Contacts of the helix formed by residues 222 - 263 (chain B) in PDB entry 5E1T
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 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLN* 1.3 78.4 - - - +
223B GLN* 1.3 65.4 + - - +
225B ASP* 3.1 8.9 + - - +
226B ARG* 3.0 39.8 + - - +
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Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLN 3.5 1.8 - - - +
222B SER* 1.3 82.7 - - - +
224B LEU* 1.3 58.4 + - - +
226B ARG* 3.3 13.1 - - + +
227B GLU* 2.9 32.5 + - + +
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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
----------------------------------------------------------
221B GLN* 3.6 16.8 + - - +
222B SER 3.2 0.8 - - - -
223B GLN* 1.3 76.4 - - - +
225B ASP* 1.3 62.7 + - - +
227B GLU* 3.2 15.0 + - + +
228B ARG* 3.0 44.9 + - + +
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Residues in contact with ASP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 6.1 0.2 - - - -
221B GLN* 3.1 19.7 + - - +
222B SER* 3.1 11.3 + - - +
224B LEU* 1.3 77.9 - - - +
226B ARG* 1.3 57.6 + - + +
228B ARG* 3.4 24.6 + - - +
229B ILE* 3.0 33.9 + - + +
226C ARG* 3.0 42.3 + - - +
229C ILE* 3.9 11.8 - - + +
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Residues in contact with ARG 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 5.8 8.0 - - - +
225A ASP* 3.5 39.7 + - - +
228A ARG* 3.8 15.7 + - - +
222B SER* 3.0 28.6 + - - +
223B GLN* 3.3 15.8 - - - +
224B LEU 3.1 0.2 - - - -
225B ASP* 1.3 74.1 - - - +
227B GLU* 1.3 66.6 + - + +
229B ILE* 3.1 7.7 + - - +
230B LEU* 2.9 24.1 + - - +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLN* 2.9 23.8 + - + +
224B LEU* 3.2 18.4 + - + +
226B ARG* 1.3 71.9 - - + +
228B ARG* 1.3 57.2 + - + +
230B LEU* 3.4 9.8 + - - +
231B SER* 2.9 35.2 + - - +
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Residues in contact with ARG 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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224B LEU* 3.0 33.6 + - + +
225B ASP* 3.6 26.7 + - - +
226B ARG 3.1 0.2 - - - -
227B GLU* 1.3 73.1 - - + +
229B ILE* 1.3 65.3 + - - +
230B LEU 3.3 0.2 + - - -
231B SER* 3.3 6.0 + - - +
232B LEU* 3.0 29.4 + - - +
226C ARG* 4.1 16.2 + - - +
229C ILE* 3.3 25.0 - - + +
230C LEU* 4.0 15.0 - - - +
233C GLU* 2.2 45.2 + - - +
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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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225A ASP* 4.6 22.2 - - + +
228A ARG* 3.4 34.5 - - + +
229A ILE* 3.7 25.4 - - + -
232A LEU* 3.9 16.8 - - + +
225B ASP* 3.0 15.2 + - + +
226B ARG* 3.1 7.8 + - - +
228B ARG* 1.3 74.4 - - - +
230B LEU* 1.3 56.7 + - - +
232B LEU* 3.1 12.9 + - + +
233B GLU* 3.0 26.9 + - - +
229C ILE* 3.4 36.1 - - + -
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Residues in contact with LEU 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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228A ARG* 4.1 16.6 - - - +
226B ARG 2.9 15.5 + - - +
227B GLU* 3.7 10.5 - - - +
229B ILE* 1.3 75.4 - - - +
231B SER* 1.3 62.9 + - - +
233B GLU* 3.1 19.7 + - - +
234B GLN* 3.0 57.1 + - + +
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU* 2.9 18.9 + - - +
228B ARG* 3.3 5.5 + - - -
230B LEU* 1.3 73.8 - - - +
232B LEU* 1.3 60.2 + - - +
234B GLN* 3.7 15.6 + - - +
235B ARG* 3.0 40.6 + - - +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.0 15.9 - - + -
228B ARG 3.0 20.4 + - - +
229B ILE* 3.1 13.7 + - + +
231B SER* 1.3 75.9 - - - +
233B GLU* 1.3 64.1 + - - +
235B ARG* 3.2 5.9 + - + +
236B VAL* 2.9 30.6 + - + +
229C ILE* 3.9 24.2 - - + +
232C LEU* 4.1 10.5 - - + -
233C GLU* 3.5 50.9 - - + +
236C VAL* 3.9 21.8 - - + -
