Contacts of the helix formed by residues 183 - 208 (chain B) in PDB entry 4YVF
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 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 4.3 1.8 - - - +
179B ASN 5.1 0.6 + - - -
180B VAL* 3.2 12.3 + - - +
182B ASP* 1.3 78.1 - - - +
184B VAL* 1.3 54.0 + - - +
185B THR* 3.5 1.9 + - - -
186B LYS* 3.2 18.4 + - - +
187B SER* 2.8 35.6 + - - -
364B ASN* 3.0 25.8 + - - -
386B LEU* 4.2 16.2 - - - -
391B ASP* 3.5 14.4 - - - -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.7 25.6 - - + -
251A GLN* 5.3 2.0 - - + +
431A ARG* 3.3 26.9 - - - +
182B ASP 3.8 0.6 + - - -
183B SER* 1.3 70.6 - - - +
185B THR* 1.3 57.5 + - - +
187B SER* 3.6 6.3 - - - -
188B LYS* 2.9 53.0 + - + +
388B LYS* 4.9 2.2 - - - +
391B ASP* 2.7 19.6 + - - +
432B TYR* 3.3 44.0 - - + +
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 4.5 7.6 - - + -
250A LEU* 4.7 4.5 - - + -
183B SER* 3.5 0.5 + - - -
184B VAL* 1.3 77.2 - - + +
186B LYS* 1.3 61.2 + - - +
188B LYS* 5.1 0.4 - - - -
189B PHE* 3.2 32.8 + - - +
360B ASN* 3.7 15.9 - - - +
364B ASN* 2.8 26.6 + - - -
391B ASP* 2.5 41.2 + - - +
394B VAL* 3.6 6.2 - - + +
395B ALA* 3.6 28.9 - - + +
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU* 2.7 38.9 + - + -
157B THR* 4.7 1.2 - - - +
180B VAL* 3.2 19.1 - - + +
181B ASN* 2.9 25.5 + - - +
183B SER* 3.2 17.5 + - - +
185B THR* 1.3 82.6 + - - +
187B SER* 1.3 57.2 + - - +
189B PHE* 4.1 0.5 - - - +
190B ASP* 2.7 71.4 + - + +
191B ASN* 5.6 1.8 + - - +
360B ASN* 4.6 2.9 - - - -
361B SER* 3.8 27.0 + - - +
364B ASN* 3.4 12.3 - - - +
502B XFA 5.6 0.4 - - - -
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 4.0 7.5 + - - -
181B ASN 3.8 11.9 - - - -
182B ASP* 4.8 3.1 - - - -
183B SER 2.8 28.3 + - - -
184B VAL* 3.3 8.5 + - - -
186B LYS* 1.3 80.6 - - - +
188B LYS* 1.3 69.9 + - - -
191B ASN* 2.8 52.8 + - - +
223B ASP* 4.4 3.3 - - - +
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN* 5.1 17.3 - - + +
431A ARG* 4.4 20.0 - - - +
432A TYR 4.3 14.1 + - - +
184B VAL* 2.9 38.6 + - + +
185B THR* 4.6 1.3 - - - +
187B SER* 1.3 86.3 + - - +
189B PHE* 1.3 59.9 + - + +
192B LEU* 2.9 32.2 + - + +
193B TYR* 2.9 46.7 + - + +
223B ASP* 3.6 26.7 + - - +
431B ARG 5.1 7.2 - - - -
432B TYR* 5.3 2.5 - - - -
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Residues in contact with PHE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 3.7 28.3 - - + -
254A MET* 3.3 41.7 - - + -
185B THR* 3.2 26.7 + - - +
186B LYS 3.4 1.7 + - - +
187B SER 3.3 0.2 - - - -
188B LYS* 1.3 80.9 - - + +
190B ASP* 1.3 59.6 + - - +
193B TYR* 3.7 29.6 - + + -
194B GLY* 2.7 31.0 + - - -
356B PHE* 3.6 18.8 - + - -
357B VAL* 3.2 27.1 - - + +
360B ASN* 3.5 31.0 - - + -
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LYS* 2.7 59.5 + - + +
187B SER* 4.2 1.3 - - - +
189B PHE* 1.3 74.3 - - - +
191B ASN* 1.3 64.4 + - - +
353B HIS* 2.9 41.8 + - - -
357B VAL* 4.2 4.0 - - - +
358B MET* 5.3 2.6 - - - +
361B SER* 4.0 9.6 + - - +
501B NAI 3.2 10.0 - - - -
502B XFA 3.4 26.8 - - - -
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Residues in contact with ASN 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASN* 5.5 1.4 + - - -
