Contacts of the helix formed by residues 170 - 199 (chain L) in PDB entry 1JH0
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 170 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L PHE* 2.9 30.0 + - + +
168L HIS 3.7 0.2 - - - +
169L TYR* 1.3 69.1 - - - +
171L PRO* 1.3 72.3 - - - +
172L ALA* 2.9 20.6 + - - +
173L HIS* 3.2 16.2 + - + +
174L MET* 3.1 21.3 + - - +
247L CYS* 2.8 31.5 + - - +
250L ILE* 4.2 1.2 - - - +
251L THR* 3.1 17.0 + - - -
259L TRP* 3.5 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 171 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169L TYR 3.0 8.3 - - - +
170L ASN* 1.3 84.2 - - - +
172L ALA* 1.3 57.7 + - + +
174L MET* 3.2 15.5 + - + +
175L ILE* 3.1 30.3 + - - +
250L ILE* 5.3 3.8 - - + -
259L TRP* 3.3 26.5 - - + -
262L TRP* 4.0 36.6 - - + -
263L TRP* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170L ASN* 2.9 8.1 + - - +
171L PRO* 1.3 74.2 - - - +
173L HIS* 1.3 60.8 + - - +
175L ILE* 3.7 9.9 - - - +
176L ALA* 3.0 28.2 + - - +
243L PHE* 3.6 11.4 - - + +
246L LEU* 4.4 16.2 - - + -
247L CYS* 3.4 32.1 - - + +
250L ILE* 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 173 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L PHE* 3.7 31.7 + + - -
168L HIS* 4.3 13.1 + + - -
170L ASN* 3.2 28.0 + - + +
172L ALA* 1.3 75.6 - - - +
174L MET* 1.3 61.5 + - - +
176L ALA* 3.8 3.6 - - - +
177L ILE* 3.0 68.8 + - + +
247L CYS* 3.4 16.1 - - - +
851L BCL 2.6 63.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168L HIS 3.4 20.6 - - - +
169L TYR* 4.3 4.3 - - - -
170L ASN 3.1 14.8 - - - +
171L PRO* 3.2 9.8 + - - +
173L HIS* 1.3 79.1 - - - +
175L ILE* 1.3 61.8 + - + +
177L ILE* 3.4 3.1 + - - +
178L SER* 2.8 27.8 + - - -
263L TRP* 3.6 28.0 - - + -
90M PHE* 5.9 0.7 - - + -
180M PHE* 3.7 26.7 - - + -
183M LEU* 3.8 7.4 - - + -
850M BCL 2.9 56.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171L PRO 3.1 13.7 + - - +
172L ALA* 3.7 9.6 - - - +
174L MET* 1.3 78.8 - - + +
176L ALA* 1.3 61.3 + - - +
178L SER* 3.3 11.7 + - - +
179L PHE* 3.3 28.3 + - + -
243L PHE* 3.3 47.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L ALA 3.0 17.8 + - - +
173L HIS* 3.8 6.5 - - - +
175L ILE* 1.3 76.8 - - - +
177L ILE* 1.3 64.3 + - - +
179L PHE* 3.4 3.8 + - - +
180L PHE* 3.1 29.4 + - - -
240L ALA* 3.7 5.6 - - - +
243L PHE* 3.7 7.9 - - + -
244L SER* 3.4 40.8 - - - +
247L CYS* 5.8 0.2 - - - -
851L BCL 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173L HIS* 3.0 46.8 + - + +
174L MET 3.7 4.3 - - - +
175L ILE 3.3 0.2 - - - -
176L ALA* 1.3 74.0 - - - +
178L SER* 1.3 67.5 + - - +
180L PHE* 3.3 6.4 + - - +
181L PHE* 3.0 51.1 + - + -
