Contacts of the helix formed by residues 230 - 255 (chain B) in PDB entry 1OHV
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 PHE 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B LYS* 3.7 52.3 - - + +
225B TYR 3.4 19.7 - - - -
226B PRO* 3.4 20.6 - - + +
227B LEU 3.2 6.2 + - - -
229B GLU* 1.3 96.9 - - + +
231B VAL* 1.3 59.8 + - - +
232B LYS 3.4 2.5 - - - -
233B GLU* 3.4 28.9 - - + +
234B ASN* 2.9 33.4 + - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU 3.5 14.1 + - - +
228B GLU* 4.0 17.0 - - + +
229B GLU 3.8 1.0 - - - -
230B PHE* 1.3 76.0 - - - +
232B LYS* 1.3 62.7 + - + +
233B GLU* 4.2 0.6 + - - -
234B ASN* 3.9 3.2 - - - +
235B GLN* 3.0 57.2 + - + +
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Residues in contact with LYS 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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230B PHE 3.4 0.2 - - - -
231B VAL* 1.3 80.4 - - + +
233B GLU* 1.3 69.3 + - - +
235B GLN* 3.3 16.9 + - - +
236B GLN* 2.9 30.4 + - - +
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LYS* 4.3 20.7 + - + +
229B GLU 4.1 2.8 - - - +
230B PHE* 3.4 48.0 - - + +
231B VAL 3.4 0.4 + - - -
232B LYS* 1.3 84.0 + - - +
234B ASN* 1.3 58.9 + - - +
236B GLN* 3.4 6.0 + - - +
237B GLU* 3.0 28.6 + - - +
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Residues in contact with ASN 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ARG 4.7 0.7 - - - +
223B LEU* 3.7 18.8 - - + +
224B LYS* 2.9 54.3 + - - +
227B LEU* 3.8 23.8 + - - +
230B PHE* 2.9 24.3 + - - +
231B VAL* 4.0 3.6 - - - +
233B GLU* 1.3 75.4 - - - +
235B GLN* 1.3 65.1 + - - +
237B GLU* 3.4 5.9 + - - +
238B GLU* 3.0 31.9 + - - +
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Residues in contact with GLN 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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231B VAL* 3.0 43.2 + - + +
232B LYS* 3.3 16.8 + - - +
234B ASN* 1.3 76.8 - - - +
236B GLN* 1.3 56.1 + - - +
238B GLU* 3.4 9.6 + - - +
239B ALA* 3.0 28.3 + - - +
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Residues in contact with GLN 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 LYS 2.9 16.8 + - - +
233B GLU* 3.7 6.5 - - - +
235B GLN* 1.3 73.9 - - - +
237B GLU* 1.3 60.9 + - - +
239B ALA* 3.8 7.2 - - - +
240B ARG* 2.9 31.4 + - - +
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Residues in contact with GLU 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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220B PHE 4.3 0.7 - - - +
221B PRO* 3.7 10.3 - - + +
222B ARG* 2.8 52.2 + - - +
223B LEU* 4.9 2.2 - - + -
224B LYS* 4.9 10.5 + - - +
233B GLU 3.0 17.3 + - - +
234B ASN* 3.6 8.5 - - - +
236B GLN* 1.3 74.7 - - - +
238B GLU* 1.3 63.3 + - - +
240B ARG* 3.4 38.4 + - - +
241B CYS* 3.0 24.6 + - - -
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Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PRO* 3.9 28.5 - - + -
223B LEU* 3.7 16.7 - - + +
234B ASN* 3.0 22.0 + - - +
235B GLN* 3.7 8.5 - - - +
237B GLU* 1.3 74.5 - - - +
239B ALA* 1.3 64.5 + - - +
241B CYS* 3.2 3.6 + - - +
242B LEU* 3.0 31.2 + - + +
276B ALA* 3.8 1.0 - - - -
277B SER* 2.6 47.8 + - - -
279B ASP* 4.7 4.5 - - - +
280B PHE* 3.6 20.0 + - + +
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Residues in contact with ALA 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 GLN 3.0 17.6 + - - +
236B GLN* 3.8 7.6 - - - +
237B GLU 3.4 0.2 - - - -
238B GLU* 1.3 74.6 - - - +
