Contacts of the strand formed by residues 183 - 189 (chain B) in PDB entry 2WO6
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 GLU 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B TYR* 3.6 10.4 - - - -
178B ASP* 2.8 32.1 + - + +
181B GLU* 3.9 30.9 - - + +
182B GLN* 1.3 79.4 - - - +
184B TRP* 1.3 67.4 + - - +
185B VAL* 4.2 7.2 - - + +
225B LYS* 2.6 40.5 + - - +
226B ARG* 5.1 1.0 + - - -
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Residues in contact with TRP 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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160B GLU 4.8 0.4 - - - -
162B ASP* 3.7 35.9 - - + -
175B LYS* 3.6 28.5 - - + +
176B ALA 3.3 21.1 - - - -
177B TYR* 3.6 42.6 - + + -
183B GLU* 1.3 80.6 - - - +
185B VAL* 1.3 64.2 + - - +
225B LYS* 5.5 0.5 - - - -
239B GLU* 5.3 0.3 - - - -
240B MET* 3.6 31.5 + - + +
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Residues in contact with VAL 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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159B TYR* 4.2 12.3 - - + -
174B VAL 3.6 0.2 - - - +
175B LYS* 3.6 4.5 - - - +
176B ALA* 2.8 49.1 + - + +
178B ASP* 4.6 9.0 - - + +
183B GLU* 4.2 15.9 - - + +
184B TRP* 1.3 80.7 - - - +
186B ALA* 1.3 60.0 + - - +
187B ILE* 4.0 14.6 - - + -
225B LYS* 4.0 16.4 - - + -
226B ARG* 5.3 0.2 - - - +
237B VAL* 3.6 28.7 - - + -
238B PHE 3.5 13.5 - - - +
240B MET* 4.3 7.9 - - - +
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Residues in contact with ALA 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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165B ILE* 4.6 0.9 - - + -
173B VAL* 3.9 15.5 - - + -
174B VAL 3.3 6.3 - - - +
185B VAL* 1.3 73.4 - - - +
187B ILE* 1.3 61.6 + - - +
188B LYS 3.7 0.7 + - - -
236B LEU 3.6 1.6 - - - +
238B PHE* 2.9 39.4 + - - +
239B GLU 4.3 0.2 - - - +
240B MET* 4.3 10.9 - - + +
600B D15 3.5 41.7 - - + +
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Residues in contact with ILE 187 (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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155B TRP* 4.2 24.5 - - + -
159B TYR* 4.0 25.4 - - + -
161B ILE* 4.6 0.4 - - + -
172B GLN 3.5 0.2 - - - +
173B VAL* 3.3 4.5 - - - -
174B VAL* 2.8 42.4 + - + +
176B ALA* 3.8 24.7 - - + -
185B VAL* 4.0 14.1 - - + -
186B ALA* 1.3 76.1 - - - +
188B LYS* 1.3 64.9 + - - +
189B ILE* 3.4 5.5 + - + +
228B PHE* 4.5 5.4 - - + -
235B CYS* 3.9 27.4 - - + -
236B LEU 3.5 7.9 - - - +
237B VAL* 4.4 8.5 - - + -
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Residues in contact with LYS 188 (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* 5.8 2.0 - - - -
172B GLN 3.3 4.7 - - - +
173B VAL* 4.3 11.0 - - + +
186B ALA 3.7 1.6 + - - -
187B ILE* 1.3 72.3 - - - +
189B ILE* 1.3 60.6 + - - +
190B ILE* 3.6 25.5 + - + +
203B GLU* 2.7 33.8 + - - +
234B LEU 3.6 0.5 - - - +
235B CYS* 3.3 5.5 - - - -
236B LEU* 2.9 40.9 + - + +
238B PHE* 3.9 17.4 - - + -
307B ASP* 3.7 12.4 + - - -
309B GLY* 5.3 0.2 - - - -
600B D15 3.6 32.1 - - + -
700B CL 2.8 32.0 - - + +
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Residues in contact with ILE 189 (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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146B ASP* 4.9 1.2 - - - +
147B TYR* 4.1 18.2 - - + +
149B VAL* 4.2 14.1 - - + -
155B TRP* 3.7 29.4 - - + -
171B GLY* 3.1 6.5 - - - -
172B GLN* 2.6 40.4 + - + +
174B VAL* 3.5 28.0 - - + -
187B ILE* 3.9 15.0 - - + +
188B LYS* 1.3 71.2 - - - +
190B ILE* 1.3 60.3 + - - +
230B PHE* 6.4 0.4 - - + -
233B HIS* 3.6 33.2 + - + +
234B LEU 3.9 2.0 - - - -
235B CYS* 3.9 8.7 - - - -
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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