Contacts of the strand formed by residues 233 - 239 (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 HIS 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B ASP* 2.5 30.2 + - - -
145B TYR 3.1 26.7 - - - -
147B TYR* 3.4 36.8 + + - +
189B ILE* 3.6 23.6 - - + +
190B ILE 2.9 24.7 + - - +
191B LYS 5.4 0.2 - - - -
192B ASN* 4.0 6.6 + - + +
229B MET* 3.4 5.4 - - - -
230B PHE* 2.9 38.2 + + - +
231B ARG 3.2 23.1 - - - -
232B ASN* 1.3 74.4 - - - +
234B LEU* 1.3 61.4 + - - +
235B CYS* 3.6 3.1 - - - -
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE* 2.8 44.0 + - + +
191B LYS 5.5 1.2 + - - -
197B LEU* 3.9 23.3 - - + +
200B ALA* 3.6 36.3 - - + +
201B GLN* 4.4 7.9 - - + +
204B VAL* 4.4 3.8 - - + -
227B HIS* 4.5 14.1 - - + +
228B PHE 3.7 13.5 - - - +
229B MET* 3.9 23.8 - - + +
232B ASN 4.3 0.4 + - - -
233B HIS* 1.3 71.2 - - - +
235B CYS* 1.3 65.3 - - - +
236B LEU* 3.8 19.5 - - + -
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Residues in contact with CYS 235 (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 9.9 - - - -
187B ILE* 3.9 12.1 - - + -
188B LYS 3.3 4.0 - - - -
189B ILE* 3.9 23.8 - - - -
227B HIS* 3.1 8.1 - - - +
228B PHE* 2.8 65.2 + - + +
230B PHE* 4.2 9.6 - - - -
233B HIS* 3.6 13.5 - - - -
234B LEU* 1.3 78.9 - - - +
236B LEU* 1.3 63.1 + - - +
237B VAL 4.0 0.4 + - - -
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Residues in contact with LEU 236 (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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186B ALA 3.6 1.0 - - - +
187B ILE* 3.5 2.5 - - - -
188B LYS* 2.9 41.7 + - + +
190B ILE* 4.9 4.9 - - + -
200B ALA* 4.8 2.2 - - + +
203B GLU* 3.9 32.5 - - + +
204B VAL* 3.6 33.9 - - + -
207B LEU* 4.5 2.5 - - + -
224B LEU* 3.5 15.3 - - + -
226B ARG 3.7 4.0 - - - -
227B HIS* 4.0 4.7 - - + -
234B LEU* 3.8 20.6 - - + -
235B CYS* 1.3 80.8 - - - +
237B VAL* 1.3 63.1 + - - +
238B PHE* 3.6 21.3 + - + -
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Residues in contact with VAL 237 (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* 3.8 13.9 - - + +
185B VAL* 3.6 39.3 - - + -
186B ALA 3.8 3.1 - - - -
187B ILE* 4.4 7.4 - - + +
224B LEU* 3.5 5.4 - - - +
225B LYS* 2.8 30.8 + - + -
226B ARG* 2.8 40.9 + - + +
228B PHE* 3.5 33.4 - - + -
236B LEU* 1.3 72.1 - - - +
238B PHE* 1.3 61.8 + - - +
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Residues in contact with PHE 238 (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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185B VAL* 3.5 8.3 - - - +
186B ALA 2.9 32.8 + - - +
188B LYS* 3.9 22.9 - - + -
203B GLU* 4.2 7.4 - - - -
207B LEU* 3.9 18.6 - - + -
222B VAL* 3.8 26.5 - - + -
223B HIS 3.4 16.2 - - - -
224B LEU* 3.8 23.3 - - + -
225B LYS* 4.2 5.4 - - - +
236B LEU* 3.6 36.1 - - + -
237B VAL* 1.3 72.8 - - - +
239B GLU* 1.3 72.6 + - - +
307B ASP 6.1 2.7 - - - -
600B D15 4.0 20.9 - + + -
700B CL 4.6 4.9 - - + -
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Residues in contact with GLU 239 (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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185B VAL* 5.2 0.4 - - - +
186B ALA* 4.3 0.2 - - - +
222B VAL* 3.6 9.7 - - + +
223B HIS* 2.7 46.7 + - + +
225B LYS* 3.6 25.7 - - - +
238B PHE* 1.3 74.3 - - - +
240B MET* 1.3 62.4 + - - +
241B LEU* 4.1 11.2 - - + +
304B LYS* 2.7 36.2 + - - -
600B D15 2.9 22.0 + - - -
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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