Contacts of the helix formed by residues 284 - 315 (chain C) in PDB entry 5J0Z
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 GLN 284 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU* 3.2 22.8 + - + +
282C GLU* 3.3 32.1 - - - +
283C SER* 1.3 78.9 - - - +
285C PRO* 1.4 52.6 - - - +
286C ALA* 2.6 20.5 + - + -
287C ARG* 2.6 49.4 + - + +
288C ALA* 3.1 8.3 + - - -
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Residues in contact with PRO 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU 4.6 2.7 - - - +
280C LYS* 3.8 33.6 + - + +
283C SER* 3.3 14.6 - - - -
284C GLN* 1.4 86.5 - - - +
286C ALA* 1.3 60.6 + - - +
288C ALA* 3.9 6.2 - - + +
289C ALA* 3.1 27.0 + - - +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLN* 2.6 6.4 + - + +
285C PRO* 1.3 76.3 - - - +
287C ARG* 1.3 50.1 + - - +
289C ALA* 3.5 1.6 - - - +
290C SER* 2.8 40.5 + - - +
293C ARG* 4.8 4.0 + - - +
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU* 3.9 15.7 - - + +
284C GLN* 2.6 41.4 + - + +
286C ALA* 1.3 71.6 - - - +
288C ALA* 1.3 66.2 + - - +
290C SER* 3.3 16.5 + - - -
291C ILE* 3.3 24.7 + - + +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLN* 3.7 25.8 - - + +
279C LEU* 3.5 32.7 - - + +
280C LYS* 4.2 9.0 - - + +
284C GLN 3.1 7.4 + - - +
285C PRO* 3.9 14.4 - - + +
287C ARG* 1.3 80.4 - - - +
289C ALA* 1.3 58.2 + - - +
290C SER 3.2 0.2 + - - -
291C ILE* 3.2 7.1 + - - +
292C THR* 3.1 23.2 + - - -
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C THR* 5.3 5.6 - - + -
276C GLN* 5.4 1.1 - - + +
280C LYS* 4.4 13.2 - - - +
285C PRO 3.1 16.3 + - - +
286C ALA 3.5 2.9 - - - -
288C ALA* 1.3 75.8 - - + +
290C SER* 1.3 60.3 + - - +
292C THR* 3.7 22.2 - - + -
293C ARG* 3.0 38.1 + - - +
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Residues in contact with SER 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ALA* 2.8 24.8 + - - +
287C ARG* 3.4 12.6 - - - -
288C ALA 3.1 0.6 - - - -
289C ALA* 1.3 75.6 - - - +
291C ILE* 1.3 57.1 + - - +
293C ARG* 3.1 19.6 + - - +
294C ALA* 2.8 35.1 + - - +
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C GLU* 4.0 25.1 - - + +
275C VAL* 3.8 30.5 - - + -
276C GLN* 5.7 0.9 - - + +
279C LEU* 3.9 13.7 - - + -
287C ARG* 3.4 27.6 - - + +
288C ALA 3.3 6.7 - - - +
290C SER* 1.3 78.5 - - - +
292C THR* 1.3 56.3 + - - +
294C ALA* 2.8 28.6 + - - +
295C SER* 2.8 18.7 + - - +
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Residues in contact with THR 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C PHE* 3.5 27.3 + - - +
218C SER 5.1 0.4 - - - +
219C THR* 5.1 3.4 - - + -
272C GLU* 2.6 27.0 + - - -
276C GLN* 2.7 29.7 + - - +
288C ALA 3.1 9.7 + - - -
289C ALA* 3.7 22.4 - - + +
291C ILE* 1.3 78.4 - - - +
293C ARG* 1.3 65.0 + - + +
295C SER* 3.5 5.3 - - - -
296C ARG* 3.4 33.6 + - - +
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Residues in contact with ARG 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ALA* 4.8 4.6 + - - +
289C ALA* 3.0 33.7 + - + +
290C SER* 3.1 14.9 + - - +
292C THR* 1.3 78.6 - - + +
294C ALA* 1.3 66.3 + - - +
296C ARG* 3.2 53.9 - - - +
297C ILE* 4.1 6.8 + - - +
278D TYR* 5.8 1.3 - - - -
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C SER 2.8 15.8 + - - +
291C ILE* 2.8 14.5 + - - +
293C ARG* 1.3 69.8 - - - +
295C SER* 1.3 54.9 + - - +
297C ILE* 2.7 31.4 + - - +
298C ALA* 3.0 14.0 + - + -
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Residues in contact with SER 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C PHE* 3.7 28.4 - - - -
