Contacts of the helix formed by residues 312 - 342 (chain A) in PDB entry 2RFQ
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 PRO 312 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A LEU* 3.6 21.1 - - + -
310A GLU* 3.5 24.0 - - + +
311A VAL* 1.3 89.5 - - + +
313A PHE* 1.3 66.3 + - - +
314A GLU* 4.2 20.2 - - + +
315A LEU* 3.0 25.9 + - + +
316A ARG* 3.2 9.3 + - - +
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLU* 4.7 1.6 + - - -
311A VAL 3.6 2.0 + - - -
312A PRO* 1.3 72.0 - - - +
314A GLU* 1.3 61.9 + - - +
316A ARG* 3.1 33.9 + - - +
317A LEU* 2.9 52.7 + - + +
386A ILE* 3.8 28.3 - - + -
391A VAL* 3.7 40.4 - - + -
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PRO* 3.2 18.4 - - + +
313A PHE* 1.3 77.9 - - - +
315A LEU* 1.3 63.4 + - - +
317A LEU* 3.3 14.1 + - + +
318A ARG* 2.8 72.1 + - - +
377A TYR* 5.3 0.5 - - - -
381A GLU* 6.0 2.0 - - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ASN* 4.0 19.3 - - + +
300A ASP* 4.0 15.7 - - + -
301A GLU* 3.6 34.1 - - + +
304A LEU* 3.7 29.4 - - + -
311A VAL* 4.1 4.7 - - + -
312A PRO* 3.0 13.9 + - + +
314A GLU* 1.3 90.8 - - - +
316A ARG* 1.3 60.4 + - - +
318A ARG* 3.5 29.4 - - - +
319A ALA* 2.8 27.9 + - - +
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER* 5.4 11.3 + - - -
229A PRO* 3.8 28.0 - - + +
232A THR* 4.6 1.2 + - - +
301A GLU* 4.0 7.2 - - - +
311A VAL* 3.8 32.0 + - + -
312A PRO 3.2 5.7 + - - +
313A PHE* 3.1 36.4 + - - +
315A LEU* 1.3 75.8 - - - +
317A LEU* 1.3 61.6 + - - +
319A ALA* 3.4 3.7 + - - +
320A ARG* 3.1 26.7 + - - +
391A VAL* 2.8 53.2 + - + +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 2.9 40.7 + - + +
314A GLU* 3.5 13.7 - - - +
316A ARG* 1.3 73.9 - - - +
318A ARG* 1.3 64.4 + - - +
320A ARG* 3.3 4.7 + - - +
321A ARG* 3.0 23.0 + - - +
376A MSE 3.6 46.1 - - + +
377A TYR* 3.9 20.9 - - + +
380A GLY* 4.2 16.4 - - - -
381A GLU* 6.1 1.1 - - - +
386A ILE* 3.9 14.8 - - + -
391A VAL* 3.9 10.3 - - + -
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ASN* 3.7 19.0 - - - +
300A ASP* 4.8 7.1 + - - -
314A GLU* 2.8 53.0 + - - +
315A LEU* 3.5 34.6 - - - +
317A LEU* 1.3 76.9 - - - +
319A ALA* 1.3 63.3 + - - +
321A ARG* 3.3 38.8 + - - +
322A ASP* 2.9 29.3 + - - -
377A TYR* 3.9 10.3 - - + -
288D ASP* 5.6 4.0 + - - -
292D ARG* 4.8 5.3 - - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 3.4 32.5 - - + +
297A ASN* 3.7 24.5 - - + +
301A GLU* 3.4 8.3 - - - +
315A LEU 2.8 16.0 + - - +
316A ARG 3.5 3.4 - - - +
318A ARG* 1.3 76.9 - - - +
320A ARG* 1.3 57.7 + - - +
322A ASP* 3.8 1.0 - - - +
323A GLN* 2.9 34.1 + - - +
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Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLY 3.4 26.9 - - - +
235A PRO* 4.1 5.9 - - - +
316A ARG 3.1 13.2 + - - +
317A LEU 3.8 6.5 - - - +
319A ALA* 1.3 80.0 - - + +
321A ARG* 1.3 63.2 + - - +
323A GLN* 2.9 24.7 + - - +
324A VAL* 3.1 36.0 + - - +
366A ALA 5.1 0.2 + - - -
367A ALA 3.0 21.8 + - - -
