Contacts of the helix formed by residues 217 - 258 (chain C) in PDB entry 5C5B
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 217 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU* 3.0 29.9 + - - +
213C MET* 3.1 12.0 + - + +
216C GLU* 1.3 73.8 - - - +
218C LEU* 1.3 59.2 - - - +
219C ASN 3.2 2.5 - - - -
220C GLU* 2.8 46.2 + - - +
221C GLN* 3.1 20.5 + - - +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C VAL* 3.7 18.6 - - + +
95C GLU* 3.9 13.5 - - + +
96C LEU* 3.5 44.4 - - + +
99C CYS* 4.7 7.0 - - - -
213C MET 4.1 0.8 + - - -
214C GLY* 3.1 17.4 + - - +
217C ASN* 1.3 82.3 - - - +
219C ASN* 1.3 58.2 + - - +
221C GLN* 3.3 6.0 + - - +
222C LEU* 2.9 46.4 + - + +
207D GLN* 5.1 0.7 - - + +
211D PHE* 3.5 40.6 - - + -
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Residues in contact with ASN 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C GLY 3.4 4.4 + - - +
215C SER* 2.5 32.9 + - - +
216C GLU* 4.3 4.4 - - - +
217C ASN 4.2 0.3 - - - +
218C LEU* 1.3 76.0 - - - +
220C GLU* 1.3 85.0 + - - +
222C LEU* 3.6 9.0 - - - +
223C GLU* 2.8 30.8 + - - +
208D ILE* 4.2 20.5 - - + +
211D PHE* 5.7 6.2 - - + +
212D LYS* 6.0 7.7 - - + +
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Residues in contact with GLU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C GLU* 5.7 1.3 - - + -
217C ASN* 2.8 29.7 + - - +
219C ASN* 1.3 89.7 + - - +
221C GLN* 1.3 61.8 + - + +
223C GLU* 3.1 9.1 + - - +
224C GLU* 3.0 22.3 + - + +
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Residues in contact with GLN 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LYS* 3.1 31.0 + - - +
92C VAL* 3.4 40.4 - - + +
95C GLU* 3.2 34.3 + - - +
217C ASN* 3.1 25.6 + - - +
218C LEU* 4.0 3.9 - - - +
220C GLU* 1.3 77.7 - - + +
222C LEU* 1.3 57.8 + - - +
224C GLU* 3.4 5.6 + - - +
225C PHE* 2.9 32.1 + - - +
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C VAL* 3.7 26.0 - - + -
218C LEU* 2.9 38.2 + - + +
219C ASN* 3.6 1.3 - - - +
221C GLN* 1.3 77.8 - - - +
223C GLU* 1.3 56.0 + - - +
225C PHE* 3.6 6.3 - - + +
226C LEU* 2.9 35.0 + - - +
203D PHE* 5.0 7.4 - - + -
204D ALA* 3.8 28.9 - - + +
207D GLN* 3.7 25.1 - - + -
208D ILE* 3.5 32.5 - - + +
211D PHE* 5.5 0.9 - - + -
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Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASN 2.8 17.9 + - - +
220C GLU* 3.1 7.6 + - - +
222C LEU* 1.3 73.5 - - - +
224C GLU* 1.3 65.4 + - - +
226C LEU* 3.1 12.2 + - - +
227C ALA* 3.0 21.3 + - - +
208D ILE* 4.9 2.2 - - + +
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Residues in contact with GLU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C GLU* 3.0 14.9 + - + +
221C GLN* 4.0 5.8 - - - +
223C GLU* 1.3 75.5 - - - +
225C PHE* 1.3 63.1 + - - +
227C ALA* 3.1 7.0 + - - +
228C ASN* 3.0 34.9 + - - +
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Residues in contact with PHE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C THR 3.9 1.1 - - - -
88C GLN* 4.1 21.8 - - + +
89C PHE* 3.3 56.8 - + + -
92C VAL* 4.7 7.9 - - + -
221C GLN 2.9 18.5 + - - +
222C LEU* 3.6 9.2 - - + +
224C GLU* 1.3 76.6 - - - +
226C LEU* 1.3 64.3 + - - +
228C ASN* 3.2 2.5 + - - +
229C ILE* 2.9 64.1 + - + +
200D MET* 3.4 35.7 - - + -
201D ILE* 4.5 1.6 - - - -
204D ALA* 3.9 17.7 - - + -
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Residues in contact with LEU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C LEU 2.9 24.6 + - - +
223C GLU* 3.4 10.1 - - - +
225C PHE* 1.3 76.8 - - + +
227C ALA* 1.3 63.6 + - - +
229C ILE* 4.1 1.7 - - - +
230C GLY* 2.9 22.3 + - - -
201D ILE* 4.0 18.4 - - + +
204D ALA* 3.7 26.5 - - + +
205D HIS* 3.5 50.3 - - + +
