Contacts of the helix formed by residues 232 - 243 (chain B) in PDB entry 2I2X
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 ALA 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B TYR* 6.2 4.0 - - + -
89B ASP* 4.8 13.0 - - - +
146B LEU* 4.9 13.5 - - + +
230B GLU* 3.9 15.0 - - + +
231B ALA* 1.3 78.0 - - - +
233B ASP* 1.3 60.4 + - - +
234B ALA 3.1 0.2 - - - -
235B PRO* 3.1 18.0 - - - +
236B LYS* 3.7 12.3 + - - +
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Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B GLY* 3.8 17.3 - - - -
229B GLU* 3.5 12.1 + - - +
230B GLU* 2.8 41.5 + - - +
231B ALA 3.0 0.6 - - - -
232B ALA* 1.3 77.5 - - - +
234B ALA* 1.3 56.1 + - - +
236B LYS* 3.9 17.1 - - - +
237B ILE* 3.1 33.5 + - - +
255B PHE* 5.2 9.8 - - + -
258B HIS* 5.5 5.3 - - - -
500B B13 5.1 1.8 - - + -
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Residues in contact with ALA 234 (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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143B VAL* 3.7 32.1 - - + +
147B LEU* 3.7 13.6 - - + +
177B MET* 4.3 2.3 - - - +
179B THR* 5.0 2.7 - - + -
230B GLU 4.3 0.6 + - - -
231B ALA 2.9 17.6 + - - +
233B ASP* 1.3 75.3 - - - +
235B PRO* 1.4 65.7 - - + +
237B ILE* 3.0 24.9 - - - +
238B ALA* 3.3 10.6 + - - +
500B B13 4.4 12.0 - - + +
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Residues in contact with PRO 235 (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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146B LEU* 3.3 38.1 - - + +
147B LEU* 3.8 10.8 - - + -
150B ASN* 3.5 34.8 - - + +
152B TYR* 4.7 2.0 - - + -
231B ALA 3.6 5.6 - - - +
232B ALA* 3.1 19.1 - - - +
234B ALA* 1.4 87.3 - - + +
236B LYS* 1.3 54.0 + - - +
238B ALA* 2.9 6.3 + - + +
239B ASP* 2.7 40.4 + - - +
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Residues in contact with LYS 236 (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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232B ALA 3.7 9.6 + - - +
233B ASP* 3.7 18.8 + - - +
234B ALA 3.4 0.6 - - - -
235B PRO* 1.3 79.0 - - - +
237B ILE* 1.3 59.1 + - - +
239B ASP* 3.6 17.0 + - - +
240B ALA* 3.7 6.9 + - - +
254B LYS* 6.1 3.6 - - - +
255B PHE* 3.4 35.1 - - + -
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Residues in contact with ILE 237 (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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177B MET* 3.8 24.8 - - + +
208B ALA* 4.1 10.8 - - + -
226B VAL* 3.1 37.5 - - + -
227B TYR 4.5 5.2 - - - +
233B ASP 3.1 19.6 + - - +
234B ALA* 3.0 26.9 - - - +
236B LYS* 1.3 75.8 - - - +
238B ALA* 1.3 58.8 + - - +
239B ASP 3.4 0.2 - - - -
240B ALA* 3.9 7.7 + - - +
241B ILE* 3.4 20.7 + - + +
251B LEU* 5.0 7.6 - - + +
255B PHE* 3.5 40.6 - - + -
500B B13 5.6 0.7 - - + +
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Residues in contact with ALA 238 (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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126B VAL* 4.9 1.8 - - + -
147B LEU* 4.9 4.5 - - + -
152B TYR* 3.2 31.7 + - + -
176B ILE* 4.5 5.3 - - + +
177B MET* 3.9 14.1 - - + -
234B ALA 3.3 14.2 + - - +
235B PRO* 2.9 10.6 + - + +
237B ILE* 1.3 75.1 - - - +
239B ASP* 1.3 63.1 + - - +
240B ALA 3.3 1.8 - - - -
241B ILE* 3.3 13.2 + - - +
242B ILE* 3.3 21.1 + - - +
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Residues in contact with ASP 239 (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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123B LYS* 3.5 11.7 + - - -
150B ASN* 4.0 13.9 + - - +
152B TYR* 2.3 33.3 + - - -
235B PRO* 2.7 22.9 + - - +
236B LYS* 3.8 11.0 - - - +
237B ILE 3.4 0.2 - - - -
238B ALA* 1.3 75.8 - - - +
240B ALA* 1.3 50.5 + - - +
242B ILE* 3.3 6.9 + - - +
243B ALA* 2.8 31.9 + - - +
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Residues in contact with ALA 240 (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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236B LYS 3.7 5.4 + - - +
237B ILE 4.0 6.3 - - - +
238B ALA 3.3 0.8 - - - -
239B ASP* 1.3 75.4 - - - +
241B ILE* 1.3 59.8 + - - +
243B ALA* 3.5 9.7 - - + +
244B GLY 3.1 6.4 + - - -
245B THR* 2.8 35.5 + - - +
251B LEU* 3.9 21.3 - - + -
254B LYS* 5.5 5.8 - - + +
255B PHE* 4.1 20.2 - - + -
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Residues in contact with ILE 241 (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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176B ILE* 3.8 39.7 - - + +
177B MET* 4.4 9.2 - - + -
206B PRO* 3.3 35.2 - - + -
237B ILE 3.4 20.9 - - - +
238B ALA* 3.5 13.7 - - - +
239B ASP 3.3 0.2 - - - -
240B ALA* 1.3 76.1 - - - +
242B ILE* 1.3 60.8 + - + +
244B GLY* 3.0 17.8 + - - -
245B THR 3.4 18.3 + - - +
246B THR* 5.3 8.8 + - + +
251B LEU* 3.9 8.5 - - + -
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Residues in contact with ILE 242 (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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123B LYS* 3.1 41.3 - - + +
152B TYR* 4.0 13.2 - - + +
176B ILE* 4.0 24.0 - - + -
238B ALA 3.3 13.7 + - - +
239B ASP* 3.5 10.1 - - - +
241B ILE* 1.3 76.1 - - + +
243B ALA* 1.3 58.1 + - - +
244B GLY* 3.2 3.2 + - - -
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Residues in contact with ALA 243 (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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239B ASP 2.8 16.1 + - - +
240B ALA* 3.5 14.4 - - + +
241B ILE 3.2 0.2 - - - -
242B ILE* 1.3 75.8 - - - +
244B GLY* 1.3 59.1 + - - +
245B THR* 4.6 5.0 + - - +
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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