369A ASP 4.6 1.4 + - - -
372A ARG* 4.0 20.8 - - - +
373A ALA* 3.6 27.8 - - + +
376A MSE 3.8 17.5 - - + +
388A ASP* 5.2 0.2 + - - -
390A MSE 2.9 51.4 + - - +
391A VAL* 4.1 4.7 - - - -
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU 3.0 13.9 + - - +
318A ARG* 3.3 34.7 + - - +
320A ARG* 1.3 78.2 - - - +
322A ASP* 1.3 95.2 + - - +
324A VAL* 3.4 5.2 - - - +
325A ARG* 3.3 15.8 + - - +
373A ALA* 4.3 5.5 + - - +
374A TYR* 3.5 15.2 - - + -
377A TYR* 3.1 38.5 + - + -
281D ALA* 3.4 26.2 - - + +
284D SER* 2.9 35.6 + - - -
285D SER* 3.6 13.7 - - - +
288D ASP* 4.2 16.2 - - - +
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLN* 3.5 36.3 + - + +
294A LEU* 5.2 1.5 + - - -
297A ASN* 3.0 32.5 + - - +
318A ARG 2.9 11.5 + - - +
321A ARG* 1.3 107.7 + - - +
323A GLN* 1.3 55.1 + - - +
325A ARG* 3.7 5.6 - - - +
326A ALA* 2.8 34.5 + - - +
285D SER* 2.7 24.3 + - - -
288D ASP* 4.1 2.6 - - - +
292D ARG* 5.3 0.3 + - - -
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Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PRO* 3.2 33.9 + - + +
236A THR* 4.1 5.6 - - - +
239A SER* 2.9 39.8 + - - +
294A LEU* 3.7 25.3 - - + +
319A ALA 2.9 19.8 + - - +
320A ARG* 2.9 29.7 + - - +
322A ASP* 1.3 74.4 - - - +
324A VAL* 1.3 69.9 + - - +
326A ALA* 3.2 9.9 + - - +
327A THR 3.2 4.5 + - - -
367A ALA 2.9 22.6 + - - -
368A ASN* 3.6 8.3 - - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ARG* 3.1 35.7 + - - +
321A ARG 3.4 4.9 - - - +
323A GLN* 1.3 79.9 - - - +
325A ARG* 1.3 65.1 + - - +
327A THR* 3.3 8.8 + - - +
328A GLY* 3.1 17.3 + - - -
367A ALA 3.5 11.0 - - - +
368A ASN* 3.9 9.3 - - - +
369A ASP 3.6 15.7 - - - +
370A PRO* 3.6 24.7 - - + +
373A ALA* 3.7 12.6 - - + -
374A TYR* 3.4 28.4 + - + -
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Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ARG 3.3 12.4 + - - +
322A ASP 3.7 5.2 - - - +
323A GLN 3.1 0.6 - - - -
324A VAL* 1.3 83.6 - - - +
326A ALA* 1.3 49.1 - - - +
328A GLY* 3.1 4.1 + - - +
329A ARG* 2.7 58.4 + - + +
374A TYR* 2.9 43.2 + - - +
282D GLU* 3.7 32.7 + - - +
285D SER* 3.3 28.3 - - - +
286D ASP* 2.8 37.6 + - - -
336D LYS* 4.8 5.5 - - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A SER* 4.8 0.7 - - - -
243A VAL* 4.2 11.7 - - + -
290A ALA* 3.7 40.0 - - + +
293A GLN* 6.0 0.4 - - - +
294A LEU* 4.3 12.6 - - + -
322A ASP 2.8 20.8 + - - +
323A GLN 3.5 6.5 - - - +
325A ARG* 1.3 69.5 - - - +
327A THR* 1.3 67.0 + - - +
329A ARG* 3.3 3.3 + - - +
330A ALA* 2.9 25.8 + - - +
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Residues in contact with THR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A SER* 2.7 35.2 + - - -
242A ILE* 3.9 13.3 - - + +
243A VAL* 5.3 0.4 - - - -
323A GLN 3.2 2.2 + - - -
324A VAL 3.5 7.9 - - - -
326A ALA* 1.3 79.9 - - - +
328A GLY* 1.3 63.6 + - - +
330A ALA* 3.2 5.9 + - - +
331A ILE* 3.0 43.7 + - + +
363A ARG* 4.0 10.5 - - - -
368A ASN* 2.8 34.4 + - + +
