Contacts of the helix formed by residues 293 - 318 (chain C) in PDB entry 2GPV
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 293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C THR 3.7 0.8 + - - -
292C LEU* 1.3 77.7 - - - +
294C LEU* 1.3 65.0 + - - +
295C ALA* 4.0 3.6 - - - -
296C ASP* 3.2 24.6 + - - +
297C GLN* 3.0 21.8 + - - +
383C GLU* 2.7 28.8 + - - -
384C ASP* 5.8 2.5 - - - +
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LEU 3.7 0.4 + - - -
293C SER* 1.3 72.6 - - - +
295C ALA* 1.3 56.7 + - - +
297C GLN* 3.4 20.6 + - - +
298C MET* 2.9 30.1 + - - +
1328I LEU* 4.1 37.7 - - + +
1329I MET* 5.6 10.3 - - + -
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C SER* 3.1 2.3 - - - +
294C LEU* 1.3 78.9 - - - +
296C ASP* 1.3 58.3 + - - +
298C MET* 3.4 8.6 + - - +
299C SER* 2.8 31.6 + - - +
381C HIS 5.9 0.9 - - - +
383C GLU* 3.5 31.2 - - + +
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Residues in contact with ASP 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LEU* 4.3 19.2 - - + +
293C SER* 3.2 19.5 + - - +
295C ALA* 1.3 75.8 - - - +
297C GLN* 1.3 67.1 + - - +
299C SER* 3.1 3.6 + - - -
300C LEU* 2.9 30.8 + - - +
381C HIS 4.1 3.1 - - - +
382C ILE* 3.3 21.7 - - + +
383C GLU* 2.7 28.2 + - - +
384C ASP* 2.9 36.4 + - - +
388C VAL* 4.5 2.4 - - + +
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Residues in contact with GLN 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LYS* 5.5 2.3 - - - +
289C PHE* 3.4 49.5 + - + +
290C SER* 3.4 19.8 + - - +
292C LEU* 2.6 30.7 + - + +
293C SER 3.0 15.3 + - - +
294C LEU* 3.6 20.9 - - - +
296C ASP* 1.3 74.4 - - - +
298C MET* 1.3 63.7 + - - +
300C LEU* 3.6 0.4 + - - -
301C LEU* 3.3 30.7 + - - +
1328I LEU* 3.8 22.2 - - + +
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Residues in contact with MET 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU 2.9 18.4 + - - +
295C ALA* 3.5 7.6 - - - +
297C GLN* 1.3 77.9 - - - +
299C SER* 1.3 57.1 + - - +
301C LEU* 3.7 1.8 - - - +
302C GLN* 2.9 49.8 + - - +
1321I GLU* 3.7 27.6 - - + +
1324I ILE* 3.6 20.7 - - + +
1325I ARG* 3.6 38.8 - - + +
1328I LEU* 4.0 12.7 - - + +
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Residues in contact with SER 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ALA* 2.8 22.8 + - - +
296C ASP* 3.1 6.0 + - - -
298C MET* 1.3 74.2 - - - +
300C LEU* 1.3 62.2 + - - +
302C GLN* 3.2 13.2 + - - +
303C SER* 3.1 26.3 + - - -
379C SER* 3.7 16.5 + - - -
381C HIS* 3.7 25.3 + - - +
382C ILE* 4.1 15.0 - - - -
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C PHE* 4.3 11.2 - - + -
292C LEU* 3.7 29.2 - - + -
296C ASP 2.9 20.3 + - - +
297C GLN 4.1 2.7 - - - +
299C SER* 1.3 71.2 - - - +
301C LEU* 1.3 63.1 + - - +
303C SER 3.4 0.3 + - - -
304C ALA* 3.1 22.5 + - - +
374C LEU* 3.5 24.0 - - + +
375C ALA* 4.5 5.6 - - - +
377C SER* 3.3 23.3 + - - +
378C ASP 5.7 0.9 - - - +
379C SER* 4.9 4.0 - - - +
382C ILE* 3.3 30.1 - - + -
388C VAL* 4.2 18.6 - - + -
391C LEU* 4.4 12.3 - - + -
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 4.6 15.0 - - + -
280C ILE* 4.2 28.5 - - + -
283C ALA* 4.3 14.8 - - + -
289C PHE* 4.1 16.2 - - + -
297C GLN 3.3 20.0 + - - +
298C MET 3.7 2.9 - - - +
300C LEU* 1.3 73.3 - - - +
302C GLN* 1.3 59.5 + - - +
303C SER 3.0 4.7 - - - -
305C TRP* 2.8 38.5 + - + +
308C ILE* 5.1 2.5 - - + -
374C LEU* 3.9 16.8 - - + -
1324I ILE* 4.1 16.8 - - + -
1328I LEU* 4.2 24.9 - - + -
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Residues in contact with GLN 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C MET* 2.9 45.8 + - - +
