Contacts of the helix formed by residues 219 - 252 (chain B) in PDB entry 3D0G
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 ARG 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B HIS 4.7 8.1 + - - -
196B TYR* 3.4 26.5 - - - +
197B GLU* 5.3 3.6 - - - +
201B ASP* 2.6 61.0 + - - +
204B ARG* 4.2 21.1 - - + +
205B GLY* 3.8 20.0 - - - -
208B GLU* 3.1 41.0 + - + +
218B SER* 1.3 69.3 - - - +
220B GLY* 1.3 60.2 + - - +
221B GLN 3.0 9.7 + - - -
222B LEU* 3.1 20.0 + - - +
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Residues in contact with GLY 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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201B ASP* 4.7 1.4 + - - -
204B ARG* 5.3 1.8 - - - -
218B SER* 3.5 4.2 + - - -
219B ARG* 1.3 77.9 - - - +
221B GLN* 1.3 59.6 + - - +
222B LEU 3.3 0.9 - - - -
223B ILE* 3.9 16.0 + - - +
224B GLU* 3.7 17.5 + - - +
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Residues in contact with GLN 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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216B ASP 4.6 3.7 + - - +
217B TYR* 3.4 31.1 - - + +
218B SER* 2.9 46.0 + - - +
219B ARG 3.0 0.8 - - - -
220B GLY* 1.3 76.3 - - - +
222B LEU* 1.3 63.4 + - - +
224B GLU* 3.6 15.9 - - + +
225B ASP* 3.0 38.8 + - - +
578B ASN* 4.5 3.8 + - - -
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Residues in contact with LEU 222 (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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204B ARG* 4.7 12.6 - - + +
207B TYR* 3.6 49.1 - - + -
217B TYR* 3.3 24.2 + - + +
219B ARG 3.1 12.9 + - - +
221B GLN* 1.3 76.5 - - - +
223B ILE* 1.3 66.5 + - - +
225B ASP* 3.1 1.7 + - - +
226B VAL* 2.8 29.3 + - + +
461B TRP* 4.4 16.2 - - + -
513B ILE* 4.2 17.3 - - + -
517B THR* 4.5 2.2 - - + -
566B TRP* 5.7 0.2 - - + -
579B MET* 4.0 22.9 - - + -
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Residues in contact with ILE 223 (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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204B ARG* 3.6 39.3 - - - +
219B ARG 4.3 0.4 + - - +
220B GLY* 3.9 14.2 + - - +
221B GLN 3.5 0.2 - - - -
222B LEU* 1.3 79.2 - - - +
224B GLU* 1.3 65.5 + - - +
225B ASP 3.0 0.2 + - - -
226B VAL* 3.8 1.6 - - - +
227B GLU* 3.1 50.4 + - + +
458B LYS* 4.6 11.0 - - - +
461B TRP* 3.6 31.9 - - + -
465B LYS* 5.9 4.7 - - + -
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Residues in contact with GLU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLY 3.7 11.6 + - - +
221B GLN* 3.6 18.8 + - + +
222B LEU 3.3 0.2 - - - -
223B ILE* 1.3 79.1 - - - +
225B ASP* 1.3 62.3 + - - +
227B GLU* 4.2 5.4 - - - +
228B HIS* 3.0 30.2 + - + +
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Residues in contact with ASP 225 (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 TYR* 2.6 31.7 + - - +
221B GLN* 3.0 15.6 + - - +
222B LEU 3.1 3.9 + - - +
224B GLU* 1.3 83.0 - - - +
226B VAL* 1.3 65.1 + - - +
227B GLU 3.2 0.2 - - - -
228B HIS* 3.8 8.1 + - - +
229B THR* 3.0 28.2 + - - +
578B ASN* 3.1 28.6 + - - -
579B MET* 5.0 16.6 - - + +
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Residues in contact with VAL 226 (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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222B LEU* 2.8 35.7 + - + +
223B ILE* 3.8 5.4 - - - +
225B ASP* 1.3 72.9 - - - +
227B GLU* 1.3 59.7 + - + +
229B THR* 2.9 11.8 - - - +
230B PHE* 2.8 23.9 + - - +
454B TYR* 3.3 35.0 - - + -
461B TRP* 4.9 5.4 - - + -
513B ILE* 4.1 29.2 - - + -
516B TYR* 3.0 26.3 + - + -
517B THR* 5.0 3.6 - - + -
579B MET* 5.1 4.3 - - + -
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Residues in contact with GLU 227 (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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223B ILE* 3.1 31.4 + - + +
224B GLU* 4.2 3.8 - - - +
226B VAL* 1.3 73.9 - - + +
228B HIS* 1.3 66.5 + - - +
229B THR 3.0 1.3 - - - -
230B PHE* 3.7 8.5 - - - +