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Residues in contact with GLY 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL 3.1 10.4 + - - -
325A ARG* 3.1 8.5 + - - -
327A THR* 1.3 78.5 - - - +
329A ARG* 1.3 55.0 + - - +
331A ILE* 3.4 6.3 + - - +
332A SER* 2.9 31.3 + - - -
363A ARG* 5.8 4.3 - - - -
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASP* 3.6 37.3 - - + +
289A ALA* 4.2 4.9 - - - +
290A ALA* 3.9 15.0 - - + +
293A GLN* 3.0 27.2 + - - -
325A ARG* 2.7 39.6 + - + +
326A ALA* 3.7 4.5 - - - +
328A GLY* 1.3 71.9 - - - +
330A ALA* 1.3 60.8 + - - +
332A SER* 3.5 5.7 + - - -
333A SER* 2.7 34.1 + - - -
285D SER* 3.0 21.0 + - - -
286D ASP* 2.9 29.7 + - - -
289D ALA* 4.0 9.3 - - - +
329D ARG* 3.8 19.4 - - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.8 20.6 - - + +
243A VAL* 4.0 12.8 - - + +
246A ALA* 3.8 23.0 - - + +
287A ILE* 4.8 3.6 - - + -
290A ALA* 4.8 2.6 - - + +
326A ALA 2.9 17.5 + - - +
327A THR 3.6 4.5 - - - +
329A ARG* 1.3 77.7 - - - +
331A ILE* 1.3 58.2 + - - +
333A SER* 3.3 4.9 + - - -
334A ILE* 3.0 34.5 + - - +
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 4.1 4.7 - - + -
327A THR* 3.0 31.8 + - + +
328A GLY* 3.9 4.5 - - - +
330A ALA* 1.3 72.9 - - - +
332A SER* 1.3 60.5 + - - +
334A ILE* 3.2 6.6 + - + +
335A ASP* 2.8 32.4 + - - +
359A ALA* 3.6 24.5 - - + +
360A HIS* 3.3 38.8 - - + +
363A ARG* 3.4 40.4 - - + -
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASP* 5.4 1.3 + - - -
328A GLY 2.9 18.7 + - - -
329A ARG* 3.8 6.5 - - - -
331A ILE* 1.3 76.2 - - - +
333A SER* 1.3 57.7 + - - +
335A ASP* 3.4 10.1 + - - +
336A LYS* 2.8 58.4 + - - +
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA* 3.5 16.9 + - - +
286A ASP* 3.4 24.4 + - - +
287A ILE* 3.6 26.6 - - - +
329A ARG 2.7 22.8 + - - -
330A ALA 3.6 4.5 - - - -
331A ILE 3.2 0.2 - - - -
332A SER* 1.3 75.0 - - - +
334A ILE* 1.3 64.4 + - - +
336A LYS* 3.2 8.8 + - - +
337A LEU* 3.1 29.1 + - - +
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Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE 4.6 1.3 - - - +
245A MSE 4.2 6.1 - - + +
246A ALA* 3.7 35.7 - - + +
249A ALA* 4.0 16.2 - - + -
287A ILE* 5.9 0.2 - - + -
330A ALA 3.0 22.9 + - - +
331A ILE* 3.7 4.3 - - + +
333A SER* 1.3 74.4 - - - +
335A ASP* 1.3 59.4 + - - +
337A LEU* 3.1 10.3 + - + +
338A PHE* 2.8 29.0 + - + +
352A LEU* 4.7 5.2 - - + -
355A PHE 4.2 4.7 - - - +
356A TRP* 3.6 37.5 - - + +
359A ALA* 3.5 28.5 - - + -
360A HIS* 5.9 0.2 - - + -
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Residues in contact with ASP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 2.8 23.0 + - - +
332A SER* 3.4 9.4 - - - +
333A SER 3.2 0.2 - - - -
334A ILE* 1.3 76.9 - - - +
336A LYS* 1.3 55.7 - - + +
338A PHE* 3.9 1.8 - - - +
339A GLU* 2.9 34.2 + - - +
356A TRP* 3.1 20.0 + - - +
360A HIS* 2.7 38.0 + - - -
335B ASP* 4.8 10.1 - - - +
360B HIS* 5.9 4.5 - - + -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 4.4 25.7 - - + +
