Contacts of the strand formed by residues 247 - 251 (chain C) in PDB entry 6F0X
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 247 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C GLN* 3.9 2.2 - - - +
210C ILE* 4.2 15.0 - - + -
236C ILE* 4.3 15.9 - - + -
239C LEU* 3.8 15.3 - - + +
240C ILE* 3.6 37.7 - - + +
245C ALA* 5.5 1.1 - - + -
246C LEU* 1.3 76.2 - - - +
248C PHE* 1.3 71.1 + - - +
249C VAL* 3.9 4.7 - - + +
292C ASN* 3.7 9.9 + - - +
293C VAL* 3.6 34.1 - - + -
294C VAL* 2.9 23.7 + - - +
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Residues in contact with PHE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 4.8 13.5 - - + -
153C VAL* 5.7 0.2 - - + -
192C LEU* 5.9 0.4 - - + -
193C ALA* 4.1 23.1 - - + -
196C LEU* 3.6 38.4 - - + -
197C THR* 5.3 2.2 - - - -
208C GLN 2.9 19.7 + - - +
209C LEU* 3.1 18.8 - - + +
210C ILE* 2.8 28.4 + - - +
246C LEU* 3.1 63.0 - - + -
247C VAL* 1.3 76.0 - - - +
249C VAL* 1.3 66.6 + - - +
294C VAL* 3.5 21.3 - - + -
296C LEU* 5.0 8.3 - - + -
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Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ILE* 4.2 8.3 - - + -
212C ILE* 4.1 8.1 - - + -
233C PHE* 5.8 2.9 - - + -
236C ILE* 4.4 28.7 - - + -
247C VAL* 3.9 2.7 - - + -
248C PHE* 1.3 73.6 - - - +
250C LEU* 1.3 62.0 + - - +
251C ILE* 3.6 29.2 - - + -
293C VAL* 4.2 14.1 - - + -
294C VAL 2.9 8.2 + - - +
295C ILE* 3.6 38.6 - - + -
296C LEU* 2.8 29.0 + - - +
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Residues in contact with LEU 250 (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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186C THR* 4.8 9.4 - - + -
189C CYS* 3.7 30.3 - - + -
190C LYS* 4.5 20.2 - - + +
209C LEU* 3.7 31.0 - - + -
210C ILE 2.9 17.6 + - - +
211C GLU* 3.9 24.4 - - - +
212C ILE* 2.9 23.8 + - - +
249C VAL* 1.3 75.2 - - - +
251C ILE* 1.3 59.5 + - - +
252C ASP* 3.5 12.7 + - + +
296C LEU* 3.8 16.2 - - + +
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Residues in contact with ILE 251 (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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212C ILE* 3.6 25.8 - - + -
214C SER* 5.1 2.2 - - - -
232C MET* 5.9 0.4 - - + -
233C PHE* 5.0 14.8 - - + -
249C VAL* 3.6 26.2 - - + -
250C LEU* 1.3 70.6 - - - +
252C ASP* 1.3 64.3 + - - +
253C GLN 3.3 1.0 + - - -
254C VAL* 3.2 38.7 - - + +
257C LEU* 3.5 34.5 - - + -
280C VAL* 5.4 2.0 - - + -
284C ILE* 5.9 2.7 - - + -
295C ILE* 4.3 11.0 - - + -
296C LEU 2.9 18.5 + - - +
297C THR* 3.7 8.0 - - + -
298C THR 4.0 0.2 + - - -
309C PHE* 5.6 4.3 - - + -
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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