Contacts of the helix formed by residues 202 - 226 (chain E) in PDB entry 5FWP
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 LYS 202 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E LEU* 2.8 34.8 + - + +
200E GLU* 2.7 43.6 + - + +
201E GLU* 1.3 77.7 - - - +
203E CYS* 1.3 57.8 + - - +
204E ALA 3.3 2.7 - - - -
205E LEU* 3.3 15.4 + - + +
206E MET* 2.9 27.1 + - - +
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Residues in contact with CYS 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E GLU* 5.0 10.8 - - - -
201E GLU* 3.4 15.0 + - - +
202E LYS* 1.3 73.4 - - - +
204E ALA* 1.3 61.0 + - - +
206E MET* 3.4 25.9 - - + +
207E GLU* 2.9 40.8 + - - +
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Residues in contact with ALA 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E LYS 3.3 0.8 - - - -
203E CYS* 1.3 77.9 - - - +
205E LEU* 1.3 63.7 + - - +
207E GLU* 3.6 12.6 + - - +
208E GLN* 3.3 18.7 + - - +
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Residues in contact with LEU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E MET* 4.2 25.8 - - + -
193E TRP* 3.8 16.2 - - + -
197E LEU* 3.7 27.4 - - + -
202E LYS* 3.3 18.9 + - + +
204E ALA* 1.3 76.2 - - - +
206E MET* 1.3 56.5 + - - +
208E GLN* 2.9 13.5 + - + +
209E VAL* 2.8 47.9 + - + +
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Residues in contact with MET 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E CYS* 3.4 38.2 - - + +
197E LEU* 3.6 19.0 - - + +
198E GLU* 3.6 28.9 - - + +
202E LYS 2.9 16.8 + - - +
203E CYS* 3.2 30.5 + - + +
205E LEU* 1.3 76.7 - - - +
207E GLU* 1.3 60.7 + - + +
209E VAL* 3.3 0.6 + - - -
210E ALA* 2.8 34.8 + - + +
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Residues in contact with GLU 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E CYS* 2.9 26.3 + - - +
204E ALA* 3.7 10.3 - - - +
206E MET* 1.3 86.9 - - + +
208E GLN* 1.3 58.3 + - - +
210E ALA* 3.3 7.8 + - - +
211E HIS* 2.9 26.7 + - - +
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Residues in contact with GLN 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLY 3.7 7.2 - - - +
164E MET* 4.6 7.0 - - - +
165E LEU 2.7 30.2 + - - +
166E ARG* 2.9 50.3 + - + +
204E ALA 3.3 9.2 + - - +
205E LEU* 2.9 15.7 + - + +
207E GLU* 1.3 76.0 - - - +
209E VAL* 1.3 61.1 + - - +
211E HIS* 3.3 27.3 + - - +
212E GLN* 3.0 27.0 + - - +
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Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLY 3.6 13.2 - - - +
190E LEU* 3.5 23.5 - - + +
193E TRP* 3.4 44.9 - - + -
194E CYS* 3.4 18.4 - - - +
197E LEU* 3.7 11.9 - - + -
205E LEU* 2.8 25.1 + - + +
206E MET 3.6 4.3 - - - +
208E GLN* 1.3 75.0 - - - +
210E ALA* 1.3 51.5 + - - +
212E GLN* 3.2 3.9 + - - +
213E THR* 2.6 37.1 + - - -
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Residues in contact with ALA 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E CYS* 3.4 10.9 - - - -
206E MET* 2.8 20.1 + - + +
207E GLU* 3.5 9.4 - - - +
209E VAL* 1.3 71.8 - - - +
211E HIS* 1.3 64.9 + - - +
213E THR* 3.2 11.1 + - - -
214E ILE* 3.0 29.9 + - + +
260E LYS* 5.3 9.0 - - - +
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Residues in contact with HIS 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E ARG* 4.3 19.0 + - + +
