Contacts of the helix formed by residues 300 - 330 (chain H) in PDB entry 6V3O
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 THR 300 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293H ARG* 3.9 2.2 - - - -
297H PRO 3.7 17.7 - - - +
298H ARG* 3.2 9.0 + - - +
299H VAL* 1.3 73.7 - - - +
301H PRO* 1.3 76.8 - - + +
302H GLU* 3.6 9.8 + - - +
303H VAL* 3.3 25.4 + - + +
304H THR* 3.2 23.4 + - - -
513H ASP* 4.5 7.4 - - - +
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Residues in contact with PRO 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293H ARG* 4.3 6.5 - - - +
300H THR* 1.3 88.7 - - - +
302H GLU* 1.3 57.0 + - - +
304H THR* 3.3 7.3 + - - +
305H ARG 3.0 21.5 + - - -
513H ASP* 3.9 28.0 - - - +
516H GLY* 3.7 13.0 - - - +
517H ALA* 3.6 22.4 - - - +
520H VAL* 3.6 30.3 - - + +
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Residues in contact with GLU 302 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H GLN* 5.2 2.4 + - - -
300H THR* 3.2 8.4 + - - +
301H PRO* 1.3 76.3 - - - +
303H VAL* 1.3 63.3 + - - +
305H ARG* 3.2 20.9 + - - +
306H ASP* 2.8 60.3 + - - +
520H VAL* 5.3 0.7 - - - -
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Residues in contact with VAL 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H PRO* 3.8 28.0 - - + -
238H GLN* 3.6 31.9 - - - +
290H GLY* 4.1 17.7 - - - +
298H ARG 3.9 14.4 - - - +
299H VAL* 4.4 6.5 - - + -
300H THR* 3.3 26.1 + - + +
302H GLU* 1.3 79.3 - - - +
304H THR* 1.3 62.9 + - - +
306H ASP* 3.2 2.8 + - - +
307H VAL* 3.1 26.0 + - + +
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Residues in contact with THR 304 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H GLY 2.9 12.6 + - - +
293H ARG* 2.5 32.3 + - - +
299H VAL* 4.4 0.2 - - - +
300H THR 3.2 8.3 + - - -
301H PRO* 3.5 9.4 - - - -
302H GLU 3.2 0.6 - - - -
303H VAL* 1.3 74.7 - - - +
305H ARG* 1.3 64.3 + - - +
306H ASP 3.2 0.3 + - - -
307H VAL* 3.2 8.1 - - - +
308H CYS* 3.1 28.2 - - - -
453H LEU* 3.7 23.8 - - + -
455H ILE* 4.2 9.4 - - + -
520H VAL* 4.5 10.3 - - + -
521H LEU* 5.0 3.4 - - + -
529H PHE* 4.4 6.7 - - + -
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Residues in contact with ARG 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301H PRO 3.0 12.7 + - - +
302H GLU* 3.5 22.5 + - - +
304H THR* 1.3 76.3 - - - +
306H ASP* 1.3 74.9 + - - +
308H CYS* 3.6 2.4 + - - +
309H LEU* 3.3 46.0 + - + +
392H LEU* 3.1 33.3 + - - +
393H LEU* 4.0 12.9 + - - +
396H GLY* 4.3 15.5 + - - +
520H VAL* 4.1 11.9 - - + +
523H GLU* 5.1 11.0 - - - -
524H LEU* 4.1 27.3 - - + +
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Residues in contact with ASP 306 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H GLN* 3.1 33.7 + - + +
302H GLU* 2.8 44.3 + - - +
303H VAL 3.6 4.9 - - - +
304H THR 3.1 0.4 - - - -
305H ARG* 1.3 86.5 + - - +
307H VAL* 1.3 57.5 - - - +
309H LEU* 3.2 3.1 + - - +
310H LEU* 2.9 36.1 + - + +
393H LEU* 3.1 28.7 - - + +
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Residues in contact with VAL 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H PRO 4.4 1.3 - - - +
238H GLN* 4.4 16.8 - - + -
241H MET* 3.5 46.4 - - + +
289H MET 4.0 8.1 - - - +
290H GLY* 4.0 18.8 - - - -
303H VAL* 3.1 18.1 + - + +
304H THR* 3.2 21.3 - - - +
306H ASP* 1.3 75.8 - - - +
308H CYS* 1.3 57.3 + - - +
311H ALA* 3.0 28.4 + - - +
453H LEU* 4.0 15.5 - - + -
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Residues in contact with CYS 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304H THR 3.1 23.8 + - - +
305H ARG 4.1 3.4 - - - +
306H ASP 3.2 0.6 - - - -
