Contacts of the helix formed by residues 220 - 244 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D SER* 3.2 11.3 + - - -
219D THR* 1.3 75.4 - - - +
221D TYR* 1.3 55.1 + - - +
222D GLU* 3.2 16.5 + - - +
223D ALA* 2.9 12.9 + - - +
224D ASN* 2.7 38.2 + - - +
221E TYR* 4.8 5.8 - - - -
222E GLU* 3.8 28.2 + - - +
277E HIS* 4.9 5.6 - - - -
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Residues in contact with TYR 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C THR 3.8 9.9 + - - -
218C SER* 3.3 28.0 - - - -
220C SER* 4.8 2.7 - - - -
223C ALA* 4.1 17.0 - - + -
227C LEU* 3.3 22.2 - - + +
219D THR 3.9 3.0 + - - -
220D SER* 1.3 70.1 - - - +
222D GLU* 1.3 73.6 + - - +
223D ALA 2.8 0.7 + - - -
224D ASN* 2.8 7.0 + - - +
225D VAL* 2.8 50.9 + - + +
273D VAL* 3.6 23.6 - - + -
274D THR* 3.4 29.3 + - + +
277D HIS* 3.4 50.3 - + + +
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Residues in contact with GLU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C SER* 4.0 23.4 + - - +
222C GLU* 4.5 14.6 - - + -
223C ALA* 4.2 18.0 - - + +
226C THR* 5.6 1.4 + - - +
219D THR 5.1 0.5 - - - +
220D SER* 3.5 16.2 + - - +
221D TYR* 1.3 97.1 + - + +
223D ALA* 1.3 55.0 + - - +
225D VAL* 4.5 2.9 - - - +
226D THR* 3.1 19.1 + - - -
277D HIS* 5.1 6.2 + - - -
222E GLU* 5.5 8.3 - - + -
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Residues in contact with ALA 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D SER* 2.9 20.9 + - - +
221D TYR 2.8 2.8 + - - -
222D GLU* 1.3 74.5 - - - +
224D ASN* 1.3 59.2 + - - +
225D VAL 3.3 2.0 - - - -
226D THR* 3.1 9.6 + - - -
227D LEU* 2.8 27.7 + - - +
221E TYR* 4.1 23.1 - - + -
222E GLU* 4.1 23.5 - - - +
225E VAL* 4.0 8.6 - - + +
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Residues in contact with ASN 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D ALA* 3.1 36.0 + - + +
218D SER* 2.7 39.6 + - - -
219D THR 4.8 0.2 - - - -
220D SER 2.7 21.7 + - - +
221D TYR* 2.8 3.9 + - - +
223D ALA* 1.3 69.4 - - - +
225D VAL* 1.3 66.9 + - - +
227D LEU* 3.4 9.1 - - - +
228D VAL* 2.8 28.8 + - - +
273D VAL* 3.7 22.5 - - + +
276D GLN* 3.5 14.1 + - - -
221E TYR* 4.5 1.4 - - - -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ALA* 4.0 8.7 - - + +
226C THR* 4.0 12.3 - - + -
227C LEU* 3.9 42.2 - - + +
221D TYR* 2.8 55.9 + - + +
222D GLU 4.5 3.1 - - - +
224D ASN* 1.3 73.4 - - - +
226D THR* 1.3 58.4 + - - +
228D VAL* 5.1 2.0 - - - -
229D VAL* 2.8 47.9 + - + +
273D VAL* 4.7 4.0 - - + -
274D THR* 5.8 0.2 - - - +
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Residues in contact with THR 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C THR* 4.2 20.4 + - + +
222D GLU 3.1 16.3 + - - -
223D ALA* 3.1 10.9 + - - -
225D VAL* 1.3 77.4 - - - +
227D LEU* 1.3 64.5 + - - +
229D VAL* 5.1 0.4 - - - -
230D SER* 2.7 41.4 + - - +
222E GLU 5.5 1.5 + - - -
225E VAL* 4.0 15.7 - - + -
226E THR* 4.0 25.3 + - + +
229E VAL* 5.6 1.6 - - + -
230E SER* 6.0 0.4 - - - +
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Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ILE* 3.4 34.1 - - + +
212D SER* 4.7 1.6 - - - +
214D THR* 3.1 28.7 - - - +
215D ALA* 4.0 20.4 - - + +
223D ALA 2.8 14.8 + - - +
224D ASN* 3.4 11.9 - - - +
226D THR* 1.3 75.0 - - - +
228D VAL* 1.3 53.0 + - + +
230D SER* 4.2 0.7 - - - -
231D THR* 2.7 37.8 + - - +
221E TYR* 3.2 27.1 - - + +
225E VAL* 3.8 21.6 - - + +
229E VAL* 4.5 9.9 - - + -
270E VAL* 5.0 2.7 - - + -
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D SER* 3.8 25.1 - - - +
