Contacts of the helix formed by residues 198 - 223 (chain B) in PDB entry 3NMV
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 GLY 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B CYS 3.4 5.8 + - - -
197B ASP* 1.3 82.5 + - - +
199B ASP* 1.3 58.3 + - - +
200B THR 3.3 0.2 - - - -
201B TRP* 3.5 20.5 - - - +
202B GLN* 2.9 28.4 + - - +
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Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASP* 3.4 10.8 + - - +
198B GLY* 1.3 74.7 - - - +
200B THR* 1.3 62.3 + - - +
202B GLN* 3.4 10.5 + - - +
203B GLU* 3.1 26.9 + - - +
324B ARG* 4.9 10.4 + - - -
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B CYS* 3.8 26.5 - - - -
197B ASP* 2.9 24.4 + - - -
199B ASP* 1.3 75.8 - - - +
201B TRP* 1.3 59.1 + - - +
203B GLU* 3.3 23.1 + - - +
204B LYS* 2.9 40.5 + - - +
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Residues in contact with TRP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PRO* 4.9 12.7 - - + +
155B HIS* 3.1 21.9 + + - -
193B PRO* 3.4 44.9 - - + +
194B GLU* 4.0 4.7 - - - +
196B CYS* 3.9 4.5 - - + +
198B GLY* 3.3 27.2 + - - +
200B THR* 1.3 77.5 - - - +
202B GLN* 1.3 78.7 + - + +
204B LYS* 3.5 1.2 + - - +
205B TRP* 3.0 32.2 + + - +
240B PHE* 3.6 38.1 - + + -
243B HIS* 4.1 27.8 - + + -
245B PHE* 3.8 28.0 - + - -
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLY 2.9 14.0 + - - +
199B ASP* 3.5 13.7 - - - +
201B TRP* 1.3 83.2 - - + +
203B GLU* 1.3 62.9 + - - +
205B TRP* 3.3 3.6 + - - +
206B LYS* 3.2 40.5 + - - +
243B HIS* 2.9 35.7 + - + +
245B PHE* 3.8 21.5 - - + -
322B SER* 3.5 18.6 + - - +
324B ARG* 5.1 7.1 - - - +
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP* 3.1 16.3 + - - +
200B THR* 3.3 31.8 + - + +
202B GLN* 1.3 76.2 - - - +
204B LYS* 1.3 62.1 + - + +
206B LYS* 3.4 10.9 + - + +
207B LYS* 2.9 32.1 + - + +
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU* 2.8 62.7 + - + +
193B PRO* 3.9 16.6 - - + -
196B CYS* 3.7 31.6 - - - -
200B THR* 2.9 27.3 + - + +
201B TRP 3.9 3.6 - - - +
202B GLN 3.3 0.2 - - - -
203B GLU* 1.3 77.7 - - + +
205B TRP* 1.3 62.1 + - - +
207B LYS* 3.7 10.3 - - + +
208B ALA* 2.8 31.5 + - - +
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Residues in contact with TRP 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 3.8 17.5 - + - -
136B LEU* 3.7 30.3 - - + -
155B HIS* 3.1 28.1 + + - -
184B LEU* 4.3 7.0 - - + -
188B ILE* 3.6 30.7 - - + -
193B PRO* 3.7 8.7 - - + +
201B TRP* 3.0 46.9 + + - +
202B GLN 3.3 0.4 + - - +
204B LYS* 1.3 76.7 - - - +
206B LYS* 1.3 57.9 + - - +
208B ALA* 3.4 2.9 + - - +
209B LEU* 3.0 40.6 + - + +
238B VAL* 3.9 28.7 - - + -
240B PHE* 3.6 23.1 - + - -
245B PHE* 3.6 25.4 - + + -
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLN* 3.2 30.8 + - - +
203B GLU* 3.7 12.1 - - + +
204B LYS 3.3 0.2 - - - -
205B TRP* 1.3 77.2 - - - +
207B LYS* 1.3 56.8 + - - +
209B LEU* 3.4 3.4 + - - +
210B PHE* 2.9 28.6 + - - +
245B PHE* 4.2 8.5 - - + -
320B VAL* 3.9 37.2 + - + +
321B THR* 4.4 3.1 - - - +