208D ILE* 4.6 13.2 - - + -
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Residues in contact with ALA 227 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C GLU 3.0 11.7 + - - +
224C GLU* 3.3 12.1 - - - +
226C LEU* 1.3 77.3 - - - +
228C ASN* 1.3 68.9 + - - +
230C GLY* 3.2 0.9 + - - -
231C THR* 3.1 30.1 + - + +
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Residues in contact with ASN 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C THR* 6.0 2.0 - - + -
88C GLN* 3.2 38.1 + - - +
224C GLU* 3.0 20.3 + - - +
225C PHE* 3.8 3.3 - - - +
227C ALA* 1.3 78.5 - - - +
229C ILE* 1.3 64.1 + - + +
231C THR* 2.7 28.1 + - - -
232C SER* 3.0 12.7 + - - +
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Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C THR* 3.5 39.3 - - + -
88C GLN* 4.6 4.3 - - - +
225C PHE* 2.9 50.6 + - + +
226C LEU 4.2 0.4 - - - +
228C ASN* 1.3 75.5 - - - +
230C GLY* 1.3 57.5 + - - +
232C SER* 3.3 4.1 + - - -
233C VAL* 2.9 31.4 + - + +
197D MET* 3.9 29.4 - - + +
200D MET* 4.6 4.9 - - + -
201D ILE* 3.5 26.9 - - + -
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Residues in contact with GLY 230 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C LEU 2.9 19.0 + - - -
227C ALA 3.6 1.3 - - - -
229C ILE* 1.3 76.0 - - - +
231C THR* 1.3 62.5 + - - +
233C VAL* 3.1 11.9 - - - +
234C GLN* 3.1 24.4 + - - +
201D ILE* 4.7 5.3 - - - +
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Residues in contact with THR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ALA* 3.1 17.4 + - + +
228C ASN* 2.7 20.1 + - - +
230C GLY* 1.3 76.8 - - - +
232C SER* 1.3 68.9 + - - +
234C GLN* 3.3 4.7 + - - +
235C ASN* 2.8 36.2 + - - +
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Residues in contact with SER 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C VAL* 3.9 26.8 - - - +
85C THR* 4.4 5.6 - - - +
228C ASN* 3.0 17.0 + - - +
229C ILE* 3.7 4.9 - - - -
230C GLY 3.3 0.2 - - - -
231C THR* 1.3 85.1 + - - +
233C VAL* 1.3 62.9 + - - +
235C ASN* 3.1 11.6 + - - +
236C VAL* 3.0 28.2 + - - +
197D MET* 3.9 20.0 - - - -
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C ILE* 2.9 21.4 + - + +
230C GLY* 3.1 22.4 - - - +
232C SER* 1.3 69.7 - - - +
234C GLN* 1.3 66.9 + - - +
236C VAL* 3.4 2.5 + - - +
237C ARG* 3.0 25.7 + - + +
194D MET* 4.6 20.8 - - + +
197D MET* 3.6 28.6 - - + +
198D GLU* 5.3 7.6 - - + +
201D ILE* 4.9 19.7 - - + -
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Residues in contact with GLN 234 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLY 3.1 13.6 + - - +
231C THR* 3.5 11.7 - - - +
233C VAL* 1.3 81.1 - - + +
235C ASN* 1.3 66.1 + - - +
237C ARG* 3.3 5.8 + - - +
238C ARG* 3.1 24.3 + - - +
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Residues in contact with ASN 235 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C THR* 2.8 25.7 + - - +
232C SER* 3.3 10.3 - - - +
234C GLN* 1.3 79.3 - - - +
236C VAL* 1.3 65.5 + - + +
238C ARG* 3.3 5.4 + - - +
239C GLU* 3.0 25.7 + - - +
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C VAL* 5.8 4.5 - - + -
232C SER* 3.0 17.5 + - - +
233C VAL 4.0 1.8 - - - +
235C ASN* 1.3 75.5 - - + +
237C ARG* 1.3 63.2 + - - +
239C GLU* 3.4 5.1 + - - +
240C MET* 3.0 23.4 + - - +
190D TYR* 3.7 25.6 - - + +
193D GLN* 3.6 31.2 - - + +
194D MET* 3.5 27.4 - - + -
197D MET* 4.0 15.0 - - + -
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Residues in contact with ARG 237 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C VAL* 3.0 15.2 + - + +
234C GLN* 3.4 11.2 - - - +
236C VAL* 1.3 77.8 - - - +
238C ARG* 1.3 64.0 + - - +
240C MET* 3.7 1.2 - - - +
