Contacts of the helix formed by residues 293 - 322 (chain A) in PDB entry 3PRJ
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 LEU 293 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A CYS* 2.8 17.9 + - + +
289A GLU 4.4 0.4 + - - -
291A LEU* 4.0 17.0 - - + +
292A ASN* 1.3 84.8 - - - +
294A PRO* 1.3 64.8 - - - +
295A GLU* 3.2 5.6 + - - -
296A VAL* 3.3 16.7 + - + -
297A ALA* 3.1 20.3 + - - +
239B ALA* 4.1 15.0 - - + +
240B LEU* 3.9 38.8 - - + +
243B ALA* 4.3 13.5 - - + -
309B TYR* 3.6 21.1 - - - +
313B ARG* 5.7 0.9 - - - -
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Residues in contact with PRO 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A CYS 5.2 0.2 - - - +
289A GLU* 5.4 8.7 - - + +
292A ASN* 3.4 18.6 - - - +
293A LEU* 1.3 87.1 - - - +
295A GLU* 1.3 75.8 + - - +
297A ALA* 3.2 8.4 + - + +
298A ARG* 2.9 54.0 + - - +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 4.2 1.0 - - - -
294A PRO* 1.3 98.0 - - - +
296A VAL* 1.3 62.4 + - - +
298A ARG* 3.7 24.6 + - - +
299A TYR* 3.3 16.5 + - - +
302B GLN* 4.3 1.9 - - - +
305B ASP 5.8 0.4 - - - +
306B MET* 3.5 11.3 - - + +
309B TYR* 3.3 61.8 + - + -
312B ARG* 4.5 10.5 + - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A CYS* 3.5 24.2 - - - -
293A LEU* 3.3 18.3 + - + +
294A PRO 3.3 0.2 - - - -
295A GLU* 1.3 77.2 - - - +
297A ALA* 1.3 63.9 + - - +
299A TYR* 3.1 16.5 + - - +
300A TRP* 3.2 25.9 + - + +
236B SER* 3.7 31.9 - - - +
239B ALA* 4.0 17.5 - - + -
240B LEU* 5.2 4.5 - - + -
306B MET* 3.6 15.7 - - + -
309B TYR* 4.2 7.2 - - + -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A VAL* 3.5 25.6 - - + +
288A CYS* 3.9 17.9 - - + +
289A GLU* 4.2 20.0 - - + +
293A LEU 3.1 11.5 + - - +
294A PRO* 3.4 12.8 - - + +
296A VAL* 1.3 80.0 - - - +
298A ARG* 1.3 62.4 + - - +
300A TRP* 3.5 1.2 + - - -
301A GLN* 3.1 23.1 + - - +
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PRO* 2.9 40.7 + - - +
295A GLU* 3.8 31.6 + - - +
297A ALA* 1.3 71.7 - - - +
299A TYR* 1.3 66.3 + - - +
301A GLN* 3.7 9.8 + - + +
302A GLN* 3.6 22.9 + - - +
302B GLN* 3.9 22.4 - - - +
305B ASP* 6.1 0.2 - - - -
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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
----------------------------------------------------------
229A GLN* 3.3 19.2 + - - -
295A GLU 3.3 14.6 + - - +
296A VAL 3.1 10.0 + - - +
298A ARG* 1.3 77.9 - - - +
300A TRP* 1.3 84.9 + + - +
302A GLN* 3.4 18.4 + - - +
303A VAL* 4.5 2.9 + - - +
229B GLN* 3.2 14.8 + - + +
232B SER* 3.7 6.6 - - - -
233B SER* 2.7 51.1 + - - -
236B SER* 4.1 5.6 - - - -
302B GLN* 3.3 52.3 + - + +
303B VAL* 4.2 4.7 - - + -
306B MET* 3.7 22.0 - - + -
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Residues in contact with TRP 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA* 3.6 33.7 - - + -
226A PHE* 3.8 29.4 - + - -
229A GLN* 3.8 21.8 - - + -
281A VAL* 3.5 12.3 - - + +
284A LEU* 3.6 30.3 - - + +
285A VAL* 4.3 9.6 - - + -
288A CYS* 5.4 0.7 - - - -
296A VAL* 3.2 32.3 + - + +
297A ALA* 4.3 2.9 - - - +
