Contacts of the helix formed by residues 178 - 205 (chain R) in PDB entry 6NIY
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 CYS 178 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN* 4.3 20.6 - - - -
176R LEU 3.2 5.3 + - - +
177R GLY* 1.3 75.0 - - - +
179R GLN* 1.3 76.4 + - - +
180R ARG* 3.4 16.6 - - + +
181R VAL* 3.8 21.3 - - + +
182R THR* 3.2 24.6 + - - +
243R TYR* 5.8 0.4 - - - -
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Residues in contact with GLN 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R CYS* 1.3 79.3 - - - +
180R ARG* 1.3 65.8 + - - +
182R THR* 3.3 21.4 - - - +
183R LEU* 3.4 9.4 + - - +
243R TYR* 3.4 27.6 - - + +
254R THR* 4.7 13.0 - - + -
255R GLU 4.5 0.9 + - - +
256R LYS* 3.3 52.1 - - + +
259R LEU* 3.4 36.0 - - - +
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Residues in contact with ARG 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN* 3.3 59.6 + - - +
391A TYR* 3.4 40.3 - - - +
170R PHE* 5.8 2.2 - - - -
178R CYS* 4.2 11.0 - - - +
179R GLN* 1.3 77.6 - - - +
181R VAL* 1.3 69.2 + - + +
183R LEU* 3.2 5.7 + - - +
184R HIS* 2.7 64.0 + - + +
243R TYR* 3.6 18.2 + - + +
247R LEU* 5.5 1.1 - - + -
391R TYR* 5.7 5.3 + - - -
395R ASN* 4.3 6.5 + - - +
397R GLU* 3.8 31.3 + - - +
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Residues in contact with VAL 181 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170R PHE* 3.6 45.0 - - + +
176R LEU 3.3 28.7 - - - +
177R GLY* 5.1 1.6 - - - -
178R CYS* 3.5 19.3 + - + +
179R GLN 3.3 0.6 - - - -
180R ARG* 1.3 101.1 - - + +
182R THR* 1.3 56.9 + - - +
184R HIS* 3.1 8.8 + - - +
185R LYS* 2.8 29.9 + - + +
397R GLU* 4.8 6.1 - - - +
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Residues in contact with THR 182 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R CYS 3.2 15.0 + - - +
179R GLN* 3.3 32.3 - - - +
181R VAL* 1.3 77.5 - - - +
183R LEU* 1.3 63.7 + - - +
185R LYS* 3.3 30.9 + - - +
186R ASN* 3.0 21.6 + - - +
259R LEU* 4.9 8.7 - - + +
263R TYR* 4.7 5.2 + - - +
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Residues in contact with LEU 183 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R GLN* 3.4 10.3 + - - +
180R ARG* 3.2 10.4 + - - +
182R THR* 1.3 82.1 - - - +
184R HIS* 1.3 62.7 + - + +
186R ASN* 3.5 5.1 + - - +
187R MET 3.4 5.7 + - - -
236R TRP* 3.4 49.0 + - + +
239R CYS* 4.7 2.0 - - + +
240R GLU* 3.5 13.9 - - + +
243R TYR* 3.8 44.2 - - + -
259R LEU* 4.1 24.2 - - + -
262R TYR* 4.4 21.1 - - + -
263R TYR* 4.8 6.1 - - + -
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Residues in contact with HIS 184 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TYR* 3.9 26.9 - + - -
170R PHE* 3.9 19.7 - + + -
180R ARG* 2.7 48.2 + - - +
181R VAL* 3.1 10.3 + - - +
183R LEU* 1.3 72.5 - - - +
185R LYS* 1.3 59.4 + - - +
187R MET* 3.2 7.8 + - - +
188R PHE* 2.9 39.5 + + + -
240R GLU* 2.9 38.3 + - + -
351R LEU* 3.5 21.6 - - + +
391R TYR* 4.8 11.4 - + + +
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Residues in contact with LYS 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167R LEU* 3.4 23.8 - - + +
170R PHE* 3.7 34.8 - - + +
171R VAL* 4.2 18.0 - - + +
174R ARG* 4.6 16.0 - - - +
181R VAL* 2.8 18.3 + - + +
182R THR* 3.5 25.8 - - - +
183R LEU 3.3 0.4 - - - -
184R HIS* 1.3 76.6 - - - +
186R ASN* 1.3 64.9 + - - +
188R PHE* 3.4 0.8 + - - -
189R LEU* 3.3 22.8 + - - +
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Residues in contact with ASN 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182R THR* 3.0 17.7 + - - +
183R LEU* 3.9 1.8 - - - +
184R HIS 3.3 0.2 - - - -
185R LYS* 1.3 75.6 - - - +
187R MET* 1.3 64.5 + - - +
189R LEU* 3.3 23.0 - - + +
190R THR* 3.0 25.9 + - - -
236R TRP* 3.5 27.1 - - + -
263R TYR* 2.5 40.3 + - - -
267R TRP* 4.3 8.7 - - - +
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Residues in contact with MET 187 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183R LEU 3.4 2.8 + - - -
184R HIS* 3.2 12.2 + - - +
186R ASN* 1.3 79.1 - - - +
188R PHE* 1.3 76.9 + - + +
