Contacts of the helix formed by residues 231 - 245 (chain B) in PDB entry 4IRX
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 ASN 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLN* 4.7 1.8 + - - +
50B PRO* 6.2 0.4 - - - +
168B ASN* 4.8 0.2 - - + -
203B SER* 3.8 14.6 + - - +
229B CYS* 3.2 4.6 - - - +
230B LEU* 1.3 82.4 - - - +
232B ASP* 1.3 60.2 + - - +
233B ASP* 3.8 15.3 - - - +
234B MSE 2.8 46.8 + - + +
235B ALA* 3.0 22.2 + - - +
257B PHE* 3.2 13.9 - - - +
258B ASP* 3.5 4.7 - - - +
401B INS 3.0 48.2 + - - +
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Residues in contact with ASP 232 (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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231B ASN* 1.3 73.6 - - - +
233B ASP* 1.3 66.0 + - - +
235B ALA* 3.4 4.0 - - - +
236B MSE 2.9 29.9 + - + +
256B GLY* 3.5 5.9 - - - -
257B PHE 2.7 23.1 + - - +
258B ASP* 3.4 2.5 + - + +
259B ALA* 2.8 27.2 + - - -
260B ILE* 2.8 36.7 + - + -
263B ALA* 3.4 14.7 - - + +
272B MSE 3.5 5.7 - - - +
275B THR* 2.7 19.2 + - - -
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Residues in contact with ASP 233 (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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50B PRO* 3.4 35.8 - - + +
203B SER 4.1 9.7 - - - +
204B LYS* 4.6 0.7 - - - +
205B ARG* 2.8 86.2 + - - +
231B ASN* 3.3 15.6 + - - +
232B ASP* 1.3 76.7 - - - +
234B MSE 1.3 62.0 + - + +
236B MSE 3.3 6.1 + - - -
258B ASP* 5.2 1.0 + - - +
260B ILE* 4.4 4.9 - - + +
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Residues in contact with MSE 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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166B ILE* 3.7 15.0 - - + +
167B THR 3.3 29.8 - - - +
168B ASN* 3.5 18.8 - - + +
201B ALA* 3.6 15.9 - - - -
203B SER* 3.5 18.2 - - - -
204B LYS 3.8 24.9 - - - +
205B ARG* 4.5 0.9 - - - +
208B ALA* 3.2 19.9 - - + +
229B CYS* 4.4 7.5 - - + -
230B LEU 3.7 0.4 - - - +
231B ASN* 2.8 47.3 + - - +
233B ASP* 1.3 69.1 - - - +
235B ALA* 1.3 66.1 + - - +
237B GLY 3.0 3.1 + - - -
238B ALA* 2.9 20.4 + - - +
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Residues in contact with ALA 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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229B CYS* 3.7 23.3 - - + +
231B ASN 3.0 15.0 + - - +
232B ASP* 3.4 9.9 - - - +
234B MSE 1.3 76.5 - - - +
236B MSE 1.3 57.3 + - + +
238B ALA* 3.2 2.3 + - - +
239B LEU* 2.9 33.6 + - - +
254B VAL* 4.0 7.6 - - + +
256B GLY* 4.0 1.6 - - - -
272B MSE 3.5 31.2 - - + -
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Residues in contact with MSE 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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205B ARG* 3.5 37.5 - - - +
232B ASP* 2.9 29.7 + - + +
233B ASP 3.4 7.4 - - - +
234B MSE 3.1 0.2 - - - -
235B ALA* 1.3 76.3 - - - +
237B GLY* 1.3 63.4 + - - +
239B LEU* 3.4 12.0 + - + +
240B GLU* 3.1 32.1 + - - +
260B ILE* 5.1 1.6 - - + -
262B GLU* 3.9 24.7 - - + +
263B ALA* 3.5 35.4 - - + +
266B ARG* 4.0 18.6 - - + -
272B MSE 4.1 14.8 - - + -
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Residues in contact with GLY 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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205B ARG* 3.8 26.1 - - - +
209B LEU* 3.6 19.7 - - - +
233B ASP 3.5 4.2 + - - -
234B MSE 3.0 8.1 + - - -
236B MSE 1.3 77.7 - - - +
238B ALA* 1.3 58.8 + - - +
240B GLU* 3.3 12.3 + - - +
241B ALA* 2.9 22.9 + - - +