307H VAL* 1.3 77.7 - - - +
309H LEU* 1.3 61.9 + - - +
311H ALA* 3.3 7.8 + - - +
312H ARG* 3.1 32.2 + - - +
449H SER* 6.3 0.2 - - - -
453H LEU* 3.9 18.6 - - - -
524H LEU* 4.3 14.1 - - + -
528H SER* 4.2 19.7 - - - +
529H PHE* 3.9 28.7 - - - -
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Residues in contact with LEU 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305H ARG* 3.3 49.9 + - + +
306H ASP 3.2 4.8 + - - +
308H CYS* 1.3 75.4 - - - +
310H LEU* 1.3 65.0 + - - +
312H ARG* 3.2 16.2 + - - +
313H MET* 3.2 27.1 + - - +
389H ALA* 4.0 15.8 - - + +
392H LEU* 4.0 25.4 - - + -
393H LEU* 3.8 35.2 - - + +
524H LEU* 4.9 14.6 - - + -
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Residues in contact with LEU 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H GLN* 4.4 18.2 - - + +
241H MET* 3.5 27.4 - - + -
242H ARG* 4.2 34.1 - - + +
306H ASP* 2.9 25.2 + - + +
309H LEU* 1.3 75.0 - - - +
311H ALA* 1.3 62.5 + - - +
313H MET* 3.1 16.9 + - + +
314H MET* 2.9 33.8 + - + +
393H LEU* 3.6 26.5 - - + -
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Residues in contact with ALA 311 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H MET* 4.4 6.2 - - + +
245H MET* 5.8 2.9 - - - -
307H VAL 3.0 19.4 + - - +
308H CYS* 3.5 9.2 - - - +
310H LEU* 1.3 76.5 - - - +
312H ARG* 1.3 57.0 + - - +
314H MET* 3.3 11.4 + - - +
315H ALA* 2.9 28.9 + - - +
449H SER* 3.4 29.0 - - - +
450H LEU* 4.5 3.1 - - + +
451H VAL* 5.1 9.4 - - + +
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Residues in contact with ARG 312 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H CYS* 3.1 21.6 + - - +
309H LEU* 3.7 18.4 - - - +
310H LEU 3.2 0.4 - - - -
311H ALA* 1.3 75.7 - - - +
313H MET* 1.3 62.1 + - - +
315H ALA* 3.6 1.9 + - - +
316H ALA* 3.2 23.2 + - - +
385H THR* 5.5 7.8 - - + +
386H ARG* 5.2 0.3 - - - -
388H ARG* 6.2 1.8 - - - +
389H ALA* 4.5 11.7 - - + -
448H LEU* 3.6 25.1 + - + +
449H SER* 3.8 18.4 + - - -
524H LEU* 5.9 1.3 - - - +
525H PRO* 3.6 21.9 - - - +
527H ASP* 2.8 35.2 + - - -
528H SER* 2.4 34.7 + - - +
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Residues in contact with MET 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H LEU 3.2 13.0 + - - +
310H LEU* 3.1 17.3 + - + +
312H ARG* 1.3 74.1 - - - +
314H MET* 1.3 65.1 + - + +
316H ALA* 3.1 11.7 + - - +
317H ASN* 3.2 20.9 + - - +
386H ARG* 3.9 21.3 - - + +
389H ALA* 3.7 17.0 - - + -
390H ARG* 3.6 59.7 - - + +
393H LEU* 4.6 17.3 - - - -
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Residues in contact with MET 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H ARG* 4.5 11.0 - - - +
241H MET* 3.7 34.1 - - + -
242H ARG* 4.2 22.4 - - + -
245H MET* 3.6 30.5 - - + +
310H LEU* 2.9 22.3 + - + +
311H ALA* 3.6 9.0 - - - +
313H MET* 1.3 76.0 - - + +
315H ALA* 1.3 63.7 + - - +
317H ASN* 3.4 4.5 + - - +
318H LEU* 3.2 29.3 + - + +
450H LEU* 4.0 12.8 - - + -
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Residues in contact with ALA 315 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H ALA 2.9 14.6 + - - +
312H ARG 3.9 1.6 - - - +
314H MET* 1.3 76.0 - - - +
316H ALA* 1.3 64.1 + - - +
318H LEU* 3.2 4.8 + - - +
319H TYR* 2.9 41.2 + - + -
448H LEU* 3.5 32.3 - - + +
450H LEU* 4.0 24.6 - - + +
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Residues in contact with ALA 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ARG 3.2 15.0 + - - +
313H MET 3.1 3.4 + - - +
315H ALA* 1.3 78.8 - - - +
317H ASN* 1.3 58.8 + - - +
319H TYR* 3.4 8.9 + - - +
320H ILE* 2.9 34.5 + - - +
382H LEU* 4.0 18.5 - - + +
385H THR* 5.0 5.8 - - + -