168E TRP* 3.6 38.1 - + - -
207E GLU 2.9 13.8 + - - +
208E GLN* 3.3 24.4 + - - +
210E ALA* 1.3 76.3 - - - +
212E GLN* 1.3 89.5 + - - +
214E ILE* 2.9 36.2 - - + +
215E VAL* 3.1 13.2 + - + +
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Residues in contact with GLN 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E PHE* 3.1 53.0 - - + +
163E GLY* 3.5 18.2 - - - +
165E LEU 3.2 28.7 + - - +
166E ARG* 4.2 2.2 + - - +
168E TRP* 5.1 1.0 - - - -
171E SER* 2.8 27.1 + - - -
190E LEU* 4.0 1.5 - - + +
208E GLN 3.0 11.5 + - - +
209E VAL 3.7 6.3 - - - +
211E HIS* 1.3 103.1 + - - +
213E THR* 1.3 64.3 + - - +
215E VAL* 3.2 9.4 + - - +
216E MET* 3.1 18.5 + - - +
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Residues in contact with THR 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ALA* 4.0 9.9 - - - +
190E LEU* 3.2 29.6 + - - +
191E VAL* 3.6 30.1 - - + -
194E CYS* 3.9 2.1 - - - -
209E VAL 2.6 27.9 + - - -
210E ALA* 3.2 14.0 + - - -
212E GLN* 1.3 71.6 - - - +
214E ILE* 1.3 57.4 + - - +
216E MET* 3.2 5.0 + - - +
217E GLN* 2.9 35.8 + - + +
260E LYS* 4.0 15.9 - - + -
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Residues in contact with ILE 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ALA* 3.0 14.7 + - + +
211E HIS* 2.9 35.7 - - + +
213E THR* 1.3 72.4 - - - +
215E VAL* 1.3 56.5 + - + +
217E GLN* 3.9 7.0 - - - -
218E PHE* 2.7 35.7 + - - +
253E ASN* 5.1 12.3 - - + +
256E LEU* 3.2 29.6 - - + +
257E GLU* 3.7 25.1 - - + +
260E LYS* 3.8 22.9 - - + +
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Residues in contact with VAL 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E PHE* 3.9 18.4 - - + -
168E TRP* 3.5 35.9 - - + -
211E HIS* 3.1 17.7 + - + +
212E GLN* 3.4 22.4 - - - +
213E THR 3.2 0.2 - - - -
214E ILE* 1.3 79.2 - - + +
216E MET* 1.3 57.3 + - - +
218E PHE* 3.2 8.7 + - - +
219E ILE* 3.0 33.5 + - + +
237E PHE* 6.4 0.7 - - + -
238E PHE* 4.0 22.0 - - + -
241E ILE* 5.2 5.8 - - + -
256E LEU* 5.0 0.7 - - + -
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Residues in contact with MET 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E PHE* 3.9 16.1 - - + -
175E LEU* 3.8 33.2 - - + -
181E LEU 3.4 16.8 - - - +
182E VAL* 3.6 29.6 - - - -
183E CYS 3.7 21.5 - - - +
186E THR* 4.1 7.9 - - + -
187E ALA* 3.8 17.0 - - + +
190E LEU* 4.5 4.5 - - + -
212E GLN 3.1 13.1 + - - +
213E THR 3.7 7.0 - - - +
215E VAL* 1.3 74.0 - - - +
217E GLN* 1.3 60.2 + - - +
219E ILE* 3.2 9.5 + - - +
220E LEU* 3.0 34.7 + - + +
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Residues in contact with GLN 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ALA* 3.5 28.1 + - + +
188E ASN* 4.6 7.7 + - - -
191E VAL* 4.7 4.6 - - - +
213E THR* 2.9 23.5 + - + +
214E ILE* 3.6 8.1 - - - +
216E MET* 1.3 74.0 - - - +
218E PHE* 1.3 54.1 + - - +
220E LEU* 3.5 9.8 - - - +
221E GLU 2.7 29.1 + - - -
256E LEU* 3.8 7.0 - - + -
259E PHE* 3.0 36.6 - - + +
260E LYS* 3.8 40.7 + - + +
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Residues in contact with PHE 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A MET* 6.5 0.2 - - + -
214E ILE 2.7 21.1 + - - +
215E VAL* 3.3 7.6 - - - +
217E GLN* 1.3 69.7 - - - +
