Contacts of the helix formed by residues 223 - 257 (chain B) in PDB entry 6KJV
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 SER 223 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 5.6 6.5 - - - +
219B SER 3.5 8.4 + - - -
220B TYR* 2.9 30.9 + - - -
221B GLN 4.2 0.7 - - - +
222B ASP* 1.3 83.9 - - - +
224B LEU* 1.3 61.4 + - - +
225B ALA* 4.1 8.2 - - - +
226B CYS* 3.5 18.0 + - - +
227B ARG* 3.3 18.5 + - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B SER* 1.3 72.3 - - - +
225B ALA* 1.3 66.8 + - - +
226B CYS 3.2 2.0 - - - -
227B ARG* 3.1 15.9 + - + +
228B LEU* 3.0 47.8 + - + +
289B TYR* 4.2 31.4 - - + +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 5.6 7.4 - - + -
220B TYR* 4.7 6.7 - - + -
223B SER* 3.5 8.4 - - - +
224B LEU* 1.3 79.0 - - - +
226B CYS* 1.3 56.1 + - - +
228B LEU* 3.2 11.7 + - - +
229B VAL* 2.9 38.0 + - + +
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Residues in contact with CYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LYS* 5.7 5.8 - - - -
220B TYR* 3.2 57.5 - - + +
223B SER* 3.5 5.7 + - - +
224B LEU 3.2 0.4 - - - -
225B ALA* 1.3 78.5 - - - +
227B ARG* 1.3 56.1 + - - +
229B VAL* 3.2 2.6 + - - +
230B PHE* 2.9 28.0 + - - +
296B CYS* 2.0 50.3 - - - -
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Residues in contact with ARG 227 (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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221B GLN 3.5 17.0 + - - -
222B ASP* 3.5 17.2 + - - +
223B SER 3.3 17.3 + - - +
224B LEU* 3.1 16.4 + - + +
226B CYS* 1.3 74.4 - - - +
228B LEU* 1.3 58.0 + - + +
230B PHE* 3.4 5.6 + - - +
231B LEU* 2.9 28.9 + - - +
289B TYR* 5.2 6.1 - - - -
293B ASP* 2.8 41.5 + - - -
294B GLU* 3.9 1.0 - - - +
295B GLY 3.8 11.1 - - - +
296B CYS* 3.0 38.8 - - - +
297B TRP* 3.3 43.7 - - + +
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Residues in contact with LEU 228 (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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224B LEU* 3.0 40.1 + - + +
225B ALA* 3.2 11.9 + - - +
227B ARG* 1.3 75.5 - - + +
229B VAL* 1.3 60.9 + - + +
231B LEU* 3.2 15.8 + - + +
232B LEU* 2.9 29.9 + - - +
297B TRP* 6.2 1.6 - - + -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B CYS* 3.9 33.7 - - + +
196B PHE* 3.6 32.3 - - + -
197B LYS* 4.5 11.2 - - + +
220B TYR* 4.1 14.6 - - - +
225B ALA* 2.9 22.1 + - + +
226B CYS 3.2 4.2 + - - +
228B LEU* 1.3 75.9 - - + +
230B PHE* 1.3 57.4 + - - +
232B LEU* 3.4 8.6 + - + +
233B MET* 2.9 29.8 + - + +
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Residues in contact with PHE 230 (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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197B LYS* 6.5 0.9 - - - -
226B CYS* 2.9 18.2 + - - +
227B ARG* 3.7 4.9 - - - +
229B VAL* 1.3 75.0 - - - +
231B LEU* 1.3 58.4 + - - +
233B MET* 3.3 16.3 + - + +
234B GLN* 2.9 52.5 + - + +
284B TRP* 3.3 34.1 - + - -
296B CYS* 3.4 29.4 - - + +
297B TRP* 3.9 17.9 - + - -
298B THR* 6.0 1.3 - - - -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ARG 2.9 18.2 + - - +
228B LEU* 3.6 17.0 - - + +
230B PHE* 1.3 76.6 - - - +
232B LEU* 1.3 57.9 + - - +
234B GLN* 3.2 5.5 + - - +
235B TYR* 2.9 27.2 + - - +
281B VAL* 3.6 30.9 - - + +
282B VAL* 5.4 9.4 - - + -
284B TRP* 3.5 30.3 - - + -
285B GLY* 4.1 13.5 - - - -
297B TRP* 4.4 9.2 - - + -
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Residues in contact with LEU 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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189B LEU* 5.1 11.9 - - + +
193B CYS* 3.5 21.5 - - - -
228B LEU 2.9 17.1 + - - +
229B VAL* 3.7 8.1 - - + +
231B LEU* 1.3 75.4 - - - +
233B MET* 1.3 58.4 + - - +
