Contacts of the strand formed by residues 226 - 236 (chain B) in PDB entry 1WYK
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 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 5.3 0.9 - - + -
132B MET* 3.7 28.7 - - + -
178B PHE* 3.6 39.5 - - + -
179B THR 2.9 6.3 + - - +
180B TYR* 3.3 7.2 - - + -
181B THR 3.0 25.6 + - - +
218B PRO* 4.0 16.6 - - + -
219B ILE 3.5 6.5 - - - +
220B MET* 4.0 11.0 - - + -
225B ARG* 1.3 73.4 - - - +
227B VAL* 1.3 63.0 + - - +
228B ALA 3.5 24.0 - - - +
229B ILE* 4.6 3.1 - - + -
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Residues in contact with VAL 227 (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 TYR* 2.6 29.1 + - - -
181B THR* 3.7 18.4 - - + -
183B GLU 4.0 2.2 - - - +
184B HIS* 3.3 31.6 + - + -
189B TYR* 3.8 30.5 - - + -
203B PHE* 4.0 12.7 - - + -
219B ILE* 2.8 37.8 + - + +
220B MET 4.4 0.2 - - - +
221B ASP* 4.4 4.0 - - + -
225B ARG 4.2 5.8 - - - +
226B VAL* 1.3 75.5 - - - +
228B ALA* 1.3 62.8 + - - +
246B THR* 3.3 4.9 - - - +
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 4.4 2.7 - - - -
203B PHE* 3.8 18.8 - - + -
218B PRO* 3.5 3.5 - - - +
219B ILE* 2.9 36.9 + - + +
226B VAL* 3.5 5.7 - - - +
227B VAL* 1.3 83.9 - - - +
229B ILE* 1.3 66.0 + - - +
244B VAL* 4.0 9.9 - - + -
245B VAL 3.3 8.1 - - - +
246B THR* 3.4 17.5 - - + -
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Residues in contact with ILE 229 (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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130B LEU* 4.2 21.3 - - + -
132B MET* 4.0 13.2 - - + -
137B MET* 4.0 3.8 - - + +
138B LYS* 6.4 0.4 - - - -
139B PRO* 5.1 2.2 - - + -
164B MET* 3.8 28.5 - - + -
216B GLY* 4.0 18.2 - - - +
217B ARG 3.6 10.5 - - - +
226B VAL* 4.6 5.4 - - + -
228B ALA* 1.3 77.0 - - - +
230B VAL* 1.3 73.9 + - - +
231B LEU* 4.4 4.1 - - + +
244B VAL* 3.2 7.6 - - - +
245B VAL* 2.9 39.5 + - + +
247B TRP* 3.8 28.9 - - + -
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TRP* 4.2 15.0 - - + -
214B ASP 4.1 11.9 - - - +
215B SER* 3.3 1.6 - - - -
216B GLY* 2.8 28.9 + - - -
217B ARG 3.0 17.4 + - - +
219B ILE* 3.9 30.7 - - + -
229B ILE* 1.3 74.3 - - - +
231B LEU* 1.3 65.7 + - - +
232B GLY 3.7 15.3 - - - +
242B LEU* 4.1 13.7 - - + -
243B SER 3.8 4.0 - - - +
244B VAL* 4.3 1.6 - - + -
264B TRP* 3.8 28.9 - - + -
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Residues in contact with LEU 231 (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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139B PRO* 4.2 12.3 - - + -
141B HIS* 3.2 15.2 + - + -
163B ASP* 3.6 33.4 - - + +
164B MET* 4.7 5.4 - - - -
215B SER* 3.5 8.6 - - - -
229B ILE* 4.4 3.1 - - + +
230B VAL* 1.3 79.6 - - - +
232B GLY* 1.3 58.6 + - - +
243B SER* 2.8 25.5 + - - +
244B VAL* 4.3 3.8 - - - -
245B VAL* 3.5 35.7 - - + -
255B LYS* 3.6 34.5 - - + -
261B THR* 5.6 0.2 - - - -
263B GLU* 3.7 5.2 - - + +
264B TRP 3.1 16.8 + - - -
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Residues in contact with GLY 232 (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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230B VAL* 3.7 3.6 - - - +
231B LEU* 1.3 81.3 - - - +
233B GLY* 1.3 56.5 + - - -
242B LEU* 3.5 10.9 - - - +
243B SER* 2.9 23.6 + - - +
261B THR* 4.0 5.4 - - - -
262B GLU 3.3 13.2 - - - -
263B GLU* 4.1 1.3 - - - -
264B TRP* 3.7 22.2 - - - -
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Residues in contact with GLY 233 (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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232B GLY* 1.3 75.4 - - - -
234B ALA* 1.3 60.8 + - - -
235B ASP 4.1 1.7 + - - -
240B THR* 3.9 5.6 - - - -
241B ALA 3.2 9.9 - - - -
242B LEU* 4.2 0.7 - - - -
260B GLY 4.1 0.5 - - - +
261B THR* 3.7 5.7 - - - +
262B GLU* 2.8 33.1 + - - +
264B TRP* 3.5 22.3 + - - -
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Residues in contact with ALA 234 (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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233B GLY* 1.3 73.4 - - - -
235B ASP* 1.3 60.0 + - - +
236B GLU* 2.9 20.9 + - + +
240B THR* 3.4 5.2 - - - +
241B ALA* 2.7 33.8 + - + +
258B PRO* 3.8 16.6 - - + -
259B GLU 3.6 22.9 - - - +
260B GLY* 3.8 6.7 - - - -
261B THR* 3.9 8.5 - - - +
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Residues in contact with ASP 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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207B ARG* 3.0 47.4 + - - +
233B GLY 4.1 2.0 + - - -
234B ALA* 1.3 67.1 - - - +
236B GLU* 1.3 59.3 + - - +
237B GLY* 3.6 13.0 + - - +
240B THR* 4.4 9.3 - - - +
260B GLY 4.6 3.4 + - - -
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Residues in contact with GLU 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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202B ARG* 2.7 41.7 + - - -
204B THR* 5.5 0.9 - - - +
234B ALA* 2.9 19.2 + - + +
235B ASP* 1.3 73.2 + - - +
237B GLY* 1.3 59.6 + - - +
238B THR 3.9 1.2 + - - -
239B ARG* 3.5 19.4 + - - +
241B ALA* 3.6 15.1 + - - +
258B PRO* 4.1 9.2 - - - +
259B GLU 4.8 4.9 + - - +
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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