231B GLU* 3.0 30.5 + - + +
454B TYR* 2.9 35.3 + - + +
458B LYS* 3.0 25.6 + - - +
461B TRP* 6.3 0.2 - - + -
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Residues in contact with HIS 228 (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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224B GLU* 3.0 24.5 + - + +
225B ASP* 3.4 9.9 + - - +
227B GLU* 1.3 77.6 - - - +
229B THR* 1.3 67.0 + - - +
231B GLU* 3.7 17.0 - - - +
232B GLU* 4.0 22.0 + - + +
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Residues in contact with THR 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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225B ASP 3.0 15.4 + - - +
226B VAL* 2.9 24.7 - - - +
227B GLU 3.0 0.6 - - - -
228B HIS* 1.3 82.5 - - - +
230B PHE* 1.3 61.8 + - - +
231B GLU 3.3 0.2 - - - -
232B GLU* 3.3 18.3 + - - +
233B ILE* 3.4 15.6 - - + +
516B TYR* 2.9 23.8 - - + +
520B LEU* 3.5 16.9 - - + +
579B MET* 4.6 6.2 + - - +
580B ASN* 5.2 1.2 - - - -
581B VAL* 3.4 28.6 + - - +
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Residues in contact with PHE 230 (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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226B VAL 2.8 18.0 + - - +
227B GLU* 3.1 8.9 + - + +
229B THR* 1.3 74.0 - - - +
231B GLU* 1.3 66.3 + - - +
232B GLU 3.1 1.6 - - - -
233B ILE* 3.1 24.3 + - + -
234B LYS* 3.3 40.3 + - + +
237B TYR* 5.8 2.0 - + + -
450B LEU* 4.3 4.3 - - + -
451B PRO* 3.7 47.8 - - + -
454B TYR* 3.9 24.0 - + + -
484B ILE* 3.8 25.8 - - + -
516B TYR* 3.3 22.7 - + + +
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Residues in contact with GLU 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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227B GLU* 3.0 18.6 + - + +
228B HIS* 3.7 11.4 - - - +
230B PHE* 1.3 78.0 - - - +
232B GLU* 1.3 63.3 + - + +
233B ILE 3.3 0.9 + - - -
234B LYS* 3.3 54.9 + - - +
235B PRO* 3.7 4.9 - - - +
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Residues in contact with GLU 232 (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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228B HIS* 4.1 28.5 + - + +
229B THR* 3.3 11.5 + - - +
230B PHE 3.1 0.6 - - - -
231B GLU* 1.3 79.4 - - + +
233B ILE* 1.3 55.9 + - - +
235B PRO* 3.4 14.9 - - - +
236B LEU 5.2 0.3 + - - -
581B VAL* 3.4 29.9 - - + +
582B ARG* 4.7 12.3 + - - -
585B LEU* 3.7 18.7 - - + +
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Residues in contact with ILE 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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229B THR 3.4 14.8 - - - +
230B PHE* 3.1 19.0 + - + +
232B GLU* 1.3 76.2 - - - +
234B LYS* 1.3 64.1 - - - +
235B PRO* 3.4 1.6 - - - -
236B LEU* 3.2 10.4 + - + +
237B TYR* 3.0 24.4 + - + +
447B VAL* 4.7 12.3 - - + -
450B LEU* 4.2 31.6 - - + -
451B PRO* 5.8 0.2 - - + -
516B TYR* 3.3 31.0 - - + +
520B LEU* 4.4 8.3 - - + -
581B VAL* 3.7 26.2 - - + -
584B LEU* 5.2 5.2 - - + -
585B LEU* 4.9 7.9 - - + -
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Residues in contact with LYS 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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230B PHE* 3.3 41.1 + - + +
231B GLU* 3.3 48.3 + - - +
233B ILE* 1.3 76.5 - - - +
235B PRO* 1.4 60.7 - - + +
237B TYR* 3.3 6.5 + - - +
238B GLU* 2.8 47.4 + - + +
484B ILE* 6.2 3.2 - - - +
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Residues in contact with PRO 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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231B GLU 3.7 5.6 - - - +
232B GLU* 3.4 18.6 - - - +
233B ILE 3.5 0.9 - - - -
234B LYS* 1.4 92.6 - - + +
236B LEU* 1.3 61.5 + - - +
238B GLU* 3.3 10.0 + - + +
239B HIS* 3.2 31.4 + - + -
592B PHE* 3.8 22.2 - - + -
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Residues in contact with LEU 236 (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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233B ILE* 3.2 10.9 + - + +
