Contacts of the helix formed by residues 214 - 238 (chain B) in PDB entry 4JYI
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 ASP 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B SER* 2.7 26.7 + - - -
206B SER* 2.7 26.0 + - - +
211B VAL* 3.7 7.4 - - + +
213B LEU* 1.3 70.3 - - - +
215B LEU* 1.3 54.0 + - - +
216B GLY* 2.9 17.5 + - - -
217B LEU* 3.1 21.3 + - + +
218B TRP* 2.7 35.2 + - - +
292B ASN* 2.8 20.8 + - + +
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Residues in contact with LEU 215 (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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213B LEU* 3.4 30.9 + - + +
214B ASP* 1.3 71.3 + - - +
216B GLY* 1.3 57.6 + - - +
218B TRP* 3.7 7.5 - - + +
219B ASP* 2.9 30.5 + - - +
394B GLU 4.9 3.6 - - - +
396B PRO* 4.2 33.0 - - + -
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B SER* 5.3 2.7 - - - -
214B ASP* 2.9 8.6 + - - -
215B LEU* 1.3 78.2 - - - +
217B LEU* 1.3 62.5 + - - +
219B ASP* 3.4 7.5 + - - +
220B LYS* 3.3 20.1 + - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B THR* 4.0 18.8 - - + -
205B SER* 3.8 24.2 + - - +
206B SER* 3.4 24.7 - - - +
214B ASP* 3.1 24.6 + - + +
216B GLY* 1.3 73.8 - - - +
218B TRP* 1.3 60.9 + - - +
220B LYS* 3.3 8.0 + - + +
221B PHE* 2.8 29.6 + - - +
283B LEU* 5.8 3.4 - - + -
285B LEU* 4.3 14.9 - - + +
289B GLN* 3.7 26.7 - - + +
292B ASN* 4.0 3.1 - - + -
293B ALA* 3.8 16.0 - - + +
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Residues in contact with TRP 218 (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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213B LEU* 4.0 10.8 - - + -
214B ASP 2.7 20.7 + - - +
215B LEU* 3.7 9.0 - - - +
217B LEU* 1.3 71.4 - - - +
219B ASP* 1.3 62.2 + - + +
221B PHE* 3.8 13.2 - + - -
222B SER* 2.8 59.6 + - - -
293B ALA 3.5 28.6 + - - +
391B LEU* 3.9 17.9 - - + -
395B ILE* 3.4 43.0 - - + +
396B PRO* 4.7 13.0 + - + +
399B MET* 3.6 35.2 - - + -
400B PRO* 4.6 3.1 - - + +
403B ILE* 5.3 0.2 - - + -
501B JYI 3.7 24.9 - + - -
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Residues in contact with ASP 219 (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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215B LEU 2.9 18.8 + - - +
216B GLY* 3.5 8.5 - - - +
218B TRP* 1.3 80.4 - - + +
220B LYS* 1.3 61.9 + - - +
222B SER* 3.0 18.2 + - - -
223B GLU* 3.4 16.5 + - - +
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Residues in contact with LYS 220 (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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201B TYR* 2.6 30.3 + - - -
216B GLY 3.3 8.1 + - - +
217B LEU* 3.3 10.2 + - + +
218B TRP 3.2 0.4 - - - -
219B ASP* 1.3 79.7 + - - +
221B PHE* 1.3 66.0 + - - +
223B GLU* 3.3 27.9 + - - +
224B LEU* 3.0 41.2 + - + +
281B ASP* 2.6 19.8 + - - -
283B LEU* 3.7 24.6 - - + +
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Residues in contact with PHE 221 (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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217B LEU 2.8 17.5 + - - +
218B TRP* 3.1 21.3 + + - +
220B LYS* 1.3 77.5 - - - +
222B SER* 1.3 60.3 + - - +
224B LEU* 3.2 8.5 + - - +
225B ALA* 2.8 27.0 + - + +
279B PHE* 3.9 27.1 - + - -
283B LEU* 6.4 0.2 - - - -
290B MET* 4.5 2.7 - - + -
293B ALA* 3.9 28.3 - - + +
294B GLY* 5.1 3.4 - - - -
295B PHE* 4.0 24.9 - + - -
501B JYI 3.4 81.1 - + + +
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Residues in contact with SER 222 (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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218B TRP* 2.8 47.7 + - - -
219B ASP* 3.0 21.3 + - - -
221B PHE* 1.3 77.0 - - - +
223B GLU* 1.3 57.8 + - - +
225B ALA* 3.5 6.9 + - - +
226B THR* 3.0 32.4 + - - -
400B PRO* 4.0 19.5 - - - +
403B ILE* 4.0 3.2 - - - +
