Contacts of the helix formed by residues 218 - 241 (chain B) in PDB entry 5FN2
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 PRO 218 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B SER* 5.3 0.3 + - - -
217B GLY* 1.4 86.7 - - - +
219B LEU* 1.3 65.2 + - - +
220B ARG* 3.4 4.0 - - + +
221B LEU* 3.7 23.0 - - + +
222B GLN* 3.3 18.0 + - - +
32D VAL* 4.1 16.2 - - + +
35D PHE* 6.2 1.3 - - + -
36D TRP* 3.3 54.8 - - + +
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Residues in contact with LEU 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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217B GLY 3.7 2.2 + - - -
218B PRO* 1.3 71.5 - - - +
220B ARG* 1.3 60.9 + - + +
222B GLN* 3.2 12.9 + - + +
223B GLN* 2.9 42.6 + - + +
287B ILE* 3.9 32.3 - - + -
288B TYR 3.5 24.5 - - - +
2D ASN* 3.8 35.9 - - + +
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Residues in contact with ARG 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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84B MET* 5.0 16.6 - - - +
218B PRO* 3.4 2.6 - - + +
219B LEU* 1.3 77.7 - - - +
221B LEU* 1.3 57.3 + - - +
223B GLN* 3.2 29.6 + - - +
224B ALA* 2.9 28.3 + - - +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 5.4 1.8 - - + +
211B ILE* 5.6 1.1 - - + -
212B SER* 3.3 21.3 - - - +
217B GLY* 5.5 0.2 - - - -
218B PRO* 3.5 23.5 + - + +
219B LEU 3.2 0.2 - - - -
220B ARG* 1.3 77.9 - - - +
222B GLN* 1.3 59.0 + - - +
224B ALA* 3.2 10.6 + - + +
225B TYR* 2.9 47.8 + - + -
28D PHE* 4.5 8.7 - - + -
32D VAL* 3.4 48.9 - - + -
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Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER* 3.2 38.8 + - - +
213B ILE* 4.3 1.8 - - - +
216B LYS 4.9 2.5 - - - +
217B GLY 5.1 0.4 - - - +
218B PRO 3.3 10.5 + - - +
219B LEU* 3.2 16.8 + - + +
221B LEU* 1.3 80.3 - - - +
223B GLN* 1.3 60.8 + - - +
225B TYR* 3.2 2.8 + - - +
226B LEU* 2.9 62.0 + - + +
281B THR* 3.0 25.6 + - - +
284B PRO* 5.1 1.1 - - - +
287B ILE* 4.4 25.5 - - - +
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Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET* 5.5 3.7 - - - +
88B PRO* 4.3 19.5 - - + +
219B LEU* 2.9 32.7 + - + +
220B ARG* 3.2 34.1 + - - +
222B GLN* 1.3 81.1 - - - +
224B ALA* 1.3 57.8 + - - +
226B LEU* 3.2 4.4 + - - +
227B ILE* 2.9 35.9 + - + +
286B LEU* 3.6 24.8 - - + +
287B ILE 4.7 4.3 + - - +
288B TYR 3.0 30.6 + - - +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG 2.9 12.6 + - - +
221B LEU* 3.2 15.7 + - + +
223B GLN* 1.3 76.1 - - - +
225B TYR* 1.3 61.2 + - + +
227B ILE* 3.0 18.8 - - + +
228B MET* 2.9 30.0 + - - +
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Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.3 10.8 - - + -
205B PHE* 3.0 68.8 + + - -
208B VAL* 3.0 24.8 - - + +
209B GLY* 3.3 18.2 - - - -
212B SER* 4.2 4.5 - - - -
213B ILE* 4.2 14.6 - - + -
221B LEU* 2.9 43.4 + - + +
222B GLN* 3.6 9.6 - - - +
224B ALA* 1.3 78.2 - - + +
226B LEU* 1.3 57.4 + - - +
228B MET* 3.2 7.8 + - + +
229B ILE* 2.9 35.0 + - + +
28D PHE* 4.2 11.4 - + - -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 3.4 30.5 - - + -
222B GLN* 2.9 39.3 + - - +
223B GLN 3.3 8.3 - - - +
225B TYR* 1.3 76.9 - - - +
227B ILE* 1.3 50.9 + - - +
229B ILE* 3.2 10.7 + - + +
230B SER* 2.5 35.9 + - - -
281B THR 4.6 8.3 - - - +
282B LEU 4.6 11.0 - - - +
284B PRO* 4.4 9.2 - - + -
