Contacts of the helix formed by residues 229 - 254 (chain F) in PDB entry 6MZL
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 LEU 229 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F SER* 1.3 85.8 - - - +
230F ASP* 1.3 69.7 + - - +
231F CYS* 3.7 2.0 - - - +
232F HIS* 3.5 30.8 - - + +
233F ARG* 3.2 20.4 + - - +
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Residues in contact with ASP 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F LEU* 1.3 80.0 - - - +
231F CYS* 1.3 61.1 + - - +
233F ARG* 3.9 2.1 - - - +
234F ALA* 2.9 30.0 + - - +
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Residues in contact with CYS 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F LEU* 5.5 0.7 - - - -
230F ASP* 1.3 79.9 - - - +
232F HIS* 1.3 82.9 + - - +
234F ALA* 3.7 6.9 - - - -
235F GLU* 2.9 43.9 + - - +
312F ASP* 5.2 3.6 - - - -
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Residues in contact with HIS 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F ILE* 5.6 0.2 - - - -
228F SER* 3.8 19.1 - - - -
229F LEU* 3.5 39.9 - - + +
230F ASP 3.2 0.2 - - - -
231F CYS* 1.3 89.5 - - - +
233F ARG* 1.3 57.9 + - - +
235F GLU* 3.3 2.6 + - - +
236F LEU* 2.9 39.4 + - + +
310F SER* 5.0 0.4 + - - -
312F ASP* 3.1 40.6 + - + -
313F SER* 4.2 13.6 + - - +
316F LEU* 3.5 30.0 - - + +
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Residues in contact with ARG 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F ILE* 4.2 22.9 - - - +
226F GLU* 4.3 41.2 + - - +
228F SER* 4.4 2.8 - - - -
229F LEU 3.2 16.5 + - - +
230F ASP* 4.1 2.2 - - - +
232F HIS* 1.3 78.0 - - - +
234F ALA* 1.3 57.4 + - - +
236F LEU* 4.4 3.6 - - - +
237F SER* 2.8 40.0 + - - +
240F PHE* 4.6 11.6 - - + -
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Residues in contact with ALA 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F ASP 2.9 19.9 + - - +
231F CYS* 3.7 9.0 - - - +
233F ARG* 1.3 77.9 - - - +
235F GLU* 1.3 62.3 + - + +
236F LEU 4.0 0.2 + - - -
237F SER* 4.3 12.0 - - - -
238F GLN* 5.3 0.7 + - - +
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Residues in contact with GLU 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F CYS* 2.9 28.2 + - + +
232F HIS 4.2 1.6 - - - +
234F ALA* 1.3 82.2 - - + +
236F LEU* 1.3 70.1 + - + +
237F SER 3.6 1.1 - - - -
238F GLN* 2.8 32.3 + - - +
308F ARG 4.2 16.6 - - - +
309F ILE* 4.3 1.1 - - - +
310F SER* 3.4 34.6 + - - -
313F SER* 4.4 2.5 + - - +
342F PHE* 4.2 17.1 - - + +
343F ASP* 4.6 7.4 - - - +
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Residues in contact with LEU 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F ILE* 3.8 33.4 - - + +
228F SER* 5.5 2.5 - - - +
232F HIS* 2.9 23.9 + - + +
233F ARG 3.7 1.6 - - - +
235F GLU* 1.3 88.4 - - + +
237F SER* 1.3 61.2 + - - +
238F GLN 3.1 1.3 - - - -
239F LEU* 2.8 51.0 + - + +
240F PHE* 3.0 18.9 + - - -
309F ILE* 4.3 9.4 - - + -
313F SER* 3.7 38.8 - - - +
316F LEU* 5.9 5.4 - - + -
317F LEU* 6.5 0.7 - - + -
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Residues in contact with SER 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ARG* 2.8 28.2 + - - +
234F ALA* 4.3 10.6 - - - -
235F GLU 3.6 0.6 - - - -
236F LEU* 1.3 77.8 - - - +
238F GLN* 1.3 59.3 + - - +
240F PHE* 3.5 27.6 + - - +
241F TYR* 4.2 1.0 + - - +
271F GLN* 4.1 6.1 - - - +
272F GLU* 4.8 20.2 + - - +
275F TYR* 5.0 4.9 + - - -
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Residues in contact with GLN 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F ALA 5.3 0.6 + - - +
235F GLU* 2.8 30.9 + - - +
237F SER* 1.3 78.8 - - - +
239F LEU* 1.3 59.8 + - + +
241F TYR* 4.2 1.6 + - - +
242F PRO* 3.2 24.7 - - - +
275F TYR* 5.5 4.7 - - - -