186B LYS* 5.6 1.4 + - - +
187B SER* 2.8 42.4 + - - +
189B PHE 4.5 0.2 - - - -
190B ASP* 1.3 83.8 + - - +
192B LEU* 1.3 64.1 + - - +
195B CYS* 3.2 27.4 - - - +
223B ASP* 3.4 25.1 + - + -
224B VAL* 3.8 7.1 - - + -
501B NAI 3.0 46.5 + - + +
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LYS* 2.9 29.7 + - + +
191B ASN* 1.3 75.5 - - - +
193B TYR* 1.3 87.7 + - + +
196B ARG* 3.0 27.6 + - - +
223B ASP* 3.5 40.6 - - + +
226B LYS* 4.2 17.9 - - + -
227B GLY* 3.8 19.1 - - - +
230B GLN* 4.1 14.8 - - - +
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Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN* 3.7 35.1 + - + +
254A MET* 3.7 30.6 - - + +
255A GLU* 3.8 16.3 + - - -
188B LYS* 2.9 42.0 + - + +
189B PHE* 3.7 47.8 - + + -
192B LEU* 1.3 80.4 - - + +
194B GLY* 1.3 69.2 + - - +
196B ARG* 3.2 34.4 + - - +
197B GLU* 3.2 20.6 + - + +
357B VAL* 4.3 3.1 - - + -
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Residues in contact with GLY 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE 2.7 25.7 + - - -
192B LEU 3.3 0.6 - - - -
193B TYR* 1.3 75.0 - - - +
195B CYS* 1.3 61.4 + - - +
197B GLU* 3.3 11.4 + - - +
198B SER* 3.4 12.1 + - - -
353B HIS* 3.4 27.6 + - - -
354B PRO* 4.1 0.7 - - - +
357B VAL* 3.5 14.1 - - - +
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Residues in contact with CYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN 3.2 21.2 + - - +
192B LEU 3.5 2.5 + - - +
193B TYR 3.4 0.2 - - - -
194B GLY* 1.3 72.4 - - - +
196B ARG* 1.3 64.2 + - - +
198B SER* 4.4 2.9 - - - +
199B LEU* 3.0 29.7 + - - +
224B VAL* 3.9 22.2 - - + +
227B GLY 5.0 1.3 - - - -
228B CYS* 4.4 5.0 - - - -
299B ILE* 3.7 19.1 - - + -
346B ASN* 4.7 0.4 - - - +
353B HIS* 4.1 2.5 - - - -
501B NAI 3.7 42.4 - - - -
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A MET* 2.9 31.3 + - - +
255A GLU* 3.1 16.1 + - - -
192B LEU* 3.0 21.7 + - - +
193B TYR* 3.2 31.6 + - - +
195B CYS* 1.3 76.3 - - - +
197B GLU* 1.3 70.5 + - + +
199B LEU 4.8 1.0 + - - -
200B ILE* 5.5 1.0 + - - +
227B GLY* 3.2 28.4 + - - +
230B GLN* 2.9 49.0 + - - +
231B ALA* 3.4 24.5 - - + +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A MET* 5.4 9.2 - - + +
193B TYR* 3.2 17.9 + - + +
194B GLY* 3.6 7.0 - - - +
195B CYS 3.1 0.4 - - - -
196B ARG* 1.3 91.9 + - + +
198B SER* 1.3 59.9 + - - +
199B LEU 3.9 0.2 - - - -
200B ILE* 5.4 1.0 - - - +
201B ASP* 3.9 12.1 + - - +
354B PRO* 3.6 28.5 - - + +
357B VAL* 5.2 3.4 - - + -
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Residues in contact with SER 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLY 3.4 13.9 + - - -
195B CYS* 4.6 0.7 - - - -
197B GLU* 1.3 80.7 + - - +
199B LEU* 1.3 66.8 + - - +
200B ILE 3.4 2.2 - - - -
201B ASP* 2.9 10.4 + - - +
202B GLY* 2.8 21.7 + - - -
346B ASN* 3.7 28.6 - - - +
350B ALA* 4.4 6.9 - - - +
352B GLY 3.0 24.3 + - - -
353B HIS* 5.4 0.2 - - - -
354B PRO* 4.0 8.0 - - - +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B CYS 3.0 18.3 + - - +
196B ARG 4.8 0.2 - - - -
197B GLU 3.9 0.2 - - - -
198B SER* 1.3 78.4 - - - +
200B ILE* 1.3 67.0 + - + +
202B GLY* 3.1 2.1 + - - -
203B ILE* 3.0 41.0 + - + +
228B CYS* 3.3 43.7 - - + +
231B ALA* 5.1 3.4 - - + -
