Contacts of the helix formed by residues 270 - 304 (chain A) in PDB entry 2OR0
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 270 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLN* 3.8 21.0 - - + +
266A LYS 3.4 1.0 + - - +
267A ILE* 2.8 29.1 + - + +
268A LYS 3.6 0.4 - - - -
269A GLU* 1.3 76.3 - - - +
271A PRO* 1.3 60.0 - - - +
272A TYR* 3.0 34.0 + - - +
273A VAL* 3.0 27.1 + - + +
274A LEU* 3.0 33.1 + - - +
369B PRO* 5.4 4.2 - - - +
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Residues in contact with PRO 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLN* 5.4 1.1 - - - +
269A GLU 3.4 9.8 - - - +
270A ASP* 1.3 86.7 - - - +
272A TYR* 1.3 80.9 + - + +
274A LEU* 4.7 4.0 - - + -
275A SER* 2.7 39.2 + - - -
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Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASP* 3.0 19.7 + - - +
271A PRO* 1.3 96.9 - - + +
273A VAL* 1.3 64.7 + - + +
275A SER* 3.3 6.0 + - - -
276A ALA* 3.2 23.2 + - - +
337A ARG* 4.5 5.1 + - - +
368B GLY* 3.7 31.0 - - - +
369B PRO* 3.8 34.3 - - + -
372B HIS* 2.6 40.3 + + + +
387B MSE 4.1 15.9 - - + -
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS* 4.8 4.3 - - - +
256A GLN* 4.6 6.1 - - - +
267A ILE* 3.8 32.3 - - + -
270A ASP* 3.0 32.5 + - + +
272A TYR* 1.3 74.5 - - + +
274A LEU* 1.3 61.0 + - - +
276A ALA* 3.4 2.9 + - - +
277A ILE* 3.0 40.3 + - + +
337A ARG* 4.5 34.9 - - + +
366B VAL* 6.1 4.9 - - + -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLN* 5.6 2.0 - - + -
267A ILE* 3.7 18.8 - - + +
268A LYS* 3.3 33.4 - - - +
269A GLU* 5.0 0.7 - - - -
270A ASP 3.0 22.4 + - - +
271A PRO* 4.4 3.4 - - + +
273A VAL* 1.3 76.2 - - - +
275A SER* 1.3 62.7 + - - +
277A ILE* 3.3 25.0 + - + +
278A GLY* 3.2 17.3 + - - -
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO 2.7 24.1 + - - -
272A TYR* 3.3 7.8 + - - -
274A LEU* 1.3 76.9 - - - +
276A ALA* 1.3 57.6 + - - +
278A GLY* 3.3 3.4 + - - +
279A GLU* 3.0 37.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR 3.2 15.1 + - - +
273A VAL 3.7 2.0 - - - +
274A LEU 3.3 0.2 - - - -
275A SER* 1.3 78.6 + - - +
277A ILE* 1.3 63.9 - - - +
279A GLU* 3.3 18.1 + - - +
280A SER* 3.1 26.7 + - - -
333A GLU* 5.6 2.1 - - + +
334A ILE* 4.7 4.0 - - + -
337A ARG* 3.5 41.3 - - - +
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 4.0 20.8 - - + +
252A HIS* 3.7 34.3 - - + +
253A ILE* 4.2 19.7 - - + -
256A GLN* 4.1 15.7 - - + -
273A VAL* 3.0 24.4 + - + +
274A LEU* 3.6 28.0 - - + +
275A SER 3.3 0.2 - - - -
276A ALA* 1.3 76.1 - - - +
278A GLY* 1.3 57.0 + - - +
280A SER* 3.4 1.9 + - - -
281A ALA* 2.9 29.6 + - + +
334A ILE* 4.2 8.7 - - + -
337A ARG* 6.5 0.2 - - - -
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU 3.2 13.3 + - - -
275A SER* 3.3 4.9 + - - -
277A ILE* 1.3 73.5 - - - +
279A GLU* 1.3 65.6 + - - +
281A ALA* 3.4 7.2 + - - +