219E ILE* 1.3 65.2 + - - +
221E GLU* 3.0 36.0 + - - +
222E LEU* 3.2 25.5 + - + -
237E PHE* 2.9 41.0 - + + -
240E LYS* 4.9 8.7 - - + -
241E ILE* 3.7 38.8 - - + -
249E MET* 4.8 4.9 - - + -
252E PHE* 4.6 30.3 - + + -
256E LEU* 3.3 22.0 - - + +
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Residues in contact with ILE 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E LEU* 3.8 28.9 - - + -
182E VAL* 3.6 24.7 - - + -
215E VAL* 3.0 18.3 + - + +
216E MET* 3.4 18.8 - - - +
218E PHE* 1.3 75.8 - - - +
220E LEU* 1.3 61.9 + - + +
223E ALA* 3.1 13.2 - - - +
230E PRO* 3.8 10.5 - - + +
234E PHE* 3.6 23.6 - - + -
237E PHE* 3.0 47.0 - - + -
238E PHE* 4.3 9.6 - - + -
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Residues in contact with LEU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E CYS* 4.0 12.3 - - - +
184E GLU* 3.8 49.8 - - + +
187E ALA* 4.0 8.1 - - + -
216E MET* 3.0 20.2 + - + +
217E GLN* 3.5 24.9 - - - +
219E ILE* 1.3 78.1 - - + +
221E GLU* 1.3 61.3 + - - +
223E ALA* 3.7 3.3 - - - +
224E LYS* 3.0 37.6 + - - +
230E PRO* 3.7 26.5 - - + -
259E PHE* 3.9 11.0 - - + -
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Residues in contact with GLU 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E GLN 2.7 16.8 + - - +
218E PHE* 3.0 33.6 + - + +
220E LEU* 1.3 75.3 - - - +
222E LEU* 1.3 71.4 + - + +
224E LYS* 3.6 4.7 + - - +
225E SER* 3.2 25.1 + - - +
255E GLU* 3.9 24.5 - - - +
256E LEU* 3.4 19.0 + - - +
259E PHE* 3.6 37.9 - - + +
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Residues in contact with LEU 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E PHE* 3.2 29.6 + - + -
221E GLU* 1.3 90.6 - - + +
223E ALA* 1.3 56.3 + - - +
224E LYS 3.2 1.3 - - - -
225E SER* 3.7 19.5 - - - +
226E LEU* 2.7 41.1 + - + +
237E PHE* 3.4 25.4 - - + -
240E LYS* 3.6 31.4 - - + +
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Residues in contact with ALA 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ILE 3.1 21.7 + - - +
220E LEU 3.7 2.5 - - - +
222E LEU* 1.3 77.7 - - - +
224E LYS* 1.3 57.3 + - - +
226E LEU 3.4 0.5 + - - -
227E LYS 3.0 7.3 + - - -
228E VAL* 2.9 45.5 + - - +
230E PRO* 3.6 37.2 - - + -
233E CYS* 3.8 8.1 - - - -
237E PHE* 3.6 1.0 - - - -
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Residues in contact with LYS 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E GLU* 2.8 31.2 + - - +
220E LEU* 3.0 30.2 + - + +
221E GLU 3.7 4.9 - - - +
223E ALA* 1.3 77.7 - - + +
225E SER* 1.3 61.0 + - - +
227E LYS* 3.0 19.3 + - - +
228E VAL 5.1 0.4 - - - -
230E PRO* 6.1 1.8 - - + -
259E PHE* 3.9 28.6 - - + -
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Residues in contact with SER 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E GLU* 3.2 13.6 + - - +
222E LEU* 3.2 28.6 + - - +
224E LYS* 1.3 79.5 - - - +
226E LEU* 1.3 62.3 + - - +
227E LYS* 3.2 9.2 + - - +
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Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E LEU* 2.7 37.9 + - + +
225E SER* 1.3 73.4 - - - +
227E LYS* 1.3 71.3 + - - +
228E VAL* 3.4 30.6 - - + +
233E CYS* 4.7 5.6 - - + -
236E GLN* 4.1 19.3 - - - +
237E PHE* 5.2 2.9 - - + -
240E LYS* 4.9 13.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il