Contacts of the helix formed by residues 281 - 308 (chain C) in PDB entry 5TIN
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 LYS 281 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 3.3 39.0 - - + +
143C LYS 3.2 7.2 - - - -
145C PHE* 4.2 9.9 - - + +
271C ARG* 3.9 22.8 - - - +
274C LEU* 3.8 30.5 - - + -
275C PRO 5.4 0.6 + - - -
277C VAL* 3.6 26.8 + - + +
279C TYR* 3.7 13.8 + - + +
280C VAL* 1.3 81.6 - - - +
282C ALA* 1.3 65.4 + - - +
283C ILE* 3.3 6.7 - - + +
284C ASP* 3.0 41.6 + - - +
285C ILE* 3.2 11.8 + - - +
345C TYR* 5.0 0.7 - - - -
222D TYR* 6.1 0.2 - - - -
225D ILE* 5.2 2.0 - - - +
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LYS 2.9 7.9 + - - +
144C ASN 3.7 12.8 - - - +
145C PHE 3.3 12.2 + - - +
147C MET* 4.0 5.2 - - + -
281C LYS* 1.3 72.4 - - - +
283C ILE* 1.3 62.2 + - - +
285C ILE* 3.3 3.1 + - - +
286C TRP 3.2 13.5 + - - -
341C TYR* 2.8 25.9 + - - +
345C TYR* 3.5 42.8 - - + -
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Residues in contact with ILE 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C PHE* 3.0 34.8 + - + +
146C PRO* 4.1 6.9 - - + +
227C MET* 4.0 25.6 - - + -
228C TYR* 3.6 37.2 - - + +
270C SER* 3.9 30.1 - - - +
271C ARG* 5.4 0.2 - - + -
281C LYS* 4.3 10.8 - - + -
282C ALA* 1.3 76.3 - - - +
284C ASP* 1.3 70.5 + - - +
286C TRP* 3.5 2.6 + - + +
287C MET* 3.0 37.6 + - + +
341C TYR* 3.9 2.6 + - - -
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Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C SER* 4.5 0.9 + - - -
271C ARG* 3.0 39.2 + - - +
279C TYR 4.0 0.5 - - - +
280C VAL* 3.9 12.6 - - + -
281C LYS* 3.0 52.5 + - - +
283C ILE* 1.3 80.0 - - - +
285C ILE* 1.3 59.8 + - - +
287C MET* 3.3 5.6 + - - +
288C ALA* 2.9 32.5 + - - +
225D ILE* 4.4 13.3 - - + +
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Residues in contact with ILE 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C VAL* 3.5 21.5 - - + -
281C LYS 3.2 12.9 + - - +
282C ALA 3.3 7.4 + - - +
284C ASP* 1.3 76.5 - - - +
286C TRP* 1.3 58.8 + - - +
288C ALA* 3.6 4.8 - - + +
289C VAL* 3.0 40.6 + - + +
337C PHE* 4.7 4.5 - - + -
341C TYR* 4.3 17.5 - - + -
345C TYR* 4.0 16.8 - - + +
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Residues in contact with TRP 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C TYR* 3.4 42.7 - + + -
231C SER* 2.8 24.2 + - - -
232C LEU* 4.8 9.4 - - + -
282C ALA 3.2 2.6 + - - -
283C ILE* 3.6 8.3 - - + +
285C ILE* 1.3 80.1 - - - +
287C MET* 1.3 74.1 + - + +
289C VAL* 3.4 2.1 + - - +
290C CYS* 2.9 46.6 + - - +
334C PHE* 4.3 8.7 - + - -
337C PHE* 3.7 25.1 - + - -
338C ASN* 3.6 37.9 - - - -
341C TYR* 3.7 38.8 - + + +
342C TRP* 4.1 14.4 - + - -
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Residues in contact with MET 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C MET* 3.7 45.1 - - + +
231C SER* 4.1 0.7 - - - -
263C MET* 3.4 26.6 - - - +
266C GLN* 4.0 24.2 - - + +
267C SER* 4.0 30.7 - - - +
270C SER* 4.0 10.1 - - - +
271C ARG* 5.8 0.2 - - - +
283C ILE* 3.0 26.3 + - + +
284C ASP* 3.9 5.4 - - - +
286C TRP* 1.3 90.4 - - + +
288C ALA* 1.3 57.3 + - - +
290C CYS* 3.5 3.1 + - - +
291C LEU* 2.9 30.2 + - - +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ASP 2.9 18.8 + - - +
285C ILE* 3.6 6.5 - - + +
287C MET* 1.3 77.6 - - - +
289C VAL* 1.3 58.7 + - + +
291C LEU* 3.2 11.0 + - - +
292C LEU* 2.9 30.7 + - - +
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ILE* 3.0 26.4 + - + +
286C TRP 3.9 0.2 - - - +
