Contacts of the helix formed by residues 193 - 217 (chain B) in PDB entry 6E8Y
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 GLU 193 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLY* 4.7 0.7 - - - -
191B VAL* 3.4 4.7 - - + +
192B GLN* 1.3 76.8 - - + +
194B VAL* 1.3 66.4 + - - +
195B ASP 3.4 2.2 - - - -
196B THR* 3.2 15.9 + - - +
197B VAL* 3.0 25.9 + - - +
246B PRO* 3.0 48.0 - - + +
248B SER* 2.7 32.1 + - - -
251B THR* 2.8 26.2 + - + +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B SER* 4.5 7.9 - - - +
144B MET 4.0 20.6 - - - +
146B VAL* 3.9 24.5 - - + +
167B GLY* 3.5 30.3 - - - +
168B CYS* 3.8 0.7 - - - -
169B LYS* 3.7 24.7 - - + +
192B GLN 3.1 5.5 + - - +
193B GLU* 1.3 70.7 - - - +
195B ASP* 1.3 72.7 + - - +
197B VAL* 3.2 4.3 + - - +
198B GLU* 3.1 21.3 + - - +
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.7 27.7 - - + +
133B SER* 5.5 0.7 + - - -
134B GLU* 3.9 13.3 - - - +
193B GLU 3.4 0.8 - - - -
194B VAL* 1.3 83.8 - - - +
196B THR* 1.3 62.7 + - - +
198B GLU* 3.3 1.2 + - - +
199B ILE* 2.9 27.5 + - - +
243B CYS* 4.0 14.8 - - + +
244B SER* 2.9 45.6 + - - +
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Residues in contact with THR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU* 3.2 28.1 + - - +
195B ASP* 1.3 79.7 - - - +
197B VAL* 1.3 64.3 + - - +
199B ILE* 3.5 8.0 - - - +
200B CYS* 3.4 21.1 + - - -
239B ALA* 4.9 0.2 - - + -
243B CYS* 4.6 1.8 - - - -
246B PRO 3.6 4.2 + - - -
247B VAL* 3.4 25.8 - - + +
251B THR* 3.7 19.7 - - + -
252B PHE* 3.4 37.5 - - + -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 3.6 20.4 - - + -
148B MET* 3.8 18.1 - - + +
165B THR* 3.9 17.9 - - + +
167B GLY* 4.1 8.3 - - - +
191B VAL* 3.5 26.9 - - + -
193B GLU 3.0 13.9 + - - +
194B VAL 3.2 6.7 + - - +
196B THR* 1.3 78.7 - - - +
198B GLU* 1.3 62.9 + - - +
200B CYS* 3.4 15.8 + - - +
201B GLY 4.0 2.3 + - - -
251B THR* 4.0 4.5 - - + -
256B CYS* 3.9 27.9 - - + +
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 4.8 1.6 + - - -
119B ILE 4.8 4.4 - - - +
121B GLY 4.8 13.0 + - - +
122B VAL* 5.3 0.2 - - - +
131B LEU* 3.4 30.4 - - + +
132B ILE* 3.2 12.5 + - - +
133B SER* 2.5 52.1 + - - -
146B VAL* 3.5 16.1 - - + +
148B MET* 4.4 18.4 - - + +
194B VAL* 3.1 16.7 + - - +
195B ASP 3.9 3.1 - - - +
197B VAL* 1.3 75.8 - - - +
199B ILE* 1.3 65.7 + - - +
200B CYS 3.3 0.3 + - - -
201B GLY* 3.3 12.6 + - - -
202B ALA* 4.0 3.6 + - - +
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Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 4.7 9.2 - - + -
129B LEU* 4.4 18.6 - - + -
131B LEU* 3.8 22.4 - - + +
195B ASP 2.9 15.9 + - - +
196B THR* 3.5 11.7 - - - +
198B GLU* 1.3 77.1 - - - +
200B CYS* 1.3 68.5 + - - +
202B ALA* 3.2 4.8 + - + +
203B LEU* 3.1 43.3 + - + +
238B PHE* 4.9 4.5 - - + -
239B ALA* 4.0 16.8 - - + -
242B PHE* 4.3 20.2 - - + -
243B CYS* 3.9 20.0 - - - -
252B PHE* 5.2 0.9 - - + -
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Residues in contact with CYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B THR* 3.4 15.9 - - - -
197B VAL 3.4 11.1 + - - +
198B GLU 3.1 0.2 - - - -
199B ILE* 1.3 81.5 - - - +
201B GLY* 1.3 62.1 + - - +
203B LEU* 4.9 0.4 - - - -
204B LYS* 3.1 29.6 + - - +
235B MET* 3.9 13.5 - - + +
251B THR 5.6 0.4 - - - -
252B PHE* 3.4 37.0 - - - -
256B CYS* 3.2 33.7 - - + +
257B GLY* 4.1 8.1 - - - -
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LYS* 3.8 32.8 - - - +