299C SER* 3.2 13.8 + - - +
301C LEU* 1.3 76.5 - - - +
303C SER* 1.3 57.2 + - - +
305C TRP* 3.2 22.6 + - - -
381C HIS* 5.9 3.1 - - - -
1320I LEU* 4.2 16.5 - - + +
1321I GLU* 4.5 19.2 - - - +
1324I ILE* 4.1 10.5 - - + +
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Residues in contact with SER 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C SER 3.1 8.1 + - - -
301C LEU 3.0 0.4 - - - -
302C GLN* 1.3 80.0 - - - +
304C ALA* 1.3 57.9 + - - +
305C TRP* 3.7 4.0 + - - -
306C MET* 5.3 0.7 + - - +
307C GLU* 4.5 10.7 + - - +
377C SER* 3.6 34.8 + - - +
379C SER* 3.4 27.0 + - - -
428C SER* 5.2 3.3 + - - -
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Residues in contact with ALA 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU 3.1 15.9 + - - +
301C LEU 3.0 1.8 + - - -
303C SER* 1.3 75.1 - - - +
305C TRP* 1.3 70.2 + - - +
306C MET 3.3 2.2 - - - -
307C GLU* 3.2 14.3 + - + +
308C ILE* 3.0 24.2 + - + +
373C ALA 3.7 5.6 - - - +
374C LEU* 3.6 32.5 - - + +
377C SER* 3.6 10.3 - - - -
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Residues in contact with TRP 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 3.7 29.8 - - + -
279C ILE* 4.9 4.7 - - + +
301C LEU* 2.8 20.3 + - + +
302C GLN 3.2 28.3 + - - -
303C SER 4.3 3.2 + - - -
304C ALA* 1.3 80.1 - - - +
306C MET* 1.3 92.6 + - + +
308C ILE* 2.8 18.6 + - - +
309C LEU* 3.1 18.6 + - + +
432C VAL* 4.4 27.3 - - + +
435C PHE* 6.0 3.1 - + + -
436C TYR* 4.9 10.1 - + - -
502C OHT 4.0 46.4 - + - -
1320I LEU* 3.3 39.0 - - + +
1324I ILE* 5.3 1.6 - - + -
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Residues in contact with MET 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C SER 5.3 1.0 + - - +
304C ALA 3.3 0.6 - - - -
305C TRP* 1.3 99.1 - - + +
307C GLU* 1.3 63.7 + - - +
309C LEU* 3.1 9.4 + - - +
310C ILE* 2.9 45.0 + - + +
428C SER* 3.6 17.5 - - - +
431C ALA* 3.3 43.1 - - + +
432C VAL* 3.6 19.3 - - + +
435C PHE* 5.3 2.9 - - + -
502C OHT 3.8 42.6 - - + -
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Residues in contact with GLU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C SER 4.5 7.9 - - - +
304C ALA* 3.2 17.7 + - - +
306C MET* 1.3 75.2 - - - +
308C ILE* 1.3 57.6 + - - +
310C ILE* 3.4 1.2 + - - -
311C LEU* 2.8 33.0 + - - +
373C ALA* 3.7 31.6 - - + +
377C SER* 5.2 2.6 - - - +
421C LEU* 5.1 2.9 - - - +
424C LEU* 3.9 29.7 - - + +
425C ARG* 2.7 47.3 + - - +
428C SER* 3.5 26.9 + - - +
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 3.5 37.9 - - + +
282C TRP* 4.3 15.3 - - + -
301C LEU* 5.1 1.8 - - + -
304C ALA* 3.0 27.7 + - + +
305C TRP* 2.8 13.5 + - - +
307C GLU* 1.3 70.9 - - - +
309C LEU* 1.3 61.0 - - - +
311C LEU* 3.4 7.4 + - - +
312C GLY* 3.1 18.7 + - - -
370C LYS* 3.8 39.9 - - + +
373C ALA* 4.9 4.5 - - + -
374C LEU* 4.0 33.2 - - + +
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Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ALA* 3.8 28.0 - - + +
275C GLU* 3.2 50.1 - - + +
276C LEU* 4.6 6.3 - - + -
279C ILE* 3.7 16.2 - - + -
305C TRP* 3.1 30.3 + - + +
306C MET* 3.6 9.4 - - - +
308C ILE* 1.3 75.6 - - - +
310C ILE* 1.3 62.8 + - - +
312C GLY* 3.2 11.3 + - - -
313C VAL 3.2 10.7 + - - -
502C OHT 3.4 38.0 + - + +
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Residues in contact with ILE 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C MET* 2.9 31.7 + - + +
307C GLU* 3.9 3.4 - - - +
309C LEU* 1.3 76.3 - - - +
311C LEU* 1.3 65.7 + - - +
