Contacts of the helix formed by residues 189 - 220 (chain B) in PDB entry 2IAG
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 THR 189 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ALA* 5.9 0.4 - - + -
187B PRO* 4.3 11.9 - - + -
188B ARG* 1.3 83.7 - - - +
190B HIS* 1.3 62.3 + - - +
191B GLU* 3.4 16.3 + - - +
192B SER* 3.0 27.6 + - - +
193B GLN* 3.2 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 1.3 74.5 - - - +
191B GLU* 1.3 95.5 + - + +
193B GLN* 4.2 5.2 - - - +
194B ALA* 3.1 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 3.4 20.2 + - - +
190B HIS* 1.3 110.5 + - + +
192B SER* 1.3 59.1 + - - +
194B ALA* 3.6 5.6 + - - +
195B GLN* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLU* 3.6 29.1 - - - +
185B ALA* 4.0 18.9 + - - -
188B ARG* 3.7 7.6 - - - +
189B THR* 3.0 34.5 + - - -
191B GLU* 1.3 76.9 - - - +
193B GLN* 1.3 57.0 + - - +
195B GLN* 3.2 4.2 + - - +
196B ASP* 2.8 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 4.3 21.4 + - + +
188B ARG* 3.0 51.1 + - + +
189B THR 3.2 19.1 + - - +
190B HIS* 4.2 4.7 - - - +
192B SER* 1.3 79.6 + - - +
194B ALA* 1.3 60.9 + - - +
196B ASP* 3.2 12.9 + - - +
197B ARG* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B HIS* 3.1 21.6 + - - +
191B GLU* 3.7 7.0 - - - +
193B GLN* 1.3 76.2 - - - +
195B GLN* 1.3 61.5 + - - +
197B ARG* 3.4 24.2 + - - +
198B VAL* 3.2 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLU* 4.0 28.7 - - + +
191B GLU 3.0 18.3 + - - +
192B SER 3.2 5.8 + - - +
194B ALA* 1.3 74.4 - - - +
196B ASP* 1.3 59.8 + - - +
198B VAL* 3.3 20.2 + - - +
199B HIS* 2.9 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASN* 5.2 0.2 - - - +
178B LEU* 3.6 35.2 - - + +
183B ILE* 3.6 19.4 - - - +
184B GLU* 2.9 27.0 + - - +
185B ALA 5.3 0.7 + - - +
188B ARG* 4.4 9.7 + - - +
192B SER* 2.8 23.1 + - - +
193B GLN* 3.2 18.6 + - - +
195B GLN* 1.3 71.7 - - - +
197B ARG* 1.3 59.1 + - + +
199B HIS* 4.8 2.9 - - - -
200B SER* 2.8 34.2 + - - -
249B ARG* 3.9 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 3.6 22.2 - - + +
147B VAL* 4.0 16.4 - - + -
150B GLY* 3.5 19.0 + - - -
151B ASP* 2.9 28.0 + - - +
154B GLU* 2.5 45.7 + - - +
174B ARG* 2.8 30.7 + - - +
193B GLN* 3.0 16.9 + - - +
194B ALA* 3.7 27.7 + - - +
195B GLN 3.2 0.4 - - - -
196B ASP* 1.3 76.5 - - + +
198B VAL* 1.3 59.6 + - + +
200B SER* 3.7 1.6 - - - -
201B ALA* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ALA* 3.2 16.5 + - + +
195B GLN* 3.3 24.4 + - - +
197B ARG* 1.3 72.9 - - + +
199B HIS* 1.3 67.7 + - - +
201B ALA* 3.3 5.8 + - - +
202B ASP* 3.1 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 2.6 44.8 + + - -
178B LEU* 5.1 0.9 - - + -
184B GLU* 6.2 0.2 - - - +
195B GLN* 2.9 34.0 + - + +
196B ASP* 4.3 2.0 - - - +
198B VAL* 1.3 73.2 - - - +
200B SER* 1.3 64.3 + - - +
202B ASP* 3.0 22.4 + - - +
203B VAL* 3.0 26.8 + - + +
240B LEU* 4.5 22.8 + - + +
245B ARG* 5.6 11.2 + - + +
249B ARG* 3.5 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 4.7 0.9 - - - +
173B LEU* 4.9 0.2 - - - +
174B ARG* 3.0 55.2 + - - +
177B TYR* 4.3 8.5 - - - -
178B LEU* 4.2 12.9 - - - +
196B ASP 2.8 23.9 + - - -
197B ARG* 3.2 5.0 + - - -
199B HIS* 1.3 77.4 - - - +
201B ALA* 1.3 56.5 + - - +
