Contacts of the helix formed by residues 279 - 303 (chain C) in PDB entry 6GYS
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 279 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ILE* 5.0 0.5 - - - +
567B PRO* 3.1 16.5 - - - +
568B LEU* 2.4 47.8 + - - +
569B ASN* 3.0 28.6 + - + +
278C ASP* 1.3 74.2 - - - +
280C PRO* 1.3 72.2 - - - +
281C VAL* 3.1 18.9 + - - +
282C GLU* 3.0 15.6 + - + +
283C SER* 2.7 33.6 + - - -
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Residues in contact with PRO 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 4.0 15.5 - - + -
278C ASP 3.5 8.5 - - - +
279C ASP* 1.3 87.5 - - - +
281C VAL* 1.3 60.0 + - + +
283C SER* 2.8 23.1 + - - +
284C ILE* 2.9 31.8 + - + +
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ILE* 3.7 34.1 - - + +
562B LEU* 6.5 0.4 - - + -
565B LEU* 3.7 30.0 - - + +
566B VAL 3.6 21.3 - - - +
567B PRO* 3.8 2.2 - - + -
568B LEU* 5.5 1.6 - - + -
279C ASP* 3.1 19.4 + - - +
280C PRO* 1.3 77.1 - - + +
282C GLU* 1.3 58.2 + - - +
284C ILE* 3.8 7.8 - - - +
285C ALA* 2.8 30.1 + - + +
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B MET* 4.9 16.9 - - + +
559B ILE* 5.0 11.8 - - + +
569B ASN* 3.3 15.1 + - - +
278C ASP* 3.5 22.2 - - + +
279C ASP* 3.0 30.6 + - + +
281C VAL* 1.3 80.5 - - - +
283C SER* 1.3 56.5 + - - +
285C ALA* 3.2 8.3 + - - +
286C LYS* 2.9 49.5 + - + +
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Residues in contact with SER 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C PRO* 3.6 28.4 - - - +
275C LEU 5.9 0.2 - - - -
278C ASP* 4.4 4.7 - - - -
279C ASP 2.7 16.1 + - - -
280C PRO* 2.8 20.1 + - - +
282C GLU* 1.3 70.0 - - - +
284C ILE* 1.3 72.0 + - - +
286C LYS* 3.2 5.5 + - - +
287C VAL* 3.0 36.0 + - - +
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Residues in contact with ILE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B LEU* 6.3 0.2 - - + -
565B LEU* 5.2 15.3 - - + -
280C PRO* 2.9 25.5 + - + +
281C VAL* 3.9 6.1 - - - +
283C SER* 1.3 84.1 + - - +
285C ALA* 1.3 52.5 + - - +
287C VAL* 3.4 7.3 + - - +
288C THR* 2.4 45.8 + - - +
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B MET* 5.5 2.2 - - - -
558B LEU* 3.7 15.7 - - + -
559B ILE* 4.9 7.9 - - + -
562B LEU* 3.7 25.8 - - + -
281C VAL* 2.8 21.6 + - + +
282C GLU* 3.3 11.0 - - - +
284C ILE* 1.3 76.7 - - - +
286C LYS* 1.3 58.6 + - + +
288C THR* 3.2 1.7 + - - -
289C LEU* 2.9 35.0 + - - +
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Residues in contact with LYS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B MET* 5.4 13.5 - - + -
269C VAL* 4.9 13.0 - - + -
271C ASP 4.9 7.6 - - - +
272C PHE* 3.2 34.7 - - + +
273C ARG 5.9 0.2 - - - -
274C PRO* 3.4 20.7 - - + +
275C LEU* 4.4 2.2 - - - +
278C ASP* 2.1 37.6 + - - -
282C GLU* 2.9 41.7 + - + +
283C SER 3.2 2.4 + - - +
285C ALA* 1.3 76.2 - - + +
287C VAL* 1.3 58.2 + - - +
289C LEU* 3.3 6.8 + - + -
290C GLY 2.9 21.8 + - - -
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PHE* 3.6 19.1 - - - +
273C ARG* 4.7 7.0 - - + -
274C PRO* 4.0 13.0 - - + -
283C SER 3.0 18.8 + - - +
284C ILE* 3.9 6.7 - - - +
286C LYS* 1.3 76.5 - - - +
288C THR* 1.3 58.5 + - - +
290C GLY* 2.9 15.3 + - - +
291C ARG* 3.3 13.0 + - - +
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Residues in contact with THR 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B LEU* 3.8 22.9 - - + +
235C GLN* 4.6 0.2 - - - +
