Contacts of the helix formed by residues 212 - 243 (chain B) in PDB entry 1J38
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 212 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASP* 2.9 7.6 + - - +
211B ASP* 1.3 85.5 - - + +
213B PHE* 1.3 58.8 + - - +
214B GLU 3.4 2.5 - - - +
215B GLN* 3.4 14.8 + - - +
216B GLN* 3.0 45.2 + - - +
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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
----------------------------------------------------------
205B LEU* 4.7 9.2 - - + +
208B TYR* 3.2 59.0 - + + -
210B ASP* 3.0 22.9 + - + +
211B ASP 3.6 1.0 - - - -
212B THR* 1.3 75.2 - - - +
214B GLU* 1.3 61.4 + - - +
216B GLN* 3.3 12.7 + - - +
217B LEU* 2.9 55.0 + - + +
390B ASN* 5.2 0.7 - - - -
505B LEU* 4.0 5.2 - - + -
509B VAL* 3.6 18.2 - - + -
564B TRP* 3.7 31.2 - + - -
577B MET* 3.8 20.4 - - + -
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.9 19.8 - - + +
211B ASP 5.5 0.2 + - - -
212B THR 3.4 0.6 - - - -
213B PHE* 1.3 81.3 - - - +
215B GLN* 1.3 57.4 + - - +
217B LEU* 3.5 8.3 + - - +
218B GLU* 3.0 31.7 + - - +
446B PHE* 4.4 3.3 - - + -
450B LYS* 4.5 10.8 + - - +
453B TRP* 3.7 28.8 - - + -
457B ARG* 2.9 37.1 + - - -
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Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B THR* 3.4 18.0 + - - +
213B PHE 3.2 0.8 - - - -
214B GLU* 1.3 75.9 - - - +
216B GLN* 1.3 67.1 + - + +
218B GLU* 3.0 17.6 + - - +
219B ASP* 2.7 61.9 + - - +
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Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASP* 2.4 34.1 + - - +
212B THR* 3.0 37.9 + - - +
213B PHE* 3.3 13.2 + - + +
215B GLN* 1.3 76.7 - - + +
217B LEU* 1.3 63.8 + - + +
219B ASP* 3.3 9.4 + - - +
220B ILE* 3.3 30.7 + - + +
564B TRP* 4.7 7.1 - - - -
576B ILE* 5.1 4.5 - - - +
577B MET* 4.3 29.4 + - + +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE* 2.9 46.9 + - + +
214B GLU* 3.7 7.4 - - - +
216B GLN* 1.3 77.1 - - - +
218B GLU* 1.3 60.9 + - - +
220B ILE* 4.2 3.4 - - + +
221B PHE* 3.5 13.3 + - - +
446B PHE* 3.2 26.5 - - + -
453B TRP* 5.5 0.2 - - + -
505B LEU* 3.4 30.5 - - + -
508B LEU* 4.2 11.2 - - + +
509B VAL* 3.9 10.5 - - + -
512B ILE* 3.7 30.0 - - + +
577B MET* 4.0 18.4 - - - -
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLU* 3.0 19.9 + - - +
215B GLN* 3.0 23.5 + - - +
217B LEU* 1.3 79.9 - - - +
219B ASP* 1.3 60.2 + - - +
221B PHE* 3.6 8.1 + - - +
222B ALA* 3.0 27.5 + - - +
446B PHE* 4.1 9.0 - - - -
450B LYS* 3.1 25.3 + - - -
476B TYR* 3.8 23.4 + - - -
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLN* 2.7 47.8 + - - +
216B GLN* 3.3 9.6 + - - +
218B GLU* 1.3 76.3 - - - +
220B ILE* 1.3 66.8 + - + +
222B ALA* 3.3 8.5 + - - +
223B ASP* 3.0 29.5 + - - +
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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
----------------------------------------------------------
216B GLN* 3.3 18.9 + - + +
217B LEU* 4.6 2.2 - - + +
219B ASP* 1.3 73.6 - - + +
221B PHE* 1.3 68.0 + - - +
223B ASP* 2.9 19.9 + - + +
224B ILE* 3.0 21.8 + - + +