235B TYR* 3.2 19.5 + - + +
236B CYS* 2.9 37.7 + - - -
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Residues in contact with MET 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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148B TYR* 5.6 2.5 - - - +
152B TYR* 5.6 0.4 - - - -
190B ARG* 4.1 18.4 - - - +
193B CYS* 3.9 28.2 - - + +
194B VAL* 4.0 33.4 - - + +
197B LYS* 4.9 15.7 - - + -
229B VAL* 2.9 15.8 + - + +
230B PHE* 3.5 22.4 - - + +
232B LEU* 1.3 73.4 - - - +
234B GLN* 1.3 65.9 - - + +
236B CYS* 3.1 7.0 + - - +
237B VAL* 2.9 34.7 + - + +
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Residues in contact with GLN 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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230B PHE* 2.9 42.8 + - + +
231B LEU 3.5 8.7 - - - +
233B MET* 1.3 75.8 - - - +
235B TYR* 1.3 62.0 + - - +
237B VAL* 3.2 13.5 + - - +
238B ALA* 3.0 23.9 + - - +
281B VAL* 4.2 10.3 - - + +
284B TRP* 3.9 29.2 - - + -
309B ILE* 3.8 26.5 - - + +
310B ARG* 4.7 19.2 + - - +
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Residues in contact with TYR 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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189B LEU* 5.8 2.7 - - + -
231B LEU* 2.9 14.2 + - + +
232B LEU* 3.4 25.1 - - + +
234B GLN* 1.3 77.7 - - - +
236B CYS* 1.3 63.0 + - - +
237B VAL 3.4 0.2 + - - -
238B ALA* 3.4 2.1 + - - +
239B ALA* 2.9 28.0 + - + +
274B TRP* 2.5 69.3 + + - +
277B PRO* 3.8 13.9 - - + -
278B LEU* 3.7 40.1 - - + +
281B VAL* 4.2 15.6 - - + +
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Residues in contact with CYS 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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186B SER* 3.9 13.2 - - - +
189B LEU* 3.4 43.7 - - - -
190B ARG* 3.6 18.2 - - + +
193B CYS* 4.5 3.6 - - - -
232B LEU* 2.9 26.3 + - - -
233B MET 3.1 7.6 + - - +
235B TYR* 1.3 81.1 - - - +
237B VAL* 1.3 57.6 + - - +
239B ALA* 3.2 7.9 + - - +
240B ASN* 2.9 35.6 + - - +
274B TRP* 5.8 1.1 - - - -
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Residues in contact with VAL 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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190B ARG* 4.0 34.1 - - - +
233B MET* 2.9 27.3 + - + +
234B GLN* 3.2 16.5 + - - +
236B CYS* 1.3 73.9 - - - +
238B ALA* 1.3 67.0 + - - +
240B ASN* 3.1 16.2 + - - +
241B TYR* 3.1 43.9 + - + -
310B ARG* 5.1 4.3 - - - +
313B ILE* 4.4 11.9 - - + -
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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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234B GLN 3.0 16.2 + - - +
235B TYR 3.8 0.4 - - - +
237B VAL* 1.3 78.1 - - - +
239B ALA* 1.3 57.6 + - - +
241B TYR* 3.3 6.6 + - - +
242B TYR* 3.0 34.3 + - - +
277B PRO* 3.5 23.6 - - + -
280B PHE* 3.5 29.8 - - + -
281B VAL* 4.2 3.6 - - + -
309B ILE* 6.1 0.2 - - + -
313B ILE* 4.9 7.6 - - + +
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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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186B SER* 3.8 16.2 - - - -
235B TYR* 2.9 16.4 + - + +
236B CYS* 3.3 10.8 - - - +
237B VAL 3.1 0.2 - - - -
238B ALA* 1.3 75.0 - - - +
240B ASN* 1.3 65.6 + - - +
243B TRP* 2.9 32.0 + - + +
273B GLY 3.5 20.2 - - - +
274B TRP* 4.0 19.7 - - + -
277B PRO* 3.8 2.6 - - + +
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Residues in contact with ASN 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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183B LEU* 3.9 7.5 - - - +
186B SER* 2.7 38.7 + - - -
187B PHE* 3.7 26.7 + - + -
190B ARG* 3.2 42.6 - - - +
236B CYS 2.9 21.6 + - - +
237B VAL* 3.1 10.3 + - - +
