Contacts of the helix formed by residues 188 - 213 (chain B) in PDB entry 5M4G
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 THR 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.9 1.7 + - - +
25B LEU* 3.7 22.4 - - + +
26B ASN* 3.8 5.7 + - - +
29B ARG* 3.5 44.9 - - - +
187B LYS* 1.3 76.9 - - - +
189B ASP* 1.3 66.1 + - - +
190B MET* 3.3 7.4 + - - +
191B GLU* 2.9 32.2 + - - +
192B LEU* 2.9 22.3 + - - +
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 5.6 0.2 - - - +
187B LYS 5.2 0.9 - - - +
188B THR* 1.3 74.1 - - - +
190B MET* 1.3 64.6 + - + +
192B LEU* 3.3 17.0 + - - +
193B GLU* 3.1 26.1 + - - +
196B ARG* 4.6 2.3 + - - +
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Residues in contact with MET 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO* 3.9 22.0 - - + -
21B ALA* 3.5 27.1 - - + +
22B LEU* 3.7 33.9 - - + +
25B LEU* 3.5 30.3 - - + +
188B THR* 3.1 5.8 + - - +
189B ASP* 1.3 81.1 - - + +
191B GLU* 1.3 62.4 + - - +
193B GLU* 3.2 18.7 + - + +
194B VAL* 3.4 15.1 + - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.0 23.6 - - + -
26B ASN* 3.5 11.8 + - - +
29B ARG* 4.2 1.2 + - - -
73B TRP* 3.3 31.0 + - - -
183B CYS 5.3 0.2 - - - +
184B ARG 5.4 1.6 - - - +
186B PHE 4.0 3.1 - - - +
187B LYS* 3.2 25.0 - - + +
188B THR* 2.9 42.4 + - - +
190B MET* 1.3 77.1 - - - +
192B LEU* 1.3 63.7 + - - +
194B VAL* 3.0 7.2 + - - +
195B LEU* 3.0 26.4 + - + +
284B PHE* 4.0 21.7 - - + -
374B ILE* 5.0 1.0 - - - +
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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
----------------------------------------------------------
187B LYS* 3.7 28.0 - - + +
188B THR 2.9 19.5 + - - +
189B ASP* 3.6 19.1 - - - +
190B MET 3.2 0.2 - - - -
191B GLU* 1.3 72.1 - - - +
193B GLU* 1.3 61.4 + - - +
195B LEU* 3.3 7.4 + - + +
196B ARG* 2.8 62.9 + - + +
406B GLY* 5.9 2.5 - - - -
408B VAL* 3.9 8.3 - - + -
456B VAL* 3.8 41.3 - - + -
463B GLU* 5.1 0.9 - - - +
465B LEU* 5.1 0.8 - - + +
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Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.8 14.6 - - + +
189B ASP* 3.1 17.4 + - + +
190B MET* 3.5 11.0 - - + +
191B GLU 3.2 0.4 - - - -
192B LEU* 1.3 77.0 - - - +
194B VAL* 1.3 62.8 + - + +
196B ARG* 2.8 36.9 + - - +
197B TYR* 3.2 21.3 + - - +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.6 19.7 - - + -
18B VAL* 4.0 17.5 - - + -
22B LEU* 3.9 19.5 - - + -
190B MET 3.6 13.0 - - - +
191B GLU 3.0 6.7 + - - +
193B GLU* 1.3 78.6 - - + +
195B LEU* 1.3 56.8 + - - +
197B TYR* 3.1 4.0 + - - +
198B THR* 2.9 26.9 + - + +
281B TYR* 4.2 17.7 - - + +
284B PHE* 3.6 39.3 - - + -
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS* 4.0 20.4 - - + -
191B GLU* 3.0 19.7 + - + +
192B LEU* 3.9 8.5 - - + +
194B VAL* 1.3 74.6 - - - +
196B ARG* 1.3 63.7 + - - +
198B THR* 3.1 14.6 + - - +
199B ASN* 3.1 17.8 + - - +
284B PHE* 4.2 22.4 - - + -
285B ALA 3.3 26.5 - - - +
372B LEU* 4.1 13.7 - - + +
373B GLY* 4.4 5.4 - - - +
408B VAL* 4.0 33.0 - - + -
465B LEU* 4.3 15.1 - - + +
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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
----------------------------------------------------------
189B ASP* 4.6 2.2 + - - +
192B LEU* 2.8 42.2 + - - +
193B GLU* 2.8 51.0 + - - +