285B ALA 4.4 0.9 - - - -
286B LEU* 3.5 42.8 - - + +
383B LEU* 4.3 13.4 - - + +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PRO* 4.0 20.4 - - + +
91B LEU* 3.4 44.6 - - + -
92B CYS* 4.0 12.6 - - + +
95B VAL* 5.0 5.6 - - + -
223B GLN* 2.9 22.9 + - + +
224B ALA* 3.0 22.4 - - + +
226B LEU* 1.3 76.6 - - - +
228B MET* 1.3 60.2 + - + +
230B SER* 2.7 18.4 + - - -
231B ALA* 2.9 21.0 + - - +
286B LEU* 4.4 4.9 - - + -
386B PHE* 4.0 24.6 - - + -
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Residues in contact with MET 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.6 22.4 - - + -
174B LEU* 6.4 0.9 - - + -
178B SER* 4.4 4.5 - - - +
181B TYR* 4.0 32.5 - - + -
205B PHE* 3.5 40.4 - - + -
224B ALA 2.9 13.0 + - - +
225B TYR* 3.2 14.3 + - + +
227B ILE* 1.3 82.0 - - + +
229B ILE* 1.3 62.2 + - + +
231B ALA* 3.2 6.3 + - - +
232B LEU* 3.0 40.7 + - + +
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Residues in contact with ILE 229 (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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170B SER* 4.6 18.4 - - - +
173B LEU* 3.8 28.4 - - + +
174B LEU* 4.0 26.7 - - + -
213B ILE* 4.7 12.3 - - + -
225B TYR* 2.9 28.5 + - + +
226B LEU* 3.2 12.1 - - + +
228B MET* 1.3 76.0 - - + +
230B SER* 1.3 65.9 + - - +
232B LEU* 3.1 23.4 - - - +
233B MET* 3.2 19.7 + - + +
282B LEU* 6.2 5.4 - - + -
383B LEU* 5.1 13.2 - - + -
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU 2.5 25.0 + - - -
227B ILE* 2.7 9.4 + - - -
229B ILE* 1.3 75.0 - - - +
231B ALA* 1.3 57.1 + - - +
233B MET 3.5 0.2 + - - -
234B ALA* 2.9 27.1 + - - +
383B LEU* 3.5 9.8 - - - +
386B PHE* 3.1 38.8 - - - -
387B ILE* 3.4 31.7 - - - +
390B SER* 5.6 0.9 - - - -
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Residues in contact with ALA 231 (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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92B CYS* 4.6 4.7 - - - +
95B VAL* 3.9 23.6 - - + -
96B VAL* 3.9 25.1 - - + -
227B ILE 2.9 13.0 + - - +
228B MET* 3.2 12.3 + - - +
230B SER* 1.3 70.8 - - - +
232B LEU* 1.3 59.3 + - - +
233B MET 3.0 1.1 - - - -
234B ALA* 2.4 29.1 + - - +
235B LEU* 2.8 15.9 + - + -
386B PHE* 5.2 0.6 - - - -
390B SER* 4.9 1.8 - - - -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TYR* 5.7 0.4 - - - +
173B LEU* 3.2 28.7 - - + +
174B LEU* 5.5 1.1 - - + -
177B PHE* 4.2 6.5 - - + +
178B SER* 3.3 49.4 - - - +
181B TYR* 4.7 12.8 - - + -
205B PHE* 5.5 0.9 - - + -
228B MET* 3.0 28.9 + - + +
229B ILE* 3.1 30.1 - - - +
231B ALA* 1.3 76.7 - - - +
233B MET* 1.3 57.6 + - - +
235B LEU* 3.5 17.7 - - + +
236B VAL* 2.9 35.6 + - + +
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Residues in contact with MET 233 (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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173B LEU* 3.8 24.0 - - + -
177B PHE* 6.1 2.2 - - + -
229B ILE* 3.2 25.8 + - + +
230B SER 3.5 4.3 - - - +
231B ALA 2.7 4.0 + - - -
232B LEU* 1.3 72.3 - - - +
234B ALA* 1.3 65.4 + - - +
236B VAL* 3.2 9.0 + - + +
237B PHE* 3.0 53.1 + - + -
387B ILE* 3.5 31.2 - - + -
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Residues in contact with ALA 234 (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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96B VAL* 4.2 4.3 - - + -
230B SER 2.9 13.8 + - - +