282A ALA* 3.0 24.8 + - - +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A SER* 3.0 24.8 + - - +
276A ALA* 3.6 18.2 - - - +
277A ILE 3.3 0.2 - - - -
278A GLY* 1.3 75.1 - - - +
280A SER* 1.3 63.9 + - - +
282A ALA* 3.3 7.4 + - - +
283A GLU* 3.2 27.5 + - + +
337A ARG* 5.9 0.7 + - - -
----------------------------------------------------------
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 5.3 0.7 - - - -
276A ALA 3.1 12.1 + - - -
277A ILE 3.9 1.6 - - - -
279A GLU* 1.3 74.2 - - - +
281A ALA* 1.3 64.4 + - - +
283A GLU* 3.2 3.1 + - - -
284A ILE* 3.0 32.4 + - - +
330A ALA* 3.0 38.4 + - - +
333A GLU* 3.6 14.0 - - - +
334A ILE* 3.5 24.4 - - - +
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 4.0 31.4 - - + +
277A ILE* 2.9 20.0 + - + +
278A GLY* 3.7 6.7 - - - +
280A SER* 1.3 75.3 - - - +
282A ALA* 1.3 57.7 + - - +
284A ILE* 4.0 2.3 - - - +
285A ASN* 3.0 28.9 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLY 3.0 17.8 + - - +
279A GLU* 3.6 7.6 - - - +
280A SER 3.2 0.2 - - - -
281A ALA* 1.3 73.9 - - - +
283A GLU* 1.3 64.8 + - - +
285A ASN* 3.4 6.0 + - - +
286A ALA* 2.9 29.7 + - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU 3.2 17.0 + - - +
280A SER* 3.6 6.1 - - - +
282A ALA* 1.3 78.9 - - - +
284A ILE* 1.3 65.6 + - - +
286A ALA* 3.2 4.2 + - - +
287A SER* 3.1 23.6 + - - -
326A ARG* 3.5 36.2 - - + +
330A ALA* 3.8 17.0 - - + -
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 4.2 4.1 - - + +
245A THR* 3.7 40.2 - - - +
246A GLU* 3.5 34.1 - - + +
249A LEU* 4.3 22.9 - - + -
280A SER* 3.0 23.5 + - - +
281A ALA* 4.0 4.5 - - - +
283A GLU* 1.3 75.0 - - - +
285A ASN* 1.3 63.3 + - - +
287A SER* 3.2 8.9 + - - +
288A ARG* 3.1 20.3 + - - +
327A ALA* 4.1 7.4 - - - +
330A ALA* 3.7 20.2 - - + -
331A ALA* 4.6 6.1 - - - +
334A ILE* 5.2 1.3 - - + -
----------------------------------------------------------
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 5.4 1.8 - - - -
281A ALA 3.0 19.0 + - - +
282A ALA* 3.7 6.4 - - - +
284A ILE* 1.3 78.7 - - - +
286A ALA* 1.3 64.9 + - - +
287A SER 3.1 0.3 + - - -
288A ARG* 3.2 15.0 + - - +
289A VAL* 3.1 42.7 + - - +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ALA 2.9 16.2 + - - +
283A GLU* 3.2 13.0 + - - +
285A ASN* 1.3 78.2 + - - +
287A SER* 1.3 55.7 + - - +
289A VAL* 3.5 8.3 - - - +
290A SER* 2.8 38.4 + - - +
326A ARG* 4.0 18.2 - - - +
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.5 15.8 - - - +
283A GLU 3.1 7.5 + - - -
284A ILE 3.5 8.5 - - - -
285A ASN 3.1 0.8 - - - -
286A ALA* 1.3 75.6 - - - +
288A ARG* 1.3 65.5 + - - +
290A SER* 4.5 0.2 - - - -
291A LEU* 3.0 27.9 + - - +
323A ALA* 2.8 32.3 + - - +
326A ARG* 3.3 29.0 + - - +
327A ALA* 3.6 7.3 + - - -
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 4.0 26.1 + - - +
65A MSE 3.5 44.9 - - + +
66A GLY* 5.1 1.4 - - - +
242A ILE* 3.9 7.1 - - + +