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Residues in contact with GLU 223 (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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219B ASP* 3.4 14.8 + - - +
220B LYS* 3.3 30.2 + - - +
221B PHE 3.2 0.4 - - - -
222B SER* 1.3 80.7 + - - +
224B LEU* 1.3 66.8 + - + +
226B THR* 3.3 7.5 + - - -
227B LYS* 3.1 57.7 + - + +
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Residues in contact with LEU 224 (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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220B LYS* 3.0 45.8 + - + +
221B PHE* 3.6 3.8 - - - +
223B GLU* 1.3 77.6 - - - +
225B ALA* 1.3 61.5 + - - +
227B LYS* 3.4 13.9 + - + +
228B CYS* 3.0 30.0 + - - +
279B PHE* 3.5 35.2 - - + -
280B SER* 5.5 1.3 - - - -
281B ASP* 3.9 30.5 - - + +
283B LEU* 4.0 9.4 - - + -
501B JYI 3.8 22.6 - - + +
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Residues in contact with ALA 225 (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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221B PHE* 2.8 18.1 + - + +
222B SER* 3.7 6.7 - - - +
224B LEU* 1.3 74.9 - - - +
226B THR* 1.3 64.8 + - - +
228B CYS* 3.3 2.6 + - - +
229B ILE* 2.9 32.1 + - + +
262B LEU* 4.6 2.4 - - + +
403B ILE* 4.1 7.6 - - + -
501B JYI 3.4 49.2 - - + +
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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
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222B SER 3.0 15.6 + - - -
223B GLU* 3.3 11.5 + - - -
225B ALA* 1.3 77.0 - - - +
227B LYS* 1.3 65.2 + - + +
229B ILE* 3.3 11.0 + - - +
230B ILE* 3.1 36.0 + - + +
400B PRO* 3.6 23.2 - - + +
402B LEU* 3.8 18.0 - - + +
403B ILE* 3.9 5.1 - - - +
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Residues in contact with LYS 227 (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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223B GLU* 3.1 50.0 + - + +
224B LEU* 3.8 14.3 - - + +
226B THR* 1.3 79.3 - - + +
228B CYS* 1.3 57.6 + - - +
230B ILE* 3.4 16.1 + - + +
231B LYS* 3.1 33.7 + - + +
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Residues in contact with CYS 228 (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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192B PHE* 4.6 1.6 - - - -
224B LEU 3.0 17.9 + - - +
225B ALA 3.8 3.6 - - - +
227B LYS* 1.3 74.4 - - - +
229B ILE* 1.3 61.8 + - - +
231B LYS* 3.1 10.0 + - - +
232B ILE* 2.8 34.0 + - - +
262B LEU* 3.7 17.9 - - + -
265B ARG* 3.8 30.3 - - - -
280B SER* 5.3 2.0 - - - +
501B JYI 3.7 37.9 - - + -
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Residues in contact with ILE 229 (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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225B ALA* 2.9 23.8 + - + +
226B THR* 3.6 6.5 - - - +
228B CYS* 1.3 74.2 - - - +
230B ILE* 1.3 62.3 + - - +
232B ILE* 3.1 9.4 + - - +
233B VAL* 3.0 23.2 + - + +
258B CYS* 3.8 19.1 - - - -
262B LEU* 4.1 17.0 - - + -
402B LEU* 3.6 22.2 - - + -
403B ILE* 3.8 38.6 - - + +
406B MET* 3.8 32.8 - - + -
407B MET* 5.4 1.8 - - + -
501B JYI 5.4 1.1 - - + -
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Residues in contact with ILE 230 (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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226B THR* 3.1 28.5 + - + +
227B LYS* 3.4 17.5 - - + +
229B ILE* 1.3 75.4 - - - +
231B LYS* 1.3 65.1 + - + +
233B VAL* 3.2 10.4 + - - +
234B GLU* 3.1 22.6 + - + +
402B LEU* 3.6 16.6 - - + -
636F LEU* 4.7 22.0 - - + -
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Residues in contact with LYS 231 (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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190B GLU 4.9 7.5 + - - -
191B THR* 3.4 34.3 - - - +
193B PRO* 6.2 2.9 - - - -
227B LYS* 3.1 17.7 + - - +