121B GLY* 4.6 5.1 + - - -
148B MET* 5.3 3.9 - - - +
197B VAL 4.0 2.0 + - - -
198B GLU 3.3 9.8 + - - -
199B ILE 3.2 1.4 - - - -
200B CYS* 1.3 78.0 - - - +
202B ALA* 1.3 58.5 + - - +
204B LYS* 3.5 23.6 - - - +
205B ASN* 3.7 10.2 + - - -
256B CYS 4.8 1.3 + - - -
260B ASP* 4.9 1.8 - - - -
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLY* 4.4 8.8 - - - -
122B VAL* 3.5 44.0 - - + -
129B LEU* 5.9 0.7 - - + -
198B GLU 4.0 2.2 + - - +
199B ILE* 3.2 13.8 + - + +
201B GLY* 1.3 77.4 - - - +
203B LEU* 1.3 66.7 + - + +
204B LYS 3.2 0.6 + - - -
205B ASN* 3.4 18.9 + - - +
206B VAL* 4.0 1.7 + - - +
302B THR* 4.0 19.8 + - + +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 4.9 1.1 - - + -
199B ILE* 3.1 45.1 + - + +
200B CYS 4.3 1.6 - - - +
202B ALA* 1.3 79.6 - - + +
204B LYS* 1.3 62.0 + - - +
206B VAL* 3.0 21.4 + - - +
207B VAL* 3.4 12.5 + - - +
235B MET* 3.6 47.6 - - + +
238B PHE* 4.2 13.9 - - + -
239B ALA 4.9 0.2 - - - +
252B PHE* 5.9 0.7 - - + -
302B THR* 4.4 6.1 - - + -
306B LEU* 4.0 36.3 - - + -
322B PHE* 4.5 5.3 - - + -
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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
----------------------------------------------------------
120B LYS* 3.7 16.4 - - - +
200B CYS 3.1 15.8 + - - +
201B GLY* 3.5 19.3 - - - +
203B LEU* 1.3 77.4 - - - +
205B ASN* 1.3 85.1 + - - +
207B VAL* 3.3 4.8 + - - +
208B ALA* 2.9 27.0 + - - +
235B MET* 4.2 7.8 - - + +
256B CYS 5.4 1.1 - - - +
257B GLY 5.8 0.2 - - - +
260B ASP* 3.1 40.1 + - + +
261B LEU* 3.9 29.2 - - + +
264B THR* 3.0 26.7 + - + +
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Residues in contact with ASN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLY* 5.8 3.8 - - - -
201B GLY 3.7 14.6 + - - -
202B ALA* 3.8 8.7 + - - +
203B LEU 3.1 0.8 - - - -
204B LYS* 1.3 102.7 + - - +
206B VAL* 1.3 62.9 + - - +
208B ALA* 3.4 6.4 + - - +
209B VAL* 3.2 27.0 + - - +
264B THR* 3.7 8.1 - - - +
270B ASN* 3.6 22.0 + - - +
298B GLN* 4.2 16.5 - - - +
299B GLY* 3.7 18.7 - - - -
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ALA 4.2 0.9 - - - +
203B LEU* 3.0 12.0 + - - +
205B ASN* 1.3 74.3 - - - +
207B VAL* 1.3 65.8 + - - +
209B VAL* 3.2 14.5 + - - +
210B GLY 3.3 8.5 + - - -
299B GLY* 3.4 23.6 - - - +
302B THR* 3.7 27.1 - - + -
303B ALA* 3.9 11.9 - - + +
306B LEU* 4.2 7.2 - - + -
321B LEU* 5.1 0.2 - - + -
322B PHE* 3.6 30.5 - - + -
325B VAL* 3.7 28.7 - - + +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU 3.7 11.9 - - - +
204B LYS 3.3 7.1 + - - +
206B VAL* 1.3 76.0 - - - +
208B ALA* 1.3 57.4 + - - +
210B GLY* 3.0 3.6 + - - -
211B ALA* 2.8 25.1 + - - +
227B VAL* 3.9 13.7 - - + +
228B ILE* 4.0 11.2 - - + -
231B GLY* 3.6 43.5 - - - +
235B MET* 4.0 11.0 - - - -
261B LEU* 3.8 17.3 - - + -
265B CYS* 4.2 3.1 - - - -
321B LEU* 4.3 9.6 - - + -
322B PHE* 4.0 12.1 - - + -
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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
----------------------------------------------------------
204B LYS 2.9 17.8 + - - +
205B ASN* 3.7 7.4 - - - +
206B VAL 3.2 0.2 - - - -
207B VAL* 1.3 76.6 - - - +
209B VAL* 1.3 57.4 + - - +
211B ALA* 3.2 2.7 + - - +
212B GLY 2.9 24.4 + - - -
264B THR* 3.6 32.5 - - + +
265B CYS* 3.7 17.9 - - - -
270B ASN* 4.1 9.0 - - + -
271B ARG* 3.7 12.6 - - - +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASN 3.2 16.0 + - - +