240B ARG* 1.3 62.9 + - - +
242B LEU* 3.6 12.1 - - + +
243B GLU* 3.0 25.3 + - - +
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Residues in contact with ARG 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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219B PRO* 4.0 14.7 - - - +
220B PHE 5.2 0.8 + - - -
236B GLN 2.9 18.5 + - - +
237B GLU* 3.4 37.8 + - - +
239B ALA* 1.3 76.1 - - - +
241B CYS* 1.3 73.4 + - - +
243B GLU* 3.4 7.1 + - - +
244B GLU* 2.9 60.2 + - + +
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Residues in contact with CYS 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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219B PRO* 3.4 34.0 - - - +
220B PHE 3.8 1.8 - - - -
221B PRO* 3.6 33.7 - - + -
237B GLU* 3.0 17.9 + - - +
238B GLU 3.2 7.6 + - - +
240B ARG* 1.3 100.7 - - - +
242B LEU* 1.3 56.1 + - - +
244B GLU* 3.2 3.5 + - - +
245B VAL* 2.9 33.0 + - - +
280B PHE* 4.2 4.7 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU* 3.0 25.3 + - + +
239B ALA* 3.6 8.5 - - - +
241B CYS* 1.3 75.6 - - - +
243B GLU* 1.3 62.0 + - - +
245B VAL* 3.3 7.9 + - - +
246B GLU* 3.2 18.2 + - - +
280B PHE* 3.5 42.6 - - + +
283B LYS* 3.7 34.3 - - + +
284B LEU* 3.8 25.4 - - + +
287B ILE* 3.7 23.4 - - + +
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Residues in contact with GLU 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 ALA 3.0 16.4 + - - +
240B ARG* 3.6 7.4 - - - +
242B LEU* 1.3 76.9 - - - +
244B GLU* 1.3 58.3 + - + +
246B GLU* 3.2 9.2 + - - +
247B ASP* 3.0 36.9 + - - +
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Residues in contact with GLU 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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219B PRO* 3.3 32.6 - - + +
240B ARG* 2.9 49.2 + - + +
241B CYS 3.6 4.5 - - - +
243B GLU* 1.3 73.9 - - + +
245B VAL* 1.3 65.5 + - - +
247B ASP* 3.4 10.5 + - - +
248B LEU* 3.0 32.7 + - + +
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Residues in contact with VAL 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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183B LEU* 3.9 10.9 - - + +
185B PHE* 3.6 22.7 - - + -
218B ALA* 3.6 26.7 - - + -
241B CYS 2.9 19.5 + - - +
242B LEU* 3.4 10.1 - - + +
244B GLU* 1.3 75.0 - - - +
246B GLU* 1.3 65.2 + - - +
248B LEU* 3.1 6.6 + - - +
249B ILE* 3.0 39.3 + - + +
262B ILE* 4.4 4.3 - - + -
280B PHE* 5.8 0.4 - - + -
284B LEU* 3.9 22.9 - - + -
287B ILE* 4.2 7.4 - - + -
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Residues in contact with GLU 246 (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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242B LEU 3.2 8.6 + - - +
243B GLU* 3.5 11.2 - - - +
245B VAL* 1.3 83.9 - - - +
247B ASP* 1.3 63.5 + - - +
249B ILE* 3.2 10.5 + - - +
250B VAL* 3.0 26.4 + - + +
287B ILE* 4.0 20.7 - - + +
290B LYS* 2.7 31.6 + - - +
291B HIS* 2.6 36.1 + - + +
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Residues in contact with ASP 247 (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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243B GLU* 3.0 25.7 + - - +
244B GLU* 3.8 10.7 - - - +
245B VAL 3.3 0.2 - - - -
246B GLU* 1.3 79.9 - - - +
248B LEU* 1.3 58.7 + - + +
250B VAL* 3.4 7.6 + - - +
251B LYS* 2.8 31.9 + - - +
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Residues in contact with LEU 248 (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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183B LEU* 4.0 3.6 - - + -
