Contacts of the helix formed by residues 169 - 194 (chain B) in PDB entry 5E9W
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 ILE 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 1.3 86.7 - - + +
170B PHE* 1.3 62.3 + - - +
171B TYR 3.3 2.5 - - - -
172B LEU* 3.0 17.7 + - + +
173B ARG* 3.0 62.5 + - + +
340B ILE* 4.3 26.5 - - + -
362B LEU* 4.3 23.1 - - + +
363B GLU* 4.3 36.3 - - + +
460B GLU* 5.9 2.7 - - - -
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Residues in contact with PHE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 3.3 22.2 - - + +
169B ILE* 1.3 79.1 - - - +
171B TYR* 1.3 97.0 + + + +
173B ARG* 3.4 11.3 + - + +
174B ASN* 3.0 35.6 + - + +
415B MET 5.1 0.7 - - - -
416B GLN* 3.1 38.1 - - + -
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG 5.4 4.9 - - - -
169B ILE 3.3 0.6 - - - -
170B PHE* 1.3 101.4 - + + +
172B LEU* 1.3 61.0 + - - +
174B ASN* 3.8 4.8 + - + +
175B PHE* 2.9 29.8 + - - +
416B GLN* 3.2 32.7 + - + +
455B THR 5.5 7.2 - - - +
456B LEU* 5.2 4.4 - - + +
460B GLU* 3.9 28.0 + - - +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 3.0 17.3 + - + +
171B TYR* 1.3 76.5 - - - +
173B ARG* 1.3 60.5 + - + +
175B PHE* 3.3 5.1 + - + +
176B ASN* 2.9 42.0 + - - +
340B ILE* 4.1 13.9 - - + -
362B LEU* 4.1 29.8 - - + -
456B LEU* 4.5 8.3 - - + -
460B GLU* 3.8 25.4 + - + +
463B ALA* 3.8 20.6 - - + -
464B THR* 3.7 33.0 - - - +
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 6.2 1.4 - - - +
169B ILE* 3.0 48.9 + - + +
170B PHE* 3.8 12.7 - - + +
172B LEU* 1.3 74.2 - - + +
174B ASN* 1.3 61.7 + - - +
176B ASN* 3.2 13.5 + - - +
177B ASN* 2.9 30.1 + - - +
362B LEU* 5.7 5.8 - - + +
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Residues in contact with ASN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PHE* 3.0 27.2 + - + +
171B TYR* 3.8 7.8 + - - +
172B LEU 3.3 0.2 - - - -
173B ARG* 1.3 78.9 - - - +
175B PHE* 1.3 57.9 + - - +
177B ASN* 3.3 7.3 + - - +
178B TRP* 2.9 25.6 + - - +
412B LEU* 4.4 10.1 + - - +
415B MET* 2.7 50.3 + - - +
416B GLN* 3.1 20.5 - - - +
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR 2.9 17.7 + - - +
172B LEU* 3.5 6.3 - - - +
173B ARG 3.2 0.2 - - - -
174B ASN* 1.3 76.1 - - - +
176B ASN* 1.3 61.5 + - - +
178B TRP* 3.1 18.2 + + - +
179B MET* 2.9 60.7 + - + +
395B PHE* 4.4 3.4 - + + -
399B TYR* 3.5 38.4 - + + -
412B LEU* 4.3 5.8 - - + -
455B THR* 4.3 7.4 - - + -
456B LEU* 3.5 33.9 - - + -
461B TRP* 3.7 12.3 - + - -
464B THR* 3.5 34.5 - - + -
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Residues in contact with ASN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 2.9 28.7 + - - +
173B ARG* 3.5 15.9 - - - +
175B PHE* 1.3 75.8 - - - +
177B ASN* 1.3 57.9 + - - +
179B MET* 3.4 8.5 + - - +
180B LYS* 3.0 36.1 + - - +
285B PHE* 4.0 33.3 - - + -
362B LEU* 5.7 5.3 - - - +
395B PHE* 3.9 6.9 - - - -
464B THR* 3.6 20.1 + - - -
467B TYR* 5.6 4.7 - - - -
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG 2.9 13.2 + - - +
174B ASN* 3.4 12.7 + - - +
176B ASN* 1.3 77.9 - - - +
178B TRP* 1.3 56.3 + - - +
180B LYS* 3.4 16.0 + - - +
181B SER* 2.9 32.4 + - - -
210B GLY* 4.1 5.1 + - - +
214B LYS* 2.6 36.5 + - - +
415B MET* 3.8 15.8 - - + +