203B VAL* 3.5 8.7 + - - +
204B PHE 2.9 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG* 3.6 23.6 - - - +
197B ARG 3.1 16.3 + - - +
198B VAL* 3.8 6.5 - - - +
199B HIS 3.2 0.2 - - - -
200B SER* 1.3 77.2 + - - +
202B ASP* 1.3 59.5 + - - +
204B PHE* 3.3 1.6 + - - +
205B HIS* 2.9 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B VAL* 3.1 13.4 + - + +
199B HIS* 3.0 17.0 + - - +
201B ALA* 1.3 77.5 - - - +
203B VAL* 1.3 62.9 + - - +
205B HIS* 3.3 3.5 + - - +
206B THR* 3.0 28.2 + - - -
236B ARG* 2.5 47.5 + - - -
240B LEU* 3.9 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 4.4 9.2 - - + -
177B TYR* 4.0 28.0 - - + -
199B HIS* 3.0 38.8 + - + +
200B SER* 3.6 9.6 - - - +
202B ASP* 1.3 75.6 - - + +
204B PHE* 1.3 53.1 + - - +
206B THR* 3.5 1.0 + - - -
207B PHE* 2.7 37.4 + - - +
237B LEU* 4.2 6.7 - - + +
240B LEU* 4.4 17.3 - - + -
241B LEU* 4.5 6.5 - - + -
281B LEU* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 4.3 14.1 - - - -
169B TYR* 3.6 35.7 - + + -
170B SER* 3.6 36.6 - - - -
173B LEU* 3.9 24.0 - - + -
174B ARG* 3.9 12.8 - - + -
200B SER 2.9 20.7 + - - +
201B ALA* 3.7 3.6 - - - +
202B ASP 3.3 0.2 - - - -
203B VAL* 1.3 73.9 - - - +
205B HIS* 1.3 87.5 + + - +
207B PHE* 3.2 2.1 + - - +
208B ARG* 2.8 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 4.8 9.4 - - - -
170B SER* 6.0 0.6 - - - -
201B ALA* 2.9 45.6 + - + +
202B ASP* 4.1 4.5 - - - +
204B PHE* 1.3 97.1 - + - +
206B THR* 1.3 62.5 + - - +
208B ARG* 3.3 12.1 + - - +
209B GLN* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ASP* 3.0 11.8 + - - -
203B VAL* 3.9 2.5 - - - -
205B HIS* 1.3 76.6 - - - +
207B PHE* 1.3 62.8 + - - +
209B GLN* 3.1 25.8 + - - +
210B LEU 3.3 8.5 + - - -
233B VAL* 3.3 26.5 - - + +
236B ARG* 2.8 44.2 + - + -
237B LEU* 3.7 24.9 - - + -
240B LEU* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B TYR* 3.3 28.5 - + - -
173B LEU* 3.3 28.3 - - + -
203B VAL 2.7 24.6 + - - +
204B PHE* 3.5 6.3 - - - +
206B THR* 1.3 73.6 - - - +
208B ARG* 1.3 62.5 + - + +
210B LEU* 3.1 10.0 + - + +
211B ASP* 2.8 31.2 + - + -
237B LEU* 4.0 15.1 - - + +
278B VAL* 5.4 1.8 - - + -
281B LEU* 3.7 27.6 - - + -
282B TRP* 3.6 55.0 - + + -
286B GLY* 4.1 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.9 20.0 - - - +
169B TYR* 3.5 34.0 - - - -
204B PHE* 2.8 49.6 + - + +
205B HIS* 3.8 7.9 - - - +
206B THR 3.3 0.4 - - - -
207B PHE* 1.3 74.9 - - + +
209B GLN* 1.3 57.6 + - - +
211B ASP* 2.8 35.9 + - - +
212B ARG* 2.9 84.1 + - - +
487B GLN* 3.0 16.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B HIS* 3.7 9.4 + - - +
206B THR* 3.1 35.4 + - - +
208B ARG* 1.3 75.3 - - - +
210B LEU* 1.3 67.2 + - - +
212B ARG* 3.5 15.6 + - - +
213B LEU* 3.4 26.1 + - - +
229B HIS* 3.2 29.2 + - + +
233B VAL* 3.8 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 4.0 23.3 - - + -
206B THR 3.3 3.9 + - - +
207B PHE* 3.1 13.7 + - + +
209B GLN* 1.3 77.1 - - - +
211B ASP* 1.3 61.9 + - + +
213B LEU* 2.9 19.4 + - - -
214B LEU* 3.0 34.5 + - + -
230B MET* 3.6 23.8 - - + +
233B VAL* 3.4 14.9 - - + +
234B LYS* 3.8 29.6 - - + -
237B LEU* 4.0 22.2 - - + -
278B VAL* 4.5 7.9 - - + -
282B TRP* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B TYR* 3.0 17.6 + - - -