322B SER* 3.5 34.6 + - - +
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Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B GLU* 3.1 37.9 + - - +
203B GLU* 2.9 18.7 + - + +
204B LYS* 3.7 9.9 - - + +
206B LYS* 1.3 77.7 - - - +
208B ALA* 1.3 55.8 + - - +
210B PHE* 3.3 8.4 + - + +
211B ASN* 3.0 46.8 + - - +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B LEU* 3.8 7.4 - - + +
187B GLU* 3.8 28.5 - - + +
188B ILE* 3.6 27.8 - - + -
191B GLU* 4.5 6.5 - - + +
204B LYS 2.8 21.9 + - - +
205B TRP 3.7 3.4 - - - +
206B LYS 3.3 0.2 - - - -
207B LYS* 1.3 72.4 - - - +
209B LEU* 1.3 57.6 + - - +
211B ASN* 3.4 1.9 + - - +
212B SER* 2.9 31.5 + - - -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.7 29.4 - - + -
205B TRP* 3.0 25.2 + - + +
206B LYS 3.6 4.0 - - - +
207B LYS 3.3 0.2 - - - -
208B ALA* 1.3 73.7 - - - +
210B PHE* 1.3 69.0 + - - +
212B SER* 2.7 23.1 + - - +
213B PHE* 3.2 13.3 + - + -
236B VAL* 3.9 24.7 - - + +
238B VAL* 4.2 8.5 - - + -
245B PHE* 3.7 35.4 - - + +
247B ALA* 4.0 20.0 - - + +
320B VAL* 4.1 13.0 - - + -
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Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B LYS 2.9 14.8 + - - +
207B LYS* 3.5 11.9 - - + +
209B LEU* 1.3 78.3 - - - +
211B ASN* 1.3 76.3 + - - +
213B PHE* 3.1 13.2 + - - +
214B MET* 3.2 33.4 + - + +
317B ASP* 3.5 35.9 - - + -
318B PRO* 3.7 39.1 - - + +
320B VAL* 4.2 7.7 - - + +
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Residues in contact with ASN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B GLU* 3.7 25.2 + - - +
191B GLU* 4.4 4.0 + - - -
207B LYS* 3.0 44.3 + - - +
208B ALA* 4.0 2.6 - - - +
210B PHE* 1.3 89.0 - - - +
212B SER* 1.3 60.8 + - - +
214B MET* 3.2 8.3 + - - +
215B ARG* 2.8 36.5 + - + +
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B MET* 2.9 25.8 - - - +
183B ALA* 4.0 7.8 - - - +
184B LEU* 3.7 30.2 - - - +
187B GLU* 4.1 5.3 - - - +
208B ALA 2.9 15.5 + - - -
209B LEU* 2.7 24.9 + - - +
211B ASN* 1.3 76.8 - - - +
213B PHE* 1.3 58.5 + - - +
215B ARG* 3.3 3.5 + - - +
216B VAL* 2.9 29.8 + - - +
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Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B MET* 3.9 13.7 - - + -
209B LEU* 3.3 14.1 - - + -
210B PHE 3.1 9.3 + - - +
212B SER* 1.3 87.5 + - - +
214B MET* 1.3 59.4 + - - +
216B VAL* 2.8 24.0 - - - +
217B ASP* 2.9 16.5 + - - +
234B SER* 3.1 41.7 - - - -
236B VAL* 4.0 15.5 - - + -
247B ALA* 3.6 34.5 - - + -
249B CYS* 4.0 10.3 - - - -
305B ILE* 3.7 8.9 - - + +
316B PRO* 4.0 11.7 - - - +
318B PRO* 3.6 35.2 - - + -
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Residues in contact with MET 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B PHE* 3.2 34.7 + - + +
211B ASN* 3.2 11.0 + - - +
213B PHE* 1.3 75.2 - - - +
215B ARG* 1.3 65.4 + - + +
217B ASP* 3.4 6.8 + - - +
218B SER* 3.1 22.7 + - - -
316B PRO* 3.7 22.4 - - + -
317B ASP* 3.4 44.6 - - - +
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG* 3.5 13.8 - - - +