288C ALA* 1.3 73.3 - - + +
290C CYS* 1.3 66.8 + - - +
292C LEU* 3.1 14.8 + - + +
293C PHE* 2.9 43.0 + - + -
334C PHE* 5.1 0.7 - - + -
337C PHE* 3.5 53.6 - - + -
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Residues in contact with CYS 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C SER* 4.3 7.4 - - - -
235C VAL* 3.8 24.6 - - + +
263C MET* 3.7 22.0 - - + -
286C TRP* 2.9 54.2 + - - +
287C MET 3.7 0.7 - - - +
289C VAL* 1.3 78.5 - - - +
291C LEU* 1.3 61.7 + - - +
293C PHE* 3.4 5.1 + - - +
294C VAL* 3.1 27.5 + - - +
334C PHE* 4.1 11.2 - - - -
337C PHE* 5.5 0.7 - - - -
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C VAL* 3.8 25.4 - - + +
263C MET* 3.7 30.7 - - + +
264C THR* 4.1 18.6 - - + -
267C SER* 5.6 5.8 - - - -
287C MET 2.9 18.8 + - - +
288C ALA* 3.4 9.6 - - - +
290C CYS* 1.3 76.5 - - - +
292C LEU* 1.3 57.1 + - - +
294C VAL* 3.4 1.5 + - - -
295C PHE* 2.9 35.2 + - + +
230D PRO* 6.1 0.7 - - + -
233D LEU* 3.3 33.4 - - + -
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ALA 2.9 15.4 + - - +
289C VAL* 3.1 19.7 + - + +
291C LEU* 1.3 76.9 - - - +
293C PHE* 1.3 55.9 + - + +
295C PHE* 3.3 6.9 + - + +
296C SER* 2.8 48.7 + - - +
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Residues in contact with PHE 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C VAL* 4.5 12.8 - - + -
238C SER* 4.6 1.8 + - - -
239C TRP* 4.8 5.2 - - - +
289C VAL* 2.9 46.0 + - + +
290C CYS* 3.7 7.0 - - - +
291C LEU 3.4 0.2 - - - -
292C LEU* 1.3 78.2 - - + +
294C VAL* 1.3 57.8 + - - +
296C SER* 3.5 4.8 + - - -
297C ALA* 3.1 23.6 + - - +
330C PHE* 3.5 40.7 - + + -
333C ALA* 3.7 18.4 - - + -
334C PHE* 3.5 54.3 - + + -
337C PHE* 4.7 5.2 - - + -
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Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ILE* 3.9 19.5 - - + +
235C VAL* 3.9 13.0 - - + -
238C SER* 3.7 27.5 - - - +
256C GLY* 4.8 1.0 - - - +
259C THR* 3.3 16.5 + - - +
260C VAL* 3.2 44.0 - - + +
263C MET* 4.6 5.2 - - + -
290C CYS 3.1 17.2 + - - +
291C LEU* 3.9 4.3 - - - +
293C PHE* 1.3 76.4 - - - +
295C PHE* 1.3 64.3 + - - +
297C ALA* 3.5 4.6 + - - +
298C LEU* 3.5 15.2 + - - +
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Residues in contact with PHE 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C VAL* 3.8 32.5 - - + -
291C LEU* 2.9 22.7 + - + +
292C LEU* 3.7 9.2 - - + +
294C VAL* 1.3 74.3 - - - +
296C SER* 1.3 61.5 + - - +
298C LEU* 3.2 13.8 + - + +
299C LEU* 3.0 55.3 + - + +
233D LEU* 3.8 40.8 - - + -
236D ILE* 4.3 24.7 - - + -
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LEU* 2.8 34.2 + - - +
293C PHE* 3.6 8.3 - - - -
295C PHE* 1.3 77.8 - - - +
297C ALA* 1.3 51.5 + - - +
299C LEU* 3.3 13.6 + - - +
300C GLU* 2.8 34.0 + - - +
330C PHE* 3.7 17.5 - - - -
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C SER* 4.0 26.5 - - - +
241C SER* 5.2 4.9 + - - -
242C PHE* 3.8 22.4 - - + -
256C GLY* 6.3 1.1 - - - -
293C PHE 3.1 13.4 + - - +
294C VAL 3.7 9.6 - - - +
295C PHE 3.2 0.4 - - - -
296C SER* 1.3 74.2 - - - +
298C LEU* 1.3 64.8 + - - +
300C GLU* 3.3 8.9 - - - +
301C TYR* 3.2 18.9 + - - +
330C PHE* 3.6 10.7 - - + -
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ARG 4.7 2.7 - - - +
253C VAL* 4.4 29.2 - - + +
256C GLY* 4.0 39.4 - - - +
257C ILE* 4.4 9.2 - - + +
260C VAL* 4.6 8.1 - - + -
294C VAL 3.5 7.0 + - - +
295C PHE* 3.2 20.5 + - + +
297C ALA* 1.3 76.2 - - - +
299C LEU* 1.3 68.2 + - + +
301C TYR* 3.0 9.6 + - + -
302C ALA* 3.0 21.2 + - + +
