Contacts of the helix formed by residues 266 - 276 (chain B) in PDB entry 2CSX
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 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B LEU* 4.7 8.3 - - + -
173B LEU* 3.7 25.9 - - + +
177B TYR* 3.8 10.3 - - - +
193B ILE* 4.4 6.5 - - + -
196B PHE* 4.6 10.5 - - + -
197B VAL* 4.1 16.2 - - + -
262B ARG* 3.1 28.8 + - + +
265B THR* 1.3 87.8 - - - +
267B TYR* 1.3 84.2 + - + +
268B TRP 3.4 0.7 - - - -
269B PRO* 3.2 9.7 - - - +
270B ALA* 3.2 16.7 + - - +
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Residues in contact with TYR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LEU* 3.8 24.5 - - + -
196B PHE* 4.8 17.8 - + - -
204B LEU* 4.0 24.3 - - + +
230B TRP* 3.7 37.0 - + - -
234B LEU* 4.5 4.3 - - + -
262B ARG* 4.4 10.3 + - + -
263B PHE* 3.5 35.3 + + - +
266B VAL* 1.3 95.0 - - + +
268B TRP* 1.3 64.6 + - - +
270B ALA* 3.5 5.0 + - - +
271B PHE* 3.0 47.0 + - + -
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Residues in contact with TRP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU* 3.5 46.6 - - + +
235B PHE* 3.7 44.0 - + - -
237B TYR* 4.0 12.3 - + + -
238B ILE* 4.3 3.4 - - + -
249B TRP* 4.0 15.5 - + - -
254B HIS* 3.1 28.9 + + - -
263B PHE 3.0 12.0 + - - +
264B HIS* 3.3 25.6 - + - +
267B TYR* 1.3 73.4 - - - +
269B PRO* 1.3 72.7 - - + +
271B PHE* 3.3 5.9 + + - -
272B LEU* 3.1 48.6 + - + +
280B PRO* 3.5 21.6 - - + +
283B VAL* 5.6 0.2 - - + -
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Residues in contact with PRO 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B LEU* 3.7 17.3 - - + -
176B LEU* 4.6 9.0 - - + -
183B PHE* 3.5 27.8 - - + -
264B HIS 3.4 6.3 - - - +
265B THR 3.5 16.4 - - - +
266B VAL 3.2 13.7 - - - +
268B TRP* 1.3 95.9 - - + +
270B ALA* 1.3 50.2 + - - +
272B LEU* 3.1 9.5 + - + +
273B MET* 2.5 47.3 + - - +
279B LEU* 4.5 8.5 - - + -
280B PRO* 5.7 0.7 - - + -
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B PHE* 3.4 31.0 - - + -
166B LEU* 3.6 16.2 - - + -
169B TYR* 3.9 12.1 - - + -
173B LEU* 4.1 2.8 - - + +
266B VAL 3.2 15.9 + - - +
267B TYR 3.6 4.7 - - - +
269B PRO* 1.3 78.1 - - - +
271B PHE* 1.3 63.8 + - - +
273B MET* 2.9 13.2 + - - +
274B SER* 2.9 19.8 + - - -
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Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B PHE* 3.6 37.7 - + - -
204B LEU* 4.2 9.0 - - + -
206B VAL* 5.1 0.2 - - + -
230B TRP* 3.7 28.3 - - + -
231B PHE* 3.4 41.7 - + + -
234B LEU* 3.9 13.5 - - + -
235B PHE* 3.6 29.4 - + + -
267B TYR* 3.0 28.2 + - + -
268B TRP* 3.6 14.4 - + + +
270B ALA* 1.3 74.5 - - - +
272B LEU* 1.3 63.3 + - - +
274B SER* 3.1 18.5 + - - -
275B LEU* 3.1 14.0 + - + +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B PHE* 4.5 3.6 - - + -
238B ILE* 3.7 18.2 - - + -
249B TRP* 4.3 1.8 - - + -
268B TRP* 3.1 49.0 + - + +
269B PRO* 3.5 6.5 - - + +
271B PHE* 1.3 80.0 - - - +
273B MET* 1.3 62.1 + - - +
275B LEU* 3.4 2.7 + - - +
276B GLY 3.1 3.3 + - - -
277B TYR* 3.0 62.3 + - + +
278B GLU 4.1 8.3 - - - +
279B LEU* 3.6 13.2 - - + -
280B PRO* 3.7 27.4 - - + -
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Residues in contact with MET 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B TYR* 3.7 20.0 - - + -
172B LYS* 3.7 52.3 + - + +
173B LEU* 3.9 20.9 - - + +
176B LEU* 4.5 10.8 - - + -
269B PRO* 2.5 29.9 + - + +
270B ALA* 2.9 5.4 + - - +
272B LEU* 1.3 73.8 - - - +
274B SER* 1.3 62.8 + - - +
276B GLY* 3.3 11.8 + - - +
277B TYR 5.2 0.9 - - - -
279B LEU* 4.3 26.9 - - + -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B CYS* 3.3 23.0 - - - -
116B ARG* 2.9 28.7 + - - -
118B ASP* 3.2 14.5 + - - +
164B PHE* 4.1 7.2 - - - -
169B TYR* 2.9 30.2 - - - -
270B ALA 2.9 8.5 + - - -
271B PHE 3.1 9.5 + - - -
273B MET* 1.3 78.5 - - - +
275B LEU* 1.3 61.8 + - - +
276B GLY 3.5 0.2 + - - -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 3.5 31.0 - - + +
112B GLU* 3.8 28.3 - - + -
113B CYS* 4.0 24.2 - - + +
116B ARG* 3.4 21.8 + - - +
231B PHE* 5.4 1.1 - - + -
235B PHE* 3.5 20.2 - - + -
271B PHE* 3.1 18.9 + - + +
272B LEU 4.0 0.4 - - - +
273B MET 3.2 0.2 - - - -
274B SER* 1.3 82.9 + - - +
276B GLY* 1.3 63.1 + - - +
277B TYR* 3.3 39.4 - - + +
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Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG* 3.9 5.4 - - - +
272B LEU 3.1 4.3 + - - -
273B MET* 3.3 7.4 + - - -
274B SER 3.3 4.6 + - - -
275B LEU* 1.3 80.1 - - - +
277B TYR* 1.3 64.1 + - - +
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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