272C GLU* 3.5 18.4 - - - +
291C ILE* 2.8 18.8 + - - +
292C THR 3.5 9.4 - - - -
294C ALA* 1.3 70.4 - - - +
296C ARG* 1.3 54.4 + - - +
297C ILE 2.6 13.0 + - - -
298C ALA* 3.0 21.6 + - - +
299C PHE* 3.1 27.4 + - - +
300C PRO* 3.8 0.3 - - - +
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Residues in contact with ARG 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C PHE* 3.1 32.1 + - + -
217C TRP* 3.4 73.6 - - + +
219C THR* 6.0 2.2 - - - +
292C THR* 3.4 20.7 + - - +
293C ARG* 3.2 46.6 - - - +
295C SER* 1.3 75.0 - - - +
297C ILE* 1.3 68.0 + - + +
300C PRO* 3.5 17.1 - - - +
278D TYR* 3.9 26.6 + - - -
----------------------------------------------------------
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Residues in contact with ILE 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C TRP* 6.4 0.2 - - + -
293C ARG 4.4 5.8 - - - +
294C ALA* 2.7 10.5 + - - +
295C SER 2.6 2.4 + - - -
296C ARG* 1.3 88.0 - - + +
298C ALA* 1.3 65.8 + - - +
299C PHE 3.1 2.5 + - - -
300C PRO* 3.3 4.8 - - - +
301C VAL* 3.0 40.6 + - + +
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ALA* 3.0 10.8 + - + +
295C SER* 3.0 18.8 + - - +
297C ILE* 1.3 76.7 - - - +
299C PHE* 1.3 61.1 + - + +
301C VAL* 3.7 4.0 - - - +
302C VAL* 2.8 47.5 + - + +
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Residues in contact with PHE 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TRP* 3.5 28.0 - + + -
216C PHE* 3.4 37.2 - + + -
265C PHE* 4.0 17.4 - + - -
268C VAL* 3.4 30.1 - - + -
269C ALA* 3.7 27.1 - - + -
272C GLU* 4.5 5.8 - - + -
295C SER* 3.1 31.0 + - - +
298C ALA* 1.3 82.9 - - + +
300C PRO* 1.3 74.4 - - + +
301C VAL 3.1 0.3 + - - -
302C VAL* 3.8 2.6 - - - -
303C PHE* 2.9 25.1 + - - +
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Residues in contact with PRO 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TRP* 4.0 32.3 - - + -
216C PHE* 5.6 1.3 - - + -
295C SER 3.8 1.1 - - - +
296C ARG 3.5 23.1 - - - +
297C ILE* 3.3 8.5 - - - +
299C PHE* 1.3 93.9 - - + +
301C VAL* 1.3 57.8 + - + +
303C PHE* 3.7 1.1 - - + +
304C LEU* 3.1 36.1 + - + +
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ILE* 3.0 39.3 + - + +
298C ALA* 3.7 5.4 - - - +
300C PRO* 1.3 72.6 - - + +
302C VAL* 1.3 75.6 - - + +
303C PHE 3.0 1.1 - - - -
304C LEU* 2.8 17.7 + - - +
305C LEU* 2.9 32.0 + - + +
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Residues in contact with VAL 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C PHE* 3.9 18.8 - - + -
298C ALA* 2.8 32.7 + - + +
299C PHE* 4.0 2.0 - - - +
301C VAL* 1.3 80.0 - - + +
303C PHE* 1.3 56.0 + - - +
305C LEU* 3.7 11.9 - - + +
306C ALA* 2.9 32.6 + - + +
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 3.6 28.5 - - + -
209C LEU* 3.6 23.6 - - + -
210C PHE* 4.9 4.9 - + - -
213C TRP* 4.0 17.7 - + + -
258C ILE* 5.8 1.3 - - + -
261C MET* 3.3 28.5 - - + -
262C ILE* 4.2 15.3 - - + -
265C PHE* 3.3 28.1 - + + -
299C PHE 2.9 16.2 + - - +
300C PRO 3.7 4.5 - - - +
301C VAL 2.9 0.4 + - - -
302C VAL* 1.3 74.5 - - - +
304C LEU* 1.3 69.6 + - + +
306C ALA* 3.2 0.8 + - - -
307C ASN* 2.8 52.9 + - + +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C PRO* 3.1 20.5 + - + +
301C VAL* 2.8 10.0 + - - +
303C PHE* 1.3 81.7 - - + +
305C LEU* 1.3 67.2 + - + +
307C ASN* 4.9 3.1 - - + -
308C ILE* 3.3 30.4 + - + +
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C VAL* 2.9 33.8 + - + +