190R THR* 3.2 8.5 + - - -
191R TYR* 3.1 42.3 + - + -
233R ASN* 5.0 4.3 - - - +
236R TRP* 3.4 27.7 - - + +
237R MET* 5.0 6.1 - - + +
240R GLU* 3.2 42.2 - - - +
351R LEU* 4.2 13.7 - - + +
387R VAL* 3.7 28.7 - - + -
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Residues in contact with PHE 188 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163R LEU* 3.6 21.9 - - + +
166R SER* 3.7 15.3 - - - -
167R LEU* 3.7 28.7 - - + -
170R PHE* 3.6 30.5 - + - -
184R HIS* 2.9 22.8 + + + +
185R LYS 3.7 5.4 - - - +
186R ASN 3.3 0.2 - - - -
187R MET* 1.3 87.6 - - + +
189R LEU* 1.3 57.3 + - - +
191R TYR* 3.2 6.9 + + - +
192R ILE* 3.0 28.9 + - - +
387R VAL* 3.6 37.7 - - + -
388R ALA* 4.5 2.2 - - - -
391R TYR* 4.8 7.4 - - + -
392R CYS* 3.6 21.3 - - - -
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Residues in contact with LEU 189 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167R LEU* 3.8 20.7 - - + +
185R LYS 3.3 16.0 + - - +
186R ASN* 3.3 31.2 - - - +
188R PHE* 1.3 79.4 - - - +
190R THR* 1.3 52.9 + - - +
192R ILE* 3.1 7.5 + - + +
193R LEU* 2.6 45.7 + - + +
267R TRP* 3.8 27.1 - - + -
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Residues in contact with THR 190 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186R ASN 3.0 14.9 + - - -
187R MET* 3.2 14.6 + - - -
189R LEU* 1.3 79.3 - - - +
191R TYR* 1.3 51.2 + - - +
193R LEU* 3.5 7.0 - - + +
194R ASN* 2.6 37.8 + - - +
229R MET* 4.5 2.5 - - - +
232R CYS* 3.7 27.8 - - - +
233R ASN* 3.7 29.6 - - + +
236R TRP* 5.1 7.7 - - + -
267R TRP* 3.3 20.5 - - + -
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Residues in contact with TYR 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163R LEU* 3.6 35.5 - - + +
187R MET* 3.1 29.4 + - + -
188R PHE* 3.2 9.6 + + - +
190R THR* 1.3 75.5 - - - +
192R ILE* 1.3 58.2 + - - +
194R ASN* 3.9 4.5 - - - +
195R SER* 2.9 31.7 + - - -
233R ASN* 3.1 39.5 - - - -
237R MET* 3.3 23.8 - - + +
350R PRO 4.0 2.4 + - - -
351R LEU 4.6 0.3 + - - -
383R GLN* 3.4 18.4 + - - -
384R GLY* 4.1 12.1 - - - -
387R VAL* 3.6 38.0 - - + +
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Residues in contact with ILE 192 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160R ILE* 3.6 35.2 - - + +
163R LEU* 3.7 10.5 - - + -
164R VAL* 3.4 40.2 - - + +
167R LEU* 4.5 9.9 - - + -
188R PHE 3.0 19.7 + - - +
189R LEU* 3.3 13.0 - - + +
191R TYR* 1.3 75.2 - - - +
193R LEU* 1.3 63.5 + - - +
196R MET* 3.2 27.1 + - + +
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Residues in contact with LEU 193 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189R LEU* 2.6 27.4 + - + +
190R THR* 3.6 5.6 - - - +
192R ILE* 1.3 76.5 - - - +
194R ASN* 1.3 60.0 + - - +
196R MET* 3.3 35.9 - - + +
197R ILE* 3.3 13.3 + - + +
229R MET* 3.6 42.2 - - + -
267R TRP* 4.4 19.1 - - + -
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Residues in contact with ASN 194 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R HIS* 5.3 3.8 + - - -
190R THR 2.6 21.4 + - - +
191R TYR* 3.9 7.4 - - - +
193R LEU* 1.3 71.9 - - - +
195R SER* 1.3 64.9 + - - +
197R ILE* 3.3 10.3 - - - +
198R ILE* 3.1 43.6 + - - +
226R HIS* 4.8 1.6 + - - -
229R MET* 4.7 15.2 - - + +
230R MET* 4.4 18.2 + - - +
233R ASN* 3.6 24.3 - - - +
234R TYR* 5.9 1.6 + - - -
----------------------------------------------------------
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Residues in contact with SER 195 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R HIS* 3.5 38.6 + - - +
159R SER* 5.6 2.5 - - - -
160R ILE* 3.5 33.0 - - - +
163R LEU* 6.0 0.9 - - - -
191R TYR 2.9 18.5 + - - -
194R ASN* 1.3 77.4 - - - +
196R MET* 1.3 62.6 + - - +
198R ILE* 3.4 2.9 + - - +
199R ILE* 3.0 27.4 + - - +
----------------------------------------------------------
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Residues in contact with MET 196 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160R ILE* 4.0 12.0 - - + +
192R ILE* 3.2 22.9 + - + +
193R LEU* 3.3 29.6 - - + +
195R SER* 1.3 76.7 + - - +
197R ILE* 1.3 83.0 + - - +
