Contacts of the strand formed by residues 239 - 245 (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 ARG 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B PHE* 5.1 9.6 - - - -
195B ALA* 5.3 2.8 + - - +
197B GLN* 3.4 25.9 - - - +
204B THR* 2.7 59.6 + - + -
205B ILE* 3.3 16.0 + - - +
206B PRO* 3.6 30.7 - - - +
207B ARG 4.7 0.2 - - - -
236B GLU* 3.5 32.0 + - - +
237B GLY 4.3 2.5 - - - -
238B THR* 1.3 90.6 + - - +
240B THR* 1.3 60.6 + - - +
241B ALA 4.0 0.2 + - - -
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Residues in contact with THR 240 (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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204B THR* 3.2 6.6 - - - -
205B ILE* 2.9 42.3 + - - +
206B PRO 4.3 1.1 + - - -
207B ARG* 3.9 21.5 - - - +
208B GLY 4.7 1.6 + - - -
210B GLY 6.2 0.4 - - - -
233B GLY* 3.9 12.1 - - - -
234B ALA 3.4 27.8 + - - +
235B ASP* 4.4 7.9 + - - +
236B GLU 4.4 0.4 - - - +
239B ARG* 1.3 71.2 - - - +
241B ALA* 1.3 63.4 + - - +
242B LEU* 3.7 2.9 + - + +
264B TRP* 4.0 20.0 - - + -
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Residues in contact with ALA 241 (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* 3.5 33.9 - - + +
203B PHE 3.7 5.8 - - - +
204B THR* 4.0 6.3 - - + -
233B GLY* 3.2 1.4 - - - -
234B ALA* 2.7 37.9 + - - +
236B GLU* 3.6 20.6 + - - +
239B ARG 4.0 2.2 + - - -
240B THR* 1.3 71.2 - - - +
242B LEU* 1.3 63.0 + - - +
258B PRO* 3.9 11.7 - - + +
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Residues in contact with LEU 242 (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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191B TRP* 5.5 2.7 - - + -
196B VAL* 4.1 8.7 - - + -
202B ARG* 5.9 1.4 - - - +
203B PHE* 2.9 24.5 + - + +
205B ILE* 3.9 31.6 - - + -
219B ILE* 4.0 24.5 - - + -
230B VAL* 4.1 12.3 - - + -
232B GLY 3.5 7.6 - - - +
240B THR* 4.4 7.2 - - + +
241B ALA* 1.3 75.8 - - - +
243B SER* 1.3 62.9 - - - +
244B VAL* 3.6 20.9 + - + +
256B THR* 4.1 4.2 - - - +
258B PRO* 3.7 11.2 - - - +
264B TRP* 3.4 36.3 - - + -
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Residues in contact with SER 243 (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* 3.8 0.5 - - - +
231B LEU* 2.8 41.5 + - - +
232B GLY 2.9 15.4 + - - +
241B ALA 3.8 1.4 + - - -
242B LEU* 1.3 71.4 - - - +
244B VAL* 1.3 61.3 + - - +
255B LYS* 4.6 0.7 + - - -
256B THR 3.1 8.3 + - - -
257B THR* 3.2 23.1 + - - +
258B PRO* 3.7 3.5 - - - +
261B THR* 3.4 33.5 - - - +
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Residues in contact with VAL 244 (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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203B PHE* 3.9 22.7 - - + -
219B ILE* 4.1 21.3 - - + -
228B ALA* 4.0 5.2 - - + -
229B ILE 3.2 14.1 - - - +
230B VAL* 4.3 3.6 - - - -
231B LEU* 4.3 2.7 - - - -
242B LEU* 3.9 24.0 - - + +
243B SER* 1.3 79.7 + - - +
245B VAL* 1.3 66.0 + - - +
246B THR* 4.0 14.6 - - + -
254B ILE 3.6 0.5 - - - +
255B LYS* 3.4 5.0 - - - +
256B THR* 3.0 48.6 + - + +
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Residues in contact with VAL 245 (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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162B TYR 3.5 24.0 - - - +
164B MET* 4.3 17.5 - - + -
228B ALA* 3.3 4.3 - - - -
229B ILE* 2.9 35.8 + - + +
231B LEU* 3.5 29.4 - - + -
244B VAL* 1.3 73.4 - - - +
246B THR* 1.3 63.3 + - - +
247B TRP* 3.8 23.1 - - + -
253B THR* 3.7 27.8 - - + -
254B ILE 3.4 4.3 - - - +
255B LYS* 4.4 5.8 - - + -
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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