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C PHE* 3.0 44.7 + - + +
296C SER* 3.3 15.5 + - - +
298C LEU* 1.3 74.8 - - + +
300C GLU* 1.3 66.3 + - - +
302C ALA* 3.2 13.4 + - + +
303C ALA* 3.0 22.7 + - - +
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C PHE* 3.6 17.8 - - + -
252C ARG* 3.9 5.0 + - - -
296C SER 2.8 18.0 + - - +
297C ALA* 3.3 13.3 - - - +
298C LEU 3.2 0.4 - - - -
299C LEU* 1.3 73.2 - - - +
301C TYR* 1.3 62.7 + - - +
303C ALA* 3.2 8.7 + - - +
304C VAL* 3.0 25.5 + - - +
322C ILE* 3.5 20.4 - - + +
323C ASP* 2.8 27.2 - - - +
326C SER* 3.0 31.9 + - - +
330C PHE* 4.4 7.2 - - + -
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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
----------------------------------------------------------
241C SER* 4.9 1.3 - - - +
246C MET* 2.9 26.3 + - - -
249C ALA* 3.1 28.2 - - + +
252C ARG* 3.0 55.2 - - + +
253C VAL* 3.9 31.2 - - + -
297C ALA 3.2 6.5 + - - +
298C LEU* 3.0 13.6 + - + +
300C GLU* 1.3 81.3 + - - +
302C ALA* 1.3 62.3 + - - +
304C VAL* 3.1 18.1 + - + -
305C ASN* 2.8 58.4 + - + +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LEU* 3.0 13.9 + - + +
299C LEU* 3.4 20.2 - - + +
301C TYR* 1.3 77.4 - - - +
303C ALA* 1.3 58.1 + - - +
305C ASN* 3.8 5.5 - - - +
306C PHE* 2.9 31.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LEU 3.0 12.1 + - - +
300C GLU* 3.4 11.9 - - - +
301C TYR 3.1 0.2 - - - -
302C ALA* 1.3 74.4 - - - +
304C VAL* 1.3 59.0 + - - +
306C PHE* 4.4 4.3 - - - -
307C VAL* 2.8 41.2 + - + +
322C ILE* 4.6 15.9 - - + -
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Residues in contact with VAL 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C MET* 3.8 30.5 - - + -
300C GLU* 3.0 20.7 + - - +
301C TYR* 3.1 19.3 + - + +
303C ALA* 1.3 76.4 - - - +
305C ASN* 1.3 53.4 + - - +
307C VAL* 4.3 5.8 - - - -
308C SER* 2.7 35.5 + - - -
319C ALA* 3.7 20.5 - - + +
322C ILE* 3.7 24.7 - - + -
323C ASP* 3.7 24.0 - - - +
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Residues in contact with ASN 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C MET 4.8 2.7 + - - -
249C ALA* 4.1 10.7 - - - +
301C TYR* 2.8 55.3 + - + +
302C ALA* 3.8 5.4 - - - +
304C VAL* 1.3 75.1 - - - +
306C PHE* 1.3 62.8 + - - +
308C SER* 3.5 12.2 + - - -
309C ARG* 3.6 16.6 + - - +
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ALA 2.9 20.4 + - - +
303C ALA* 3.2 5.1 + - - +
305C ASN* 1.3 75.0 + - - +
307C VAL* 1.3 73.0 + - + +
308C SER 3.2 2.3 + - - -
309C ARG* 3.0 75.9 + - - -
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Residues in contact with VAL 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA* 2.8 31.3 + - + +
306C PHE* 1.3 82.2 - - + +
308C SER* 1.3 60.2 + - - +
309C ARG* 3.4 1.8 + - - +
310C ALA 5.0 0.9 + - - +
315C PHE* 3.4 35.6 - - + +
318C ARG* 4.5 5.8 - - + -
319C ALA* 3.6 36.1 - - + +
322C ILE* 4.2 15.0 - - + -
----------------------------------------------------------
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C MET* 4.3 10.5 + - - +
304C VAL* 2.7 22.1 + - - +
305C ASN* 3.5 9.2 + - - -
306C PHE 3.2 0.4 - - - -
307C VAL* 1.3 78.5 - - - +
309C ARG* 1.3 64.3 + - - +
310C ALA 3.4 13.2 + - - +
311C GLY* 4.2 1.6 + - - -
315C PHE 4.2 5.8 - - - -
316C ILE* 4.1 23.4 - - - +
319C ALA* 3.8 16.8 - - - -
----------------------------------------------------------
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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