Contacts of the strand formed by residues 226 - 236 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C LEU* 5.2 1.1 - - + -
132C MET* 3.7 28.3 - - + -
178C PHE* 3.7 38.4 - - + -
179C THR 2.9 6.7 + - - +
180C TYR* 3.3 6.7 - - + -
181C THR 3.0 25.5 + - - +
218C PRO* 4.0 22.0 - - + -
219C ILE 3.5 6.3 - - - +
220C MET* 4.0 5.6 - - + -
225C ARG* 1.3 73.4 - - - +
227C VAL* 1.3 63.9 + - - +
228C ALA 3.5 24.9 - - - +
229C ILE* 4.6 2.9 - - + -
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TYR* 2.6 28.6 + - - -
181C THR* 3.7 21.1 - - + -
183C GLU 4.1 2.9 - - - +
184C HIS* 3.3 26.3 + - + -
189C TYR* 3.8 30.5 - - + -
203C PHE* 3.9 13.6 - - + -
219C ILE* 2.8 37.8 + - + +
220C MET 4.4 0.2 - - - +
221C ASP* 4.4 4.3 - - + -
225C ARG 4.2 5.6 - - - +
226C VAL* 1.3 75.7 - - - +
228C ALA* 1.3 63.2 + - - +
246C THR* 3.3 6.9 - - - +
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TYR* 4.4 2.9 - - - -
203C PHE* 3.8 19.7 - - + -
218C PRO* 3.5 3.6 - - - +
219C ILE* 2.9 35.3 + - + -
226C VAL* 3.5 6.7 - - - +
227C VAL* 1.3 83.2 - - - +
229C ILE* 1.3 66.4 + - - +
244C VAL* 4.0 9.4 - - + -
245C VAL 3.3 8.1 - - - +
246C THR* 3.4 18.6 - - + -
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Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 4.2 19.7 - - + -
132C MET* 4.0 16.4 - - + -
137C MET* 4.0 4.5 - - + +
138C LYS* 6.2 0.7 - - - -
139C PRO* 5.2 2.0 - - + -
164C MET* 3.7 35.7 - - + -
216C GLY* 4.0 17.9 - - - +
217C ARG 3.6 10.8 - - - +
226C VAL* 4.6 2.2 - - + -
228C ALA* 1.3 77.3 - - - +
230C VAL* 1.3 72.7 + - - +
231C LEU* 4.4 4.1 - - + +
244C VAL* 3.2 7.6 - - - +
245C VAL* 3.0 38.6 + - + +
247C TRP* 3.7 20.2 - - + -
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Residues in contact with VAL 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C TRP* 4.1 15.0 - - + -
214C ASP 4.1 12.1 - - - +
215C SER* 3.3 1.3 - - - -
216C GLY* 2.8 28.9 + - - -
217C ARG 2.9 18.7 + - - +
219C ILE* 3.9 30.7 - - + -
229C ILE* 1.3 75.0 - - - +
231C LEU* 1.3 65.8 + - - +
232C GLY 3.7 15.5 - - - +
242C LEU* 4.1 14.4 - - + -
243C SER 3.9 4.0 - - - +
244C VAL* 4.3 1.6 - - + -
264C TRP* 3.8 29.2 - - + -
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C PRO* 4.3 11.9 - - + -
141C HIS* 3.2 15.1 + - + -
163C ASP* 3.6 33.7 - - + +
164C MET* 4.7 5.2 - - - -
215C SER* 3.6 8.8 - - - -
229C ILE* 4.4 3.6 - - + +
230C VAL* 1.3 79.4 - - - +
232C GLY* 1.3 60.3 + - - +
243C SER* 2.8 25.3 + - - +
244C VAL* 4.3 3.6 - - - -
245C VAL* 3.5 35.0 - - + -
255C LYS* 3.6 34.3 - - + -
263C GLU* 3.7 6.2 - - + +
264C TRP 3.1 16.8 + - - -
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Residues in contact with GLY 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C VAL* 3.7 3.2 - - - +
231C LEU* 1.3 80.5 - - - +
233C GLY* 1.3 57.8 + - - -
242C LEU* 3.5 11.8 - - - +
243C SER* 2.9 22.8 + - - +
261C THR* 4.0 5.2 - - - -
262C GLU 3.3 13.2 - - - -
263C GLU* 4.1 1.3 - - - -
264C TRP* 3.7 21.1 - - - -
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Residues in contact with GLY 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C GLY* 1.3 75.4 - - - -
234C ALA* 1.3 61.0 + - - -
235C ASP 4.1 0.9 + - - -
240C THR* 3.9 5.8 - - - -
241C ALA 3.2 10.1 - - - -
242C LEU* 4.2 0.7 - - - -
260C GLY 4.1 0.3 - - - +
261C THR* 3.7 5.7 - - - +
262C GLU* 2.9 32.7 + - - +
264C TRP* 3.5 22.5 + - - -
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A VAL* 4.0 4.7 - - + -
233C GLY* 1.3 72.3 - - - -
235C ASP* 1.3 60.3 + - - +
236C GLU* 2.9 17.5 + - + +
240C THR* 3.4 5.0 - - - +
241C ALA 2.7 34.0 + - - +
258C PRO* 3.8 15.7 - - + -
259C GLU 3.6 24.0 - - - +
260C GLY 3.8 6.7 - - - -
261C THR* 3.9 8.5 - - - +
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Residues in contact with ASP 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A HIS* 3.1 34.1 + - + -
149A PRO* 3.8 25.5 - - + +
150A VAL* 3.2 11.9 - - - +
173A MET* 3.7 0.2 - - - +
207C ARG* 3.0 47.9 + - - +
233C GLY 4.1 2.0 + - - -
234C ALA* 1.3 66.9 - - - +
236C GLU* 1.3 58.8 + - - +
237C GLY 3.6 11.3 + - - +
240C THR* 4.4 9.4 - - - +
260C GLY 4.6 1.0 + - - -
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Residues in contact with GLU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 4.5 4.0 - - + -
170A PRO* 3.8 28.9 - - + +
172A ASN* 3.0 31.6 + - + +
173A MET* 3.4 19.7 - - + +
202C ARG* 2.7 41.5 + - - -
204C THR* 5.5 0.7 - - - +
234C ALA* 2.9 18.8 + - + +
235C ASP* 1.3 72.7 + - - +
237C GLY* 1.3 58.2 + - - +
239C ARG 3.4 16.3 + - - +
241C ALA* 3.6 14.7 + - - +
258C PRO* 4.1 9.4 - - - +
259C GLU 4.8 3.3 + - - +
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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