216B PRO* 4.0 21.5 - - + -
217B ILE 3.5 31.2 - - - +
218B ALA* 3.5 23.8 - - + -
219B PRO* 4.8 2.5 - - + -
244B GLU* 3.0 23.3 + - + +
245B VAL 3.5 6.5 - - - +
247B ASP* 1.3 73.9 - - + +
249B ILE* 1.3 66.4 + - - +
251B LYS* 4.2 16.8 - - + +
252B TYR* 2.9 43.0 + - + +
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Residues in contact with ILE 249 (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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183B LEU* 3.9 13.7 - - + -
245B VAL* 3.0 19.2 + - + +
246B GLU* 3.2 7.4 + - - +
248B LEU* 1.3 77.1 - - - +
250B VAL* 1.3 62.6 + - - +
252B TYR* 3.9 1.6 - - - +
253B ARG* 3.0 24.5 + - + +
259B VAL* 4.0 19.2 + - + +
262B ILE* 3.9 26.0 - - + -
287B ILE* 3.9 22.7 - - + -
291B HIS* 3.8 34.1 - - + +
293B CYS* 4.0 17.5 - - - -
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Residues in contact with VAL 250 (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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246B GLU* 3.0 20.5 + - + +
247B ASP* 3.7 10.5 - - - +
249B ILE* 1.3 76.7 - - - +
251B LYS* 1.3 64.9 + - - +
253B ARG* 3.2 9.8 + - - +
254B LYS* 3.2 45.5 + - - +
291B HIS* 4.2 20.6 - - + +
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Residues in contact with LYS 251 (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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247B ASP 2.8 19.0 + - - +
248B LEU* 3.3 18.9 + - + +
250B VAL* 1.3 78.0 - - - +
252B TYR* 1.3 72.2 + - + +
254B LYS* 3.4 11.7 + - - +
255B LYS* 3.2 47.8 + - + +
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Residues in contact with TYR 252 (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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181B SER* 4.4 0.4 - - - -
214B ASP* 2.8 42.0 + - - -
215B TRP 4.1 5.7 + - - -
216B PRO* 3.7 37.6 - - + +
248B LEU* 2.9 27.4 + - + +
251B LYS* 1.3 91.1 + - + +
253B ARG* 1.3 65.0 + - - +
254B LYS 3.2 0.7 - - - -
255B LYS* 3.4 30.3 + - + -
256B LYS 3.4 2.8 + - - -
257B LYS* 2.9 60.9 + - + +
258B THR* 4.6 0.2 - - - -
259B VAL* 3.9 11.9 - - + -
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Residues in contact with ARG 253 (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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249B ILE* 3.0 16.1 + - + +
250B VAL* 3.4 12.6 - - - +
252B TYR* 1.3 76.5 - - - +
254B LYS* 1.3 59.8 + - + +
256B LYS* 3.2 15.8 + - - +
258B THR* 4.5 25.7 + - + +
259B VAL 5.9 0.2 - - - +
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Residues in contact with LYS 254 (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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250B VAL* 3.2 34.7 + - + +
251B LYS* 3.5 11.9 - - - +
252B TYR 3.2 0.2 - - - -
253B ARG* 1.3 74.8 - - + +
255B LYS* 1.3 59.3 + - + +
256B LYS* 3.0 17.0 + - - +
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Residues in contact with LYS 255 (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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214B ASP* 4.6 10.5 - - - -
251B LYS* 3.2 37.2 + - + +
252B TYR* 3.4 46.3 + - + +
254B LYS* 1.3 75.0 - - + +
256B LYS* 1.3 69.9 + - - +
257B LYS* 3.3 21.4 + - + +
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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
------------------------------------------------------------
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