195B LEU* 1.3 75.0 - - - +
197B TYR* 1.3 57.8 + - - +
199B ASN* 3.4 5.1 + - - +
200B LYS* 2.8 28.3 + - - +
463B GLU* 2.8 37.3 + - - +
465B LEU* 3.6 24.1 - - + +
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Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU 4.1 9.6 - - - -
15B THR* 3.3 15.4 - - - -
16B LEU* 3.7 37.2 - - + -
193B GLU 3.2 9.7 + - - +
194B VAL 3.1 8.8 + - - +
196B ARG* 1.3 77.9 - - - +
198B THR* 1.3 67.9 + - - +
200B LYS* 3.0 19.5 + - + +
201B ILE* 3.0 49.8 + - + +
233B ARG 4.3 0.2 + - - -
234B GLY* 2.7 29.5 + - - -
236B MET* 4.8 2.0 - - + -
281B TYR* 3.6 46.9 - + + -
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Residues in contact with THR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 2.9 19.2 + - + +
195B LEU* 3.1 13.5 + - - -
197B TYR* 1.3 74.1 - - - +
199B ASN* 1.3 60.2 + - - +
202B SER* 3.0 33.6 + - - -
236B MET* 3.5 13.5 - - + +
279B GLY 4.3 0.2 - - - -
281B TYR* 3.7 26.0 - - + +
284B PHE* 3.5 29.6 - - + +
285B ALA 2.8 21.8 + - - +
286B SER* 3.6 10.8 - - - -
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Residues in contact with ASN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU* 3.1 21.7 + - - +
196B ARG 3.6 2.7 - - - +
197B TYR 3.1 0.6 - - - -
198B THR* 1.3 86.7 + - - +
200B LYS* 1.3 57.6 + - - +
203B SER* 2.7 38.6 + - - -
285B ALA 4.8 1.2 + - - -
286B SER* 4.0 6.0 - - - +
288B ILE* 3.6 10.3 - - - +
372B LEU* 5.6 1.4 - - - +
454B ASP* 3.1 30.0 + - - +
465B LEU* 3.4 34.2 - - + +
466B THR* 2.8 29.5 + - - +
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 4.9 9.3 + - - +
196B ARG 2.8 14.7 + - - +
197B TYR* 3.0 24.1 + - + +
199B ASN* 1.3 77.3 - - - +
201B ILE* 1.3 76.5 + - + +
203B SER* 3.3 4.8 + - - -
204B GLU* 3.0 51.8 + - + +
465B LEU 4.9 1.3 + - - -
467B CYS* 6.3 1.6 - - - -
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 5.6 1.6 - - + +
197B TYR* 3.0 52.6 + - + +
200B LYS* 1.3 85.2 - - - +
202B SER* 1.3 64.8 + - - +
204B GLU* 3.1 21.6 + - - +
205B ALA* 2.9 21.5 + - - +
229B TYR* 3.9 9.1 - - + -
230B CYS* 3.9 19.5 - - - -
233B ARG* 4.3 7.6 - - + +
234B GLY* 3.9 13.2 - - - -
236B MET* 3.7 26.2 - - + -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B THR 3.0 15.9 + - - -
201B ILE* 1.3 75.8 - - - +
203B SER* 1.3 57.7 + - - +
205B ALA* 3.3 3.4 + - - +
206B HIS* 2.9 36.0 + - - -
226B PHE* 4.0 15.2 - - - -
230B CYS* 4.2 3.1 - - - -
236B MET* 4.2 0.7 - - - +
277B MET 4.7 0.9 - - - -
278B GLY* 4.4 2.0 - - - -
279B GLY* 2.9 20.0 + - - -
286B SER* 2.7 25.4 + - - -
288B ILE* 3.8 15.5 - - - -
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASN 2.7 25.2 + - - -
200B LYS* 3.6 5.4 - - - -
202B SER* 1.3 74.3 - - - +
204B GLU* 1.3 65.3 + - - +
206B HIS* 3.3 3.3 + - - +
207B ARG* 3.0 28.5 + - - +
288B ILE* 3.7 3.4 - - - +
466B THR* 3.6 12.0 - - - +
467B CYS* 3.0 43.9 + - - -
468B VAL* 3.7 11.4 - - - +
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LYS* 3.0 47.5 + - + +
201B ILE* 3.5 18.2 - - - +
203B SER* 1.3 75.5 - - - +
205B ALA* 1.3 57.4 + - - +
207B ARG* 3.2 15.3 + - - +
208B GLU* 2.9 31.4 + - + +
229B TYR* 2.7 39.4 + - + +
233B ARG* 5.1 0.7 + - - +
484B LYS* 6.3 2.2 - - + +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE 2.9 16.1 + - - +
204B GLU* 1.3 73.5 - - - +