199R ILE* 3.4 7.0 + - - +
200R ILE* 2.8 43.6 + - + +
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Residues in contact with ILE 197 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193R LEU* 3.3 13.9 + - + +
194R ASN* 3.3 20.2 - - - +
196R MET* 1.3 90.9 - - - +
198R ILE* 1.3 60.5 + - - +
200R ILE* 3.3 15.0 - - + +
201R HIS* 2.8 30.2 + - + +
222R LEU* 4.1 13.7 - - + +
225R PHE* 3.6 22.9 - - + +
226R HIS* 3.5 46.2 - - + +
229R MET* 4.3 15.3 - - + -
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Residues in contact with ILE 198 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P LEU* 3.9 38.6 - - + -
156R HIS* 3.9 37.5 - - + +
194R ASN* 3.1 36.1 + - - +
195R SER 3.8 3.8 - - - +
196R MET 3.3 0.2 - - - -
197R ILE* 1.3 76.2 - - - +
199R ILE* 1.3 52.6 + - - +
201R HIS* 3.1 10.2 + - + +
202R LEU* 2.7 45.6 + - + +
226R HIS* 3.3 24.0 - - + +
230R MET* 6.5 1.1 - - + -
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Residues in contact with ILE 199 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R ALA 5.4 1.1 - - - +
153R ILE* 4.8 14.8 - - + +
156R HIS* 4.0 26.2 - - + -
157R SER* 4.1 20.6 - - - +
160R ILE* 5.2 4.5 - - + -
195R SER* 3.0 23.8 + - - +
196R MET* 3.9 5.8 - - - +
197R ILE 3.3 0.2 - - - -
198R ILE* 1.3 75.5 - - + +
200R ILE* 1.3 62.3 + - - +
202R LEU* 3.0 26.1 + - + +
203R VAL* 3.0 23.7 + - + +
----------------------------------------------------------
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Residues in contact with ILE 200 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196R MET* 2.8 27.8 + - + +
197R ILE* 3.3 22.0 - - + +
199R ILE* 1.3 76.5 - - - +
201R HIS* 1.3 64.3 + - - +
203R VAL* 3.2 26.3 - - + +
204R GLU* 3.6 9.5 + - - +
222R LEU* 3.8 30.5 - - + +
----------------------------------------------------------
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Residues in contact with HIS 201 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P LEU* 6.0 3.3 - - + +
13P SER* 3.1 36.8 + - - -
197R ILE* 2.8 22.5 + - + +
198R ILE* 3.3 11.0 + - - +
200R ILE* 1.3 75.3 - - + +
202R LEU* 1.3 66.3 + - - +
204R GLU* 3.3 26.7 - - + +
205R VAL* 3.3 26.3 + - + +
222R LEU* 5.1 4.9 - - + -
223R HIS* 4.7 19.7 - + + -
226R HIS* 4.7 20.6 + + + -
291R LEU* 3.6 23.1 - - + +
----------------------------------------------------------
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Residues in contact with LEU 202 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P LEU* 5.3 5.8 - - + -
12P LEU* 6.0 3.6 - - + -
13P SER* 4.5 12.8 - - - +
149R TYR* 3.4 39.6 + - + +
152R ALA* 4.1 23.1 - - + +
153R ILE* 3.9 28.9 - - + +
156R HIS* 5.6 0.2 - - - +
198R ILE* 2.7 31.4 + - + +
199R ILE* 3.0 19.7 + - + +
201R HIS* 1.3 77.6 - - - +
203R VAL* 1.3 63.5 + - + +
205R VAL* 3.3 29.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 203 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149R TYR* 4.5 6.5 - - - +
153R ILE* 6.0 4.3 - - + -
199R ILE* 3.0 19.2 + - + +
200R ILE* 3.2 29.2 - - + +
202R LEU* 1.3 78.8 - - + +
204R GLU* 1.3 63.0 + - + +
205R VAL 3.4 4.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 204 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200R ILE 3.6 5.6 + - - +
201R HIS* 3.3 36.3 + - + +
202R LEU 3.3 0.6 - - - -
203R VAL* 1.3 82.8 - - + +
205R VAL* 1.3 61.2 + - + +
219R CYS* 3.8 41.0 - - - +
222R LEU* 4.3 21.7 - - + +
223R HIS* 5.5 1.0 + - - +
291R LEU* 6.0 0.9 - - + +
----------------------------------------------------------
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Residues in contact with VAL 205 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P SER* 4.2 13.2 - - - +
16P LEU* 5.4 12.6 - - + -
17P HIS* 3.8 37.2 - - + +
149R TYR* 5.2 5.2 - - + -
201R HIS* 3.3 29.7 + - + +
202R LEU* 3.3 33.7 - - + +
203R VAL 4.2 4.0 - - - +
204R GLU* 1.3 82.5 - - + +
291R LEU* 4.8 12.6 - - + -
----------------------------------------------------------
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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