851L BCL 3.6 43.3 - - + -
850M BCL 3.2 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174L MET 2.8 19.3 + - - -
175L ILE* 3.3 14.5 - - - +
176L ALA 3.2 0.2 - - - -
177L ILE* 1.3 82.3 - - - +
179L PHE* 1.3 59.3 + - - +
181L PHE* 3.2 1.6 + - - +
182L THR* 2.8 34.6 + - - -
850M BCL 3.1 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175L ILE* 3.3 27.2 + - + -
176L ALA 3.8 1.8 - - - +
177L ILE 3.4 0.2 - - - -
178L SER* 1.3 79.2 - - - +
180L PHE* 1.3 57.3 + - - +
182L THR* 3.6 4.3 - - - -
183L ASN* 2.8 33.1 + - - +
235L LEU 5.2 0.4 - - - -
236L LEU* 3.8 29.7 - - + +
239L SER* 4.0 22.4 - - - -
240L ALA* 3.4 27.1 - - + +
243L PHE* 3.5 37.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L ALA 3.1 23.9 + - - -
177L ILE* 3.6 8.3 - - + +
178L SER 3.2 0.2 - - - -
179L PHE* 1.3 76.5 - - - +
181L PHE* 1.3 65.6 + - + +
183L ASN* 3.2 6.7 + - - +
184L ALA* 3.1 22.9 + - - +
240L ALA* 3.5 30.5 - - + -
241L VAL* 4.6 8.5 - - + -
244L SER* 3.5 3.4 - - - -
851L BCL 3.5 50.0 - + + -
855L BPH 4.7 3.6 - - + -
209M LEU* 4.1 32.9 - - + +
210M TYR* 4.3 15.0 - + - -
213M ALA* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177L ILE* 3.0 40.1 + - + +
178L SER* 3.7 4.9 - - - +
180L PHE* 1.3 77.1 - - + +
182L THR* 1.3 62.0 + - - +
184L ALA* 4.7 0.9 - - - -
185L LEU* 3.1 19.8 + - - +
851L BCL 4.2 21.8 - - + -
209M LEU* 4.3 13.5 - - + -
850M BCL 4.1 43.5 - + + -
852M BCL 3.3 46.7 - - + -
854M BPH 3.1 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178L SER 2.8 19.1 + - - -
179L PHE* 3.6 4.9 - - - -
181L PHE* 1.3 73.5 - - - +
183L ASN* 1.3 55.3 + - - +
184L ALA 3.0 1.3 - - - -
185L LEU* 2.9 13.4 + - + +
186L ALA* 2.8 33.7 + - + +
236L LEU* 3.3 36.3 - - + -
850M BCL 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 183 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L PHE 2.8 22.6 + - - +
180L PHE* 3.5 7.2 + - - +
182L THR* 1.3 74.8 - - - +
184L ALA* 1.3 57.7 + - - +
186L ALA 3.9 0.4 - - - -
187L LEU* 3.1 22.2 + - - +
233L GLY 3.5 4.5 - - - +
236L LEU* 3.4 22.5 - - + +
237L SER* 2.8 36.4 + - - -
240L ALA* 5.6 0.7 - - + -
212M SER* 3.4 26.9 + - - -
213M ALA* 3.4 14.2 - - + +
216M PHE* 3.6 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180L PHE 3.1 11.6 + - - +
181L PHE 3.7 2.9 - - - +
182L THR 3.0 0.8 - - - -
183L ASN* 1.3 76.8 - - - +
185L LEU* 1.3 68.6 + - - +
186L ALA 3.1 1.1 - - - -
187L LEU* 3.3 1.0 + - - -
188L ALA* 2.8 26.0 + - - +
209M LEU* 4.4 13.0 - - + -
212M SER* 4.3 23.3 - - - +
273M ALA* 3.7 8.1 - - + +
276M VAL* 5.2 4.5 - - + -
854M BPH 3.5 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181L PHE 3.1 10.4 + - - +
182L THR* 2.9 14.5 + - + +