206B HIS* 1.3 66.0 + - - +
208B GLU* 3.2 4.1 + - - +
209B VAL* 3.0 26.2 + - - +
226B PHE* 3.4 30.0 - - + +
229B TYR* 3.7 31.2 - - + -
230B CYS* 3.9 10.1 - - - -
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER 2.9 26.8 + - - +
203B SER 3.6 5.2 - - - +
205B ALA* 1.3 77.4 - - - +
207B ARG* 1.3 56.1 + - - +
209B VAL* 3.3 8.3 + - - +
210B MET* 3.0 33.0 + - - +
226B PHE* 3.5 10.8 - + - -
275B PHE* 3.3 28.8 + - + +
277B MET* 2.9 45.3 + - + +
288B ILE* 3.3 27.6 + - + +
290B CYS* 3.6 31.2 - - - +
292B PHE* 6.1 0.6 - - - -
468B VAL* 4.0 5.8 - - + -
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B SER 3.0 15.8 + - - +
204B GLU* 3.2 15.7 + - - +
206B HIS* 1.3 73.9 - - - +
208B GLU* 1.3 64.4 + - + +
210B MET* 3.3 4.4 + - + +
211B LYS* 2.9 40.2 + - - +
467B CYS* 3.2 37.0 + - - -
468B VAL* 3.8 9.4 + - - +
469B PRO* 3.6 31.2 - - + +
478B CYS* 3.8 18.6 - - - +
484B LYS* 3.5 56.4 + - - +
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Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLU* 2.9 18.2 + - - +
205B ALA* 3.2 9.4 + - - +
207B ARG* 1.3 76.3 - - - +
209B VAL* 1.3 57.4 + - - +
211B LYS* 3.1 35.8 + - - +
212B ALA* 3.0 30.3 + - - +
225B LEU* 4.0 13.5 - - + +
229B TYR* 3.8 33.4 + - + -
233B ARG* 5.2 4.3 + - - -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ALA 3.0 17.3 + - - +
206B HIS* 3.6 11.2 - - - +
208B GLU* 1.3 73.7 - - - +
210B MET* 1.3 65.3 + - - +
212B ALA* 3.1 1.6 + - - +
213B VAL* 3.0 30.0 + - + +
222B LEU* 3.8 31.4 - - + +
225B LEU* 4.2 13.0 - - + -
226B PHE* 4.0 20.0 - - + +
275B PHE* 3.5 38.6 - - + -
277B MET* 4.1 6.3 - - + -
292B PHE* 4.7 2.5 - - + -
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Residues in contact with MET 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B HIS* 3.0 29.6 + - + +
207B ARG* 3.7 6.3 - - - +
209B VAL* 1.3 77.6 - - - +
211B LYS* 1.3 61.2 + - - +
213B VAL* 3.9 8.4 + - - +
290B CYS* 4.0 21.8 - - + -
291B SER 5.6 0.2 - - - +
292B PHE* 3.6 42.8 - - + -
468B VAL* 4.8 0.2 - - + -
469B PRO* 3.6 39.5 - - + +
475B ILE* 4.5 19.1 - - - -
478B CYS* 3.8 10.3 - - - -
479B MET* 3.5 33.4 - - + +
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Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 2.9 35.3 + - - +
208B GLU* 3.1 38.3 + - - +
209B VAL 3.2 0.2 - - - -
210B MET* 1.3 78.6 - - - +
212B ALA* 1.3 58.9 + - - +
213B VAL 4.7 2.1 - - - +
478B CYS* 3.4 27.4 - - - +
479B MET 4.3 9.5 - - - +
481B GLY* 4.6 14.1 - - - +
482B CYS 4.9 10.2 + - - +
483B ASP* 6.3 0.4 - - - +
484B LYS 5.9 2.4 - - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU 3.0 16.8 + - - +
209B VAL 3.1 2.6 + - - +
211B LYS* 1.3 78.1 - - + +
213B VAL* 1.3 65.3 + - - +
214B LYS* 3.3 14.6 + - - +
217B MET* 3.6 11.1 - - + +
222B LEU* 4.6 3.8 - - + -
225B LEU* 3.6 23.8 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 3.0 21.0 + - + +
210B MET 3.9 7.0 + - - +
211B LYS 3.6 4.0 - - - +
212B ALA* 1.3 77.4 - - - +
214B LYS* 1.3 71.3 + - - +
217B MET* 4.1 5.2 - - - -
222B LEU* 3.6 24.5 - - + -
267B ILE* 4.4 14.4 - - + -
273B CYS* 4.8 0.9 - - - -
275B PHE* 4.0 9.0 - - + -
292B PHE* 4.0 27.8 - - + -
294B ALA* 3.7 29.1 - - + +
479B MET* 4.6 4.9 - - + +
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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