207B PHE* 2.8 29.7 + - + +
208B ARG* 2.8 30.7 + - - +
210B LEU* 1.3 83.3 - - - +
212B ARG* 1.3 53.8 + - - +
213B LEU 3.4 0.3 + - - -
214B LEU* 3.6 8.8 + - - +
215B PRO* 3.7 0.3 - - - +
282B TRP* 3.4 22.0 + - - -
286B GLY 5.0 1.0 - - - +
480B ARG* 2.2 40.4 + - - -
487B GLN* 2.9 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B HIS 5.5 0.2 + - - -
208B ARG* 2.9 78.0 + - - +
209B GLN* 3.8 15.1 - - - +
210B LEU 3.2 0.2 - - - -
211B ASP* 1.3 78.8 - - - +
213B LEU* 1.3 64.3 + - + +
214B LEU 3.7 0.3 + - - -
215B PRO* 3.7 9.9 - - - +
216B LYS* 5.2 5.9 - - - +
480B ARG* 3.5 7.7 + - - +
487B GLN* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLN 3.4 15.1 + - - +
210B LEU 2.9 8.5 + - - +
212B ARG* 1.3 80.2 - - + +
214B LEU* 1.3 58.3 + - - +
215B PRO* 3.5 1.6 - - - -
216B LYS* 3.4 10.4 + - + +
217B LEU* 3.0 26.9 + - - +
222B LEU* 4.1 21.7 - - + +
226B ASP* 4.2 20.0 - - - +
229B HIS* 3.6 30.5 - - + +
230B MET* 3.9 37.0 - - + +
233B VAL* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 3.9 18.6 - - + +
108B PHE* 3.6 30.3 - - + -
210B LEU* 3.0 22.4 + - + +
211B ASP* 3.8 6.1 - - - +
213B LEU* 1.3 74.7 - - - +
215B PRO* 1.4 73.1 - - + +
217B LEU* 3.6 1.9 - - - +
218B ALA* 2.9 22.1 + - + +
230B MET* 4.0 9.4 - - + -
282B TRP* 3.6 34.1 - - + +
480B ARG* 5.1 2.9 - - - +
483B PHE* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG 3.7 6.1 - - - +
213B LEU 3.6 2.9 - - - -
214B LEU* 1.4 96.0 - - + +
216B LYS* 1.3 60.1 + - + +
217B LEU 3.1 0.3 + - - -
218B ALA* 3.2 1.2 + - - +
219B ARG* 2.9 41.9 + - - +
477B ASP* 5.9 0.7 - - - +
479B SER* 3.6 35.4 - - - +
480B ARG* 3.6 40.2 - - + +
483B PHE* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG 5.2 7.4 - - - +
213B LEU* 3.4 6.8 + - + +
215B PRO* 1.3 83.2 - - + +
217B LEU* 1.3 56.1 + - - +
219B ARG* 4.5 16.4 - - - +
220B GLY 3.0 6.2 + - - -
221B SER* 2.9 51.1 + - - +
222B LEU* 3.1 33.9 + - + +
479B SER* 5.1 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 3.1 28.5 + - - +
107B ILE* 3.6 21.3 - - + +
213B LEU 3.0 17.8 + - - +
214B LEU* 3.6 4.3 - - - +
215B PRO 3.1 0.4 - - - -
216B LYS* 1.3 73.4 - - - +
218B ALA* 1.3 66.6 + - - +
220B GLY* 3.0 11.7 + - - -
222B LEU* 3.9 19.9 - - + +
227B LYS* 5.3 11.7 - - + -
230B MET* 3.5 30.7 - - + -
234B LYS* 3.6 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 6.0 2.2 - - + -
106B ARG* 3.7 19.6 + - - +
107B ILE* 4.1 25.8 - - + +
214B LEU* 2.9 18.5 + - + +
215B PRO 3.7 3.1 - - - +
217B LEU* 1.3 76.1 - - - +
219B ARG* 1.3 62.1 + - + +
220B GLY 3.5 0.3 + - - -
483B PHE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY* 3.8 36.8 + - - -
48B LYS* 5.5 1.0 - - - +
106B ARG* 4.8 1.6 - - - -
215B PRO* 2.9 35.4 + - + +
216B LYS* 4.1 11.7 - - - +
218B ALA* 1.3 79.6 - - + +
220B GLY* 1.3 60.3 + - - +
221B SER* 4.1 19.4 + - - +
479B SER* 3.2 45.0 + - - +
483B PHE* 5.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 3.9 12.1 - - - -
216B LYS 3.0 3.8 + - - -
217B LEU* 3.0 13.9 + - - -
218B ALA 3.2 0.8 - - - -
219B ARG* 1.3 80.1 - - - +
221B SER* 1.3 57.9 + - - +
222B LEU 3.7 3.1 + - - +
227B LYS* 5.3 11.0 + - - -
----------------------------------------------------------
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