282A GLU* 3.5 45.5 - - + +
283A ALA* 4.4 7.6 - - + +
286A ASP* 4.4 13.1 + - - -
332A SER* 2.8 43.9 + - - +
333A SER* 3.2 10.2 + - - +
335A ASP* 1.3 74.7 - - - +
337A LEU* 1.3 58.2 + - - +
339A GLU* 3.8 10.2 - - - +
340A SER* 2.9 30.5 + - - -
325D ARG* 4.7 3.3 - - - +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ALA 4.8 1.6 - - - +
249A ALA* 4.1 4.5 - - + +
250A TYR* 3.5 45.5 - - + +
253A HIS* 3.5 36.5 - - + +
279A ARG* 4.4 5.8 - - + +
280A ILE* 4.2 12.6 - - + +
283A ALA* 3.8 19.3 - - + -
287A ILE* 4.9 2.0 - - + -
333A SER 3.1 18.6 + - - +
334A ILE* 3.1 8.5 + - - +
336A LYS* 1.3 75.3 - - - +
338A PHE* 1.3 60.5 + - - +
340A SER* 3.3 5.1 + - - -
341A SER* 2.9 30.8 + - - -
352A LEU* 4.1 9.6 - - + -
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Residues in contact with PHE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE 2.8 20.0 + - - +
335A ASP* 3.9 3.1 - - - +
337A LEU* 1.3 71.9 - - - +
339A GLU* 1.3 66.0 + - + +
341A SER* 3.3 3.3 + - - -
342A GLY* 3.3 17.7 + - - +
345A ALA* 3.7 37.2 - - + +
346A LEU* 3.9 20.6 - - + -
352A LEU* 3.8 17.2 - - + +
353A GLN* 3.9 20.2 - - + -
356A TRP* 3.5 62.4 - + + -
182B VAL* 4.5 4.5 - - + -
360B HIS* 4.1 19.5 - + + -
----------------------------------------------------------
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 5.6 4.9 - - - -
335A ASP 2.9 18.4 + - - +
336A LYS* 3.8 9.0 - - - +
338A PHE* 1.3 81.9 - - + +
340A SER* 1.3 62.8 + - - +
342A GLY* 3.3 12.8 + - - -
360B HIS* 6.0 5.2 - - + +
363B ARG* 2.8 57.4 + - + +
370B PRO* 5.1 1.4 - - - +
----------------------------------------------------------
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Residues in contact with SER 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A HIS* 4.2 13.5 + - - -
257A GLN* 5.8 0.7 - - - -
276A ALA* 3.9 28.2 - - - +
279A ARG* 4.4 16.7 - - - +
336A LYS 2.9 18.9 + - - -
337A LEU* 3.6 6.3 - - - -
339A GLU* 1.3 78.3 - - - +
341A SER* 1.3 63.7 + - - +
342A GLY* 3.3 1.4 + - - -
----------------------------------------------------------
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A HIS* 3.9 13.3 + - - -
257A GLN* 3.7 12.5 + - - +
337A LEU 2.9 16.4 + - - -
338A PHE 3.6 1.3 - - - -
339A GLU 3.3 0.4 - - - -
340A SER* 1.3 76.5 - - - +
342A GLY* 1.3 63.5 + - - +
343A ALA 3.7 1.0 + - - -
344A THR* 3.3 31.0 - - - +
345A ALA* 3.4 20.2 - - - +
352A LEU* 3.7 12.5 - - - +
392A 1PS 4.1 5.0 - - - +
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Residues in contact with GLY 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PHE* 3.3 9.2 + - - +
339A GLU* 3.3 9.2 + - - -
340A SER 3.2 3.9 - - - -
341A SER* 1.3 77.3 - - - +
343A ALA* 1.3 66.5 + - - +
345A ALA* 3.0 18.0 + - - +
346A LEU* 3.8 2.8 + - - +
364B VAL* 3.5 24.6 - - - +
----------------------------------------------------------
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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