Contacts of the strand formed by residues 261 - 266 (chain C) in PDB entry 2I6A
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 ILE 261 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ASP 2.9 9.4 + - - +
219C ILE* 3.1 25.8 - - + -
220C LEU 2.8 30.8 + - - -
259C GLN 4.0 7.9 - - - +
260C ARG* 1.3 84.3 - - - +
262C VAL* 1.3 59.9 + - - +
263C ILE* 4.2 11.2 - - + -
273C MET* 4.2 25.6 - - + -
274C ALA 3.5 9.9 - - - +
275C THR* 4.1 12.1 - - + -
306C PHE* 5.5 0.7 - - + -
316C LEU* 3.8 29.8 - - + -
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Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU* 3.4 9.2 - - + +
245C ALA* 3.7 10.8 - - - +
248C THR* 4.0 13.5 - - + -
249C GLN* 3.4 42.6 - - + +
260C ARG* 4.2 6.1 - - - -
261C ILE* 1.3 77.9 - - - +
263C ILE* 1.3 64.0 + - - +
264C PHE* 3.4 41.5 - - + -
272C ILE 3.1 6.1 - - - +
273C MET* 3.2 2.3 - - - -
274C ALA* 3.0 36.4 + - + +
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ILE* 4.9 3.4 - - + -
220C LEU 2.7 10.1 + - - +
221C PHE* 3.2 37.7 - - + -
222C GLY 3.2 5.2 + - - +
261C ILE* 4.5 8.7 - - + -
262C VAL* 1.3 77.9 - - - +
264C PHE* 1.3 66.4 + - - +
265C THR* 5.0 2.4 - - + +
271C THR* 3.5 24.0 - - + -
272C ILE 3.1 2.0 - - - +
273C MET* 3.0 40.4 - - + -
302C PHE* 4.1 16.6 - - + -
306C PHE* 3.4 25.1 - - + -
320C ILE* 3.9 7.9 - - + -
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Residues in contact with PHE 264 (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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197C LEU* 4.2 17.5 - - + -
220C LEU* 4.7 5.4 - - + -
221C PHE 4.8 0.4 - - - -
222C GLY 3.1 18.4 - - - +
223C ASN 4.8 0.4 - - - -
227C ALA* 3.8 25.1 - - + -
230C PHE* 5.7 1.3 - + - -
241C ILE* 3.7 34.8 - - + -
244C ILE* 4.1 9.2 - - + -
245C ALA* 3.5 42.4 - - + -
248C THR* 4.5 9.0 - - + -
262C VAL* 3.4 22.0 - - + -
263C ILE* 1.3 83.9 - - - +
265C THR* 1.3 64.4 + - - +
271C THR* 3.4 5.8 - - - +
272C ILE* 2.9 36.4 + - + +
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Residues in contact with THR 265 (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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222C GLY 2.9 9.0 + - - +
223C ASN* 3.2 21.4 - - - +
224C GLU* 2.9 25.1 + - - -
263C ILE* 5.0 2.0 - - + +
264C PHE* 1.3 78.3 - - - +
266C GLN* 1.3 63.3 + - - +
267C GLY 3.8 5.4 + - - -
271C THR* 4.3 15.3 - - + +
299C GLY* 5.0 12.1 - - - +
302C PHE* 4.3 36.6 - - + -
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Residues in contact with GLN 266 (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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224C GLU* 3.5 32.1 - - + +
241C ILE* 4.0 26.6 - - + +
264C PHE 4.2 0.2 + - - -
265C THR* 1.3 79.0 - - - +
267C GLY* 1.3 55.7 + - - +
268C ARG 3.2 0.7 + - - -
269C ASP* 2.8 52.2 + - + +
270C ASP* 2.5 25.5 + - - +
271C THR* 5.2 0.4 + - - -
272C ILE* 2.8 20.1 - - + +
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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