Contacts of the helix formed by residues 220 - 244 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B SER* 3.2 11.1 + - - -
219B THR* 1.3 76.6 - - - +
221B TYR* 1.3 54.2 + - - +
222B GLU* 3.2 28.8 + - - +
223B ALA* 2.9 12.7 + - - +
224B ASN* 2.7 37.6 + - - +
221C TYR* 4.7 6.7 - - - -
222C GLU* 4.4 11.1 + - - -
277C HIS* 4.8 8.3 - - - -
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Residues in contact with TYR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A THR* 3.6 10.9 + - - -
217A TRP 5.7 0.2 - - - -
218A SER* 3.3 28.0 - - - -
220A SER* 4.9 2.9 - - - -
223A ALA* 4.1 16.6 - - + -
227A LEU* 3.2 23.2 - - + +
219B THR 3.9 3.0 + - - -
220B SER* 1.3 69.9 - - - +
222B GLU* 1.3 73.5 + - - +
223B ALA 2.8 1.7 + - - -
224B ASN* 2.9 7.1 + - - +
225B VAL* 2.8 49.7 + - + +
273B VAL* 3.6 24.2 - - + -
274B THR* 3.3 29.5 + - + +
277B HIS* 3.4 48.9 - + + +
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A SER* 4.4 13.3 + - - +
222A GLU* 6.0 4.9 - - + +
223A ALA* 4.2 23.0 - - + +
226A THR* 5.5 1.7 + - - +
219B THR 5.1 0.2 - - - +
220B SER* 3.2 25.6 + - - +
221B TYR* 1.3 93.8 + - - +
223B ALA* 1.3 55.8 + - + +
225B VAL* 4.5 2.9 - - - +
226B THR* 3.1 19.4 + - - -
277B HIS* 6.1 0.2 - - - -
222C GLU* 5.0 16.2 - - + +
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B SER* 2.9 15.0 + - - +
221B TYR 2.8 0.2 + - - -
222B GLU* 1.3 77.4 - - - +
224B ASN* 1.3 60.1 + - - +
225B VAL 3.3 1.6 - - - -
226B THR* 3.1 9.8 + - - -
227B LEU* 2.8 27.6 + - - +
221C TYR* 4.0 29.6 - - + -
222C GLU* 4.2 22.2 - - - +
225C VAL* 3.9 10.0 - - + +
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Residues in contact with ASN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA* 3.2 34.8 + - + +
218B SER* 2.7 39.4 + - - -
220B SER 2.7 22.4 + - - +
221B TYR* 3.7 4.3 - - - +
223B ALA* 1.3 69.6 - - - +
225B VAL* 1.3 68.7 + - - +
227B LEU* 3.4 9.1 - - - +
228B VAL* 2.9 28.8 + - - +
273B VAL* 3.7 21.9 - - + +
276B GLN* 3.5 14.5 + - - -
221C TYR* 4.5 1.2 - - - -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ALA* 4.1 7.2 - - + +
226A THR* 4.0 11.7 - - + -
227A LEU* 3.8 45.8 - - + +
221B TYR* 2.8 58.3 + - + +
222B GLU 4.5 3.4 - - - +
224B ASN* 1.3 70.4 - - - +
226B THR* 1.3 56.9 + - - +
228B VAL* 3.9 1.7 - - - -
229B VAL* 2.8 47.4 + - + +
273B VAL* 4.7 4.0 - - + -
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 4.0 19.5 + - + +
222B GLU 3.1 16.1 + - - -
223B ALA* 3.1 10.6 + - - -
225B VAL* 1.3 77.6 - - - +
227B LEU* 1.3 63.7 + - - +
229B VAL* 5.1 0.9 - - - -
230B SER* 2.7 42.2 + - - +
222C GLU 5.6 1.0 + - - -
225C VAL* 4.0 15.9 - - + -
226C THR* 4.1 24.5 + - + +
229C VAL* 5.5 1.8 - - + -
230C SER* 6.0 0.4 - - - +
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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
----------------------------------------------------------
211B ILE* 3.5 33.7 - - + +
212B SER* 4.7 1.8 - - - +
214B THR* 3.1 29.2 - - - +
215B ALA* 4.0 20.9 - - + +
223B ALA 2.8 14.8 + - - +
224B ASN* 3.4 11.0 - - - +
226B THR* 1.3 74.6 - - - +
228B VAL* 1.3 51.7 - - + +
230B SER* 4.2 0.3 - - - -
231B THR* 2.7 38.3 + - - +
221C TYR* 3.2 27.4 - - + +
225C VAL* 3.8 21.2 - - + +
229C VAL* 4.5 10.1 - - + -
270C VAL* 4.9 2.9 - - + -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER* 3.8 24.2 - - - +
215B ALA* 4.3 9.6 - - + -
216B PHE* 6.6 0.2 - - + -
224B ASN 2.9 21.2 + - - +
225B VAL* 4.2 2.2 - - - +
227B LEU* 1.3 72.1 - - - +
229B VAL* 1.3 63.9 + - + +