442B LEU* 6.5 0.2 - - + -
512B ILE* 4.0 35.2 - - + -
577B MET* 4.2 12.1 - - + +
578B SER* 3.5 17.5 - - - +
579B GLY* 3.5 39.7 - - - +
582B ILE* 4.6 2.5 - - + -
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Residues in contact with PHE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU 3.5 18.3 + - - +
218B GLU* 3.9 11.7 - - - +
219B ASP 3.3 0.4 - - - -
220B ILE* 1.3 78.8 - - - +
222B ALA* 1.3 56.7 + - + +
224B ILE* 3.1 6.1 + - + +
225B ARG* 2.7 79.3 + - + +
228B TYR* 5.4 4.7 - + + -
442B LEU* 4.9 7.9 - - + -
443B PRO* 3.6 37.7 - - + -
446B PHE* 4.1 15.5 - + + -
476B TYR* 3.6 47.3 - + - -
508B LEU* 6.3 2.0 - - + -
512B ILE* 5.8 0.6 - - - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLU* 3.0 15.3 + - + +
219B ASP* 3.3 13.9 - - - +
221B PHE* 1.3 83.7 - - - +
223B ASP* 1.3 59.3 + - - +
225B ARG* 3.6 24.0 + - - +
226B PRO* 3.1 24.8 - - - +
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Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ASP* 3.0 17.9 + - - +
220B ILE* 2.9 13.8 + - - +
222B ALA* 1.3 80.2 - - - +
224B ILE* 1.3 70.2 + - + +
225B ARG 3.5 0.2 - - - -
226B PRO* 3.7 10.0 - - - +
227B LEU* 5.0 1.0 + - - +
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ILE* 3.0 25.5 + - + +
221B PHE* 4.2 6.1 - - + +
223B ASP* 1.3 86.6 - - + +
225B ARG* 1.3 56.9 + - - +
226B PRO* 3.2 3.1 - - - -
227B LEU* 2.6 44.5 + - + +
228B TYR* 2.8 8.4 + - + +
439B ILE* 4.2 14.4 - - + -
442B LEU* 3.9 24.9 - - + -
579B GLY* 4.2 9.2 - - - +
582B ILE* 3.5 33.2 - - + -
583B ALA* 5.2 9.0 - - + -
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Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 2.7 55.5 + - + +
222B ALA* 3.6 22.0 + - - +
224B ILE* 1.3 76.2 - - - +
226B PRO* 1.3 72.5 - - + +
228B TYR* 2.8 22.5 + - + +
229B GLN* 3.1 35.3 + - + +
476B TYR* 6.0 0.6 - - - +
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Residues in contact with PRO 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ALA 3.1 18.8 - - - +
223B ASP 3.7 8.3 - - - +
224B ILE 3.4 3.1 - - - -
225B ARG* 1.3 97.3 - - + +
227B LEU* 1.3 62.6 + - - +
229B GLN* 3.4 13.4 + - + +
230B GLN* 3.5 19.7 + - - +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ASP 5.0 1.1 + - - +
224B ILE* 2.6 33.7 + - + +
226B PRO* 1.3 76.3 - - - +
228B TYR* 1.3 61.2 + - - +
230B GLN* 3.1 14.7 + - + +
231B ILE* 3.6 26.6 + - + +
439B ILE* 3.3 29.6 - - + -
582B ILE* 6.4 0.4 - - + -
583B ALA* 5.4 8.3 - - + -
586B PHE* 4.2 13.9 - - + -
589B LEU* 4.4 11.4 - - + -
590B ARG* 3.8 29.8 - - + -
593B LEU* 4.5 5.2 - - + -
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Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 5.4 4.0 - + + -
224B ILE* 2.8 12.2 + - + +
225B ARG* 2.8 16.4 + - + +
227B LEU* 1.3 77.8 - - - +
229B GLN* 1.3 67.2 + - + +
231B ILE* 3.3 6.5 + - + +
232B HIS* 2.9 31.6 + + + +
267B TRP* 3.2 39.0 - + - -
439B ILE* 4.2 17.4 - - + +
440B VAL* 3.9 32.5 + - + +
443B PRO* 4.2 20.0 - - + -
476B TYR 3.8 19.7 - - - -
477B SER* 2.8 35.0 + - - -
606B TRP* 5.2 1.8 - + - -
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Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ARG* 3.1 39.7 + - - +