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Residues in contact with TRP 178 (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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174B ASN* 2.9 14.5 + - - +
175B PHE* 3.1 19.3 + + - +
177B ASN* 1.3 72.7 - - - +
179B MET* 1.3 94.0 + - + +
181B SER* 3.4 2.9 + - - -
182B VAL* 3.1 38.1 + - + +
398B PHE* 5.7 0.2 - + - -
399B TYR* 3.8 32.3 - + - -
402B LYS* 4.2 18.8 - - + -
403B ILE* 4.5 12.8 - - + -
408B ASN* 2.7 42.5 + - + -
411B LEU* 3.8 18.2 - - + +
412B LEU* 3.5 43.0 - - + +
415B MET* 3.7 13.2 - - - +
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Residues in contact with MET 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 2.9 48.8 + - + +
176B ASN* 3.5 8.7 - - - +
178B TRP* 1.3 91.2 - - + +
180B LYS* 1.3 57.6 + - + +
182B VAL* 3.5 0.9 + - - -
183B LEU* 3.0 29.9 + - - +
395B PHE* 3.4 61.9 - - + +
398B PHE* 3.4 39.1 - - + -
399B TYR 4.5 2.5 - - - -
469B VAL* 4.0 4.4 - - + +
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Residues in contact with LYS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASN* 3.0 24.5 + - - +
177B ASN* 3.7 21.6 + - - +
179B MET* 1.3 73.4 - - + +
181B SER* 1.3 59.0 + - - +
183B LEU* 4.3 6.1 - - - -
184B ILE* 2.8 44.1 + - + +
210B GLY* 5.1 2.0 - - - -
211B ASP* 3.1 20.9 + - - +
214B LYS* 4.1 7.9 - - + -
284B GLN* 3.6 42.8 - - + +
285B PHE* 3.8 17.6 - - + -
317B THR* 5.1 3.1 - - + +
501B SAH 2.7 30.3 + - - +
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASN 2.9 24.0 + - - -
178B TRP* 3.5 7.9 - - - -
179B MET 3.3 0.2 - - - -
180B LYS* 1.3 77.7 - - - +
182B VAL* 1.3 56.4 + - - +
184B ILE* 4.0 2.1 - - - +
185B GLY* 2.8 26.5 + - - -
214B LYS* 3.3 25.4 - - - +
411B LEU* 4.2 21.5 - - - -
415B MET* 4.4 8.0 - - - +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TRP* 3.1 47.4 + - + +
179B MET* 3.9 3.4 - - - +
180B LYS 3.2 0.2 - - - -
181B SER* 1.3 75.8 - - - +
183B LEU* 1.3 61.1 + - - +
185B GLY* 4.8 0.9 - - - -
186B GLU* 3.0 29.6 + - + +
398B PHE* 4.2 4.0 - - + -
402B LYS* 3.6 40.8 - - + +
408B ASN* 3.9 24.9 - - - +
411B LEU* 4.8 4.7 - - + -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET 3.0 18.1 + - - +
180B LYS* 3.7 4.7 - - - +
182B VAL* 1.3 78.7 - - - +
184B ILE* 1.3 61.4 + - + +
186B GLU* 3.3 1.7 + - - +
187B PHE* 3.3 47.2 + - + +
284B GLN* 4.0 25.8 - - - +
315B ILE* 4.4 8.5 - - + +
316B GLY 4.0 27.8 - - - +
317B THR* 4.4 7.9 - - + -
391B TYR* 3.3 30.5 - - + +
398B PHE* 4.0 15.2 - - + -
469B VAL* 4.4 7.6 - - + -
470B PHE 4.6 6.3 - - - +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LYS* 2.8 26.9 + - + +
181B SER* 4.0 3.4 - - - +
183B LEU* 1.3 72.4 - - + +
185B GLY* 1.3 63.0 + - - +
187B PHE* 3.4 1.7 + - - +
188B LEU* 3.0 34.4 + - + +
211B ASP* 4.1 15.7 - - - +
214B LYS* 4.0 30.7 - - + +
215B TRP* 3.5 53.6 - - + -
280B ILE* 5.2 0.7 - - - +
282B SER* 4.1 10.1 - - - +
284B GLN* 4.6 5.6 - - - +
315B ILE* 4.3 12.8 - - + -
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Residues in contact with GLY 185 (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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181B SER 2.8 19.6 + - - -
182B VAL* 3.8 2.5 - - - -
