Contacts of the strand formed by residues 239 - 245 (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 ARG 239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ASN* 2.9 25.3 + - - +
188C PHE* 5.1 9.8 - - - -
195C ALA* 5.3 2.6 + - - +
197C GLN* 3.4 25.4 - - - +
204C THR* 2.7 59.7 + - + -
205C ILE* 3.3 15.7 + - - +
206C PRO* 3.6 30.3 - - - +
207C ARG 4.7 0.2 - - - -
236C GLU* 3.4 31.9 + - - +
237C GLY 4.3 2.2 - - - -
238C THR* 1.3 88.0 - - - +
240C THR* 1.3 60.3 + - - +
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Residues in contact with THR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 3.2 6.9 - - - -
205C ILE* 2.9 41.5 + - - +
206C PRO 4.3 1.1 + - - -
207C ARG* 3.9 21.9 - - - +
208C GLY 4.7 1.9 + - - -
210C GLY 6.2 0.4 - - - -
233C GLY* 3.9 12.1 - - - -
234C ALA 3.4 27.8 + - - +
235C ASP* 4.4 7.6 - - - +
236C GLU 4.4 0.4 - - - +
239C ARG* 1.3 71.3 - - - +
241C ALA* 1.3 63.3 + - - +
242C LEU* 3.8 2.9 + - + +
264C TRP* 4.0 19.5 - - + -
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Residues in contact with ALA 241 (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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202C ARG* 3.5 33.9 - - + +
203C PHE 3.7 5.8 - - - +
204C THR* 4.0 6.5 - - + -
233C GLY* 3.2 1.7 - - - -
234C ALA* 2.7 38.6 + - - +
236C GLU* 3.6 20.8 + - - +
239C ARG 4.0 2.0 + - - -
240C THR* 1.3 71.0 - - - +
242C LEU* 1.3 62.1 + - - +
258C PRO* 3.9 11.4 - - + +
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Residues in contact with LEU 242 (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* 5.5 2.5 - - + -
196C VAL* 4.1 8.5 - - + -
202C ARG* 5.9 1.4 - - - +
203C PHE* 2.9 24.4 + - + +
205C ILE* 3.9 31.9 - - + -
219C ILE* 4.0 24.9 - - + -
230C VAL* 4.1 12.3 - - + -
232C GLY 3.5 7.6 - - - +
240C THR* 4.4 6.7 - - + +
241C ALA* 1.3 76.2 - - - +
243C SER* 1.3 62.9 - - - +
244C VAL* 3.6 20.6 + - + +
256C THR* 4.1 4.2 - - - +
258C PRO* 3.7 11.3 - - - +
264C TRP* 3.4 36.8 - - + -
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Residues in contact with SER 243 (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* 3.9 0.5 - - - -
231C LEU* 2.8 41.2 + - - +
232C GLY 2.9 16.7 + - - +
241C ALA 3.9 1.4 + - - -
242C LEU* 1.3 70.5 - - - +
244C VAL* 1.3 62.9 + - - +
255C LYS* 4.6 0.9 + - - -
256C THR 3.1 8.3 + - - -
257C THR* 3.2 23.0 + - - +
258C PRO* 3.7 3.5 - - - +
261C THR* 3.4 34.0 - - - +
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Residues in contact with VAL 244 (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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203C PHE* 3.9 22.2 - - + -
219C ILE* 4.1 21.1 - - + -
228C ALA* 4.0 5.4 - - + -
229C ILE 3.2 13.2 - - - +
230C VAL* 4.3 3.8 - - - -
231C LEU* 4.3 2.9 - - - -
242C LEU* 3.9 23.8 - - + +
243C SER* 1.3 80.2 + - - +
245C VAL* 1.3 65.2 + - - +
246C THR* 4.0 14.8 - - + -
254C ILE 3.6 0.7 - - - +
255C LYS* 3.4 4.7 - - - +
256C THR* 2.9 49.1 + - + +
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Residues in contact with VAL 245 (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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162C TYR 3.5 24.0 - - - +
164C MET* 4.3 15.9 - - + -
228C ALA* 3.3 4.7 - - - -
229C ILE* 3.0 35.0 + - + +
231C LEU* 3.5 29.6 - - + -
244C VAL* 1.3 75.5 - - - +
246C THR* 1.3 62.8 + - - +
247C TRP* 3.7 23.1 - - + -
253C THR* 3.7 28.3 - - + -
254C ILE 3.3 4.5 - - - +
255C LYS* 4.4 5.4 - - + -
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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