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Residues in contact with GLU 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG* 2.8 53.6 + - - +
231A SER* 6.2 0.2 - - - -
232A LEU* 3.6 26.1 - - + +
235A ARG* 4.7 4.9 + - - +
229B ILE* 3.0 17.7 + - - +
230B LEU* 3.1 17.3 + - - +
232B LEU* 1.3 76.3 - - - +
234B GLN* 1.3 62.6 + - + +
236B VAL* 3.4 2.5 + - - +
237B VAL* 3.1 30.4 + - + +
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Residues in contact with GLN 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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230B LEU* 3.0 38.4 + - + +
231B SER* 3.7 21.5 + - - +
232B LEU 3.3 0.4 - - - -
233B GLU* 1.3 76.3 - - + +
235B ARG* 1.3 59.4 + - + +
237B VAL* 3.3 7.5 + - - +
238B GLU* 2.9 43.2 + - - +
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Residues in contact with ARG 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B SER* 3.0 26.9 + - - +
232B LEU* 3.8 6.3 - - - +
234B GLN* 1.3 76.7 - - + +
236B VAL* 1.3 58.0 + - - +
238B GLU* 3.5 17.0 + - - +
239B LEU* 2.9 36.3 + - - +
236C VAL* 4.1 17.9 - - + +
237C VAL* 3.3 22.6 - - - +
240C GLN* 2.3 47.4 + - - +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.2 11.9 - - + -
235A ARG* 3.8 37.7 - - + +
236A VAL* 4.4 8.7 - - + -
239A LEU* 3.3 26.2 - - + +
232B LEU* 2.9 19.4 + - + +
233B GLU* 3.7 6.3 - - - +
235B ARG* 1.3 74.1 - - - +
237B VAL* 1.3 65.0 + - - +
239B LEU* 3.3 8.1 + - + +
240B GLN* 3.0 22.5 + - - +
236C VAL* 4.0 22.2 - - + -
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Residues in contact with VAL 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 3.5 31.6 - - - +
233B GLU* 3.1 18.5 + - + +
234B GLN* 3.3 9.2 + - - +
236B VAL* 1.3 74.0 - - - +
238B GLU* 1.3 64.5 + - + +
240B GLN* 2.9 24.0 + - - +
241B GLN* 3.1 20.2 + - + +
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Residues in contact with GLU 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B GLN* 2.9 28.2 + - - +
235B ARG* 3.7 19.6 - - - +
237B VAL* 1.3 79.5 - - + +
239B LEU* 1.3 62.9 + - + +
241B GLN* 3.1 8.6 + - - +
242B THR* 3.0 32.1 + - + +
240C GLN* 5.7 2.0 + - - +
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Residues in contact with LEU 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 4.1 26.7 - - + -
235B ARG 2.9 30.0 + - - +
236B VAL* 3.7 5.2 - - - +
237B VAL 3.3 0.4 - - - -
238B GLU* 1.3 75.3 - - + +
240B GLN* 1.3 57.1 + - - +
242B THR* 3.1 8.5 + - + +
243B LEU* 2.9 33.5 + - + +
236C VAL* 4.0 23.6 - - + -
239C LEU* 4.2 17.9 - - + -
240C GLN* 3.3 35.9 - - + +
243C LEU* 3.9 21.7 - - + +
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Residues in contact with GLN 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ARG* 3.1 23.7 + - - +
239A LEU* 4.2 19.2 - - + +
236B VAL 3.0 12.0 + - - +
237B VAL* 2.9 17.5 + - - +
239B LEU* 1.3 78.0 - - - +
241B GLN* 1.3 78.0 + - - +
243B LEU* 3.5 6.0 + - - +
244B ALA* 3.1 24.6 + - - +
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Residues in contact with GLN 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B VAL* 3.6 20.0 - - + +
238B GLU* 3.1 9.7 + - - +
240B GLN* 1.3 93.4 - - - +
242B THR* 1.3 65.3 + - + +
243B LEU 3.1 1.8 - - - -
244B ALA* 3.1 8.1 + - - +
245B GLN* 3.1 21.7 + - - +
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Residues in contact with THR 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLU* 3.0 19.9 + - + +
239B LEU* 3.1 12.9 + - + -
241B GLN* 1.3 75.2 - - + +
243B LEU* 1.3 66.2 + - - +
245B GLN* 3.1 5.1 + - - +
246B LYS* 3.0 38.1 + - - +
243C LEU* 3.2 22.2 - - - +
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Residues in contact with LEU 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 4.4 18.2 - - + +
242A THR* 3.0 29.6 - - - +