235B PRO* 1.3 76.9 - - + +
237B TYR* 1.3 65.9 + - - +
238B GLU 3.3 0.2 + - - -
239B HIS* 3.3 3.1 + - - +
240B LEU* 3.0 22.4 + - + +
447B VAL* 4.1 25.4 - - + -
584B LEU* 4.3 4.7 - - + -
585B LEU* 3.9 28.5 - - + +
588B PHE* 3.7 29.2 - - + -
591B LEU* 5.5 2.7 - - + -
592B PHE* 3.6 47.2 - - + +
595B LEU* 4.7 9.4 - - + -
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Residues in contact with TYR 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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230B PHE* 5.8 1.8 - + + -
233B ILE* 3.0 18.8 + - + +
234B LYS* 3.9 7.0 - - - +
236B LEU* 1.3 75.8 - - - +
238B GLU* 1.3 65.1 + - + +
240B LEU* 3.1 8.0 + - + +
241B HIS* 2.8 29.4 + + - +
275B TRP* 3.2 43.6 - + - -
447B VAL* 4.4 18.5 - - + +
448B GLY* 4.3 9.9 - - - -
451B PRO* 3.5 43.7 - - + -
484B ILE 4.2 2.9 - - - -
485B VAL* 2.4 37.9 + - + +
606B TRP* 3.8 24.0 - + - -
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Residues in contact with GLU 238 (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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234B LYS* 2.8 39.3 + - + +
235B PRO* 3.4 9.4 - - - +
237B TYR* 1.3 73.4 - - + +
239B HIS* 1.3 64.5 - - + +
241B HIS* 3.1 9.3 + - - +
242B ALA* 3.0 21.1 + - - +
604B VAL* 4.3 21.9 - - + +
605B GLY* 4.6 13.3 + - - -
606B TRP* 4.0 25.5 - - + -
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Residues in contact with HIS 239 (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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235B PRO* 3.2 23.7 + - + +
236B LEU 3.8 5.8 - - - +
238B GLU* 1.3 79.0 - - + +
240B LEU* 1.3 67.3 + - - +
242B ALA* 2.8 6.3 + - - +
243B TYR* 2.8 23.7 + - - +
592B PHE* 3.6 19.4 - + + -
595B LEU* 4.0 15.5 - - + -
596B LYS* 3.5 39.3 - - + +
599B ASN* 3.1 25.5 + - + +
604B VAL* 3.9 28.3 - - + +
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Residues in contact with LEU 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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236B LEU* 3.0 15.4 + - + +
237B TYR* 3.3 13.7 - - + +
239B HIS* 1.3 75.3 - - - +
241B HIS* 1.3 53.0 + - - +
243B TYR* 3.2 2.3 + - + +
244B VAL* 2.7 46.0 + - + +
275B TRP* 3.5 36.3 - - + -
440B LEU* 3.7 28.9 - - + -
443B ALA* 4.1 31.9 - - + +
444B LEU* 4.3 7.0 - - + -
447B VAL* 5.0 5.4 - - + -
448B GLY* 4.6 9.0 - - - +
595B LEU* 4.2 17.4 - - + +
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Residues in contact with HIS 241 (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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237B TYR* 2.8 34.0 + + + +
238B GLU* 3.1 14.3 + - - +
240B LEU* 1.3 75.9 - - - +
242B ALA* 1.3 54.2 + - - +
244B VAL* 3.3 3.9 + - - +
245B ARG* 2.7 62.8 + - - +
260B GLY 4.3 5.2 - - - -
262B LEU* 3.7 27.4 - - + +
275B TRP* 4.2 11.6 - + + -
485B VAL 4.0 0.9 - - - -
486B GLY 3.0 28.4 + - - -
605B GLY 4.8 0.6 + - - -
606B TRP* 3.8 28.7 - + + -
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Residues in contact with ALA 242 (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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238B GLU 3.0 11.9 + - - +
239B HIS 2.8 11.4 + - - +
241B HIS* 1.3 76.6 + - - +
243B TYR* 1.3 58.6 - - - +
245B ARG* 3.3 11.1 + - - +
246B ALA* 3.0 28.8 + - - +
599B ASN* 3.7 16.4 - - - +
602B SER* 5.1 3.7 + - - +
603B PHE 3.5 25.0 - - - +
604B VAL* 3.9 16.6 - - + -
605B GLY 4.9 0.2 - - - +
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Residues in contact with TYR 243 (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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239B HIS 2.8 9.5 + - - +
240B LEU* 3.5 4.7 - - + +
242B ALA* 1.3 75.0 - - - +
244B VAL* 1.3 71.4 + - + +
246B ALA* 3.3 7.6 + - + +
247B LYS* 3.2 48.1 + - + +
282B THR* 2.7 36.1 + - - -
284B PRO* 3.3 19.8 - - - +
440B LEU* 3.9 23.8 - - + -
594B TRP* 3.8 11.3 - + - -
595B LEU* 3.5 29.6 - - + -
598B GLN* 3.6 35.0 - - + -
599B ASN* 3.6 12.5 - - - +