299A TYR* 1.3 79.7 - + - +
301A GLN* 1.3 66.2 + - - +
302A GLN 3.0 2.5 - - - -
303A VAL* 2.9 36.7 + - + +
233B SER* 3.6 26.9 - - - -
236B SER* 3.0 25.6 + - - -
237B ILE* 4.0 11.6 - - + +
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Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 5.5 2.9 + - - -
281A VAL* 4.8 2.5 - - - -
282A LEU* 4.4 13.1 - - - +
285A VAL* 3.7 27.9 - - + +
297A ALA 3.1 18.8 + - - +
298A ARG* 3.7 11.7 - - + +
299A TYR 3.3 0.2 - - - -
300A TRP* 1.3 76.1 - - - +
302A GLN* 1.3 60.8 + - - +
304A ILE* 3.1 31.4 + - - +
305A ASP* 3.1 39.1 + - - +
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Residues in contact with GLN 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ARG 3.6 7.0 + - - +
299A TYR 3.4 10.9 + - - +
300A TRP 3.0 0.8 + - - -
301A GLN* 1.3 80.7 - - - +
303A VAL* 1.3 61.7 + - + +
305A ASP* 3.6 25.8 + - - +
306A MET* 3.0 27.9 + - - +
295B GLU 4.3 1.9 - - - +
298B ARG* 4.0 24.7 + - - +
299B TYR* 3.3 46.6 + - + +
302B GLN* 3.5 30.4 - - + +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA 5.0 0.2 - - - +
228A ALA* 3.8 35.0 - - + -
229A GLN* 3.9 24.5 - - + +
232A SER* 2.8 36.7 + - - +
272A PHE* 4.0 7.1 - - + -
281A VAL* 4.5 9.9 - - + -
299A TYR 5.0 1.6 - - - +
300A TRP* 2.9 37.1 + - + +
302A GLN* 1.3 77.6 - - - +
304A ILE* 1.3 62.2 + - - +
307A ASN* 3.1 12.0 + - - +
299B TYR* 4.2 6.1 - - + -
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 4.3 9.4 - - + -
278A GLN* 3.9 37.0 - - + +
281A VAL* 3.6 38.1 - - + -
282A LEU* 4.3 18.4 - - + -
301A GLN* 3.1 26.1 + - - +
303A VAL* 1.3 75.5 - - - +
305A ASP* 1.3 56.0 + - - +
307A ASN* 3.2 6.7 + - + +
308A ASP* 2.8 51.3 + - - +
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN* 3.1 39.1 + - - +
302A GLN* 3.6 30.3 + - - +
304A ILE* 1.3 78.4 - - - +
306A MET* 1.3 57.6 + - - +
308A ASP* 3.5 9.5 + - - +
309A TYR* 2.9 28.8 + - - +
312A ARG* 5.2 1.4 + - - -
295B GLU* 5.8 0.6 - - - +
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Residues in contact with MET 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 3.3 30.3 - - - +
235A ASN* 4.8 5.4 - - + -
236A SER* 3.6 30.1 - - - +
302A GLN* 3.0 19.0 + - - +
303A VAL 3.8 4.0 - - - +
305A ASP* 1.3 74.9 - - - +
307A ASN* 1.3 55.0 + - - +
309A TYR* 3.1 20.5 + - + +
310A GLN* 2.6 36.2 + - - +
295B GLU* 3.5 28.0 - - + +
296B VAL* 3.7 10.3 - - + -
299B TYR* 3.6 24.5 - - + -
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Residues in contact with ASN 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 3.7 2.3 + - - -
235A ASN* 4.3 5.1 + - - +
271A GLY* 3.3 9.3 - - - -
272A PHE* 3.0 74.3 + - + +
278A GLN* 5.3 4.4 + - - +
303A VAL 3.1 12.7 + - - +
304A ILE* 3.4 8.9 - - - +
306A MET* 1.3 80.0 - - - +
308A ASP* 1.3 63.6 + - - +
310A GLN* 3.1 14.9 + - - +
311A ARG* 3.1 32.3 + - - +
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Residues in contact with ASP 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLN* 5.1 4.3 - - - +
304A ILE* 2.8 41.1 + - - +
305A ASP* 3.6 11.4 - - - +