243A LEU* 3.6 33.0 - - + +
246A LYS* 3.9 25.6 - - + +
239B LEU* 2.9 17.1 + - + +
240B GLN* 3.5 5.4 - - - +
242B THR* 1.3 81.9 + - - +
244B ALA* 1.3 61.6 + - - +
246B LYS* 3.4 7.9 + - + +
247B ASP* 3.0 22.9 + - - +
243C LEU* 3.7 14.8 - - + -
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Residues in contact with ALA 244 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B GLN 3.1 14.2 + - - +
241B GLN* 3.1 15.4 + - - +
243B LEU* 1.3 75.9 - - - +
245B GLN* 1.4 58.4 + - - +
247B ASP* 3.0 19.9 + - - +
248B GLN* 3.1 12.8 + - - +
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Residues in contact with GLN 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B GLN 3.1 10.2 + - - +
242B THR* 3.1 6.1 + - - +
244B ALA* 1.4 74.6 - - - +
246B LYS* 1.3 63.3 + - - +
247B ASP 3.2 0.4 - - - -
248B GLN* 4.0 17.1 - - - +
249B ALA* 3.0 29.7 + - + +
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Residues in contact with LYS 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LYS* 6.2 4.5 - - + -
242B THR* 3.0 28.1 + - - +
243B LEU* 3.8 6.5 - - + +
245B GLN* 1.3 79.2 - - - +
247B ASP* 1.3 58.2 + - - +
249B ALA* 3.7 6.1 - - + +
250B LEU* 3.0 27.5 + - - +
243C LEU* 4.2 31.1 + - + -
244C ALA* 5.4 1.2 - - - +
246C LYS* 5.9 4.0 - - + -
247C ASP* 2.4 45.2 + - + +
250C LEU* 4.1 20.6 - - + +
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Residues in contact with ASP 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 2.4 42.6 + - - +
243B LEU 3.0 12.2 + - - +
244B ALA* 3.0 13.8 + - - +
246B LYS* 1.3 78.1 - - - +
248B GLN* 1.3 60.3 + - - +
250B LEU* 3.2 17.4 - - - +
251B GLY* 2.9 20.6 + - - -
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Residues in contact with GLN 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ALA 3.1 12.3 + - - +
245B GLN* 3.7 16.0 + - - +
247B ASP* 1.3 74.5 - - - +
249B ALA* 1.3 62.6 + - - +
251B GLY* 2.7 18.5 + - - +
252B LYS* 2.9 36.2 + - + +
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Residues in contact with ALA 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLN* 3.0 24.0 + - + +
246B LYS* 3.7 7.9 - - + +
248B GLN* 1.3 75.9 - - - +
250B LEU* 1.3 62.4 + - - +
252B LYS* 3.5 1.8 + - - +
253B LEU* 3.1 23.4 + - - +
250C LEU* 4.4 15.9 - - + +
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Residues in contact with LEU 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LYS* 4.8 12.1 - - + +
249A ALA* 3.9 26.7 - - + -
250A LEU* 3.5 34.3 - - + +
253A LEU* 3.4 24.7 - - + -
246B LYS 3.0 15.4 + - - +
247B ASP* 3.2 24.9 - - - +
249B ALA* 1.3 74.7 - - - +
251B GLY* 1.3 55.1 + - - +
253B LEU* 3.4 5.0 + - - +
254B GLU* 2.9 45.0 + - - +
250C LEU* 4.1 12.2 - - + +
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Residues in contact with GLY 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ASP* 2.9 12.1 + - - -
248B GLN* 2.7 19.7 + - - -
250B LEU* 1.3 71.8 - - - +
252B LYS* 1.3 58.4 + - - -
254B GLU* 2.9 33.0 + - - +
255B GLN* 2.9 11.4 + - - +
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Residues in contact with LYS 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLN* 2.9 33.0 + - + +
249B ALA* 4.7 1.8 - - - +
251B GLY* 1.3 74.5 + - - +
253B LEU* 1.3 61.2 + - - +
255B GLN* 3.5 43.3 + - - +
256B SER* 2.9 26.9 + - - -
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Residues in contact with LEU 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 3.5 31.2 - - + -
249B ALA 3.1 14.0 + - - +
250B LEU* 3.5 10.8 - - - +
252B LYS* 1.3 74.7 - - - +
254B GLU* 1.3 63.5 + - - +
256B SER* 3.3 7.3 + - - -
257B LEU* 3.0 21.1 + - + +
250C LEU* 4.2 16.8 - - + +
253C LEU* 4.0 21.3 - - + +
254C GLU* 3.8 43.5 - - + +
257C LEU* 4.2 13.6 - - + +