239B ALA* 1.3 75.7 - - - +
241B TYR* 1.3 68.1 + - + +
243B TRP 3.9 0.3 - - - -
244B LEU* 2.9 25.4 + - - +
360B LEU* 5.4 4.6 - - + +
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Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ARG* 5.7 3.6 - - - -
237B VAL* 3.1 46.6 + - + -
238B ALA* 3.9 5.6 - - - +
239B ALA 3.2 0.4 - - - -
240B ASN* 1.3 84.6 - - + +
242B TYR* 1.3 62.4 + - + +
244B LEU* 3.4 12.6 + - + +
245B LEU* 2.9 23.6 + - - +
313B ILE* 4.1 24.7 - - + -
316B ALA* 4.5 14.7 - - + +
317B CYS* 3.9 9.2 - - - -
320B ASN* 3.9 5.6 + - - +
360B LEU* 3.2 36.8 + - + -
361B CYS* 3.7 25.4 - - - -
364B GLU* 5.3 6.5 + - + +
394B GLN* 4.9 7.8 + - - -
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Residues in contact with TYR 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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238B ALA* 3.0 27.7 + - + +
241B TYR* 1.3 79.3 - - + +
243B TRP* 1.3 61.1 + - - +
245B LEU* 3.1 20.7 + - + +
246B VAL* 3.0 30.7 + - - +
272B ILE* 3.6 39.2 - - + +
273B GLY* 4.0 7.6 - - - +
276B VAL* 3.9 19.5 - - + +
277B PRO* 4.3 7.6 - - + -
280B PHE* 3.8 23.7 - + - -
312B PRO* 3.3 29.2 + - - +
313B ILE* 5.1 2.2 - - + -
315B PHE* 4.0 15.3 - + - -
316B ALA* 3.7 22.1 - - + +
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Residues in contact with TRP 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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179B ILE* 4.2 22.9 - - + +
182B ASN* 3.3 37.9 - - + -
183B LEU* 3.8 23.7 - - + +
186B SER* 4.9 1.3 - - - +
239B ALA* 2.9 25.5 + - + +
242B TYR* 1.3 74.7 - - - +
244B LEU* 1.3 59.8 + - - +
246B VAL* 3.2 34.6 - - + +
247B GLU* 2.9 28.6 + - - +
266B PHE* 5.4 2.2 - + - -
269B TYR* 3.9 10.1 - - + -
270B VAL* 3.6 31.6 - - + -
273B GLY* 3.3 28.3 - - - -
274B TRP* 3.1 52.1 - + - +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.0 11.5 - - + +
240B ASN 2.9 19.0 + - - +
241B TYR* 3.4 9.2 - - + +
243B TRP* 1.3 74.9 - - - +
245B LEU* 1.3 64.2 + - - +
247B GLU* 3.2 14.1 + - + +
248B GLY* 3.0 18.0 + - - -
320B ASN* 3.8 21.6 - - - +
353B THR* 4.9 5.1 - - + +
356B LEU* 4.2 31.0 - - + +
357B ILE* 4.4 18.7 - - + +
360B LEU* 4.0 35.9 - - + -
361B CYS* 4.7 8.1 - - - -
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Residues in contact with LEU 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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241B TYR 2.9 15.2 + - - +
242B TYR* 3.1 37.2 + - + +
244B LEU* 1.3 76.6 - - - +
246B VAL* 1.3 57.6 + - + +
248B GLY* 3.1 3.3 + - - -
249B VAL* 2.9 45.3 + - + +
272B ILE* 4.7 10.8 - - + -
315B PHE* 5.4 5.4 - - + -
316B ALA* 4.9 3.1 - - + +
319B VAL* 3.6 33.0 - - + -
320B ASN* 3.5 21.7 - - - +
323B ILE* 5.0 6.1 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 4.2 8.0 - - + +
242B TYR 3.0 13.9 + - - +
243B TRP* 3.2 42.4 - - + +
245B LEU* 1.3 74.4 - - + +
247B GLU* 1.3 63.0 + - - +
249B VAL* 3.8 8.0 - - + +
250B TYR* 2.9 31.7 + - - +
269B TYR* 4.0 28.2 - - + +
272B ILE* 3.7 38.1 - - + -
273B GLY 4.4 1.1 - - - +
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Residues in contact with GLU 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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179B ILE* 3.3 22.2 - - - +
180B HIS* 3.1 36.2 + - - -
183B LEU* 4.3 8.4 - - + +
243B TRP 2.9 15.2 + - - +
244B LEU* 3.3 16.8 - - + +
246B VAL* 1.3 78.0 - - - +
248B GLY* 1.3 56.9 + - - +
250B TYR* 3.5 12.3 + - - +
251B LEU* 3.0 27.7 + - - +
349B LEU* 4.2 8.1 - - - +
353B THR* 3.9 10.2 + - + +
402B TYR* 3.1 34.1 + - + +
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Residues in contact with GLY 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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244B LEU 3.0 13.6 + - - -