232B LEU* 4.1 19.3 - - + -
273B VAL* 4.0 24.0 - - + -
297B CYS* 4.3 0.7 - - - -
299B ILE* 4.0 15.3 - - + +
345B VAL* 4.0 24.9 - - + +
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Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ARG 5.5 0.8 + - - +
197B GLU 5.2 1.5 + - - +
198B SER 3.4 0.2 - - - -
199B LEU* 1.3 80.0 - - + +
201B ASP* 1.3 59.9 + - - +
203B ILE* 3.8 7.4 - - + -
204B LYS* 2.8 44.0 + - + +
211B ILE* 4.2 17.3 - - + -
231B ALA* 3.4 37.4 - - + +
232B LEU* 3.7 23.6 - - + +
235B PHE* 3.3 47.6 - - + -
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Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLU 3.9 8.3 + - - +
198B SER* 2.9 22.3 + - - +
200B ILE* 1.3 78.6 - - - +
202B GLY* 1.3 62.8 + - - +
204B LYS* 3.4 4.9 + - - +
205B ARG* 2.9 74.0 + - - +
350B ALA* 3.9 9.9 - - + +
351B MET* 4.7 1.6 + - - +
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER 2.8 12.7 + - - -
199B LEU 3.6 3.8 - - - -
201B ASP* 1.3 75.5 - - - +
203B ILE* 1.3 65.0 + - - +
205B ARG 3.4 0.7 + - - -
206B ALA* 3.0 25.3 + - - +
345B VAL* 4.2 9.9 - - - -
349B CYS* 3.4 32.9 - - - +
350B ALA* 3.9 5.1 - - - +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 3.0 38.5 + - + +
200B ILE* 3.9 8.5 - - - +
202B GLY* 1.3 75.6 - - - +
204B LYS* 1.3 58.7 + - - +
206B ALA* 3.4 1.2 + - - +
207B THR* 2.8 44.7 + - - +
209B VAL* 4.2 14.8 - - + -
211B ILE* 4.3 10.3 - - + -
232B LEU* 5.0 6.3 - - + -
271B ILE* 4.1 28.7 - - + -
273B VAL* 4.5 1.3 - - + -
295B ILE* 4.4 15.3 - - + -
297B CYS* 4.3 8.3 - - - -
339B LEU* 4.0 19.1 - - + -
345B VAL* 4.6 1.6 - - + -
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ILE* 2.8 37.4 + - + +
201B ASP* 3.7 6.7 - - - +
203B ILE* 1.3 74.5 - - - +
205B ARG* 1.3 65.0 + - + +
207B THR* 4.7 0.2 - - - -
208B ASP* 2.4 50.1 + - - +
209B VAL 2.9 29.6 + - - +
210B MET* 4.4 9.7 - - - +
211B ILE* 3.9 21.3 - - + +
235B PHE* 4.5 13.8 - - - -
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ASP* 2.9 47.9 + - - +
204B LYS* 1.3 76.8 - - + +
206B ALA* 1.3 57.2 + - - +
208B ASP* 4.6 6.0 - - - +
322B LYS* 3.1 25.1 + - - +
349B CYS* 3.3 26.5 - - + +
350B ALA* 4.2 3.0 - - - +
351B MET* 3.3 36.7 - - - +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLY 3.0 17.6 + - - +
203B ILE 3.7 3.6 - - - +
205B ARG* 1.3 78.9 - - - +
207B THR* 1.3 62.2 + - - +
321B ILE* 5.2 1.6 - - - +
322B LYS* 3.3 22.2 + - - +
325B VAL* 3.5 34.1 - - + +
339B LEU* 3.8 22.4 - - + -
349B CYS* 3.9 11.4 - - - +
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE 2.8 22.6 + - - +
204B LYS 3.4 0.4 - - - -
206B ALA* 1.3 85.7 - - + +
208B ASP* 1.3 75.6 + - - +
209B VAL* 2.9 29.7 + - - +
295B ILE* 3.7 21.2 - - + +
321B ILE* 6.2 0.4 - - + -
322B LYS* 5.1 1.3 - - - +
325B VAL* 4.8 1.6 - - + -
337B ILE* 4.1 26.2 - - + -
339B LEU* 4.3 4.5 - - + -
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Residues in contact with ASP 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS* 2.4 48.0 + - - +
205B ARG* 4.6 4.6 - - - +
207B THR* 1.3 71.8 + - - +
209B VAL* 1.3 64.2 + - - +
210B MET 3.9 0.3 + - - -
322B LYS* 4.5 11.6 + - - -
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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