231B THR* 2.8 17.9 + - - -
232B LEU* 3.0 13.4 + - + +
266B TYR* 3.9 19.8 - - + +
269B ALA* 4.3 17.0 - - + -
270B VAL* 3.3 36.1 - - + +
273B VAL* 4.6 9.6 - - + -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 4.4 20.9 - - + -
226A THR* 5.0 0.9 - - + +
227A LEU* 4.6 6.7 - - + +
230A SER* 3.3 36.3 - - - +
231A THR* 4.3 14.8 - - + +
234A ALA* 6.3 0.9 - - + -
225B VAL* 2.8 41.3 + - + +
226B THR* 4.5 1.3 - - - +
228B VAL* 1.3 72.5 - - + +
230B SER* 1.3 57.6 + - - +
232B LEU* 3.2 13.5 + - + +
233B ILE* 3.0 28.8 + - + +
270B VAL* 4.8 8.1 - - + -
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 2.7 36.2 + - - +
229B VAL* 1.3 75.7 - - - +
231B THR* 1.3 60.9 + - - +
233B ILE* 3.0 10.8 + - - +
234B ALA* 2.9 25.1 + - - +
229C VAL* 3.2 25.7 - - - +
233C ILE* 3.5 18.2 - - - +
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Residues in contact with THR 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 3.4 30.2 - - + +
211B ILE* 3.6 26.2 - - + -
212B SER* 3.6 6.1 - - - +
227B LEU 2.7 21.8 + - - +
228B VAL* 2.8 16.3 + - - -
230B SER* 1.3 76.3 - - - +
232B LEU* 1.3 53.3 + - - +
234B ALA* 3.4 8.9 + - - +
235B HIS* 2.9 28.6 + - - +
266B TYR* 3.4 14.5 + - - -
229C VAL* 4.5 9.9 - - + -
232C LEU* 5.4 4.3 - - + -
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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
----------------------------------------------------------
208A ILE* 4.0 17.5 - - + -
211A ILE* 3.8 29.4 - - + -
231A THR* 5.6 2.5 - - + -
234A ALA* 5.4 4.7 - - + -
228B VAL* 3.0 16.6 + - + +
229B VAL* 3.3 17.7 - - + +
230B SER 3.1 0.2 - - - -
231B THR* 1.3 74.7 + - - +
233B ILE* 1.3 59.1 + - - +
235B HIS* 3.4 5.1 + - + -
236B ILE* 2.9 43.4 + - + +
263B TYR* 4.6 17.3 - - + +
266B TYR* 3.6 35.4 - - + -
270B VAL* 6.1 1.3 - - + -
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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
----------------------------------------------------------
230A SER* 3.5 32.8 - - - +
233A ILE* 3.6 20.6 - - + -
234A ALA* 4.0 20.9 - - + -
402A LMT 4.5 22.4 - - + -
404A LMT 4.9 7.7 - - + +
229B VAL* 3.0 17.2 + - + +
230B SER* 3.3 10.8 - - - +
232B LEU* 1.3 75.6 - - + +
234B ALA* 1.3 64.4 + - - +
236B ILE* 2.9 21.0 + - - +
237B ALA* 3.0 11.0 + - - +
401B LMT 5.4 2.4 - - + +
233C ILE* 3.7 22.0 - - + -
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.0 12.6 - - + -
230B SER 2.9 13.1 + - - +
231B THR* 3.5 12.6 - - - +
233B ILE* 1.3 78.1 - - - +
235B HIS* 1.3 59.9 + - - +
237B ALA* 3.1 23.1 - - - +
238B PHE* 3.4 12.1 - - - -
401B LMT 5.7 1.3 - - - -
232C LEU* 5.4 4.0 - - + -
233C ILE* 4.2 13.0 - - + -
236C ILE* 3.4 27.8 - - + -
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Residues in contact with HIS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B MET* 3.8 38.0 + - + +
208B ILE* 3.2 20.9 - - + +
231B THR 2.9 15.7 + - - +
232B LEU* 3.6 7.4 - - + +
233B ILE 3.2 0.2 - - - -
234B ALA* 1.3 70.6 - - - +
236B ILE* 1.3 66.4 + - - +
238B PHE* 3.1 8.2 + - - +
239B ASN* 3.0 18.2 + - + +
259B ILE* 3.9 8.3 + - + +
262B ILE* 3.1 37.0 - - + +
263B TYR* 3.4 40.4 - + - -
266B TYR* 3.8 15.4 - + + +
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 4.1 15.3 - - + -
234A ALA* 3.6 30.5 - - + -
237A ALA* 3.7 21.1 - - + -
238A PHE* 3.4 31.2 - - + -
404A LMT 3.8 7.8 - - + +
232B LEU* 2.9 24.4 + - + +
233B ILE* 2.9 10.6 + - - +
235B HIS* 1.3 75.9 - - - +
237B ALA* 1.3 62.4 + - - +
239B ASN* 3.1 10.6 + - - +