306F VAL* 3.7 17.2 - - - +
307F LEU* 5.4 2.7 - - + +
308F ARG* 3.1 65.5 + - - +
309F ILE* 3.6 8.5 - - + +
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Residues in contact with LEU 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F ILE* 5.0 13.0 - - + -
236F LEU* 2.8 50.6 + - + +
238F GLN* 1.3 77.8 - - - +
240F PHE* 1.3 65.4 + - - +
241F TYR 3.3 1.6 + - - -
242F PRO* 3.7 6.2 - - + +
243F LEU* 3.6 24.6 - - + +
305F PHE* 5.8 3.4 - - + -
307F LEU* 3.7 29.8 - - + -
309F ILE* 4.8 9.2 - - + -
317F LEU* 5.3 17.9 - - + -
337F LEU* 5.4 7.2 - - + -
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Residues in contact with PHE 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F TYR* 3.1 29.3 + + - -
222F LYS* 3.6 50.3 - - + -
225F ILE* 3.6 40.2 - - + -
226F GLU* 4.0 16.4 - - + -
233F ARG* 4.6 15.3 - - + -
236F LEU 3.0 25.1 + - - -
237F SER* 3.5 17.2 + - - +
238F GLN 3.4 1.2 - - - -
239F LEU* 1.3 77.4 - - - +
241F TYR* 1.3 61.9 + - - +
243F LEU* 5.5 0.9 - - - -
244F PHE* 3.9 3.8 + - - +
270F ASP 5.9 0.7 - - - +
271F GLN* 3.1 25.2 + - - +
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Residues in contact with TYR 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F SER 4.2 1.5 + - - +
238F GLN 4.2 2.6 + - - +
240F PHE* 1.3 77.3 - - - +
242F PRO* 1.4 79.9 - - + +
244F PHE* 3.1 12.7 + + - +
245F VAL* 3.0 47.9 + - + +
271F GLN* 3.1 33.8 + - + +
275F TYR* 3.4 58.9 + + + +
278F ASP* 3.3 33.8 + - - +
279F LEU* 4.7 11.7 + - + +
282F LEU* 5.5 2.3 - - + +
300F PHE* 4.7 18.5 - + - -
649F ARG* 6.2 0.2 - - - -
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Residues in contact with PRO 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F GLN 3.2 24.2 - - - +
239F LEU* 3.7 6.3 - - + +
241F TYR* 1.4 92.4 - - + +
243F LEU* 1.3 60.9 + - - +
245F VAL* 3.6 11.6 - - + +
246F HIS* 2.9 30.7 + - - +
300F PHE* 5.4 10.8 - - + -
304F LYS 5.3 1.8 - - - +
305F PHE* 3.6 36.2 - - + -
306F VAL 6.1 1.1 - - - +
307F LEU* 6.5 1.3 - - + -
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Residues in contact with LEU 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F TYR* 3.6 29.8 - - + -
221F LEU* 3.7 26.7 - - + -
225F ILE* 5.7 4.0 - - + -
239F LEU* 3.6 18.8 + - + +
240F PHE* 6.0 0.4 - - - -
241F TYR 3.2 0.2 - - - -
242F PRO* 1.3 80.3 - - - +
244F PHE* 1.3 56.9 + - - +
246F HIS* 3.4 3.9 + - - +
247F MET* 2.9 38.0 + - + +
305F PHE* 4.9 5.2 - - - -
329F ILE* 4.1 21.3 - - + -
332F ILE* 3.8 32.8 - - + -
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Residues in contact with PHE 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F TYR* 3.3 34.0 - + - +
240F PHE 3.9 3.2 + - - +
241F TYR* 3.1 16.5 + + - +
243F LEU* 1.3 77.5 - - - +
245F VAL* 1.3 62.1 + - + +
247F MET* 3.4 4.6 + - - +
248F TYR* 2.9 33.9 + + + +
263F PHE* 3.5 34.8 - + - -
264F PHE* 3.9 26.2 - + - -
267F PHE* 3.2 39.3 - - + -
268F HIS* 4.4 3.4 - - - -
271F GLN* 5.1 6.3 - - + +
279F LEU* 5.6 2.9 - - + -
282F LEU* 4.0 24.2 - - + -
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Residues in contact with VAL 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F TYR* 3.0 51.9 + - + +
242F PRO* 3.6 9.9 - - + +
243F LEU 3.2 0.2 - - - -
244F PHE* 1.3 84.2 - - + +
246F HIS* 1.3 57.6 + - - +
248F TYR* 3.3 6.4 + - - +
249F LEU* 2.9 25.8 + - - +
282F LEU* 4.6 12.9 - - + +
300F PHE* 4.6 11.0 - - + -
301F ARG* 3.4 41.2 + - + +
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Residues in contact with HIS 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F PRO 2.9 16.9 + - - +
243F LEU* 4.0 3.4 - - - +
245F VAL* 1.3 73.4 - - - +
247F MET* 1.3 61.8 + - - +
249F LEU* 3.3 29.0 + - + +
250F GLU* 2.9 30.3 + - + +
301F ARG* 4.0 17.8 + - + +
