Contacts of the helix formed by residues 220 - 244 (chain C) in PDB entry 5J0Z
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 SER 220 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C SER* 3.2 10.9 + - - -
219C THR* 1.3 75.6 - - - +
221C TYR* 1.3 54.5 + - - +
222C GLU* 3.2 29.6 + - - +
223C ALA* 2.9 11.1 + - - -
224C ASN* 2.7 38.1 + - - +
221D TYR* 4.8 6.1 - - - -
222D GLU* 4.0 17.9 + - - +
277D HIS* 4.9 6.7 - - - -
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Residues in contact with TYR 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR 3.7 10.2 + - - -
218B SER* 3.2 28.6 - - - -
220B SER* 4.7 3.1 - - - -
223B ALA* 4.0 20.0 - - + -
224B ASN* 4.5 1.6 - - - -
227B LEU* 3.2 20.8 - - + +
219C THR 3.9 3.2 + - - -
220C SER* 1.3 69.7 - - - +
222C GLU* 1.3 73.1 + - - +
223C ALA 2.8 0.9 + - - -
224C ASN* 2.9 6.6 + - - +
225C VAL* 2.8 51.0 + - + +
273C VAL* 3.6 24.2 - - + -
274C THR* 3.3 29.1 + - + +
277C HIS* 3.4 50.5 - + + +
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Residues in contact with GLU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B SER* 4.4 13.0 + - - -
222B GLU* 5.0 15.1 - - + +
223B ALA* 4.2 18.9 - - + +
226B THR* 5.6 1.0 + - - +
219C THR 5.0 0.2 - - - +
220C SER* 3.2 25.5 + - - +
221C TYR* 1.3 94.5 + - - +
223C ALA* 1.3 55.0 + - + +
225C VAL* 4.5 2.9 - - - +
226C THR* 3.1 19.4 + - - -
277C HIS* 5.7 0.3 + - - -
222D GLU* 4.5 15.3 - - + -
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C SER* 2.9 21.1 + - - +
221C TYR 2.8 0.6 + - - -
222C GLU* 1.3 77.2 - - - +
224C ASN* 1.3 60.7 + - - +
225C VAL 3.3 1.6 - - - -
226C THR* 3.1 9.5 + - - -
227C LEU* 2.8 27.8 + - - +
221D TYR* 4.1 23.3 - - + -
222D GLU* 4.2 22.4 - - - +
225D VAL* 4.0 10.5 - - + +
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Residues in contact with ASN 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ALA* 3.1 34.6 + - + +
218C SER* 2.7 40.0 + - - -
219C THR 4.8 0.2 - - - -
220C SER 2.7 22.7 + - - +
221C TYR* 3.7 3.9 - - - +
223C ALA* 1.3 69.9 - - - +
225C VAL* 1.3 66.9 + - - +
227C LEU* 3.4 9.1 - - - +
228C VAL* 2.8 29.1 + - - +
273C VAL* 3.7 22.1 - - + +
276C GLN* 3.5 13.9 + - - -
221D TYR* 4.6 1.2 - - - -
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ALA* 3.9 10.8 - - + +
226B THR* 4.0 9.9 - - + -
227B LEU* 3.8 43.5 - - + +
221C TYR* 2.8 59.4 + - + +
222C GLU 4.5 3.6 - - - +
224C ASN* 1.3 71.7 - - - +
226C THR* 1.3 59.9 + - - +
228C VAL* 5.1 1.3 - - - -
229C VAL* 2.8 43.4 + - + +
273C VAL* 4.7 3.8 - - + -
274C THR* 5.8 0.2 - - - +
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Residues in contact with THR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 4.1 19.7 + - + +
222C GLU 3.1 16.3 + - - -
223C ALA* 3.1 11.5 + - - -
225C VAL* 1.3 77.5 - - - +
227C LEU* 1.3 64.3 + - - +
229C VAL* 5.1 0.4 - - - -
230C SER* 2.7 42.4 + - - +
222D GLU 5.6 1.1 + - - -
225D VAL* 4.0 15.5 - - + -
226D THR* 4.2 23.2 + - + +
229D VAL* 5.6 2.0 - - + -
230D SER* 6.1 0.2 - - - +
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ILE* 3.4 34.3 - - + +
212C SER* 4.7 1.1 - - - +
214C THR* 3.1 28.9 - - - +
215C ALA* 4.0 21.1 - - + +
223C ALA 2.8 14.7 + - - +
224C ASN* 3.4 11.7 - - - +
226C THR* 1.3 74.8 - - - +
228C VAL* 1.3 53.3 + - + +
230C SER* 4.2 0.7 - - - -
231C THR* 2.7 37.2 + - - +
221D TYR* 3.3 27.1 - - + +
225D VAL* 3.9 21.2 - - + +
229D VAL* 4.6 9.8 - - + +
270D VAL* 5.0 2.7 - - + -
274D THR* 5.2 0.2 - - - +
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Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C SER* 3.7 24.9 - - - +