302C VAL* 3.7 14.6 - - + +
304C LEU* 1.3 77.4 - - + +
306C ALA* 1.3 52.9 + - - +
308C ILE* 2.8 13.5 + - - +
309C ILE* 2.7 45.5 + - + +
----------------------------------------------------------
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Residues in contact with ALA 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C MET* 4.0 20.5 - - - +
265C PHE* 5.0 2.2 - - + -
302C VAL* 2.9 25.6 + - + +
303C PHE* 4.1 2.0 - - - +
305C LEU* 1.3 76.2 - - + +
307C ASN* 1.3 58.0 + - - +
309C ILE* 3.6 20.9 - - + +
310C LEU* 3.1 31.0 + - - +
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Residues in contact with ASN 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 6.1 0.8 - - - +
254C TYR* 5.1 4.9 + - - -
258C ILE* 4.0 31.0 - - - +
261C MET* 3.2 28.2 - - - +
303C PHE* 2.8 42.1 + - + +
304C LEU* 4.6 2.9 - - + +
306C ALA* 1.3 71.6 - - - +
308C ILE* 1.3 64.3 + - + +
310C LEU* 3.7 4.7 - - - +
311C ALA* 2.7 34.5 + - - +
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LEU* 3.3 20.2 + - + +
305C LEU* 2.8 12.6 + - - +
307C ASN* 1.3 85.5 - - + +
309C ILE* 1.3 64.8 + - + +
311C ALA* 3.8 10.2 - - + +
312C PHE* 3.2 24.5 + - + +
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU* 2.7 24.9 + - + +
306C ALA* 3.6 30.7 - - + +
308C ILE* 1.3 74.5 - - + +
310C LEU* 1.3 60.2 + - + +
312C PHE* 3.6 8.8 + - + +
313C LEU* 3.0 45.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C TYR* 4.6 6.3 - - + +
257C ALA* 3.8 26.7 - - + -
258C ILE* 4.0 24.0 - - + +
261C MET* 4.4 15.0 - - + -
306C ALA 3.1 17.5 + - - +
307C ASN* 3.7 5.2 - - - +
309C ILE* 1.3 77.8 - - + +
311C ALA* 1.3 69.8 + - - +
313C LEU* 2.9 33.5 + - + +
314C PHE* 2.9 37.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C TYR* 4.3 21.1 - - - +
307C ASN 2.7 22.6 + - - +
308C ILE* 3.8 16.2 - - + +
310C LEU* 1.3 72.0 - - - +
312C PHE* 1.3 64.0 + - - +
314C PHE 3.2 0.7 + - - -
315C PHE* 3.2 30.1 + - + +
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Residues in contact with PHE 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C ILE* 3.2 14.8 + - + +
309C ILE* 3.7 8.1 - - + +
310C LEU 3.1 0.8 - - - -
311C ALA* 1.3 76.0 - - - +
313C LEU* 1.3 64.4 - - + +
314C PHE 2.8 11.4 + - - -
315C PHE* 2.9 27.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C ILE* 3.0 36.1 + - + +
310C LEU* 2.9 32.1 + - + +
312C PHE* 1.3 80.4 - - + +
314C PHE* 1.3 62.6 + - + +
315C PHE 3.7 0.2 - - - -
402C HXA 5.4 7.3 - - - +
----------------------------------------------------------
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Residues in contact with PHE 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ARG* 3.6 33.7 - - + -
118C ARG* 3.4 25.1 + - + +
252C MET* 3.4 34.1 - - + -
253C THR 3.7 12.1 - - - -
254C TYR* 3.6 23.8 - + + -
257C ALA* 4.1 16.4 - - + -
310C LEU* 2.9 28.4 + - + +
312C PHE 2.8 1.8 + - - -
313C LEU* 1.3 78.9 - - + +
315C PHE* 1.3 83.4 + - + +
402C HXA 4.6 9.9 - - + +
----------------------------------------------------------
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Residues in contact with PHE 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ARG* 3.9 47.8 - - + +
121C PHE* 4.2 36.8 - + + -
254C TYR* 4.1 24.9 - + - -
311C ALA* 3.2 20.4 + - + +
312C PHE* 2.9 24.0 + - - +
313C LEU 3.7 0.4 - - - -
314C PHE* 1.3 109.0 - - + +
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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