184L ALA* 1.3 78.8 - - - +
186L ALA* 1.3 59.5 + - - +
188L ALA* 3.2 3.8 + - - +
189L LEU* 3.0 51.5 + - + +
850M BCL 4.8 18.6 - - + -
854M BPH 3.5 75.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182L THR* 2.8 16.9 + - + +
183L ASN 3.8 1.8 - - - +
185L LEU* 1.3 79.4 - - - +
187L LEU* 1.3 59.7 + - - +
189L LEU* 3.0 7.1 + - - +
190L HIS* 2.9 30.0 + - - +
229L ILE* 5.0 7.5 - - + +
232L LEU* 5.2 8.3 - - + -
236L LEU* 3.8 21.1 - - + -
216M PHE* 3.5 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L ASN 3.1 10.2 + - - +
184L ALA* 3.3 3.3 + - - +
186L ALA* 1.3 78.2 - - - +
188L ALA* 1.3 64.4 + - - +
189L LEU 3.2 0.2 + - - -
190L HIS* 4.3 2.0 - - + +
191L GLY* 3.2 20.1 + - - -
212M SER* 3.8 36.3 - - - +
215M LEU* 4.3 11.9 - - + -
216M PHE* 3.1 55.9 - - + +
219M HIS* 5.4 4.7 - - + -
269M ALA* 3.7 42.7 - - + +
272M MET* 4.3 1.3 - - + -
273M ALA* 4.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L ALA 2.8 14.7 + - - +
185L LEU 3.2 10.8 - - - +
187L LEU* 1.3 76.5 - - - +
189L LEU* 1.3 60.3 + - - +
192L ALA* 3.4 3.3 + - - +
149M ALA* 4.4 6.4 - - + +
269M ALA 4.9 1.6 - - - -
270M ILE* 2.9 33.7 - - - +
273M ALA* 3.9 16.9 - - + +
274M VAL* 5.1 2.9 - - + +
854M BPH 4.1 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L LEU* 3.0 38.0 + - + +
186L ALA* 3.5 7.6 - - - +
188L ALA* 1.3 74.4 - - - +
190L HIS* 1.3 55.7 + - - +
191L GLY 3.0 1.8 - - - -
192L ALA* 2.9 6.0 + - - +
193L LEU* 2.8 36.5 + - - +
216L PHE* 3.8 24.6 - - + -
229L ILE* 6.1 2.2 - - + -
146M THR* 3.8 18.5 + - + +
854M BPH 3.6 60.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L ALA 2.9 17.4 + - - +
187L LEU* 4.3 5.2 - - + +
189L LEU* 1.3 73.4 - - - +
191L GLY* 1.3 58.6 + - - +
193L LEU* 3.9 11.7 - - - +
194L VAL* 3.1 35.7 + - + +
226L THR* 6.2 1.1 - - - -
229L ILE* 3.5 35.2 - - + +
230L HIS* 3.1 21.1 - + - -
216M PHE* 4.1 13.5 - + + -
219M HIS* 3.8 15.0 - + - -
234M GLU* 3.2 8.3 - - - -
266M HIS* 2.7 10.6 + + - -
269M ALA* 5.7 1.6 - - + -
856M FE 2.1 32.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 191 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L LEU 3.2 13.0 + - - -
189L LEU 3.0 0.8 - - - -
190L HIS* 1.3 76.8 - - - +
192L ALA* 1.3 63.5 - - - +
193L LEU 3.2 0.4 - - - -
195L LEU* 3.0 34.4 + - - +
266M HIS* 4.0 25.8 - - - +
269M ALA* 4.6 5.2 - - - -
270M ILE* 3.7 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L ALA 3.5 7.4 - - - +
189L LEU* 2.9 5.9 + - - +
191L GLY* 1.3 76.5 - - - +
193L LEU* 1.3 54.7 + - - +
195L LEU* 4.5 0.4 - - - -
196L SER* 2.8 37.5 + - - -
145M HIS* 3.4 11.8 - - + +
146M THR* 3.5 35.0 - - - +
149M ALA* 4.6 1.3 - - + -