215C ALA* 4.3 9.9 - - + -
216C PHE* 6.6 0.2 - - + -
224C ASN 2.8 20.5 + - - +
225C VAL* 4.2 1.8 - - - +
227C LEU* 1.3 72.7 - - - +
229C VAL* 1.3 62.9 + - + +
231C THR* 2.8 17.4 + - - -
232C LEU* 3.1 13.6 + - + +
266C TYR* 3.9 20.1 - - + +
269C ALA* 4.3 16.6 - - + -
270C VAL* 3.3 34.8 - - + +
273C VAL* 4.6 10.1 - - + -
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 4.5 19.5 - - + -
226B THR* 4.8 1.3 - - + +
227B LEU* 4.5 8.3 - - + +
230B SER* 3.2 36.1 - - - +
231B THR* 4.3 13.9 - - + +
225C VAL* 2.8 41.7 + - + +
226C THR* 4.5 1.3 - - - +
228C VAL* 1.3 73.7 - - + +
230C SER* 1.3 56.8 + - - +
232C LEU* 3.2 13.0 + - + +
233C ILE* 3.0 28.4 + - + +
270C VAL* 4.8 8.3 - - + -
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Residues in contact with SER 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 6.0 0.3 - - - +
226C THR* 2.7 37.2 + - - +
229C VAL* 1.3 75.5 - - - +
231C THR* 1.3 59.9 + - - +
233C ILE* 3.1 12.1 + - - +
234C ALA* 2.9 24.3 + - - +
229D VAL* 3.3 25.2 - - - +
233D ILE* 3.6 19.0 - - - +
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Residues in contact with THR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 3.4 30.2 - - + +
211C ILE* 3.7 26.0 - - + -
212C SER* 3.6 6.1 - - - +
227C LEU 2.7 23.8 + - - +
228C VAL* 2.8 16.3 + - - -
230C SER* 1.3 78.8 - - - +
232C LEU* 1.3 54.6 - - - +
234C ALA* 3.4 9.6 + - + +
235C HIS* 2.8 27.5 + - - +
266C TYR* 3.4 13.6 + - - -
229D VAL* 4.5 9.9 - - + -
232D LEU* 5.5 4.0 - - + -
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Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.2 15.9 - - + -
211B ILE* 3.7 33.0 - - + -
231B THR* 5.4 3.6 - - + -
234B ALA* 5.4 3.4 - - + -
228C VAL* 3.1 16.4 + - + +
229C VAL* 3.3 17.9 - - + +
230C SER 3.2 0.2 - - - -
231C THR* 1.3 72.5 + - - +
233C ILE* 1.3 61.3 + - + +
235C HIS* 3.4 5.1 + - + +
236C ILE* 2.9 44.3 + - + +
263C TYR* 4.6 16.8 - - + +
266C TYR* 3.6 34.3 - - + -
270C VAL* 6.1 1.1 - - + -
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Residues in contact with ILE 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LMT 4.6 22.4 - - + -
230B SER* 3.5 40.2 - - - +
233B ILE* 3.7 19.1 - - + -
234B ALA* 4.2 15.5 - - + -
401B LMT 5.1 7.1 - - + +
229C VAL* 3.0 14.2 + - + +
230C SER* 3.1 11.9 + - - +
232C LEU* 1.3 75.7 - - + +
234C ALA* 1.3 65.1 + - - +
236C ILE* 2.9 19.2 + - - +
237C ALA* 3.0 11.7 + - - +
233D ILE* 3.7 22.2 - - + -
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 3.9 12.1 - - + -
230C SER 2.9 13.1 + - - +
231C THR* 3.4 13.0 + - - +
233C ILE* 1.3 76.8 - - - +
235C HIS* 1.3 61.5 + - - +
237C ALA* 3.1 22.5 - - - +
238C PHE* 3.4 12.0 - - - -
229D VAL* 6.5 0.2 - - + -
232D LEU* 5.5 3.8 - - + -
233D ILE* 4.2 13.0 - - + -
236D ILE* 3.5 26.9 - - + -
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Residues in contact with HIS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C MET* 3.8 40.6 + - + +
208C ILE* 3.2 21.3 - - + +
231C THR 2.8 16.9 + - - +
232C LEU* 3.6 7.6 - - + +
234C ALA* 1.3 70.8 - - - +
236C ILE* 1.3 66.7 + - - +
238C PHE* 3.1 7.8 + - - +
239C ASN* 3.0 18.7 + - + +
259C ILE* 3.9 8.3 + - + +
262C ILE* 3.2 35.4 - - + +
263C TYR* 3.4 39.9 - + - -
266C TYR* 3.8 15.4 - + + +
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.0 15.9 - - + -
234B ALA* 3.4 32.5 - - + -
237B ALA* 3.7 9.4 - - + -
238B PHE* 3.5 30.3 - - + -
401B LMT 3.7 20.6 - - + +
232C LEU* 2.9 23.8 + - + +
233C ILE* 2.9 10.7 + - - +