245B LEU 3.1 3.1 + - - -
247B GLU* 1.3 75.0 - - - +
249B VAL* 1.3 58.8 + - - +
251B LEU* 3.2 9.1 + - - +
252B TYR* 2.9 27.7 + - - +
320B ASN* 5.0 3.8 - - - -
323B ILE* 3.8 23.6 - - - +
353B THR* 4.3 11.8 - - - +
357B ILE* 5.1 3.4 - - - -
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 2.9 40.5 + - + +
246B VAL* 3.8 8.5 - - + +
248B GLY* 1.3 74.4 - - - +
250B TYR* 1.3 64.6 + - - +
252B TYR* 3.2 8.3 + - + +
253B THR* 3.0 32.7 + - + +
269B TYR* 4.6 16.2 - - + +
272B ILE* 6.1 5.4 - - + -
323B ILE* 5.3 10.8 - - + -
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Residues in contact with TYR 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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175B THR* 3.3 25.8 + - - -
176B ARG* 3.7 31.4 + - + +
179B ILE* 3.7 25.6 - - + -
246B VAL 2.9 18.5 + - - +
247B GLU* 3.7 10.8 - - - +
249B VAL* 1.3 76.2 - - - +
251B LEU* 1.3 59.4 + - - +
253B THR* 3.0 10.6 + - - -
254B LEU* 2.9 54.9 + - + +
269B TYR* 4.1 21.2 + + + +
349B LEU* 4.0 21.5 - - + -
1156B THR* 6.0 1.7 - - - +
1158B ASP* 4.8 2.4 + - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU 3.0 15.9 + - - +
248B GLY* 3.2 8.9 + - - +
250B TYR* 1.3 79.7 - - - +
252B TYR* 1.3 62.9 + - - +
254B LEU* 3.2 11.1 + - + +
255B LEU* 3.0 38.0 + - + +
323B ILE* 6.1 0.2 - - + -
327B VAL* 4.1 19.3 - - + -
346B ALA 3.9 11.7 - - - +
349B LEU* 4.0 17.7 - - + -
350B ALA* 3.7 45.1 - - + +
353B THR* 4.0 23.1 - - + +
354B LEU* 4.9 4.0 - - + -
357B ILE* 6.3 0.4 - - + -
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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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248B GLY 2.9 13.1 + - - +
249B VAL* 3.2 11.2 + - + +
251B LEU* 1.3 77.8 - - - +
253B THR* 1.3 72.3 + - + +
255B LEU* 3.0 15.2 + - + +
256B ALA* 3.0 26.8 + - + +
323B ILE* 4.8 14.8 - - + -
326B ARG* 3.3 36.5 - - + +
327B VAL* 4.2 21.3 - - + +
330B ILE* 4.6 12.8 - - + +
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B VAL* 3.0 22.0 + - + +
250B TYR* 3.0 21.0 + - - -
252B TYR* 1.3 85.3 - - + +
254B LEU* 1.3 60.5 + - - +
256B ALA* 3.1 18.9 + - + +
257B PHE* 3.1 16.1 + - - +
269B TYR* 4.3 8.3 + - - +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 5.8 1.3 - - - -
250B TYR* 2.9 43.9 + - + +
251B LEU* 3.2 7.6 + - + +
253B THR* 1.3 78.6 + - - +
255B LEU* 1.3 61.0 + - + +
256B ALA 3.5 0.2 + - - -
257B PHE* 3.7 16.1 + - + +
345B ILE* 4.7 18.4 - - + -
346B ALA* 4.4 25.5 - - + +
349B LEU* 3.9 28.5 - - + -
1157B TRP* 3.9 32.5 + - + +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 3.0 24.8 + - + +
252B TYR* 3.0 10.1 + - + +
254B LEU* 1.3 78.6 - - - +
256B ALA* 1.3 58.1 + - - +
257B PHE 3.4 4.9 + - - +
327B VAL* 4.0 35.4 - - + -
330B ILE* 4.1 27.6 - - + +
331B VAL* 4.4 13.2 - - + -
334B LYS* 4.3 23.1 + - + +
340B MET* 3.7 28.9 - - + -
346B ALA* 3.8 21.5 - - + +
1001B ASN* 5.6 1.2 + - - -
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B TYR* 3.0 23.4 + - + +
253B THR* 3.1 13.3 + - + +
255B LEU* 1.3 77.1 - - - +
257B PHE* 1.3 59.8 + - - +
1001B ASN* 4.0 10.8 + - - -
1004B GLU* 4.2 9.0 - - - +
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B THR 3.1 13.4 + - - +
254B LEU* 3.7 13.6 + - + +
255B LEU 3.4 4.7 - - - +
256B ALA* 1.3 77.8 - - - +
334B LYS* 5.6 1.6 + - - -
1001B ASN* 1.3 84.4 + - - +
1004B GLU* 3.7 20.6 - - + -
1005B MET* 3.7 22.9 - - + -
1008B ILE* 4.8 8.7 - - + -
1157B TRP* 3.6 54.4 + + + -
1160B TYR* 4.1 26.2 - + + -
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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
------------------------------------------------------------
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