307A ASN* 1.3 74.7 + - - +
309A TYR* 1.3 62.6 + - - +
311A ARG* 3.3 21.9 + - - +
312A ARG* 3.1 39.7 + - - +
352A TYR* 5.9 1.6 - - - -
356A TYR* 5.0 2.1 + - - -
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Residues in contact with TYR 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ALA* 4.2 11.7 - - + +
305A ASP 2.9 15.3 + - - +
306A MET* 3.4 25.1 - - - +
308A ASP* 1.3 76.3 - - - +
310A GLN* 1.3 64.2 + - - +
311A ARG 3.2 0.2 + - - -
312A ARG* 3.3 22.3 + - + +
313A ARG* 2.9 65.3 + - + +
293B LEU* 3.7 22.9 - - - +
295B GLU* 3.3 56.4 + - + -
296B VAL* 4.2 7.9 - - + -
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Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASN* 3.2 34.5 + - + +
238A SER* 3.2 19.7 + - - -
269A SER 2.8 30.0 + - - +
270A VAL* 3.6 10.3 - - - +
271A GLY* 4.8 0.9 - - - -
306A MET* 2.6 18.5 + - - +
307A ASN* 3.3 13.7 - - - +
309A TYR* 1.3 78.1 - - - +
311A ARG* 1.3 62.0 + - - +
313A ARG* 2.3 32.9 + - - +
314A PHE* 3.3 20.8 + - - +
462A ILE* 3.7 12.6 - - - +
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL 3.3 19.1 - - - +
271A GLY* 4.6 0.4 - - - -
272A PHE 3.0 24.3 + - - -
273A GLY* 4.2 0.2 - - - -
278A GLN* 4.3 12.3 + - - -
307A ASN* 3.1 28.0 + - - +
308A ASP* 3.6 18.9 + - - +
310A GLN* 1.3 72.3 - - - +
312A ARG* 1.3 62.3 + - - +
314A PHE* 3.2 5.1 + - - +
315A ALA* 2.9 25.7 + - - +
347A GLU* 3.1 24.5 + - - +
349A SER* 2.9 25.0 + - - +
352A TYR* 3.3 47.7 - - + -
353A ILE* 3.5 19.0 - - + +
356A TYR* 4.9 10.1 - - + +
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP 5.2 1.0 + - - -
308A ASP* 3.1 37.0 + - - +
309A TYR* 3.8 30.4 - - + +
311A ARG* 1.3 78.1 - - - +
313A ARG* 1.3 58.7 + - - +
315A ALA* 3.4 7.5 + - - +
316A SER* 2.8 28.2 + - - -
356A TYR* 3.6 34.5 + - + +
295B GLU* 4.3 12.1 + - - +
98C MET* 4.4 13.6 - - + +
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A SER* 3.1 20.4 + - - -
239A ALA* 3.7 19.2 - - - +
242A GLU* 2.6 43.4 + - - +
309A TYR* 2.9 58.0 + - + +
310A GLN* 2.3 34.5 + - - +
312A ARG* 1.3 74.2 - - - +
314A PHE* 1.3 66.4 + - - +
316A SER* 3.2 8.1 + - - -
317A ARG* 2.9 30.8 + - + +
462A ILE* 5.1 2.9 - - - +
293B LEU* 5.8 1.1 - - - -
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 3.4 27.1 - - + -
310A GLN 3.3 10.1 + - - +
311A ARG 3.2 8.4 + - - +
313A ARG* 1.3 80.5 - - - +
315A ALA* 1.3 62.6 + - - +
317A ARG* 3.3 20.4 + - + +
318A ILE* 3.3 39.5 + - + +
353A ILE* 3.9 11.9 - - + -
412A VAL* 3.9 11.7 - - + -
413A ILE 5.0 0.9 - - - -
414A CYS* 5.4 1.1 - - - -
439A PHE* 3.8 30.7 - + + -
440A ASP 4.4 2.9 - - - -
441A GLY* 3.6 26.0 - - - -
460A GLU 5.3 0.2 - - - -
461A THR* 5.3 1.8 - - - -
462A ILE* 3.6 36.8 - - + -
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG 2.9 13.0 + - - +
312A ARG* 3.6 9.0 - - - +
314A PHE* 1.3 77.7 - - - +
316A SER* 1.3 56.5 + - - +
318A ILE* 3.1 13.6 + - - +
319A ILE* 3.0 32.8 + - + +
353A ILE* 4.3 12.3 - - + +
356A TYR* 3.9 37.7 - - + -
357A LEU* 4.7 2.5 - - + +
98C MET* 5.4 0.9 - - + -