206B VAL 3.2 8.0 + - - +
208B ALA* 1.3 75.7 - - - +
210B GLY* 1.3 57.8 + - - +
213B PHE* 2.9 56.9 + - + -
270B ASN* 3.8 25.8 - - + +
274B ALA* 3.1 17.8 - - + +
297B LEU* 4.8 3.1 - - + -
299B GLY* 4.3 2.5 - - - -
300B PRO* 4.1 19.5 - - + -
325B VAL* 3.8 15.7 - - + -
329B CYS* 4.4 7.0 - - - -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL 3.3 5.0 + - - -
207B VAL* 3.0 8.2 + - - -
209B VAL* 1.3 79.0 - - - +
211B ALA* 1.3 62.4 + - - +
213B PHE* 3.2 7.2 + - - +
214B CYS* 2.9 20.3 + - - +
227B VAL* 3.8 8.7 - - - -
321B LEU* 5.2 0.9 - - - -
325B VAL* 3.9 6.2 - - - +
338B PHE* 3.5 33.2 - - - -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL 2.8 15.4 + - - +
208B ALA 3.5 7.4 - - - +
210B GLY* 1.3 73.7 - - - +
212B GLY* 1.3 58.6 + - - +
214B CYS* 3.2 6.9 + - - +
215B ASP* 3.0 31.7 + - - +
224B LYS* 4.1 15.9 - - + +
227B VAL* 3.8 10.2 - - + +
228B ILE* 4.5 8.3 - - + -
265B CYS* 3.9 31.0 - - + +
271B ARG* 4.5 0.2 - - - -
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Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ALA 2.9 11.7 + - - -
209B VAL 3.6 3.1 - - - -
211B ALA* 1.3 74.1 - - - +
213B PHE* 1.3 66.9 + - - +
215B ASP* 3.2 4.8 + - - +
216B GLY 2.9 19.4 + - - -
271B ARG* 3.6 32.0 - - - +
274B ALA* 3.8 2.2 - - - -
275B GLU* 3.4 17.1 - - - -
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Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 2.9 41.7 + - + -
210B GLY* 3.4 10.1 - - - +
212B GLY* 1.3 75.1 - - - +
214B CYS* 1.3 63.9 + - - +
216B GLY* 3.1 2.6 + - - -
217B LEU* 2.9 29.6 + - + +
274B ALA* 3.6 19.5 - - + -
277B PHE* 3.8 21.5 - + - -
278B ALA* 4.0 5.5 - - + +
325B VAL* 4.5 11.2 - - + -
328B VAL* 3.5 34.8 - - + -
329B CYS* 4.3 9.6 - - - -
335B VAL* 3.7 20.9 - - + -
338B PHE* 3.9 29.8 - + + -
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Residues in contact with CYS 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLY 2.9 12.7 + - - +
211B ALA* 3.4 11.0 - - - +
212B GLY 3.2 0.2 - - - -
213B PHE* 1.3 76.9 - - - +
215B ASP* 1.3 63.3 + - - +
217B LEU* 3.3 11.5 + - - -
219B PHE* 3.2 49.9 + - - +
220B GLY 4.4 0.9 - - - -
223B THR* 3.7 10.3 - - - -
224B LYS* 3.6 36.1 - - - -
227B VAL* 4.1 14.1 - - + -
338B PHE* 4.8 2.4 - - + -
339B ILE* 4.7 5.2 - - + -
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Residues in contact with ASP 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ALA 3.0 14.0 + - - +
212B GLY 3.2 6.9 + - - +
214B CYS* 1.3 74.9 - - - +
216B GLY* 1.3 57.4 + - - +
218B GLY* 3.0 19.6 + - - -
219B PHE 4.1 11.4 + - - +
220B GLY 6.0 0.3 - - - -
224B LYS* 2.9 43.0 + - - +
271B ARG* 2.9 26.6 + - - +
275B GLU* 3.4 17.7 - - - +
279B ARG* 3.0 13.9 + - - -
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 2.9 15.3 + - - -
213B PHE 3.6 2.9 - - - -
215B ASP* 1.3 75.6 - - - +
217B LEU* 1.3 60.0 + - - +
218B GLY 3.1 1.3 + - - -
275B GLU* 3.9 6.9 - - - +
278B ALA* 4.0 14.9 - - - +
279B ARG* 3.3 46.1 + - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE* 2.9 25.3 + - + +
214B CYS* 4.7 0.9 - - - -
215B ASP 3.2 0.6 - - - -
216B GLY* 1.3 76.3 - - - +
218B GLY* 1.3 58.6 + - - +
219B PHE* 3.5 33.3 - - + -
278B ALA* 4.6 8.5 - - + +
279B ARG* 5.2 0.4 - - - -
335B VAL* 3.8 32.3 - - + +
336B GLY* 3.9 26.2 - - - +
338B PHE* 4.5 11.7 - - + +
339B ILE* 4.6 7.2 - - + -
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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