313C VAL* 3.1 10.8 - - - +
314C VAL* 2.9 26.4 + - + +
349C ILE* 4.3 23.1 - - + -
352C LEU* 4.1 16.2 - - + -
424C LEU* 4.0 17.9 - - + -
427C THR* 4.2 8.1 - - + +
428C SER* 3.8 15.3 - - - +
431C ALA* 3.5 31.9 - - + -
502C OHT 4.4 11.9 - - + -
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLU 2.8 19.4 + - - +
308C ILE* 3.7 6.1 - - - +
310C ILE* 1.3 76.4 - - - +
312C GLY* 1.3 53.1 + - - +
314C VAL* 3.4 8.8 + - + +
315C TYR 2.8 29.7 + - - +
352C LEU* 5.5 0.2 - - + -
356C TYR* 4.0 33.4 - - + +
361C LEU* 5.4 3.6 - - + -
366C PHE* 3.6 21.2 - - + +
369C LEU* 4.0 15.7 - - + +
370C LYS* 3.6 37.5 - - + +
373C ALA* 5.1 0.9 - - + -
424C LEU* 4.0 25.6 - - + -
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Residues in contact with GLY 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLU* 5.7 0.7 - - - -
308C ILE 3.1 13.9 + - - -
309C LEU 3.5 4.9 - - - -
310C ILE 3.1 0.4 - - - -
311C LEU* 1.3 73.3 - - - +
313C VAL* 1.3 64.5 + - - +
315C TYR* 3.0 4.3 + - - +
316C ARG* 2.9 42.5 + - - +
366C PHE* 3.9 17.2 - - - -
370C LYS* 5.3 0.7 - - - -
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C LEU 3.2 7.4 + - - +
310C ILE* 3.1 26.5 - - + +
312C GLY* 1.3 73.0 - - - +
314C VAL* 1.3 52.9 + - - +
316C ARG* 3.3 21.5 - - - +
317C SER* 2.5 39.7 + - - +
324C LEU* 4.3 5.4 - - + -
325C VAL 3.3 25.8 - - - +
326C TYR* 3.4 41.1 - - + +
349C ILE* 4.4 16.2 - - + -
502C OHT 4.2 3.8 - - + +
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Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ILE* 2.9 23.1 + - + +
311C LEU* 3.4 10.1 - - + +
313C VAL* 1.3 73.8 - - - +
315C TYR* 1.3 69.7 + - - +
317C SER* 3.0 12.8 + - - -
318C LEU* 3.4 13.2 + - + +
349C ILE* 3.5 29.2 - - + +
352C LEU* 3.9 24.7 - - + +
353C VAL* 4.1 17.3 - - + +
356C TYR* 3.8 32.5 - - + -
361C LEU* 5.7 0.9 - - + -
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Residues in contact with TYR 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LEU 2.8 19.9 + - - +
312C GLY 3.8 1.8 - - - +
314C VAL* 1.3 73.9 - - - +
316C ARG* 1.3 70.0 + - + +
318C LEU* 3.2 38.3 + - + +
361C LEU* 3.8 28.8 + - + -
362C GLU* 4.2 0.6 - - - -
363C LYS* 3.4 42.3 + - + +
366C PHE* 3.7 54.5 - + + -
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Residues in contact with ARG 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C LYS* 6.0 7.6 - - - +
275C GLU* 4.0 13.2 + - - -
312C GLY* 2.9 32.7 + - - +
313C VAL* 3.3 26.0 - - - +
315C TYR* 1.3 82.8 - - + +
317C SER* 1.3 59.5 + - - +
318C LEU 3.3 0.7 + - - -
319C SER* 4.8 2.3 + - - -
320C PHE* 4.2 7.8 - - - -
325C VAL* 3.0 46.2 + - + +
326C TYR 2.8 26.3 + - - -
327C ALA* 4.3 3.9 - - - +
328C ASP 5.9 0.4 - - - +
366C PHE* 6.3 0.9 - - + -
502C OHT 3.4 16.8 + - - -
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Residues in contact with SER 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C VAL 2.5 23.9 + - - -
314C VAL 3.0 6.2 + - - -
316C ARG* 1.3 77.6 - - - +
318C LEU* 1.3 63.0 + - - +
319C SER 3.4 1.3 - - - -
320C PHE* 3.0 23.8 + - - +
323C GLU 3.6 15.5 - - - +
324C LEU* 3.3 17.6 - - - +
325C VAL* 2.8 27.7 + - - -
353C VAL* 4.0 13.1 - - - +
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C VAL* 3.4 9.5 + - + +
315C TYR* 3.2 44.4 + - + +
316C ARG 3.3 1.2 - - - -
317C SER* 1.3 76.1 - - - +
319C SER* 1.3 58.5 + - - +
353C VAL* 3.9 19.1 - - + -
356C TYR* 3.8 11.9 - - + +
357C LYS* 3.2 59.4 - - + +
361C LEU* 3.7 33.2 - - + +
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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