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Residues in contact with SER 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG 2.8 15.9 + - - -
313A ARG* 3.2 9.4 + - - -
315A ALA* 1.3 76.6 - - - +
317A ARG* 1.3 58.9 + - - +
319A ILE* 3.8 11.8 - - - +
320A ASP* 2.8 35.5 + - - +
98C MET* 4.0 23.9 - - - +
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU* 3.3 33.9 + - - +
313A ARG* 2.9 24.0 + - + +
314A PHE* 3.3 21.2 - - + +
315A ALA 3.2 0.2 - - - -
316A SER* 1.3 74.2 - - - +
318A ILE* 1.3 64.4 + - - +
320A ASP* 3.3 5.9 + - - +
321A SER* 3.1 28.1 + - - -
439A PHE* 4.2 10.5 - - + -
460A GLU* 3.3 42.7 + - - +
461A THR 2.6 33.7 + - - +
462A ILE* 4.0 3.6 - - - +
464A LYS 4.2 7.5 + - - -
466A VAL* 4.6 23.5 - - - +
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.6 37.9 - - + +
315A ALA* 3.1 8.4 + - - +
317A ARG* 1.3 76.3 - - - +
319A ILE* 1.3 64.2 + - - +
320A ASP 3.1 0.7 + - - -
321A SER 3.2 4.5 + - - -
322A LEU* 3.1 36.8 - - + +
331A ILE* 5.0 4.0 - - + -
353A ILE* 4.3 10.5 - - + -
357A LEU* 4.1 20.0 - - + -
410A ALA* 5.2 2.0 - - + -
412A VAL* 3.8 28.9 - - + -
439A PHE* 3.6 40.8 - - + -
----------------------------------------------------------
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Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA* 3.0 26.6 + - + +
316A SER* 4.0 10.5 - - - +
317A ARG 3.4 0.2 - - - -
318A ILE* 1.3 74.8 - - - +
320A ASP* 1.3 55.5 + - - +
322A LEU* 3.3 7.9 + - - +
323A PHE 3.1 3.3 + - - -
324A ASN* 2.6 60.4 + - - +
325A THR 4.6 1.1 - - - +
326A VAL* 4.9 8.7 - - + -
356A TYR* 4.7 6.1 - - + +
357A LEU* 4.1 18.8 - - + -
360A GLU* 3.8 41.5 - - + +
98C MET* 4.4 15.5 - - + -
----------------------------------------------------------
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Residues in contact with ASP 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A SER* 2.8 22.9 + - - +
317A ARG* 3.6 6.9 - - - +
318A ILE 3.1 0.4 - - - -
319A ILE* 1.3 73.1 - - - +
321A SER* 1.3 54.2 + - - +
322A LEU 2.8 5.2 + - - -
323A PHE* 2.4 32.8 + - - +
324A ASN* 4.3 14.7 + - - +
135C ARG* 4.7 15.1 + - - -
142C ARG* 4.5 2.0 + - - -
----------------------------------------------------------
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 3.1 11.3 + - - -
318A ILE 3.8 0.7 - - - -
320A ASP* 1.3 76.3 - - - +
322A LEU* 1.3 59.8 + - - +
323A PHE* 3.3 2.9 + - - -
437A PHE* 3.5 33.2 - - - -
439A PHE* 3.6 26.8 - - - -
460A GLU* 3.1 23.9 + - - -
142C ARG* 3.6 21.0 + - - +
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 3.1 25.5 + - + +
319A ILE 3.6 8.1 - - - +
320A ASP 2.8 1.0 - - - -
321A SER* 1.3 87.5 - - - +
323A PHE* 1.3 69.7 + - - +
324A ASN 3.2 0.7 - - - -
325A THR* 3.0 24.4 - - - +
326A VAL* 3.0 28.5 - - + -
329A LYS* 3.6 24.2 + - + +
331A ILE* 4.2 18.2 - - + -
409A HIS* 5.1 8.3 - - + -
410A ALA* 5.0 3.6 - - + -
437A PHE* 4.2 17.9 - - + -
439A PHE* 4.7 3.1 - - + -
110C GLU* 3.8 0.8 - - - +
----------------------------------------------------------
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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