183B ALA* 3.7 12.6 + - + -
186B GLU* 2.5 44.8 + - - +
187B GLU* 2.9 30.2 + - - +
190B LYS* 3.6 13.6 - - - +
211B ASN* 2.8 21.7 + - + +
212B SER* 3.8 4.9 - - - +
214B MET* 1.3 79.8 - - + +
216B VAL* 1.3 62.5 + - - +
218B SER* 2.9 22.0 + - - +
219B GLU* 3.0 26.5 + - - +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B TYR* 4.0 23.6 - - + -
176B CYS* 4.2 24.0 - - - -
179B ARG* 4.8 10.1 - - + -
180B MET* 3.7 20.9 - - + -
183B ALA* 5.1 2.1 - - + +
212B SER 2.9 15.7 + - - +
213B PHE* 2.8 28.9 - - - +
215B ARG* 1.3 73.2 - - - +
217B ASP* 1.3 60.3 + - - +
219B GLU* 3.2 21.9 + - - +
220B ILE* 3.3 12.5 + - - +
305B ILE* 4.0 13.0 - - + -
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Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B PHE 2.9 18.4 + - - +
214B MET* 3.7 6.1 - - - +
216B VAL* 1.3 77.2 - - - +
218B SER* 1.3 62.0 + - - +
220B ILE* 3.3 26.1 + - - +
221B GLU* 4.4 2.1 + - - +
304B SER 4.4 0.2 - - - +
305B ILE* 3.9 4.9 - - + -
306B GLY* 2.8 29.5 + - - +
311B LYS* 3.1 32.3 + - - -
316B PRO* 3.5 33.1 - - + +
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B MET 3.1 13.3 + - - -
215B ARG* 2.9 22.2 + - - +
217B ASP* 1.3 76.4 - - - +
219B GLU* 1.3 64.8 + - - +
220B ILE 3.4 0.5 + - - -
221B GLU* 3.8 5.0 + - - +
222B THR* 3.3 25.4 + - - +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B TYR* 2.6 35.1 + - + +
179B ARG* 2.7 46.2 + - - +
183B ALA* 5.8 0.2 - - - -
215B ARG* 3.0 30.1 + - - +
216B VAL* 3.2 8.4 + - - +
218B SER* 1.3 77.7 - - - +
220B ILE* 1.3 59.4 + - - +
221B GLU 3.2 0.2 - - - -
222B THR* 3.6 7.6 - - - +
223B VAL* 2.7 38.8 + - + -
224B ALA 2.9 9.9 + - - -
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Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL* 3.8 20.4 - - + -
175B TYR* 4.6 11.2 - - + -
216B VAL 3.3 8.4 + - - +
217B ASP* 3.5 16.4 - - - +
218B SER 3.2 1.4 - - - -
219B GLU* 1.3 76.4 - - - +
221B GLU* 1.3 59.7 - - + +
224B ALA* 3.4 9.6 - - + +
225B HIS 2.9 21.7 + - - -
226B ALA* 2.9 37.6 + - + +
227B PRO 5.4 1.1 - - - +
230B VAL* 5.1 2.0 - - + +
305B ILE* 3.2 35.4 - - + -
306B GLY* 3.4 23.6 - - - +
308B ARG* 5.7 5.8 - - + +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ASP 4.4 1.7 + - - +
218B SER* 3.8 6.1 + - - +
219B GLU 3.2 0.2 - - - -
220B ILE* 1.3 80.8 - - - +
222B THR* 1.3 67.0 + - + +
223B VAL 3.4 0.2 - - - -
225B HIS* 3.1 33.0 + - - +
308B ARG* 3.1 51.8 + - + +
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B SER* 3.3 19.9 + - - +
219B GLU* 3.5 3.4 + - - +
221B GLU* 1.3 83.6 - - + +
223B VAL* 1.3 73.5 + - - +
225B HIS* 3.4 19.4 + - - -
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 3.7 23.1 - - + +
219B GLU* 2.7 34.4 + - + +
221B GLU 3.4 0.2 - - - -
222B THR* 1.3 89.1 - - - +
224B ALA* 1.3 62.6 + - - +
225B HIS* 3.3 13.7 - - - -
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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) + - + + + + + -
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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