183B LEU 3.3 0.2 - - - -
184B ILE* 1.3 79.0 - - - +
186B GLU* 1.3 60.2 + - - +
188B LEU* 3.8 7.2 - - - +
189B GLU* 3.3 22.7 + - - +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 3.0 17.2 + - + +
183B LEU* 3.6 4.7 - - - +
184B ILE 3.3 0.4 - - - -
185B GLY* 1.3 76.9 - - - +
187B PHE* 1.3 61.8 + - + +
189B GLU* 3.4 7.4 + - - +
190B LYS* 3.1 53.5 + - + +
391B TYR* 3.0 38.6 + - - -
398B PHE* 4.3 1.2 - - - -
401B GLU* 4.9 1.2 - - - +
402B LYS* 3.0 33.2 + - - +
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Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 3.3 31.6 + - + +
184B ILE 4.4 1.6 - - - +
186B GLU* 1.3 84.5 - - + +
188B LEU* 1.3 62.3 + - - +
189B GLU 3.2 0.9 - - - -
190B LYS* 3.5 27.5 - - + +
191B VAL* 3.0 33.1 + - - +
280B ILE* 3.9 11.4 - - + -
313B TYR* 3.6 32.3 - + + -
315B ILE* 3.9 18.4 - - + -
390B VAL* 4.3 5.6 - - + -
391B TYR* 3.2 39.7 - + - -
471B ALA* 3.3 29.4 - - + -
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 3.0 36.5 + - + +
185B GLY* 3.8 7.9 - - - +
187B PHE* 1.3 78.3 - - - +
189B GLU* 1.3 56.9 + - - +
191B VAL* 3.5 3.6 + - - +
192B ARG* 3.0 46.6 + - - +
199B ILE* 4.1 12.6 - - + -
214B LYS 4.6 2.0 - - - +
215B TRP* 3.9 17.3 - - + -
218B GLY* 3.7 28.3 - - - +
220B ILE* 3.6 24.7 - - + -
280B ILE* 3.9 16.7 - - + +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLY 3.3 11.7 + - - +
186B GLU* 3.7 9.0 - - - +
187B PHE 3.2 0.4 - - - -
188B LEU* 1.3 77.5 - - - +
190B LYS* 1.3 58.2 + - + +
192B ARG* 3.1 9.3 + - - +
193B GLN* 2.7 38.9 + - + +
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 3.1 48.5 + - + +
187B PHE* 3.5 34.3 - - + +
188B LEU 3.4 0.2 - - - -
189B GLU* 1.3 79.5 - - + +
191B VAL* 1.3 60.7 + - - +
193B GLN* 3.2 16.7 + - - +
194B LYS* 3.3 18.7 + - - +
313B TYR* 3.8 24.2 + - + +
390B VAL* 5.1 7.3 - - - +
391B TYR* 5.3 0.7 - - - -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE 3.0 20.6 + - - +
188B LEU* 3.7 5.4 - - - +
190B LYS* 1.3 76.3 - - - +
192B ARG* 1.3 61.6 + - - +
194B LYS* 3.1 26.0 + - - +
196B LYS* 3.7 17.0 - - + +
199B ILE* 3.4 30.7 - - + -
279B ASP* 3.9 18.4 - - + +
280B ILE* 3.8 18.2 - - + -
311B GLY 5.0 2.2 - - - +
312B GLY* 5.2 0.9 - - - -
313B TYR* 3.6 25.8 - - + -
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 3.0 36.5 + - - +
189B GLU* 3.1 7.6 + - - +
191B VAL* 1.3 72.0 - - - +
193B GLN* 1.3 54.8 + - - +
194B LYS 2.5 22.2 - - - +
195B LYS* 4.6 0.5 - - - -
196B LYS 4.4 10.2 - - - +
197B ARG 5.2 3.2 + - - +
199B ILE* 4.1 28.5 - - + +
218B GLY* 2.3 35.5 + - - -
219B ARG* 3.1 24.1 + - - +
220B ILE* 4.0 1.8 - - - +
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Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 2.7 24.2 + - + +
190B LYS* 3.2 12.1 + - - +
192B ARG* 1.3 69.1 - - - +
194B LYS* 1.3 63.7 + - + +
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS 3.3 9.8 + - - +
191B VAL* 3.1 14.6 + - - +
192B ARG 2.5 23.8 - - - +
193B GLN* 1.3 77.5 - - + +
195B LYS* 1.3 61.8 + - - +
196B LYS* 3.2 6.7 - - + +
310B PRO 5.3 0.9 - - - +
311B GLY* 2.8 35.3 + - - +
313B TYR* 2.5 32.9 + - - -
473B GLU* 3.0 16.8 + - - -
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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