284C ILE* 2.4 39.3 + - - +
285C ALA* 3.3 9.4 - - - -
287C VAL* 1.3 76.3 - - - +
289C LEU* 1.3 57.1 + - - +
291C ARG* 3.2 42.3 + - - +
292C ILE* 3.0 41.8 + - + +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B MET* 6.0 0.7 - - - -
558B LEU* 3.7 41.7 - - + -
562B LEU* 4.3 8.1 - - + -
231C ILE* 4.8 9.6 - - + -
264C PHE* 3.9 29.1 - - + +
267C PHE* 5.4 4.3 - - + -
269C VAL* 4.8 17.5 - - + -
272C PHE* 3.5 15.8 - - + -
285C ALA 2.9 22.5 + - - +
286C LYS* 3.5 11.2 - - + +
288C THR* 1.3 72.6 - - - +
290C GLY* 1.3 59.4 + - - +
292C ILE* 3.8 16.1 - - + +
293C PHE* 2.8 32.2 + - - +
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PHE* 3.3 27.6 - - - -
286C LYS 2.9 10.5 + - - -
287C VAL 2.9 7.8 + - - -
289C LEU* 1.3 75.8 - - - +
291C ARG* 1.3 61.1 + - - +
293C PHE* 3.2 5.0 + - - +
294C TYR* 3.2 31.8 + - - -
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Residues in contact with ARG 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR 3.8 4.0 + - - -
127C PHE* 2.0 50.5 + - + +
128C GLY 3.3 20.9 - - - -
129C SER 3.1 26.1 + - - -
130C ILE* 3.2 21.0 + - - +
131C GLY* 3.8 5.3 - - - +
287C VAL 3.3 9.5 + - - +
288C THR* 3.2 37.1 + - - +
290C GLY* 1.3 72.2 - - - +
292C ILE* 1.3 73.5 + - - +
294C TYR* 3.4 4.7 + - - +
295C ARG* 3.0 28.9 + - - +
339C ASN 6.0 0.4 - - - +
342C GLU* 3.5 30.4 - - + +
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Residues in contact with ILE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B LEU* 4.9 0.7 - - + -
128C GLY 4.3 5.4 - - - +
129C SER 4.3 4.5 - - - +
231C ILE* 4.5 16.8 - - + -
234C VAL* 3.7 29.4 - - + -
235C GLN* 3.5 34.3 - - + +
238C LEU* 3.5 12.8 - - + +
264C PHE* 5.3 5.8 - - + -
288C THR* 3.0 33.6 + - + +
289C LEU* 3.8 12.3 - - + +
291C ARG* 1.3 86.0 - - - +
293C PHE* 1.3 58.0 + - - +
295C ARG 3.5 0.2 + - - -
296C LEU* 2.9 32.5 + - + +
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Residues in contact with PHE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C PHE* 3.4 35.0 - + + -
270C ASP 5.8 0.7 - - - -
272C PHE* 3.5 25.4 - + + -
289C LEU 2.8 20.5 + - - +
290C GLY 3.4 3.4 - - - +
291C ARG 3.1 0.2 - - - -
292C ILE* 1.3 79.6 - - - +
294C TYR* 1.3 89.4 + + - +
296C LEU* 3.2 5.9 + - + +
297C CYS* 2.9 45.2 + - - -
312C LEU* 4.7 13.7 - - + -
315C GLU* 6.0 2.7 - - + -
316C VAL* 3.6 27.1 - - + -
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Residues in contact with TYR 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PHE* 5.5 6.9 - + - -
290C GLY* 3.2 18.6 + - - +
291C ARG* 3.4 6.7 + - - +
293C PHE* 1.3 103.9 - + - +
295C ARG* 1.3 61.9 + - - +
297C CYS* 3.5 2.0 + - + -
298C GLY* 2.9 24.8 + - - -
316C VAL* 4.8 5.4 - - + +
342C GLU* 4.9 9.6 - - + +
343C VAL* 4.2 26.6 - - + +
346C TRP* 3.6 62.2 + + + +
349C ILE* 6.1 0.2 - - - +
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Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ALA* 3.2 23.4 + - - +
125C LEU* 3.6 15.7 + - - +
127C PHE* 4.7 0.6 - - - -
128C GLY* 3.1 28.4 - - - +
238C LEU* 3.7 18.4 - - + -
291C ARG 3.0 13.8 + - - +
292C ILE 3.9 3.1 - - - +
294C TYR* 1.3 76.6 - - - +
296C LEU* 1.3 61.6 + - - +
298C GLY* 3.5 2.3 + - - -
299C CYS* 3.3 28.1 + - - -
342C GLU* 2.6 46.8 + - - +
345C TYR* 3.4 36.4 - - - +
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C VAL* 4.2 22.9 - - + -
237C TYR* 4.5 5.2 - - + -
238C LEU* 3.7 18.6 - - + +