226B PRO* 3.4 7.6 + - + +
227B LEU 3.2 0.2 - - - -
228B TYR* 1.3 83.1 - - + +
230B GLN* 1.3 58.0 + - - +
231B ILE 3.0 5.4 - - - -
232B HIS* 3.7 8.3 - - + -
233B GLY* 3.1 19.9 + - - -
604B ILE* 3.8 28.8 - - + +
605B GLY* 3.7 24.9 + - - +
606B TRP* 4.6 23.1 - - + +
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Residues in contact with GLN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PRO 3.5 15.1 + - - +
227B LEU* 3.1 12.9 + - + +
229B GLN* 1.3 77.0 - - - +
231B ILE* 1.3 57.6 + - - +
234B TYR* 3.5 4.7 - - - +
590B ARG* 5.3 3.1 - - + +
593B LEU* 3.1 31.5 - - + +
594B GLU* 3.4 39.5 + - + +
597B ASN* 2.8 47.4 + - - +
604B ILE* 3.4 29.8 - - - +
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 3.6 20.6 - - + +
228B TYR* 3.3 7.6 - - + +
230B GLN* 1.3 79.1 - - - +
232B HIS* 1.3 55.1 + - - +
233B GLY 3.5 0.2 - - - -
234B TYR* 3.3 3.5 + - - +
235B VAL* 2.7 54.9 + - + +
267B TRP* 4.1 8.5 - - + -
432B PHE* 4.2 9.0 - - + -
435B ALA* 3.7 27.8 - - + +
436B LEU* 4.1 15.9 - - + -
439B ILE* 3.7 28.9 - - + -
440B VAL* 4.2 6.1 - - + -
589B LEU* 4.8 0.9 - - + -
593B LEU* 3.8 16.6 - - + -
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Residues in contact with HIS 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 2.9 32.3 + + + +
229B GLN* 3.7 10.5 - - + -
231B ILE* 1.3 76.0 - - - +
233B GLY* 1.3 69.7 + - - +
235B VAL* 3.0 4.9 + - - +
236B ARG* 2.8 32.0 + - - +
254B ILE* 3.9 27.3 - - + +
267B TRP* 4.2 11.0 - + - -
477B SER 3.2 21.1 + - - -
478B GLY 2.8 24.3 + - - -
479B ILE* 4.3 0.9 - - + -
605B GLY 5.5 0.8 + - - -
606B TRP* 3.1 39.7 + + - -
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Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLN 3.1 13.8 + - - -
232B HIS* 1.3 85.9 + - - +
234B TYR* 1.3 56.4 + - - +
236B ARG* 3.2 12.0 + - - +
237B PHE* 2.9 21.7 + - - +
250B GLU* 5.2 0.5 - - - +
602B VAL* 3.2 16.7 - - - +
603B HIS 3.6 20.4 - - - -
604B ILE* 4.8 2.7 - - - -
605B GLY 5.8 0.4 - - - +
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Residues in contact with TYR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLN 3.5 18.8 + - - +
231B ILE 3.3 4.8 + - - +
232B HIS 3.1 0.4 - - - -
233B GLY* 1.3 72.6 - - - +
235B VAL* 1.3 61.3 + - - +
236B ARG 3.0 1.3 - - - -
237B PHE* 2.8 35.7 + + - +
238B ARG* 3.3 38.8 + - + +
274B VAL 3.5 20.4 - - - -
276B PRO* 3.5 25.3 + - + +
432B PHE* 3.7 28.7 - + - -
592B TRP* 4.1 9.6 - + - -
593B LEU* 4.1 8.3 - - + -
596B GLU* 4.0 23.4 + - + +
597B ASN* 3.3 26.0 + - - +
600B ASN* 4.8 3.8 - - - -
602B VAL* 3.9 2.7 - - + +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 2.7 30.4 + - + +
232B HIS 3.5 4.5 - - - +
234B TYR* 1.3 73.6 - - - +
236B ARG* 1.3 59.5 + - - +
238B ARG 3.7 0.2 + - - -
239B LEU* 3.2 40.8 + - + +
254B ILE* 4.2 2.9 - - + -
259B LEU* 3.9 9.0 - - + -
267B TRP* 3.7 35.0 - - + -
270B ILE* 4.5 4.0 - - + -
274B VAL* 4.0 20.2 - - + +
432B PHE* 4.1 10.3 - - + -
436B LEU* 3.8 18.8 - - + -
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Residues in contact with ARG 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B HIS* 2.8 18.8 + - - +
