Contacts of the strand formed by residues 261 - 266 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D ASP 2.9 11.7 + - - +
219D ILE* 3.2 23.9 - - + -
220D LEU 2.8 30.0 + - - -
259D GLN 3.8 6.3 - - - +
260D ARG* 1.3 85.9 - - - +
262D VAL* 1.3 57.8 + - - +
263D ILE* 4.3 11.9 - - + -
273D MET* 3.9 29.6 - - + -
274D ALA 3.5 6.7 - - - +
275D THR* 4.5 6.7 - - + -
316D LEU* 3.7 33.9 - - + -
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Residues in contact with VAL 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D LEU* 3.5 9.2 - - + +
245D ALA* 3.9 15.3 - - - +
248D THR* 3.9 14.1 - - + -
249D GLN* 3.5 36.3 - - + +
260D ARG* 4.0 7.0 - - - -
261D ILE* 1.3 79.3 - - - +
263D ILE* 1.3 64.5 + - - +
264D PHE* 3.4 41.5 - - + -
272D ILE 3.5 1.3 - - - +
273D MET* 3.1 5.4 - - - +
274D ALA* 2.8 36.9 + - + +
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Residues in contact with ILE 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ILE* 5.0 2.0 - - + -
220D LEU 2.9 9.8 + - - +
221D PHE* 3.4 17.3 - - + -
222D GLY 3.2 16.6 + - - -
261D ILE* 4.4 6.7 - - + -
262D VAL* 1.3 79.6 - - - +
264D PHE* 1.3 75.0 + - - +
265D THR* 4.9 1.6 - - + -
271D THR* 3.9 14.4 - - + -
272D ILE 3.0 2.7 - - - -
273D MET* 3.5 30.5 - - + -
302D PHE* 3.8 26.2 - - + -
306D PHE* 2.9 42.6 - - + -
320D ILE* 4.1 4.0 - - + -
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Residues in contact with PHE 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LEU* 3.9 20.2 - - + -
220D LEU* 4.7 5.6 - - + -
221D PHE 4.6 3.1 - - - -
222D GLY* 3.0 17.3 - - - +
223D ASN 4.9 1.6 - - - -
227D ALA* 3.6 34.5 - - + -
230D PHE* 5.7 1.1 - + - -
241D ILE* 3.9 24.7 - - + -
244D ILE* 3.9 8.5 - - + -
245D ALA* 3.6 34.1 - - + -
248D THR* 4.4 6.1 - - + -
262D VAL* 3.4 29.2 - - + -
263D ILE* 1.3 83.6 - - - +
265D THR* 1.3 66.1 + - - +
266D GLN* 4.2 2.1 - - - +
271D THR* 3.4 3.4 - - - -
272D ILE* 2.8 40.3 + - + +
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Residues in contact with THR 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D GLY 2.8 17.9 + - - +
223D ASN* 3.2 17.0 - - - +
224D GLU* 2.9 26.2 + - - +
263D ILE* 4.9 2.0 - - + -
264D PHE* 1.3 76.3 - - - +
266D GLN* 1.3 60.6 + - - +
267D GLY 3.8 4.5 - - - -
271D THR* 4.4 15.7 - - + +
299D GLY* 5.1 11.6 - - - -
302D PHE* 4.0 40.4 - - + -
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Residues in contact with GLN 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D GLU* 3.5 25.4 - - + +
241D ILE* 2.8 51.0 - - + +
264D PHE 4.2 2.0 - - - +
265D THR* 1.3 75.8 - - - +
267D GLY* 1.3 61.2 + - - +
268D ARG 3.1 0.3 + - - -
269D ASP* 2.9 41.2 + - + +
270D ASP* 2.7 32.8 + - - +
271D THR* 4.9 0.6 + - - +
272D ILE* 3.2 11.5 - - - +
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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