246A GLU* 2.8 43.4 + - - +
284A ILE 3.1 9.6 + - - +
285A ASN* 3.2 20.6 + - - +
287A SER* 1.3 80.5 - - - +
289A VAL* 1.3 66.9 + - + +
291A LEU* 3.9 1.0 - - - +
292A ILE* 3.1 34.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 5.4 2.1 + - - +
285A ASN* 3.1 36.5 + - - +
286A ALA* 3.5 16.4 - - - +
288A ARG* 1.3 82.6 - - + +
290A SER* 1.3 65.4 + - - +
292A ILE* 3.5 4.6 + - - +
293A GLU* 2.9 31.8 + - - +
----------------------------------------------------------
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ALA* 2.8 21.7 + - - +
287A SER* 3.8 5.2 - - - -
289A VAL* 1.3 82.7 - - - +
291A LEU* 1.3 63.4 + - - +
293A GLU* 3.4 14.5 + - - +
294A THR* 3.4 9.2 + - - -
319A THR* 3.5 27.1 - - - +
323A ALA* 5.0 1.6 - - - -
326A ARG* 4.4 11.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MSE 3.9 9.0 - - + -
231A CYS* 5.9 0.7 - - - -
235A LEU* 3.7 33.9 - - + +
238A THR* 4.0 6.7 - - + -
239A ALA* 3.6 35.0 - - + +
242A ILE* 3.9 14.4 - - + -
287A SER 3.0 15.8 + - - +
288A ARG 3.9 3.1 - - - +
290A SER* 1.3 80.2 - - - +
292A ILE* 1.3 63.0 + - + +
294A THR* 3.6 15.6 + - - -
295A ALA 3.7 3.8 + - - -
319A THR* 4.6 5.6 - - - -
320A GLN* 3.6 39.3 - - + -
323A ALA* 4.4 3.8 - - + +
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.2 55.4 - - + +
61A ALA* 4.1 13.7 - - + -
62A GLU* 3.7 30.7 - - + +
65A MSE 3.8 23.3 - - + -
235A LEU* 5.3 1.6 - - - -
288A ARG* 3.1 30.3 + - + +
289A VAL* 4.0 3.8 - - - +
291A LEU* 1.3 76.1 - - + +
293A GLU* 1.3 63.2 + - - +
295A ALA* 3.2 8.3 + - + +
296A ASP* 3.0 20.5 + - - -
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 4.8 2.2 - - - +
289A VAL 2.9 19.3 + - - +
290A SER* 3.8 7.3 - - - +
291A LEU 3.3 0.6 - - - -
292A ILE* 1.3 76.6 - - - +
294A THR* 1.3 64.3 + - - +
296A ASP* 3.3 14.2 + - + +
297A ARG* 2.8 66.6 + - - +
319A THR* 6.1 0.2 - - - +
----------------------------------------------------------
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A CYS* 4.5 8.1 - - + -
290A SER 3.4 11.8 + - - -
291A LEU* 3.7 9.9 - - - -
292A ILE 3.3 0.2 - - - -
293A GLU* 1.3 81.6 + - - +
295A ALA* 1.3 56.7 + - - +
297A ARG* 3.6 17.4 + - - +
298A PHE* 2.9 63.5 + - + -
316A GLY* 3.8 19.2 + - - +
319A THR* 3.7 19.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 4.8 2.2 - - - -
57A PRO* 3.7 28.2 - - + +
58A ARG* 5.0 1.8 - - - +
227A MSE 3.7 11.0 - - + +
231A CYS* 4.2 16.1 - - - -
235A LEU* 4.5 11.9 - - + -
291A LEU 3.7 7.2 + - - +
292A ILE* 3.2 10.3 + - - +
294A THR* 1.3 75.3 - - - +
296A ASP* 1.3 60.8 + - - +
299A TYR* 2.8 33.0 + - - +
----------------------------------------------------------
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 3.4 25.4 + - - -
58A ARG* 2.9 46.0 + - - +
292A ILE 3.0 13.8 + - - +
293A GLU* 3.4 15.0 - - + +
295A ALA* 1.3 75.5 - - - +
297A ARG* 1.3 57.8 + - + +
299A TYR* 3.5 2.8 + - - +