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Residues in contact with VAL 244 (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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240B LEU* 2.7 29.2 + - + +
241B HIS 3.5 7.9 - - - +
243B TYR* 1.3 77.3 - - + +
245B ARG* 1.3 59.4 + - - +
247B LYS* 3.1 2.4 + - - +
248B LEU* 2.8 38.6 + - + +
262B LEU* 3.8 14.6 - - + -
275B TRP* 3.7 30.5 - - + -
278B LEU* 4.8 6.7 - - + -
282B THR* 4.0 22.2 - - + -
444B LEU* 4.0 27.4 - - + -
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Residues in contact with ARG 245 (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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241B HIS* 2.7 40.6 + - - +
242B ALA* 3.5 8.5 + - - +
243B TYR 3.3 0.4 - - - -
244B VAL* 1.3 71.4 - - - +
246B ALA* 1.3 64.9 + - - +
248B LEU* 3.1 3.7 + - - +
249B MET* 2.9 32.4 + - + +
256B ILE* 4.0 12.3 - - + -
257B SER 3.3 20.2 - - - +
258B PRO* 3.1 24.7 + - - +
259B ILE* 3.8 3.8 - - - -
260B GLY 2.9 24.1 + - - -
262B LEU* 3.5 24.2 - - + -
603B PHE* 2.9 31.5 + - - -
605B GLY 2.9 31.1 + - - +
606B TRP* 3.8 1.2 - - - +
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Residues in contact with ALA 246 (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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242B ALA 3.0 13.4 + - - +
243B TYR* 3.3 12.3 + - + +
245B ARG* 1.3 75.3 - - - +
247B LYS* 1.3 63.9 - - + +
249B MET* 3.1 28.5 + - - +
250B ASN* 3.3 13.1 + - - +
599B ASN* 5.9 0.9 - - - +
602B SER* 5.0 15.3 - - - +
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Residues in contact with LYS 247 (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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243B TYR* 3.2 45.2 + - + +
244B VAL 3.1 8.3 + - - +
246B ALA* 1.3 80.2 - - + +
248B LEU* 1.3 63.9 + - - +
250B ASN* 3.0 28.6 + - - +
251B ALA* 3.1 11.8 + - - +
281B LEU* 3.5 27.7 + - - +
282B THR* 3.8 19.9 - - + -
283B VAL 4.0 13.1 + - - -
284B PRO 4.8 5.1 + - - -
598B GLN* 5.9 0.7 - - - -
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Residues in contact with LEU 248 (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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244B VAL* 2.8 31.9 + - + +
245B ARG* 3.8 3.1 - - - +
247B LYS* 1.3 70.4 - - + +
249B MET* 1.3 55.9 + - - +
251B ALA* 4.1 2.7 - - - -
252B TYR* 2.6 55.4 + - + -
256B ILE* 3.6 18.2 - - + +
262B LEU* 3.9 28.7 - - + -
263B PRO* 5.9 0.4 - - + -
266B LEU* 4.0 17.0 - - + +
267B LEU* 4.8 5.2 - - + -
278B LEU* 3.9 22.9 - - + -
281B LEU* 3.4 27.6 - - + -
282B THR* 5.5 0.2 - - + -
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Residues in contact with MET 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ARG* 2.9 23.8 + - - +
246B ALA* 3.1 15.9 + - - +
248B LEU* 1.3 76.4 - - - +
250B ASN* 1.3 62.6 + - - +
252B TYR 4.5 2.7 - - - -
253B PRO* 3.1 27.2 - - - +
254B SER* 4.5 4.4 + - - +
256B ILE* 3.0 44.8 - - + +
258B PRO* 3.5 41.5 - - + -
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Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ALA* 3.3 15.6 + - - +
247B LYS* 3.0 24.9 + - - +
249B MET* 1.3 76.2 - - - +
251B ALA* 1.3 65.1 + - - +
253B PRO* 3.3 15.0 - - - +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 5.3 5.8 - - + +
247B LYS 3.1 11.7 + - - +
248B LEU* 3.6 9.6 - - - +
250B ASN* 1.3 76.3 - - - +
252B TYR* 1.3 74.4 + - + +
253B PRO* 2.9 9.9 - - - +
281B LEU* 3.6 35.4 - - + -
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Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B SER 3.4 19.8 + - - -
156B LEU* 3.3 41.5 - - + +
158B TYR* 4.1 16.6 - + + -
161B ARG* 3.5 12.4 + - - -
248B LEU* 2.6 43.4 + - + +
249B MET* 3.3 7.3 - - - +
251B ALA* 1.3 88.2 - - + +
253B PRO* 1.3 68.7 - - - +
254B SER 3.1 2.8 + - - -
255B TYR* 3.1 30.7 + + + +
256B ILE* 4.4 6.9 + - + +
266B LEU* 3.8 39.9 + - + -
281B LEU* 4.5 3.7 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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