Contacts of the strand formed by residues 226 - 236 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU* 5.3 0.9 - - + -
132A MET* 3.6 24.7 - - - -
178A PHE* 3.6 41.5 - - + -
179A THR 2.9 8.0 + - - +
180A TYR* 2.9 23.1 - - + -
181A THR* 3.0 13.9 + - - +
218A PRO* 3.9 21.5 - - + -
219A ILE 3.4 5.6 - - - +
220A MET* 4.4 3.6 - - + +
225A ARG* 1.3 71.4 - - - +
227A VAL* 1.3 63.2 + - - +
228A ALA 3.6 25.8 - - - +
229A ILE* 4.4 6.5 - - + -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 2.8 26.4 + - - -
181A THR* 3.7 25.1 - - + +
183A GLU 3.9 12.3 - - - +
184A HIS* 4.0 14.7 + - + -
189A TYR* 3.9 26.5 - - + -
203A PHE* 4.1 15.7 - - + -
219A ILE* 2.9 33.5 + - + +
221A ASP* 4.2 6.3 - - + +
225A ARG 4.1 6.7 - - - +
226A VAL* 1.3 75.3 - - - +
228A ALA* 1.3 63.3 + - - +
246A THR* 3.4 7.8 - - - +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 4.5 2.0 - - - -
203A PHE* 4.1 14.8 - - + -
218A PRO* 3.4 3.8 - - - +
219A ILE* 2.8 48.6 + - + +
226A VAL* 3.6 5.9 - - - +
227A VAL* 1.3 84.0 - - + +
229A ILE* 1.3 63.7 + - - +
230A VAL 4.2 0.2 - - - -
244A VAL* 4.1 6.5 - - + -
245A VAL 3.3 13.5 - - - +
246A THR* 3.7 10.8 - - + -
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 4.2 24.9 - - + -
132A MET* 4.6 1.8 - - + -
137A MET* 3.1 36.1 - - + -
139A PRO* 5.1 0.4 - - + -
164A MET* 3.9 21.5 - - + -
216A GLY* 4.0 25.1 - - - +
217A ARG 3.7 2.9 - - - +
226A VAL* 4.4 7.4 - - + -
228A ALA* 1.3 78.1 - - - +
230A VAL* 1.3 73.3 + - - +
231A LEU* 3.7 2.9 + - + +
244A VAL* 3.2 6.9 - - - -
245A VAL* 3.0 37.9 + - + +
247A TRP* 4.2 11.2 - - + -
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A TRP* 4.0 17.7 - - + -
214A ASP 3.9 13.2 - - - +
215A SER* 3.3 1.2 - - - -
216A GLY* 2.8 29.5 + - - -
217A ARG 3.0 18.4 + - - +
219A ILE* 3.7 32.3 - - + -
229A ILE* 1.3 73.6 - - - +
231A LEU* 1.3 66.3 - - - +
232A GLY 4.0 7.4 - - - +
242A LEU* 4.1 10.5 - - + -
243A SER 3.8 4.7 - - - +
244A VAL* 4.3 1.6 - - + -
264A TRP* 3.9 33.4 - - + -
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PRO* 4.0 17.7 - - + -
141A HIS* 3.3 13.9 - - + -
163A ASP* 3.6 30.1 - - + +
164A MET* 4.2 6.1 - - - -
215A SER* 3.6 8.1 - - - -
229A ILE* 4.2 2.9 - - + +
230A VAL* 1.3 80.4 - - - +
232A GLY* 1.3 60.3 + - - +
243A SER* 2.9 24.2 + - - +
244A VAL 4.3 2.9 - - - -
245A VAL* 3.6 34.1 - - + -
255A LYS* 3.8 33.4 - - + -
261A THR* 5.6 0.4 - - - -
263A GLU* 4.0 2.4 - - + +
264A TRP* 3.1 18.3 + - - -
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Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A VAL* 3.8 2.9 - - - +
231A LEU* 1.3 81.5 - - - +
233A GLY* 1.3 58.5 + - - -
242A LEU* 3.5 10.4 - - - +
243A SER* 2.7 26.1 + - - +
261A THR* 4.3 4.0 - - - -
262A GLU 3.2 14.1 - - - -
264A TRP* 3.6 21.5 - - - -
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLY* 1.3 75.1 - - - -
234A ALA* 1.3 61.3 + - - -
240A THR* 4.3 0.7 - - - -
241A ALA 3.1 12.8 - - - -
242A LEU* 4.1 2.0 - - - -
243A SER 4.1 2.2 - - - -
260A GLY 4.3 0.2 - - - +
261A THR* 3.8 5.0 - - - +
262A GLU* 2.8 35.3 + - - +
264A TRP* 3.6 23.0 + - - -
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Residues in contact with ALA 234 (chain A).
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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233A GLY* 1.3 74.5 - - - -
235A ASP* 1.3 67.0 + - - +
236A GLU* 3.4 2.8 + - + +
240A THR* 3.9 2.8 - - - +
241A ALA* 2.6 42.5 + - - +
258A PRO* 4.1 13.7 - - + -
259A GLU 3.5 16.4 - - - +
260A GLY 3.4 25.6 - - - +
261A THR* 3.9 2.7 - - - -
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Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ARG* 3.2 40.1 + - - +
234A ALA* 1.3 72.7 - - - +
236A GLU* 1.3 65.2 + - - +
239A ARG 3.5 4.3 - - - -
240A THR* 2.8 24.3 + - - +
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Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ARG* 2.8 49.9 + - - +
234A ALA* 3.4 10.8 + - + +
235A ASP* 1.3 79.9 - - - +
237A GLY* 1.3 61.9 + - - +
238A THR 3.4 0.2 + - - -
239A ARG* 2.9 26.7 + - - +
241A ALA* 3.4 13.7 - - + +
258A PRO* 3.2 24.8 - - - +
259A GLU* 4.0 10.6 + - - +
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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