Contacts of the strand formed by residues 233 - 238 (chain C) in PDB entry 3F7F
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 TYR 233 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C LEU* 3.3 3.6 - - - +
229C PHE* 2.7 64.4 + + + +
230C HIS* 4.6 9.4 - + + -
232C ARG* 1.3 113.0 + - + +
234C LEU* 1.3 58.4 + - - +
235C ILE* 3.6 2.0 - - + +
245C ILE* 4.2 3.4 - - + -
246C TRP 3.1 8.3 - - - +
247C ASP* 3.2 34.1 - - + -
254C ILE* 5.5 2.0 - - + -
305C VAL* 4.6 14.8 - - + +
311C LEU* 3.2 52.7 + - + +
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C PHE* 3.3 23.8 - - + -
169C VAL* 4.9 2.5 - - + -
175C VAL* 3.9 25.6 - - + -
177C PHE* 3.8 23.8 - - + -
183C LEU* 5.4 2.9 - - + -
199C PHE* 5.7 0.9 - - + -
226C CYS* 3.3 26.5 - - - -
227C LYS 3.9 0.2 - - - -
228C LEU* 4.1 15.0 - - + -
232C ARG 3.7 0.2 + - - -
233C TYR* 1.3 72.2 - - - +
235C ILE* 1.3 62.4 + - - +
236C VAL* 3.3 10.6 + - + +
245C ILE* 4.7 0.2 - - - -
246C TRP* 2.7 41.0 + - + +
248C LEU* 4.5 17.3 - - + -
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Residues in contact with ILE 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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226C CYS* 3.3 3.6 - - - -
227C LYS* 2.9 52.2 + - + +
229C PHE* 3.1 34.3 - - + -
233C TYR* 3.6 10.5 - - + +
234C LEU* 1.3 71.5 - - - +
236C VAL* 1.3 61.7 + - - +
243C LEU* 3.4 35.0 - - + -
244C LYS 4.2 2.5 - - - -
245C ILE* 4.5 20.4 - - + +
280C LEU* 5.0 5.0 - - + +
282C LEU* 5.5 1.6 - - + -
287C LEU* 4.7 17.0 - - + -
303C LEU* 4.2 16.8 - - + -
311C LEU* 5.5 0.4 - - + -
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Residues in contact with VAL 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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177C PHE* 3.9 30.5 - - + -
223C VAL* 3.5 21.1 - - + -
225C SER 3.5 4.9 - - - +
226C CYS* 4.1 5.6 - - - -
234C LEU* 3.3 12.3 - - + +
235C ILE* 1.3 81.0 - - - +
237C LEU* 1.3 61.8 + - - +
238C THR* 5.2 0.9 - - + -
242C HIS 5.1 0.4 - - - +
243C LEU* 3.2 19.8 - - - +
244C LYS* 2.8 52.5 + - + +
246C TRP* 4.2 14.1 - - + +
280C LEU* 5.0 1.3 - - - -
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Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C VAL* 3.2 2.9 - - - -
224C ILE* 2.6 50.4 + - + +
225C SER* 3.0 15.4 + - - -
236C VAL* 1.3 74.2 - - - +
238C THR* 1.3 56.1 + - - +
241C CYS* 3.5 40.2 - - + -
242C HIS 3.6 4.7 - - - +
243C LEU* 5.0 2.5 - - + -
259C MET* 4.6 4.5 - - + -
279C TYR* 3.5 32.8 - - + -
280C LEU* 3.8 18.2 - - + -
289C THR* 3.8 26.7 - - + -
290C LEU 5.0 3.1 - - - +
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Residues in contact with THR 238 (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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221C ASP* 3.1 41.6 + - - +
222C SER 3.4 8.5 - - - +
223C VAL* 4.6 8.5 - - + -
224C ILE* 3.6 11.3 - - - +
236C VAL* 5.2 1.6 - - + -
237C LEU* 1.3 77.3 - - - +
239C GLN* 1.3 56.7 + - - +
240C ASN 3.0 2.4 + - - -
241C CYS* 2.8 23.4 + - - -
242C HIS* 2.9 40.2 + - - +
244C LYS* 4.2 20.6 - - + +
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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