240B ILE* 3.2 17.5 + - + +
263B TYR* 3.5 25.6 - - + +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LMT 3.2 36.2 - - - +
233B ILE 3.0 7.5 + - - +
234B ALA* 3.1 17.7 - - - +
236B ILE* 1.3 76.3 - - - +
238B PHE* 1.3 54.0 + - + +
241B LEU 3.4 8.0 + - - -
401B LMT 3.2 38.8 - - + -
236C ILE* 3.7 12.3 - - + -
240C ILE* 3.2 9.8 - - + +
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ASN 4.0 14.8 - - - -
201B ILE* 4.3 18.3 - - + +
204B PRO* 3.7 25.8 - - + -
205B MET* 3.3 34.7 - - + +
208B ILE* 5.5 4.5 - - + -
234B ALA 3.4 13.7 - - - -
235B HIS* 3.1 7.7 + - - +
237B ALA* 1.3 79.0 - - + +
239B ASN* 1.3 63.3 + - - +
240B ILE 3.6 0.2 - - - -
241B LEU* 4.0 16.8 - - + +
242B VAL* 3.5 21.3 + - - +
236C ILE* 3.5 33.9 - - + -
239C ASN* 4.3 5.4 - - - -
240C ILE* 4.1 12.1 - - + -
243C GLU* 5.8 0.7 - - - -
263C TYR* 3.5 24.5 - + - -
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Residues in contact with ASN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PRO 5.3 2.6 + - - -
200A ASN* 4.4 17.8 + - - +
204A PRO* 4.8 3.2 - - - +
238A PHE* 4.4 6.8 - - - -
205B MET* 4.5 0.4 - - - +
235B HIS* 3.0 10.3 + - + +
236B ILE 3.1 3.9 + - - +
238B PHE* 1.3 75.1 - - - +
240B ILE* 1.3 61.7 + - + +
242B VAL* 3.3 1.7 + - - +
243B GLU* 3.0 41.4 + - - +
259B ILE* 3.7 28.5 - - + +
263B TYR* 2.7 46.0 + - + +
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA* 3.3 38.8 - - + +
238A PHE* 4.3 16.6 - - + -
241A LEU* 3.4 43.7 - - + -
403A LMT 3.9 23.8 - - + -
404A LMT 4.5 15.6 - - + +
236B ILE* 3.2 16.5 + - + +
239B ASN* 1.3 77.6 - - + +
241B LEU* 1.4 54.1 + - - +
243B GLU* 4.5 6.2 - - - +
244B THR* 2.5 34.6 + - - +
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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
----------------------------------------------------------
404A LMT 4.2 9.3 - - + +
201B ILE* 4.8 17.0 - - + -
237B ALA 3.4 19.0 + - - +
238B PHE* 4.3 13.9 - - + +
239B ASN 3.3 0.6 - - - -
240B ILE* 1.4 76.9 - - - +
242B VAL* 1.4 53.0 + - - +
244B THR* 4.2 1.8 + - - -
245B ASN* 2.7 41.2 + - - +
240C ILE* 3.6 39.0 - - + -
243C GLU* 3.4 28.5 - - - +
244C THR* 4.5 19.1 - - + -
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 5.2 5.8 - - + -
197B TYR* 6.0 0.2 - - + -
201B ILE* 3.7 42.8 - - + -
238B PHE 3.5 14.8 + - - +
239B ASN* 3.3 3.3 + - - +
241B LEU* 1.4 74.8 - - + +
243B GLU* 1.3 68.6 + - + +
244B THR 3.2 3.6 + - - -
245B ASN* 3.4 23.9 + - - +
246B LEU* 3.9 19.0 + - + +
255B THR* 4.1 19.7 - - + -
256B GLY* 5.7 2.7 - - - +
259B ILE* 3.6 24.7 - - + -
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASN* 3.1 45.3 - - - +
201A ILE* 4.9 6.6 - - - +
238A PHE* 6.0 0.2 - - - -
241A LEU* 3.5 33.9 - - - +
239B ASN* 3.0 30.9 + - - +
240B ILE* 4.6 4.9 - - - +
241B LEU 3.6 0.2 - - - -
242B VAL* 1.3 79.5 - - + +
244B THR* 1.3 61.9 + - - +
245B ASN 3.8 0.2 - - - -
246B LEU* 3.5 19.9 - - - +
247B PRO 5.6 0.7 - - - -
248B LYS* 5.0 16.3 - - - +
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Residues in contact with THR 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 4.7 19.3 - - + -
245A ASN* 5.9 1.3 - - - +
33B LYS* 3.3 33.4 - - - +
240B ILE* 2.5 29.3 + - + +
241B LEU* 4.2 3.3 + - - -
242B VAL 3.2 0.4 - - - -
243B GLU* 1.3 81.1 - - - +
245B ASN* 1.3 62.3 + - - +
246B LEU 3.2 3.4 - - - -
----------------------------------------------------------
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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