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Residues in contact with GLU 254 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ALA* 5.1 7.1 - - - +
253A LEU* 3.5 31.3 - - + +
250B LEU* 2.9 36.7 + - - +
251B GLY* 2.9 20.4 + - - +
253B LEU* 1.3 75.5 - - - +
255B GLN* 1.3 60.0 + - - +
257B LEU* 3.1 7.6 + - - +
258B ARG* 2.9 20.5 + - - +
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Residues in contact with GLN 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B GLY 2.9 9.6 + - - +
252B LYS* 3.4 42.1 + - - +
253B LEU 3.2 0.4 - - - -
254B GLU* 1.3 73.2 - - - +
256B SER* 1.3 67.5 + - - +
258B ARG* 3.0 49.6 + - + +
259B LEU* 2.9 38.9 + - + +
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Residues in contact with SER 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LYS 2.9 15.2 + - - -
253B LEU* 3.3 12.6 - - - -
255B GLN* 1.3 75.3 - - - +
257B LEU* 1.3 64.4 + - - +
259B LEU* 3.3 10.2 + - - +
260B MET* 3.0 26.0 + - - +
257C LEU* 3.5 19.7 - - - +
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Residues in contact with LEU 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.6 28.5 - - + +
256A SER* 3.7 24.7 - - - +
257A LEU* 3.9 23.1 - - + +
260A MET* 4.1 18.4 - - + -
253B LEU* 3.0 15.2 + - + +
254B GLU* 3.1 9.2 + - - +
256B SER* 1.3 76.7 - - - +
258B ARG* 1.3 61.9 + - - +
260B MET* 3.1 6.5 + - - +
261B GLU* 3.0 33.7 + - - +
257C LEU* 3.7 30.4 - - + +
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Residues in contact with ARG 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B GLU 2.9 11.5 + - - +
255B GLN* 3.0 48.4 + - + +
257B LEU* 1.3 75.7 - - - +
259B LEU* 1.3 79.0 + - - +
261B GLU* 2.8 33.5 + - - +
262B GLU* 2.9 41.0 + - - +
292B PHE 5.7 2.6 + - - -
293B SER 5.9 0.2 - - - -
294B PRO* 4.8 10.3 - - - +
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Residues in contact with LEU 259 (chain B).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B GLN* 2.9 36.6 + - + +
256B SER* 3.9 7.0 - - - +
258B ARG* 1.3 107.6 - - - +
260B MET* 1.3 66.7 + - - +
262B GLU* 4.1 10.6 - - - +
263B ALA* 3.3 24.9 + - - +
294B PRO* 4.4 14.5 - - + +
295B ALA* 4.6 15.7 - - + +
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Residues in contact with MET 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A MET* 3.7 34.1 - - + +
256B SER* 3.0 18.8 + - - +
257B LEU 3.3 8.7 - - - +
259B LEU* 1.3 79.6 - - - +
261B GLU* 1.4 62.1 + - - +
263B ALA* 3.5 15.0 + - - +
265B PHE* 5.0 12.9 - - + -
257C LEU* 3.6 27.6 - - + +
260C MET* 4.5 3.4 - - - +
261C GLU* 3.8 51.6 - - + +
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Residues in contact with GLU 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A SER* 5.1 3.8 + - - -
260A MET* 4.3 23.6 - - + -
265A PHE* 6.0 1.2 - - - -
300A LYS* 3.3 20.4 + - - -
257B LEU* 3.2 25.0 - - + +
258B ARG* 2.8 21.9 + - - +
260B MET* 1.4 78.3 - - - +
262B GLU* 1.3 64.8 + - + +
263B ALA 3.2 0.9 + - - +
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Residues in contact with GLU 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LYS* 3.4 8.9 + - - +
301A TYR* 4.1 4.2 + - - -
333A TYR* 5.3 9.7 + - - +
258B ARG* 2.9 50.6 + - - +
259B LEU* 3.5 2.0 + - - +
260B MET 3.4 0.4 - - - -
261B GLU* 1.3 79.3 - - + +
263B ALA* 1.3 60.2 + - - +
264B SER 3.8 0.3 + - - -
269B PHE* 3.2 22.3 - - + -
294B PRO* 3.1 41.2 - - + +
295B ALA 4.7 0.7 - - - -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LYS* 2.4 24.8 + - - -
259B LEU 3.3 18.4 + - - +
260B MET* 3.7 10.0 - - - +
261B GLU 3.1 3.4 - - - +
262B GLU* 1.3 73.8 - - - +
264B SER* 1.3 56.4 + - - +
265B PHE* 3.5 28.8 - - + -
295B ALA* 3.4 20.6 - - + +
296B PHE* 4.8 0.2 - - - -
297B TYR* 4.2 11.9 - - + -
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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