235C HIS* 1.3 75.2 - - - +
237C ALA* 1.3 63.1 + - - +
239C ASN* 3.1 10.2 + - - +
240C ILE* 3.2 16.5 + - + +
263C TYR* 3.5 25.1 - - + +
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Residues in contact with ALA 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LMT 3.6 21.9 - - + +
233C ILE 3.0 9.1 + - - +
234C ALA* 3.1 18.2 - - - +
235C HIS 3.2 0.2 - - - -
236C ILE* 1.3 77.5 - - - +
238C PHE* 1.3 54.7 + - + +
241C LEU* 3.4 17.0 + - - +
236D ILE* 3.8 25.1 - - + -
240D ILE* 3.3 18.2 - - + +
402D LMT 4.1 17.0 - - + -
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Residues in contact with PHE 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ASN 3.9 15.0 - - - -
201C ILE* 4.3 17.4 - - + +
204C PRO* 3.7 27.4 - - + -
205C MET* 3.3 34.6 - - + +
208C ILE* 5.5 4.9 - - + -
234C ALA 3.4 13.0 - - - -
235C HIS* 3.1 7.5 + - - +
237C ALA* 1.3 78.6 - - + +
239C ASN* 1.3 62.9 + - - +
241C LEU* 4.0 17.1 - - + +
242C VAL* 3.5 21.0 + - - +
236D ILE* 3.5 34.3 - - + -
239D ASN* 4.3 5.2 - - - -
240D ILE* 4.1 11.0 - - + -
243D GLU* 5.8 0.7 - - - -
263D TYR* 3.5 24.9 - + - -
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Residues in contact with ASN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO 5.4 1.8 + - - -
200B ASN* 4.5 13.0 + - - +
204B PRO* 4.7 4.0 - - - +
238B PHE* 4.3 10.2 - - - -
205C MET* 4.5 0.2 - - - +
235C HIS* 3.0 9.9 + - + +
236C ILE 3.1 3.7 + - - +
238C PHE* 1.3 76.3 - - - +
240C ILE* 1.3 62.3 + - + +
242C VAL* 3.3 2.3 + - - +
243C GLU* 3.0 41.5 + - - +
259C ILE* 3.7 28.7 - - + +
263C TYR* 2.7 46.1 + - + +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LMT 4.2 17.9 - - + -
237B ALA* 3.2 40.6 - - + +
238B PHE* 4.1 20.6 - - + -
241B LEU* 3.6 43.5 - - + -
401B LMT 3.9 20.1 - - + +
236C ILE* 3.2 12.3 + - + +
239C ASN* 1.3 76.8 - - + +
241C LEU* 1.4 53.9 + - - +
243C GLU* 4.5 6.6 - - - +
244C THR* 2.5 35.4 + - + +
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LMT 4.1 12.5 - - + +
201C ILE* 4.8 17.3 - - + -
237C ALA 3.4 19.0 + - - +
238C PHE* 4.3 14.4 - - + +
239C ASN 3.3 1.4 - - - -
240C ILE* 1.4 77.5 - - - +
242C VAL* 1.4 52.8 + - - +
244C THR* 4.2 2.5 + - - -
245C ASN* 2.7 41.4 + - - +
240D ILE* 3.6 39.5 - - + -
243D GLU* 3.5 29.2 - - - +
244D THR* 4.5 19.3 - - + -
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C TYR* 5.1 6.0 - - + -
197C TYR* 6.0 0.2 - - + -
201C ILE* 3.7 42.8 - - + -
238C PHE 3.5 15.5 + - - +
239C ASN* 3.3 3.6 + - - +
241C LEU* 1.4 74.0 - - + +
243C GLU* 1.3 68.0 + - + +
244C THR 3.3 3.5 + - - -
245C ASN* 3.4 25.0 + - - +
246C LEU* 3.9 18.6 + - + +
255C THR* 4.1 18.2 - - + +
256C GLY* 5.7 2.0 - - - +
259C ILE* 3.6 25.1 - - + -
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ASN* 3.1 47.1 - - + +
201B ILE* 4.9 5.8 - - - +
238B PHE* 5.8 0.5 - - - -
241B LEU* 3.4 36.2 - - - +
239C ASN* 3.0 30.0 + - - +
240C ILE* 4.6 5.3 - - - +
241C LEU 3.6 0.2 - - - -
242C VAL* 1.3 80.8 - - + +
244C THR* 1.3 60.6 + - - +
246C LEU* 3.5 19.1 - - - +
247C PRO 5.5 0.7 - - - +
248C LYS* 4.9 16.3 - - - +
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Residues in contact with THR 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.5 21.1 - - + -
245B ASN* 6.0 0.9 - - - +
401B LMT 5.8 2.6 - - - +
33C LYS* 3.3 34.3 - - - +
240C ILE* 2.5 28.7 + - + +
241C LEU* 4.2 3.9 + - - -
242C VAL 3.3 0.2 - - - -
243C GLU* 1.3 81.8 - - - +
245C ASN* 1.3 61.4 + - - +
246C LEU 3.2 3.1 - - - -
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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