241C ASP* 2.8 34.2 + - - +
194D MET* 4.0 21.7 - - + -
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Residues in contact with ARG 238 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLN 3.1 10.0 + - - +
235C ASN* 3.7 8.3 - - - +
237C ARG* 1.3 80.0 - - - +
239C GLU* 1.3 64.4 + - - +
240C MET 3.1 0.5 + - - -
241C ASP* 3.2 2.9 + - - +
242C SER* 3.1 21.7 + - - -
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ASN 3.0 17.5 + - - +
236C VAL* 4.0 4.7 - - - +
238C ARG* 1.3 76.8 - - - +
240C MET* 1.3 59.2 + - - +
242C SER* 3.1 10.4 + - - -
243C ASP* 3.0 25.3 + - - +
190D TYR* 5.1 12.5 - - + -
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Residues in contact with MET 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C VAL* 3.0 16.7 + - + +
237C ARG* 4.0 2.9 - - - +
239C GLU* 1.3 75.2 - - - +
241C ASP* 1.3 64.8 + - - +
242C SER 3.1 1.3 - - - -
243C ASP* 3.5 22.7 - - - -
244C ILE* 2.9 56.9 + - + +
247C MET* 4.7 2.7 - - + -
186D ASN 4.0 1.3 - - - +
187D ALA* 3.2 39.3 - - + +
190D TYR* 3.0 45.8 - - + -
191D ARG* 5.7 1.8 - - + -
194D MET* 5.4 4.5 - - - -
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Residues in contact with ASP 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ARG* 2.8 30.5 + - - +
238C ARG* 3.2 2.7 + - - +
240C MET* 1.3 77.9 - - - +
242C SER* 1.3 62.5 + - - +
244C ILE* 4.4 13.6 - - - +
245C GLU* 3.1 26.0 + - - +
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Residues in contact with SER 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C ARG 3.1 13.4 + - - -
239C GLU* 3.1 15.6 + - - -
241C ASP* 1.3 76.3 - - - +
243C ASP* 1.3 60.0 + - - +
245C GLU* 3.3 5.8 + - - +
246C THR* 3.0 34.2 + - - -
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Residues in contact with ASP 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C GLU 3.0 13.6 + - - +
240C MET* 3.4 19.9 + - + -
242C SER* 1.3 75.5 - - - +
244C ILE* 1.3 60.9 + - - +
246C THR* 4.5 7.1 - - - +
247C MET* 3.0 46.0 + - - +
6D LYS* 2.7 36.4 + - - +
190D TYR* 3.2 13.4 + - + +
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Residues in contact with ILE 244 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C MET* 2.9 50.7 + - + +
241C ASP* 4.4 13.0 - - - +
243C ASP* 1.3 75.2 - - - +
245C GLU* 1.3 66.0 + - - +
247C MET* 3.9 7.9 - - + +
248C GLN* 2.9 27.7 + - + +
183D CYS* 5.1 8.7 - - - -
187D ALA* 4.6 9.0 - - + -
191D ARG* 4.4 21.5 - - + +
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Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ASP 3.1 21.4 + - - +
242C SER* 3.3 5.6 + - - +
244C ILE* 1.3 78.7 - - - +
246C THR* 1.3 63.6 + - - +
248C GLN* 3.2 5.2 + - - +
249C GLN* 3.0 24.8 + - - +
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Residues in contact with THR 246 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C SER* 3.0 20.1 + - - -
243C ASP* 4.0 9.6 - - - +
245C GLU* 1.3 77.5 - - - +
247C MET* 1.3 53.4 + - + +
249C GLN* 3.5 6.4 + - - +
250C THR* 2.5 44.0 + - - +
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Residues in contact with MET 247 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C MET* 4.7 6.5 - - + -
243C ASP* 3.0 45.0 + - - +
244C ILE* 3.9 6.1 - - + +
245C GLU 3.3 0.2 - - - -
246C THR* 1.3 76.5 - - + +
248C GLN* 1.3 59.6 + - - +
250C THR* 3.3 6.9 + - - +
251C ILE* 2.9 35.4 + - - +
6D LYS* 6.4 1.1 - - + -
7D LEU 5.4 0.4 - - - +
9D LEU* 3.6 16.0 - - + +
183D CYS* 3.8 33.7 - - - +
186D ASN* 3.4 46.7 - - + -
187D ALA 4.4 4.0 - - - +
190D TYR* 5.9 0.2 - - + -
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Residues in contact with GLN 248 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ILE* 2.9 21.7 + - + +