228B CYS* 3.1 13.2 + - - +
230B ILE* 1.3 78.9 - - + +
232B ILE* 1.3 57.6 + - - +
234B GLU* 3.2 24.4 + - - +
235B PHE* 2.8 28.9 + - - +
265B ARG* 3.7 7.0 - - - +
280B SER* 6.1 2.9 - - - +
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Residues in contact with ILE 232 (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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228B CYS* 2.8 26.0 + - - +
229B ILE* 3.1 10.5 + - - +
231B LYS* 1.3 70.8 - - - +
233B VAL* 1.3 61.8 + - + +
235B PHE* 3.3 11.2 + - + +
236B ALA* 2.9 27.8 + - + +
254B LEU* 4.3 14.1 - - + -
258B CYS* 4.1 14.8 - - - +
261B ILE* 3.7 43.5 - - + -
262B LEU* 3.7 32.3 - - + +
265B ARG* 3.9 19.3 - - - +
327B LEU* 5.9 0.4 - - + -
406B MET* 5.7 0.7 - - + -
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Residues in contact with VAL 233 (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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229B ILE* 3.0 20.7 + - + +
230B ILE* 3.4 8.5 - - - +
232B ILE* 1.3 77.5 - - - +
234B GLU* 1.3 62.0 + - - +
236B ALA* 3.2 6.9 + - - +
237B LYS* 3.0 30.3 + - + +
254B LEU* 4.2 7.2 - - + -
406B MET* 4.0 12.1 - - + -
633F LEU* 4.0 25.4 - - + -
636F LEU* 4.1 28.7 - - + +
637F LEU* 4.1 24.5 - - + -
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Residues in contact with GLU 234 (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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190B GLU 4.3 5.8 - - - +
191B THR* 3.5 22.3 - - + +
230B ILE* 3.1 14.7 + - + +
231B LYS* 3.5 27.3 + - - +
233B VAL* 1.3 73.7 - - - +
235B PHE* 1.3 64.3 + - - +
237B LYS* 3.3 15.4 + - - +
238B ARG* 3.3 39.6 + - + +
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Residues in contact with PHE 235 (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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184B ILE* 4.0 5.2 - - + -
187B ALA* 3.6 26.2 - - + -
188B HIS* 3.5 31.0 - - + -
191B THR* 3.6 14.5 - - - +
231B LYS 2.8 14.5 + - - +
232B ILE* 3.4 15.5 - - + +
234B GLU* 1.3 77.9 - - - +
236B ALA* 1.3 66.0 + - - +
238B ARG* 3.1 16.8 + - - +
239B LEU* 3.5 38.6 + - + +
261B ILE* 5.5 4.0 - - + -
265B ARG* 3.8 12.1 - - - +
320B GLY* 3.5 23.1 - - - -
323B SER* 3.9 22.2 - - - -
324B ALA 4.2 3.4 - - - -
327B LEU* 5.2 4.0 - - + -
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Residues in contact with ALA 236 (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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232B ILE 2.9 13.6 + - - +
233B VAL* 3.5 9.0 - - - +
234B GLU 3.2 0.2 - - - -
235B PHE* 1.3 78.6 - - - +
237B LYS* 1.3 61.4 + - - +
238B ARG 3.0 1.4 + - - -
239B LEU* 3.1 14.8 + - - +
242B PHE* 3.2 32.5 - - + +
254B LEU* 3.8 15.0 - - + -
327B LEU* 3.4 31.9 - - + -
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Residues in contact with LYS 237 (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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233B VAL* 3.0 25.3 + - + +
234B GLU* 3.3 9.8 + - - +
236B ALA* 1.3 74.6 - - - +
238B ARG* 1.3 60.5 + - + +
239B LEU 3.4 4.3 - - - +
242B PHE* 4.1 2.7 - - + -
243B THR* 3.7 35.7 + - + +
636F LEU 3.0 27.3 + - - +
637F LEU* 3.6 35.7 + - + -
638F GLN 4.3 7.5 + - - -
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Residues in contact with ARG 238 (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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183B LYS* 5.0 9.6 + - - +
184B ILE* 5.2 0.3 - - - +
186B LYS* 4.0 6.9 - - - +
187B ALA* 3.7 36.5 + - + +
190B GLU* 2.6 49.0 + - - +
191B THR* 4.7 2.4 - - - +
234B GLU* 3.3 36.3 + - + +
235B PHE 3.1 8.2 + - - +
236B ALA 3.0 1.2 - - - -
237B LYS* 1.3 80.0 - - + +
239B LEU* 1.3 64.8 + - - +
240B PRO* 3.4 9.5 - - - +
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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