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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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208B ALA* 4.5 1.0 - - - +
212B THR* 3.9 29.1 - - + +
227B ILE* 4.3 9.6 - - + -
229B CYS* 3.7 26.7 - - - -
234B MSE 2.9 7.9 + - - +
235B ALA* 3.2 8.0 + - - +
237B GLY* 1.3 71.9 - - - +
239B LEU* 1.3 65.3 + - - +
241B ALA* 3.1 2.9 + - - +
242B VAL* 3.0 28.3 + - - +
254B VAL* 4.6 5.6 - - + -
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Residues in contact with LEU 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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235B ALA 2.9 18.6 + - - +
236B MSE 3.5 23.6 - - + +
238B ALA* 1.3 75.4 - - - +
240B GLU* 1.3 58.2 + - - +
242B VAL* 3.3 8.7 + - + +
243B ARG* 3.0 35.7 + - - +
254B VAL* 3.7 26.5 - - + -
266B ARG* 4.0 32.1 - - + -
271B GLU* 3.3 45.7 - - + +
272B MSE 4.4 7.9 - - + -
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Residues in contact with GLU 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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205B ARG* 4.8 15.6 + - - +
209B LEU* 3.9 20.3 - - + +
236B MSE 3.1 17.8 + - - +
237B GLY* 3.5 14.5 - - - +
238B ALA 3.2 0.2 - - - -
239B LEU* 1.3 74.9 - - - +
241B ALA* 1.3 59.9 + - - +
243B ARG* 3.2 33.3 + - - +
244B ALA* 2.8 30.7 + - - +
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Residues in contact with ALA 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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209B LEU* 3.5 10.4 - - + +
212B THR* 3.6 27.8 - - + -
213B GLN* 3.7 27.6 - - + +
216B LEU* 3.7 5.0 - - + +
237B GLY 2.9 13.3 + - - +
238B ALA 3.1 8.0 + - - +
240B GLU* 1.3 75.7 - - - +
242B VAL* 1.3 56.2 + - - +
244B ALA* 3.3 3.9 + - - +
245B ALA* 3.0 30.3 + - - +
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Residues in contact with VAL 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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216B LEU* 4.1 12.1 - - + -
227B ILE* 3.9 13.0 - - + -
238B ALA 3.0 18.8 + - - +
239B LEU* 3.6 9.9 - - + +
241B ALA* 1.3 74.7 - - - +
243B ARG* 1.3 63.3 + - + +
245B ALA* 3.2 7.2 + - - +
247B LEU* 3.0 53.2 + - + +
248B ASP* 4.1 9.4 - - - +
252B VAL* 3.9 37.0 - - + +
254B VAL* 4.6 7.0 - - + -
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Residues in contact with ARG 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 LEU* 3.0 26.2 + - - +
240B GLU* 3.4 38.8 + - - +
242B VAL* 1.3 78.2 - - + +
244B ALA* 1.3 56.7 + - - +
246B GLY* 2.9 20.6 + - - -
247B LEU 3.8 10.8 - - - +
248B ASP* 6.1 1.6 - - + -
266B ARG* 5.6 1.2 - - - +
271B GLU* 2.4 42.7 + - + +
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Residues in contact with ALA 244 (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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209B LEU* 5.4 2.0 - - + -
213B GLN* 3.7 22.9 - - - +
240B GLU 2.8 21.2 + - - +
241B ALA* 3.3 4.9 + - - +
243B ARG* 1.3 72.5 - - - +
245B ALA* 1.3 58.1 + - - +
246B GLY 3.2 0.8 + - - -
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Residues in contact with ALA 245 (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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216B LEU* 4.2 15.3 - - + -
241B ALA 3.0 15.7 + - - +
242B VAL 3.6 5.8 - - - +
243B ARG 3.1 0.8 - - - -
244B ALA* 1.3 78.0 - - - +
246B GLY* 1.3 60.2 + - - +
247B LEU* 3.2 22.9 + - + +
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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