231B ALA 2.4 19.1 + - - +
233B MET* 1.3 70.8 - - - +
235B LEU* 1.3 62.6 + - - +
237B PHE* 2.9 5.0 + - - +
238B ILE* 2.9 27.1 + - + +
387B ILE* 3.5 25.9 - - - +
390B SER* 3.6 19.1 - - - -
391B VAL* 3.5 15.5 - - + +
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Residues in contact with LEU 235 (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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95B VAL* 5.6 1.8 - - + -
96B VAL* 3.8 11.0 - - + +
99B THR* 3.3 35.7 - - + -
100B ILE* 3.6 25.8 - - + -
106B TYR* 3.8 29.9 - - + +
181B TYR* 4.0 24.2 - - + -
231B ALA* 2.8 17.9 + - + +
232B LEU* 3.5 25.6 - - + +
234B ALA* 1.3 72.7 - - - +
236B VAL* 1.3 57.7 + - + +
238B ILE* 3.2 9.0 + - + +
239B LYS* 2.9 28.9 + - - +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TYR* 5.4 4.0 - - + -
177B PHE* 3.7 48.0 - - + -
232B LEU* 2.9 19.5 + - + +
233B MET* 3.3 12.3 - - + +
235B LEU* 1.3 75.9 - - + +
237B PHE* 1.3 76.8 + - + +
239B LYS* 3.2 16.3 + - - +
240B TYR* 3.2 38.8 + - + +
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Residues in contact with PHE 237 (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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139B MET* 5.8 9.0 - - + -
143B ILE* 6.2 2.2 - - + -
233B MET* 3.0 47.6 + - + +
234B ALA* 2.9 9.0 + - - +
236B VAL* 1.3 85.1 - - + +
238B ILE* 1.3 63.6 + - - +
240B TYR* 5.7 0.2 - - - -
241B LEU* 3.4 49.4 + - + +
253B ILE* 5.4 3.1 - - + -
387B ILE* 5.2 3.1 - - + -
388B PHE* 3.5 39.9 - + - -
391B VAL* 3.5 19.5 - - + -
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.8 11.9 - - + -
100B ILE* 3.6 37.5 - - + -
106B TYR* 4.9 10.1 - - + +
234B ALA 2.9 24.6 + - - +
235B LEU* 3.4 8.7 - - + +
237B PHE* 1.3 76.8 - - - +
239B LYS* 1.3 66.0 - - - +
241B LEU 3.8 1.9 + - - +
391B VAL* 3.7 28.7 - - + +
394B GLY* 3.8 19.1 - - - +
395B LYS* 3.5 36.3 + - + +
398B ALA* 5.0 8.1 - - + -
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Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.1 50.2 - - + +
106B TYR* 3.4 39.3 - - + +
108B ARG 2.8 13.5 + - - +
109B LYS* 2.5 37.5 + - - +
110B ASP* 4.2 13.2 - - - +
111B GLY 4.4 5.1 + - - -
235B LEU 2.9 12.7 + - - +
236B VAL* 3.2 12.1 + - - +
238B ILE* 1.3 80.3 - - - +
240B TYR* 1.3 85.8 + - + +
241B LEU 3.7 3.5 + - - +
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Residues in contact with TYR 240 (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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243A ASN* 4.7 13.2 + - - -
105B PHE* 4.8 3.7 - + - -
110B ASP 3.7 13.0 - - - -
111B GLY 4.3 11.7 - - - -
112B GLN* 4.6 6.1 - - + -
113B LEU* 2.0 62.6 - - - +
114B ILE* 3.6 5.4 + - - +
177B PHE* 4.7 16.9 - + - -
180B ILE* 5.5 5.4 - - - +
236B VAL* 3.2 40.7 + - + +
237B PHE 4.8 0.7 - - - +
239B LYS* 1.3 106.2 - - + +
241B LEU* 1.3 60.2 + - + +
242B PRO* 3.9 0.9 - - - +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP* 5.8 1.9 - - - -
113B LEU* 4.1 2.5 - - - -
114B ILE* 4.5 18.4 - - + -
139B MET* 5.8 6.3 - - + -
237B PHE* 3.4 40.7 + - + +
238B ILE 3.9 2.4 - - - +
239B LYS 3.4 3.7 - - - +
240B TYR* 1.3 84.2 - - + +
242B PRO* 1.4 61.7 - - + +
245B THR* 4.3 14.1 - - + -
246B ALA* 3.9 18.8 - - + -
249B ILE* 3.6 28.9 - - + -
391B VAL* 5.7 6.3 - - + -
395B LYS* 3.1 21.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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