305F PHE* 5.1 9.1 - + + -
328F GLN* 5.1 7.4 + - - -
332F ILE* 3.6 34.8 - - + +
336F HIS* 3.4 36.5 + + - -
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Residues in contact with MET 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F PRO* 5.3 2.2 - - + +
214F TYR* 3.6 39.5 - - + +
215F GLU* 5.8 2.0 - - + -
218F TYR* 5.0 10.5 - - + -
243F LEU* 2.9 32.0 + - + +
244F PHE* 3.8 7.4 - - - +
245F VAL 3.3 0.2 - - - -
246F HIS* 1.3 75.0 - - - +
248F TYR* 1.3 58.7 + - - +
250F GLU* 3.2 32.0 + - + +
251F LEU* 2.9 37.3 + - + +
263F PHE* 4.8 13.5 - - + -
328F GLN* 4.6 5.6 - - + -
329F ILE* 5.1 8.7 - - + -
332F ILE* 4.0 19.5 - - + -
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Residues in contact with TYR 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F PHE* 2.9 23.4 + + + +
245F VAL* 3.8 3.6 - - - +
247F MET* 1.3 73.9 - - - +
249F LEU* 1.3 60.3 + - - +
251F LEU* 3.3 15.2 + - + +
252F VAL* 2.9 48.3 + - + +
260F ALA* 3.2 40.3 + - + +
261F LYS* 4.9 2.9 + - - -
263F PHE* 5.0 4.2 - + + -
264F PHE* 3.6 24.5 - + + +
282F LEU* 3.2 54.1 + - + -
283F SER* 5.0 2.8 + - - -
285F LEU* 3.7 22.0 + - + -
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Residues in contact with LEU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F VAL 2.9 13.8 + - - +
246F HIS* 3.3 25.8 - - + +
248F TYR* 1.3 78.0 - - - +
250F GLU* 1.3 57.3 + - - +
252F VAL* 3.3 4.7 + - + -
253F TYR* 2.9 31.1 + - + +
282F LEU* 5.5 0.8 - - - +
285F LEU* 6.0 1.6 - - - -
291F MET* 5.1 14.4 - - + -
297F MET* 3.3 55.2 - - + +
298F LEU* 4.9 8.3 - - + -
301F ARG* 3.7 25.1 - - + +
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Residues in contact with GLU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F PRO* 6.0 2.0 - - + -
214F TYR* 3.9 13.7 - - - -
246F HIS* 2.9 18.3 + - + +
247F MET* 3.2 31.6 + - + +
249F LEU* 1.3 77.4 - - - +
251F LEU* 1.3 57.3 + - + +
253F TYR* 3.4 9.0 + - + +
254F ASN* 2.8 51.5 + - - +
328F GLN* 3.3 43.6 + - - +
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Residues in contact with LEU 251 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F PRO* 3.7 28.9 - - + +
215F GLU* 3.4 32.8 - - + +
247F MET* 2.9 23.3 + - + +
248F TYR* 3.5 13.7 - - + +
249F LEU 3.2 0.2 - - - -
250F GLU* 1.3 77.9 - - + +
252F VAL* 1.3 61.1 + - - +
254F ASN* 3.5 4.8 + - - +
255F GLN 3.2 15.1 + - - -
256F HIS* 3.5 17.6 + - + +
259F GLU* 5.3 4.0 - - + -
260F ALA* 3.7 31.6 - - + +
263F PHE* 3.7 25.4 - - + -
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Residues in contact with VAL 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F TYR* 2.9 49.0 + - + +
249F LEU* 3.8 5.6 - - - +
251F LEU* 1.3 75.8 - - + +
253F TYR* 1.3 57.8 + - - +
255F GLN* 3.0 27.0 + - - +
256F HIS 5.3 0.7 - - - +
260F ALA* 5.2 3.4 - - + -
285F LEU* 3.9 16.6 - - + +
286F THR 3.5 28.1 - - - +
287F LYS* 4.1 11.7 - - - +
288F LYS* 5.7 1.2 - - - +
291F MET* 5.3 4.3 - - + -
297F MET* 4.1 21.1 - - + -
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Residues in contact with TYR 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F LEU* 2.9 20.6 + - + +
250F GLU* 3.8 9.9 - - + +
252F VAL* 1.3 78.4 - - - +
254F ASN* 1.3 69.0 + - - +
255F GLN* 3.5 7.8 + - - +
288F LYS* 4.0 31.6 + - - +
291F MET* 4.0 33.4 - - + -
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Residues in contact with ASN 254 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F PRO* 4.3 19.6 - - - +
250F GLU* 2.8 44.2 + - - +
251F LEU* 3.9 4.2 - - - +
252F VAL 3.3 0.2 - - - -
253F TYR* 1.3 83.9 - - - +
255F GLN* 1.3 69.6 + - - +
256F HIS* 3.4 29.5 + - + +
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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