215D ALA* 4.3 9.9 - - + -
224D ASN 2.8 20.5 + - - +
225D VAL* 4.2 2.0 - - - +
227D LEU* 1.3 72.0 - - - +
229D VAL* 1.3 63.0 + - + +
231D THR* 2.8 18.5 + - - -
232D LEU* 3.1 12.6 + - + +
266D TYR* 3.9 19.8 - - + +
269D ALA* 4.3 16.4 - - + -
270D VAL* 3.4 35.2 - - + +
273D VAL* 4.6 10.1 - - + -
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ILE* 4.5 19.3 - - + -
226C THR* 4.9 1.8 - - + +
227C LEU* 4.6 8.1 - - + +
230C SER* 3.3 35.9 - - - +
231C THR* 4.4 13.9 - - + +
225D VAL* 2.8 40.9 + - + +
226D THR* 5.1 1.1 - - - -
228D VAL* 1.3 73.7 - - + +
230D SER* 1.3 57.3 + - - +
232D LEU* 3.2 13.5 + - + +
233D ILE* 3.0 28.7 + - + +
270D VAL* 4.8 8.3 - - + -
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Residues in contact with SER 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D THR* 2.7 36.9 + - - +
229D VAL* 1.3 74.9 - - - +
231D THR* 1.3 61.3 + - - +
233D ILE* 3.0 11.3 + - - +
234D ALA* 2.9 24.3 + - - +
229E VAL* 3.2 25.9 - - - +
233E ILE* 3.5 18.6 - - - +
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Residues in contact with THR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 3.4 29.8 - - + +
211D ILE* 3.6 26.0 - - + -
212D SER* 3.6 5.6 - - - +
227D LEU 2.7 24.0 + - - +
228D VAL* 2.8 16.1 + - - -
230D SER* 1.3 77.8 - - - +
232D LEU* 1.3 54.9 + - - +
234D ALA* 3.4 9.2 + - - +
235D HIS* 2.9 27.4 + - - +
266D TYR* 3.4 15.4 + - - -
229E VAL* 4.4 10.8 - - + -
232E LEU* 5.5 3.8 - - + -
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 4.2 14.6 - - + -
211C ILE* 3.8 32.5 - - + -
231C THR* 5.5 3.4 - - + -
234C ALA* 5.5 3.4 - - + -
228D VAL* 3.1 17.1 + - + +
229D VAL* 3.3 17.5 - - + +
230D SER 3.2 0.2 - - - -
231D THR* 1.3 73.8 + - - +
233D ILE* 1.3 60.9 + - + +
235D HIS* 3.4 5.5 + - + +
236D ILE* 2.9 42.1 + - + +
263D TYR* 4.6 17.9 - - + +
266D TYR* 3.6 35.4 - - + -
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Residues in contact with ILE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LMT 4.4 19.1 - - + -
230C SER* 3.6 34.8 - - - +
233C ILE* 3.7 18.4 - - + -
234C ALA* 4.2 20.0 - - + -
229D VAL* 3.0 14.3 + - + +
230D SER* 3.0 10.7 + - - +
232D LEU* 1.3 75.5 - - + +
234D ALA* 1.3 66.1 + - - +
236D ILE* 2.9 20.7 + - - +
237D ALA* 3.0 11.0 + - - +
402D LMT 5.4 1.7 - - + +
403D LMT 5.2 5.0 - - + +
233E ILE* 3.7 22.4 - - + -
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 4.0 11.9 - - + -
230D SER 2.9 13.1 + - - +
231D THR* 3.5 13.0 - - - +
233D ILE* 1.3 79.2 - - - +
235D HIS* 1.3 60.3 + - - +
237D ALA* 3.1 22.9 - - - +
238D PHE* 3.4 12.0 - - - -
403D LMT 5.4 1.6 - - - -
229E VAL* 6.4 0.4 - - + -
232E LEU* 5.4 4.3 - - + -
233E ILE* 4.1 12.1 - - + -
236E ILE* 3.5 27.6 - - + -
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Residues in contact with HIS 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D MET* 3.8 41.0 + - + +
208D ILE* 3.2 21.5 - - + +
231D THR 2.9 13.1 + - - +
232D LEU* 3.6 7.2 - - + +
233D ILE 3.2 0.2 - - - -
234D ALA* 1.3 73.4 - - - +
236D ILE* 1.3 66.4 + - - +
238D PHE* 3.1 8.0 + - - +
239D ASN* 3.0 18.4 + - + +
259D ILE* 3.9 8.2 + - + +
262D ILE* 3.2 35.4 - - + +
263D TYR* 3.4 39.2 - + - -
266D TYR* 3.8 16.9 - + + +
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 4.0 15.7 - - + -
234C ALA* 3.5 31.9 - - + -
237C ALA* 3.8 21.5 - - + -
238C PHE* 3.5 30.3 - - + -
232D LEU* 2.9 23.1 + - + +
233D ILE* 2.9 10.8 + - - +
235D HIS* 1.3 75.1 - - - +
237D ALA* 1.3 63.9 + - - +
239D ASN* 3.1 10.7 + - - +
240D ILE* 3.2 16.4 + - + +
263D TYR* 3.5 26.0 - - + +
402D LMT 4.3 6.0 - - + +