257C LEU* 4.0 22.2 - - + -
260C CYS* 4.4 10.3 - - + +
261C ILE* 4.3 10.1 - - + -
264C PHE* 4.5 22.0 - - + -
292C ILE* 2.9 18.9 + - + +
293C PHE* 3.6 6.7 - - - +
294C TYR 3.2 0.2 - - - -
295C ARG* 1.3 76.9 - - - +
297C CYS* 1.3 60.4 + - - +
299C CYS* 3.1 6.0 + - + +
300C ASP* 2.9 25.3 + - - +
312C LEU* 4.2 22.2 - - + -
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Residues in contact with CYS 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C PHE* 2.9 53.1 + - - +
294C TYR* 4.1 2.0 - - - +
296C LEU* 1.3 74.0 - - - +
298C GLY* 1.3 59.3 + - - +
300C ASP* 3.3 8.8 + - - +
301C TYR* 2.9 27.4 + - - +
312C LEU* 3.8 25.6 - - - -
313C HIS* 4.0 6.4 - - + +
316C VAL* 4.3 7.2 - - - -
346C TRP* 3.6 27.8 - - + -
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Residues in contact with GLY 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C TYR 2.9 17.3 + - - -
295C ARG* 3.5 3.1 + - - -
296C LEU 3.2 0.2 - - - -
297C CYS* 1.3 77.4 - - - +
299C CYS* 1.3 56.0 + - - +
301C TYR* 3.2 4.2 + - - +
302C LEU* 2.9 36.7 + - - +
346C TRP* 3.7 2.8 - - - -
349C ILE* 4.1 27.7 - - - +
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Residues in contact with CYS 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C TYR* 4.7 14.1 - - + -
238C LEU* 3.7 18.8 - - + -
241C ALA* 3.8 24.2 - - + -
257C LEU* 4.9 3.4 - - + -
295C ARG 3.3 15.6 + - - -
296C LEU* 3.1 9.4 + - + +
298C GLY* 1.3 74.5 - - - +
300C ASP* 1.3 56.5 + - - +
302C LEU* 4.2 9.9 - - - +
303C GLN* 2.7 44.4 + - - +
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Residues in contact with ASP 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU* 4.2 10.6 - - + +
261C ILE* 3.7 9.8 - - + +
296C LEU 2.9 13.6 + - - +
297C CYS* 3.3 15.5 - - - +
299C CYS* 1.3 76.9 - - - +
301C TYR* 1.3 51.9 + - - +
304C SER* 2.4 29.3 + - - -
308C LYS* 2.9 32.5 + - - +
310C ILE 3.6 4.9 - - - +
312C LEU* 2.8 39.4 + - + +
313C HIS* 2.2 31.2 + - - +
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Residues in contact with TYR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LYS* 5.6 0.3 - - - -
297C CYS 2.9 13.0 + - - +
298C GLY 3.5 7.2 - - - +
300C ASP* 1.3 77.8 - - - +
302C LEU* 1.3 76.2 + - + +
304C SER* 2.9 23.2 + - - -
313C HIS* 3.5 29.1 + + + +
346C TRP* 5.5 0.9 - - + -
349C ILE* 4.1 22.2 - - + -
352C ASP* 2.9 51.6 + - + -
353C ARG* 3.6 23.6 - - + -
356C ASP* 3.5 18.5 + - + +
359C LEU* 5.0 2.9 - - - +
413C LYS* 5.8 0.2 + - - -
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LYS* 3.5 21.1 + - - -
247C TYR* 5.6 1.2 + - - -
298C GLY 2.9 23.2 + - - +
299C CYS* 4.0 9.9 - - - +
301C TYR* 1.3 94.0 - - + +
303C GLN* 1.3 61.3 + - + +
304C SER 3.3 0.7 - - - -
349C ILE* 5.3 13.5 - - + -
352C ASP* 5.7 0.7 - - - +
456C HIS* 6.0 6.5 - - + -
458C MET* 6.6 0.4 - - + -
461C GLN* 6.0 7.2 - - + -
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Residues in contact with GLN 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LYS* 4.4 7.7 - - - +
237C TYR* 2.6 35.3 + - - -
241C ALA* 5.1 2.6 - - - +
246C PRO* 3.4 35.1 - - + +
253C ALA* 3.8 11.4 - - - +
254C ASN* 3.6 17.2 + - - +
257C LEU* 3.4 21.0 - - + +
299C CYS* 2.7 28.0 + - - +
300C ASP 3.9 3.1 - - - +
302C LEU* 1.3 74.2 - - + +
304C SER* 1.3 62.1 + - - +
305C GLY 3.3 0.5 + - - -
308C LYS* 3.2 19.7 - - - +
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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