300A ASP* 3.0 36.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 2.8 46.0 + - - +
294A THR* 3.6 22.6 + - - +
296A ASP* 1.3 75.9 - - + +
298A PHE* 1.3 87.5 + - + +
300A ASP* 3.3 10.4 + - + +
301A LYS* 3.0 48.2 + - + +
312A GLU* 5.3 10.7 + - - +
315A ILE* 6.0 4.8 - - - +
316A GLY* 6.0 1.2 - - - -
----------------------------------------------------------
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A MSE 3.7 16.6 - - + -
228A PRO* 3.8 19.1 - - + -
230A SER* 5.8 0.2 - - - -
231A CYS* 3.8 31.0 - - + -
294A THR* 2.9 36.1 + - + +
297A ARG* 1.3 96.9 - - + +
299A TYR* 1.3 67.2 + - - +
301A LYS* 3.3 4.6 + - + +
302A VAL* 2.9 27.5 + - - +
308A ILE* 3.7 30.7 - - + +
312A GLU* 3.3 35.2 - - + -
313A ARG* 4.1 9.2 - - + -
316A GLY* 4.5 3.1 - - - -
----------------------------------------------------------
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 3.4 36.7 - + + +
57A PRO* 3.6 24.2 - - + -
223A PRO* 3.8 24.5 - - + +
224A LEU* 3.8 26.3 + - + +
227A MSE 3.5 14.7 - - - -
295A ALA 2.8 19.1 + - - +
296A ASP 3.6 4.5 - - - +
298A PHE* 1.3 77.4 - - - +
300A ASP* 1.3 59.2 + - - +
302A VAL* 3.2 2.8 + - - +
303A ASP* 2.8 53.3 + - + +
----------------------------------------------------------
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 5.5 0.7 + - - -
296A ASP* 3.0 21.7 + - - +
297A ARG* 3.5 12.0 - - + +
298A PHE 3.2 0.2 - - - -
299A TYR* 1.3 83.7 - - - +
301A LYS* 1.3 57.8 + - + +
303A ASP* 3.4 7.1 + - - +
304A ALA* 3.0 30.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 3.0 42.5 + - + +
298A PHE* 3.7 9.4 - - + +
300A ASP* 1.3 77.1 - - + +
302A VAL* 1.3 58.3 + - - +
304A ALA* 3.3 4.0 + - - -
305A GLY 3.1 3.8 + - - -
306A LYS* 2.8 65.4 + - + +
307A GLU 4.9 4.5 - - - +
308A ILE* 4.1 13.2 - - + -
312A GLU* 3.3 36.8 - - - +
----------------------------------------------------------
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO* 3.5 34.2 - - + +
226A ASN* 3.7 32.3 - - + +
227A MSE 4.3 8.7 - - - -
298A PHE 2.9 22.9 + - - +
299A TYR* 3.7 4.9 - - - +
301A LYS* 1.3 72.2 - - - +
303A ASP* 1.3 66.0 + - - +
305A GLY* 3.0 13.3 + - - -
306A LYS 4.3 5.2 - - - +
308A ILE* 3.5 21.3 - - + -
----------------------------------------------------------
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO* 3.7 24.2 - - - +
299A TYR* 2.8 42.5 + - + +
300A ASP* 3.7 7.9 - - - +
302A VAL* 1.3 73.5 - - - +
304A ALA* 1.3 58.4 + - - +
305A GLY 3.5 0.9 + - - -
----------------------------------------------------------
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASP 3.0 17.6 + - - +
301A LYS* 3.7 6.7 - - - +
302A VAL 3.2 0.2 - - - -
303A ASP* 1.3 74.4 - - - +
305A GLY* 1.3 62.0 + - - +
306A LYS* 3.3 7.7 + - + +
----------------------------------------------------------
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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