270M ILE* 3.1 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189L LEU 2.8 16.3 + - - +
190L HIS* 3.9 13.2 - - - +
191L GLY 3.2 0.2 - - - -
192L ALA* 1.3 72.0 - - - +
194L VAL* 1.3 66.8 + - + +
195L LEU 3.0 1.8 + - - -
196L SER* 2.9 25.1 + - - +
197L ALA* 3.1 11.4 + - - +
212L GLU* 3.6 39.7 - - + +
215L PHE* 3.6 34.3 - - + -
216L PHE* 4.1 22.4 - - + -
142M MET* 4.5 2.4 - - + +
146M THR* 4.3 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L HIS* 3.1 41.6 + - + +
193L LEU* 1.3 80.0 - - + +
195L LEU* 1.3 59.1 + - + +
197L ALA* 3.7 3.5 - - - +
198L ALA* 3.2 27.1 + - + +
212L GLU* 3.4 17.0 + - - +
234M GLU* 3.4 17.5 - - + +
235M LEU* 3.8 12.1 - - + +
238M ILE* 5.6 5.4 - - + -
262M MET 5.3 1.6 - - - +
263M GLU* 5.9 1.8 - - + -
266M HIS* 3.4 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191L GLY 3.0 23.6 + - - +
192L ALA 3.8 0.4 - - - +
193L LEU 3.0 0.8 - - - -
194L VAL* 1.3 75.9 - - + +
196L SER* 1.3 56.1 + - - +
197L ALA 2.9 5.4 - - - -
198L ALA* 4.8 0.7 - - + -
199L ASN* 2.8 52.5 + - - +
145M HIS* 3.5 27.8 - - + +
263M GLU* 4.0 20.9 - - + +
266M HIS* 3.8 24.5 - - + +
267M ARG* 3.8 35.9 - - + +
270M ILE* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L ALA 2.8 21.0 + - - -
193L LEU* 2.9 23.0 + - - +
195L LEU* 1.3 71.8 - - - +
197L ALA* 1.3 58.2 + - - +
199L ASN 4.2 1.3 - - - -
200L PRO* 3.9 4.0 - - - +
215L PHE* 5.6 1.6 - - - -
137M ALA* 5.9 0.2 - - - -
142M MET* 3.0 25.4 - - - +
143M GLY* 2.8 50.1 + - - +
145M HIS* 3.5 15.4 + - - -
146M THR* 4.6 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L LEU 3.1 14.2 + - - +
194L VAL 3.7 5.4 - - - +
195L LEU 2.9 1.2 - - - -
196L SER* 1.3 78.5 - - - +
198L ALA* 1.3 63.5 + - - +
199L ASN 3.2 1.7 + - - -
200L PRO* 3.4 6.9 - - - +
207L ARG* 3.0 40.9 + - + +
212L GLU* 3.9 14.8 - - + -
142M MET* 4.5 3.8 - - + -
235M LEU* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H PHE* 3.2 32.0 - - + -
194L VAL* 3.2 16.4 + - + +
195L LEU* 4.8 0.4 - - - -
197L ALA* 1.3 77.6 - - - +
199L ASN* 1.3 68.7 + - - +
200L PRO* 3.4 7.2 - - - +
206L MET* 3.6 12.6 - - + +
235M LEU* 3.7 17.9 - - + +
238M ILE* 4.8 11.2 - - + -
263M GLU* 4.3 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 199 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H LYS* 3.1 25.5 + - - -
64H PHE* 4.6 0.7 - - - -
195L LEU* 2.8 28.7 + - - +
196L SER 4.1 1.8 - - - -
198L ALA* 1.3 85.7 - - - +
200L PRO* 1.3 66.2 - - - +
143M GLY* 3.6 15.9 - - - -
145M HIS* 3.9 13.5 - - + +
263M GLU* 2.7 24.8 + - - -
267M ARG* 3.6 14.8 + - - +
----------------------------------------------------------
Back to top of page
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