7 + - + +
209F GLY 3.2 2.1 + - - -
210F GLU* 5.7 0.9 - - - -
239F LEU* 4.3 2.6 - - - +
240F VAL* 2.8 42.8 + - + +
242F VAL* 3.7 28.3 - - + -
255F MET* 4.4 17.5 - - + -
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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