Contacts of the strand formed by residues 180 - 186 (chain B) in PDB entry 4GWR
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B GLU 5.5 1.3 - - - +
179B ASP* 1.3 74.3 - - - +
181B TRP* 1.3 68.0 + - - +
214B LYS 3.0 8.0 + - - +
215B VAL* 3.3 18.8 - - + +
216B LYS* 2.9 25.6 + - - +
242B ILE* 4.1 21.1 - - + -
243B PHE 3.5 12.3 - - - +
244B GLN* 4.3 6.7 - - + +
268B LEU* 4.1 24.7 - - + +
269B PHE* 5.4 0.7 - - - -
272B ASN* 3.8 38.8 - - + +
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Residues in contact with TRP 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 3.7 40.8 - - + -
165B LEU* 4.1 5.8 - - + -
173B ASN* 3.3 40.8 + - + -
174B VAL* 3.8 33.2 - - + -
177B SER* 3.1 21.9 + - - -
179B ASP* 3.4 18.4 + - - +
180B VAL* 1.3 76.2 - - - +
182B MET* 1.3 62.4 + - - +
183B VAL* 3.9 11.7 - - + -
216B LYS* 3.4 30.5 - - + -
218B ALA* 3.8 26.9 - - + -
241B LYS 3.7 1.0 - - - +
242B ILE* 3.4 4.5 - - - +
243B PHE* 2.8 40.2 + - + +
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Residues in contact with MET 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B VAL* 5.1 0.2 - - + -
181B TRP* 1.3 73.6 - - - +
183B VAL* 1.3 60.1 + - - +
200B TRP* 3.4 21.0 - - + -
215B VAL* 4.4 9.2 - - + -
216B LYS 2.8 11.8 + - - +
217B LEU* 3.3 15.8 - - + -
218B ALA 2.9 23.9 + - - -
240B ILE* 4.8 1.8 - - + -
241B LYS 3.6 5.2 - - - +
242B ILE* 4.3 9.2 - - + -
252B TYR* 4.4 19.5 - - + -
261B ILE* 4.3 19.3 - - + +
264B ARG* 4.3 22.0 - - + -
265B ALA* 3.9 31.2 - - - -
268B LEU* 4.0 16.4 - - + -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 4.4 2.2 - - + -
170B PHE* 4.3 12.1 - - + -
174B VAL* 4.8 0.2 - - + -
181B TRP* 4.1 12.8 - - + -
182B MET* 1.3 76.0 - - - +
184B GLU* 1.3 63.3 + - - +
185B PHE* 3.7 21.8 + - + -
218B ALA* 3.5 22.7 - - + +
220B VAL* 3.7 26.0 - - + -
239B THR 3.6 1.6 - - - +
240B ILE* 3.3 5.0 - - - +
241B LYS 2.8 37.5 + - - +
243B PHE* 3.8 28.0 - - + -
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Residues in contact with GLU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B VAL* 1.3 69.0 - - - +
185B PHE* 1.3 63.0 + - - +
186B TYR* 3.6 24.4 + - - +
193B CYS* 4.3 10.9 - - - +
196B LEU* 3.5 26.2 - - + +
197B GLU* 5.5 4.6 + - - +
200B TRP* 3.6 33.4 - - + +
218B ALA 2.9 15.9 + - - +
219B ALA* 3.2 12.0 - - - +
220B VAL 2.9 25.6 + - - +
238B PRO* 4.0 12.4 - - + +
239B THR 3.7 2.7 - - - -
240B ILE* 4.0 18.2 - - + -
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PHE* 4.3 9.6 - + - -
183B VAL* 3.7 30.7 - - + -
184B GLU* 1.3 70.4 - - - +
186B TYR* 1.3 60.0 + - - +
220B VAL* 3.4 37.9 - - + +
222B ALA* 4.7 7.0 - - + -
228B LEU* 4.2 18.4 - - + -
229B ALA* 5.5 0.4 - - - -
232B TYR* 4.0 20.9 - + - -
234B ILE* 3.7 42.4 - - + -
237B PHE* 3.7 6.4 - - - -
238B PRO* 3.5 4.3 - - - +
239B THR* 2.8 42.6 + - - +
241B LYS* 4.1 20.9 - - + -
243B PHE* 4.3 3.6 - + - -
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Residues in contact with TYR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLU* 4.3 10.2 + - - -
184B GLU* 3.6 25.8 - - - +
185B PHE* 1.3 74.8 - - - +
187B ALA* 1.3 74.1 + - - +
188B PRO* 4.5 6.5 - - + -
193B CYS* 3.5 25.1 - - + -
219B ALA* 3.8 20.2 - - + -
220B VAL 3.0 35.9 + - - -
221B ASP* 3.5 31.4 + - + +
222B ALA* 2.9 28.8 + - - +
237B PHE* 3.7 6.3 - - - -
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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