Contacts of the strand formed by residues 236 - 241 (chain C) in PDB entry 6C9G
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 236 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C PRO* 4.4 11.4 - - + -
229C VAL 3.5 6.5 - - - +
230C VAL* 4.3 3.1 - - + +
234C GLY 3.7 1.6 + - - -
235C ARG* 1.3 72.3 - - - +
237C VAL* 1.3 60.0 + - - +
238C ASP 3.2 25.4 - - - +
275C VAL* 3.6 36.9 - - + +
277C LYS* 4.9 3.0 + - - -
300C VAL* 4.6 5.8 - - + -
302C VAL* 4.0 16.8 - - + -
306C ASP* 3.2 30.9 + - - +
308C VAL* 3.9 13.9 - - + -
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Residues in contact with VAL 237 (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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208C THR* 3.5 30.3 - - + -
229C VAL* 2.8 22.0 + - + +
231C ASP* 4.2 25.6 - - + +
235C ARG* 3.3 2.6 + - + +
236C VAL* 1.3 77.5 - - - +
238C ASP* 1.3 66.3 + - + +
272C PHE* 4.0 11.5 - - - -
275C VAL* 5.0 4.2 + - - -
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Residues in contact with ASP 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PRO 3.7 0.2 - - - -
229C VAL* 2.7 40.2 + - + -
236C VAL* 3.2 16.0 - - - +
237C VAL* 1.3 81.8 - - + +
239C ILE* 1.3 77.6 + - - +
262C THR* 5.9 1.2 - - - +
265C LEU* 3.6 15.7 - - + +
268C ARG* 2.9 42.1 + - - -
272C PHE* 3.4 16.9 - - - -
275C VAL* 4.6 4.2 - - - +
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Residues in contact with ILE 239 (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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226C ALA* 4.0 22.0 - - + -
227C LEU 3.6 17.9 - - - +
228C PRO* 4.0 6.7 - - + -
229C VAL* 4.0 3.8 - - - -
238C ASP* 1.3 94.3 + - - +
240C TYR* 1.3 64.3 + - - +
244C ASP* 3.5 10.6 - - - +
265C LEU* 3.5 5.4 - - - +
268C ARG* 3.6 2.8 + - - +
275C VAL* 4.2 4.5 - - + -
298C ARG* 4.2 9.2 - - - +
300C VAL* 4.2 16.2 - - + -
311C ILE* 6.1 0.4 - - + -
1102C AMP 3.4 70.9 - - + +
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Residues in contact with TYR 240 (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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206C VAL* 5.0 1.3 - - + -
212C VAL* 3.3 28.6 - - + +
215C ALA* 4.3 15.7 - - + -
216C LEU* 4.8 0.9 - - + -
219C PHE* 3.7 22.0 - + - -
226C ALA* 3.4 1.6 - - - -
227C LEU* 2.7 47.8 + - + +
229C VAL* 3.9 12.1 - - + +
239C ILE* 1.3 72.7 - - - +
241C SER* 1.3 58.0 + - - +
244C ASP* 3.7 13.1 + - + -
245C VAL* 3.7 35.0 - - + +
248C LEU* 4.7 4.0 - - - +
261C VAL* 4.0 21.3 - - + -
264C ALA* 4.1 19.1 - - + +
265C LEU* 3.4 30.5 - - + -
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Residues in contact with SER 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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219C PHE* 3.9 4.9 - - - -
225C SER 3.5 6.3 - - - -
226C ALA* 3.5 18.4 - - - +
239C ILE* 4.1 1.3 - - - -
240C TYR* 1.3 75.9 - - - +
242C LYS* 1.3 60.5 + - - +
243C PHE* 3.5 6.7 + - - -
244C ASP* 2.8 37.6 + - - +
245C VAL* 3.5 7.1 + - - +
298C ARG* 4.4 2.5 - - - -
1102C AMP 3.4 41.5 - - - -
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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