233B GLY* 3.4 10.1 + - - +
234B TYR 3.0 0.2 - - - -
235B VAL* 1.3 77.1 - - - +
237B PHE* 1.3 61.4 + - - +
238B ARG 3.4 0.2 - - - -
239B LEU* 4.2 4.7 - - - -
240B ARG* 3.5 23.0 + - - +
248B VAL* 4.0 8.1 - - + +
249B SER 3.7 18.8 - - - +
250B GLU* 3.4 16.1 + - - +
251B THR 3.2 19.6 - - - +
252B GLY 3.1 28.5 + - - -
253B PRO 5.4 0.2 - - - -
254B ILE* 3.9 22.0 - - + +
603B HIS* 2.4 35.4 + - - -
604B ILE 3.8 2.4 - - - -
605B GLY 2.7 31.5 + - - +
606B TRP* 3.5 10.7 - - - +
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Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLY 2.9 11.7 + - - +
234B TYR* 2.8 17.2 + + - +
236B ARG* 1.3 80.2 - - - +
238B ARG* 1.3 76.8 + - - +
240B ARG* 4.5 2.9 - - - +
241B LYS* 3.3 50.9 + - + +
250B GLU* 5.0 13.5 - - - +
600B ASN* 3.5 49.4 - - + -
601B ASN 5.3 1.1 - - - -
602B VAL* 3.6 28.0 - - + -
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Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TYR* 3.3 46.0 + - + +
236B ARG 3.4 0.2 - - - -
237B PHE* 1.3 94.3 - - - +
239B LEU* 1.3 54.7 + - - +
240B ARG 3.3 0.2 - - - -
241B LYS* 3.0 16.5 + - - +
242B HIS* 2.5 39.9 + - - +
273B ILE 3.6 21.2 + - - +
274B VAL* 3.7 30.2 + - + -
275B SER 3.3 22.2 + - - +
276B PRO 5.5 0.4 - - - -
278B PRO* 4.6 14.1 - - - +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 3.2 34.6 + - + +
236B ARG* 4.0 1.5 + - - +
238B ARG* 1.3 79.5 - - - +
240B ARG* 1.3 54.9 + - - +
242B HIS* 4.2 3.1 - - - -
243B TYR* 2.5 59.5 + - + +
248B VAL* 3.9 17.9 - - + -
254B ILE* 3.8 29.8 - - + -
258B LEU* 3.7 24.9 - - + +
259B LEU* 4.1 8.1 - - + -
270B ILE* 5.0 5.8 - - + -
273B ILE* 3.9 16.6 - - + -
274B VAL* 4.8 3.4 - - + -
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ARG 3.5 15.6 + - - +
237B PHE* 4.6 3.8 - - - +
238B ARG 3.3 0.4 - - - -
239B LEU* 1.3 80.1 - - - +
241B LYS* 1.3 57.6 + - - +
244B GLY* 3.2 23.4 + - - +
245B ASP* 2.9 49.5 + - - +
248B VAL* 3.0 46.7 + - + +
249B SER* 3.4 15.4 - - - +
250B GLU* 3.4 40.3 + - - +
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Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B PHE* 3.3 47.3 + - + +
238B ARG* 3.0 24.7 + - - +
240B ARG* 1.3 80.5 - - - +
242B HIS* 1.3 64.1 + - - +
244B GLY* 4.5 2.1 + - - -
600B ASN* 5.2 1.8 + - - -
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ARG* 4.3 19.0 + - + +
238B ARG* 2.5 22.6 + - - +
239B LEU* 3.7 4.9 - - - +
241B LYS* 1.3 75.6 - - - +
243B TYR* 1.3 90.2 + + - +
244B GLY 3.7 0.2 + - - -
273B ILE* 3.8 44.3 - - + +
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Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B SER 3.8 1.6 + - - -
157B ARG* 2.9 55.2 + - - +
159B HIS* 3.8 25.8 - + + -
162B LEU* 3.5 11.5 - - + +
239B LEU* 2.5 42.8 + - + +
242B HIS* 1.3 93.7 - + - +
244B GLY* 1.3 56.9 + - - +
247B VAL* 3.7 27.8 - - + +
248B VAL* 4.5 2.2 - - + -
258B LEU* 3.4 33.1 + - + -
270B ILE* 6.0 0.7 - - + +
273B ILE* 4.1 4.9 - - + -
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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