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ILE 3.0 6.6 + - - +
234D ALA 3.1 16.8 - - - +
236D ILE* 1.3 76.8 - - - +
238D PHE* 1.3 54.1 + - + +
241D LEU 3.5 7.6 + - - -
402D LMT 3.3 29.0 - - - +
403D LMT 3.2 36.1 - - + -
236E ILE* 3.7 15.7 - - + -
240E ILE* 3.2 17.5 - - + +
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Residues in contact with PHE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D ASN 3.9 15.9 - - - -
201D ILE* 4.4 17.3 - - + +
204D PRO* 3.8 26.7 - - + -
205D MET* 3.3 33.4 - - + +
208D ILE* 5.5 4.9 - - + -
234D ALA 3.4 13.2 - - - -
235D HIS* 3.1 8.5 + - - +
237D ALA* 1.3 79.3 - - + +
239D ASN* 1.3 61.5 + - - +
241D LEU* 4.0 17.0 - - + +
242D VAL* 3.6 21.0 + - - +
236E ILE* 3.5 35.0 - - + -
239E ASN* 4.3 4.9 - - - -
240E ILE* 4.2 10.8 - - + -
243E GLU* 5.5 0.4 - - - -
263E TYR* 3.5 24.7 - + - -
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Residues in contact with ASN 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C PRO 5.4 2.4 + - - -
200C ASN* 4.5 13.3 + - - +
204C PRO* 4.8 3.6 - - - +
238C PHE* 4.3 9.7 - - - -
205D MET* 4.5 0.2 - - - +
235D HIS* 3.0 10.3 + - + +
236D ILE 3.1 4.2 + - - +
238D PHE* 1.3 75.3 - - - +
240D ILE* 1.3 63.5 + - + +
242D VAL* 3.3 1.9 + - - +
243D GLU* 3.0 41.5 + - - +
259D ILE* 3.7 28.9 - - + +
263D TYR* 2.7 44.6 + - + +
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Residues in contact with ILE 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LMT 4.1 19.7 - - + -
237C ALA* 3.3 40.2 - - + +
238C PHE* 4.1 18.8 - - + -
241C LEU* 3.6 42.0 - - + -
236D ILE* 3.2 16.9 + - + +
239D ASN* 1.3 76.5 - - + +
241D LEU* 1.4 53.3 + - - +
243D GLU* 4.6 6.0 - - - +
244D THR* 2.5 34.9 + - + +
402D LMT 4.3 19.2 - - + +
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Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ILE* 4.8 17.0 - - + -
237D ALA 3.5 18.6 + - - +
238D PHE* 4.3 12.8 - - + +
239D ASN 3.2 1.0 - - - -
240D ILE* 1.4 77.1 - - - +
242D VAL* 1.4 54.2 + - - +
244D THR* 4.2 2.6 + - - -
245D ASN* 2.7 40.5 + - - +
402D LMT 3.9 23.8 - - + +
240E ILE* 3.6 33.9 - - + -
243E GLU* 3.2 30.5 - - - +
244E THR* 4.5 18.6 - - + -
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D TYR* 5.1 5.6 - - + -
197D TYR* 6.0 0.2 - - + -
201D ILE* 3.7 43.3 - - + -
238D PHE 3.6 14.6 + - - +
239D ASN* 3.3 3.2 + - - +
241D LEU* 1.4 75.5 - - + +
243D GLU* 1.3 68.8 + - + +
244D THR 3.2 3.5 + - - -
245D ASN* 3.4 24.2 + - - +
246D LEU* 3.9 19.6 + - + +
255D THR* 4.1 18.8 - - + -
256D GLY* 5.7 2.5 - - - +
259D ILE* 3.6 24.0 - - + -
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Residues in contact with GLU 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ASN* 3.1 48.0 - - + +
201C ILE* 4.9 5.6 - - - +
238C PHE* 5.8 0.5 - - - -
241C LEU* 3.5 34.9 - - - +
33D LYS* 5.7 0.2 - - - -
239D ASN* 3.0 30.1 + - - +
240D ILE* 4.0 5.6 + - - +
241D LEU 3.6 0.2 - - - -
242D VAL* 1.3 79.6 - - + +
244D THR* 1.3 61.0 + - - +
246D LEU* 3.5 19.0 - - - +
247D PRO 5.5 0.7 - - - +
248D LYS* 5.0 15.9 - - - +
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Residues in contact with THR 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LEU* 4.5 21.8 - - + -
245C ASN* 5.9 1.1 - - - +
33D LYS* 3.7 26.3 - - - +
240D ILE* 2.5 28.9 + - + +
241D LEU* 4.2 3.1 + - - -
242D VAL 3.2 0.6 - - - -
243D GLU* 1.3 81.0 - - - +
245D ASN* 1.3 61.4 + - - +
246D LEU 3.2 3.5 + - - -
402D LMT 5.3 6.2 - - - +
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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