245C GLU* 3.2 6.5 + - - +
247C MET* 1.3 75.6 - - - +
249C GLN* 1.3 58.7 + - - +
251C ILE* 3.3 13.2 + - - +
252C GLU* 3.0 25.8 + - - +
183D CYS* 4.8 3.7 - - - -
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Residues in contact with GLN 249 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C GLU 3.0 15.3 + - - +
246C THR* 4.0 4.6 - - - +
248C GLN* 1.3 74.9 - - - +
250C THR* 1.3 60.4 + - - +
252C GLU* 3.1 7.2 + - + +
253C ASP* 3.0 53.7 + - - +
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Residues in contact with THR 250 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C THR* 2.5 33.2 + - - +
247C MET* 3.5 8.8 - - - -
248C GLN 3.3 0.2 - - - -
249C GLN* 1.3 74.9 - - - +
251C ILE* 1.3 59.3 + - - +
253C ASP* 3.3 6.4 + - - -
254C LEU* 2.9 56.7 + - + +
9D LEU* 4.2 17.0 - - + -
10D GLU* 5.5 2.9 - - + +
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Residues in contact with ILE 251 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C MET 2.9 19.5 + - - +
248C GLN* 3.4 10.5 - - - +
250C THR* 1.3 74.6 - - - +
252C GLU* 1.3 60.2 + - - +
254C LEU* 3.9 1.9 - - - +
255C GLU* 2.9 32.8 + - + +
9D LEU* 3.7 13.7 - - + -
176D LEU* 6.0 2.2 - - + -
179D LEU* 3.7 45.4 - - + +
180D GLN* 3.7 29.6 - - - +
183D CYS* 3.9 20.2 - - + -
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Residues in contact with GLU 252 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C GLN 3.0 13.1 + - - +
249C GLN* 3.1 13.4 + - + +
251C ILE* 1.3 79.5 - - - +
253C ASP* 1.3 61.5 + - - +
255C GLU* 3.8 5.2 - - - +
256C VAL* 3.0 26.7 + - - +
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Residues in contact with ASP 253 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLN* 3.0 39.2 + - - +
250C THR* 3.9 6.5 - - - +
252C GLU* 1.3 81.3 - - - +
254C LEU* 1.3 65.0 + - + +
256C VAL* 3.3 8.6 + - - +
257C ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 254 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C THR* 2.9 38.7 + - + +
251C ILE 3.9 3.6 - - - +
253C ASP* 1.3 78.3 - - + +
255C GLU* 1.3 59.3 + - - +
257C ALA* 3.9 3.5 - - - -
258C SER* 2.4 43.4 + - - +
9D LEU* 3.2 45.3 - - + +
10D GLU* 3.5 16.4 - - + +
175D HIS* 4.5 10.3 - - + +
179D LEU* 4.2 9.9 - - + -
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Residues in contact with GLU 255 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ILE* 2.9 20.4 + - + +
252C GLU* 3.8 6.3 - - - +
254C LEU* 1.3 77.4 - - - +
256C VAL* 1.3 63.2 + - - +
258C SER* 3.9 5.6 + - - -
259C ASP* 4.0 15.9 + - - +
262C TYR* 4.7 11.0 + - - -
172D ARG* 5.1 1.6 + - - -
175D HIS* 4.8 3.5 - - - -
176D LEU* 4.3 22.7 - - + -
179D LEU* 4.9 3.1 - - + +
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLU 3.0 16.0 + - - +
253C ASP* 3.4 12.8 - - - +
255C GLU* 1.3 79.5 - - - +
257C ALA* 1.3 60.8 + - + +
259C ASP* 3.9 12.4 + - - +
260C PRO* 4.7 1.9 - - - +
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASP 2.9 16.4 + - - +
254C LEU* 3.3 4.2 + - - +
256C VAL* 1.3 73.6 - - - +
258C SER* 1.3 62.3 + - - +
259C ASP 3.2 6.6 + - - -
260C PRO* 3.3 16.6 - - - +
261C LEU* 4.0 8.7 - - + +
271C PHE* 5.4 0.9 - - - -
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Residues in contact with SER 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C LEU* 2.4 27.5 + - - +
255C GLU 3.9 0.6 + - - -
256C VAL 3.5 0.6 - - - -
257C ALA* 1.3 76.6 - - - +
259C ASP* 1.3 57.8 + - - +
260C PRO 3.4 1.1 - - - -
261C LEU* 2.9 35.1 + - - +
262C TYR* 3.3 33.2 + - - -
13D LEU* 4.1 15.2 - - - +
175D HIS* 3.3 16.7 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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