386H ARG* 3.7 31.6 - - + +
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Residues in contact with ASN 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H MET* 3.2 15.9 + - - +
314H MET* 4.1 4.3 - - - +
316H ALA* 1.3 75.4 - - - +
318H LEU* 1.3 65.0 + - - +
319H TYR 3.1 0.2 - - - -
320H ILE* 3.8 10.8 - - - +
321H ASP* 3.1 36.6 + - - +
386H ARG* 2.7 52.2 + - - +
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Residues in contact with LEU 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248H ILE* 5.4 0.9 - - + -
249H HIS* 4.2 44.2 - - + +
253H TRP* 3.7 45.7 + - + +
314H MET* 3.2 20.7 + - + +
315H ALA 3.2 5.4 + - - +
317H ASN* 1.3 76.4 - - - +
319H TYR* 1.3 61.5 + - - +
321H ASP* 3.7 9.3 + - + +
322H GLN* 3.2 27.4 + - - +
450H LEU* 3.7 35.7 - - + -
----------------------------------------------------------
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Residues in contact with TYR 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H TRP* 3.6 25.4 - + - -
315H ALA* 2.9 36.7 + - + +
316H ALA* 3.7 6.7 - - - +
318H LEU* 1.3 76.3 - - - +
320H ILE* 1.3 59.5 + - - +
322H GLN* 3.1 3.0 + - - +
323H ILE* 2.8 36.1 + - + +
382H LEU* 3.9 20.9 - - + -
412H PHE* 3.9 27.1 - + + -
439H LEU* 4.2 15.3 - - + -
442H GLN* 3.6 6.8 + - + -
443H VAL* 3.4 39.5 - - + +
446H PHE* 4.2 2.6 - - - +
447H GLY 2.6 32.3 + - - -
448H LEU* 4.6 6.7 - - + -
----------------------------------------------------------
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Residues in contact with ILE 320 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H ALA* 2.9 27.0 + - + +
317H ASN* 3.3 19.9 + - - +
319H TYR* 1.3 74.3 - - - +
321H ASP* 1.3 68.0 + - - +
323H ILE* 3.5 3.3 + - - +
324H GLU* 3.0 44.3 + - - +
379H ARG* 4.1 15.7 - - + +
382H LEU* 3.6 24.7 - - + +
383H TYR* 4.0 29.8 - - + +
386H ARG* 4.9 8.7 - - - +
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Residues in contact with ASP 321 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H HIS* 5.9 1.9 + - - -
317H ASN* 3.1 24.1 + - - +
318H LEU* 3.9 10.2 - - + +
320H ILE* 1.3 84.0 - - - +
322H GLN* 1.3 65.2 + - + +
324H GLU* 3.2 11.7 + - - +
325H GLU* 3.2 23.0 + - - +
----------------------------------------------------------
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Residues in contact with GLN 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H TRP* 3.5 21.9 - - + +
254H LYS* 3.5 37.4 - - - +
318H LEU 3.2 16.0 + - - +
319H TYR* 3.1 4.8 + - - +
321H ASP* 1.3 81.3 - - + +
323H ILE* 1.3 58.8 + - - +
325H GLU* 3.6 5.6 + - - +
326H LEU* 3.0 29.0 + - - +
435H SER* 5.7 4.7 - - - +
438H ASP* 6.0 2.1 - - - +
439H LEU* 3.8 21.4 - - + +
442H GLN* 3.7 16.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H TYR* 2.8 22.2 + - + +
320H ILE* 3.9 5.8 - - - +
322H GLN* 1.3 76.2 - - - +
324H GLU* 1.3 57.5 + - - +
326H LEU* 3.3 5.6 + - + +
327H MET* 2.8 29.0 + - - +
375H LEU* 3.4 39.2 - - + +
378H VAL* 4.1 9.2 - - + -
379H ARG* 4.3 14.6 - - + +
382H LEU* 4.0 15.0 - - + -
412H PHE* 4.9 3.8 - - + -
416H LEU* 3.9 16.6 - - + -
439H LEU* 3.7 32.8 - - + -
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Residues in contact with GLU 324 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H ILE* 3.0 32.3 + - - +
321H ASP* 3.2 11.9 + - - +
323H ILE* 1.3 74.4 - - - +
325H GLU* 1.3 64.7 + - - +
327H MET* 3.2 18.6 + - - +
328H PHE* 3.3 16.1 + - - +
379H ARG* 3.2 46.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 325 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G GLN* 4.3 15.2 - - - +
192G ARG* 5.2 3.7 + - - -
321H ASP 3.2 14.4 + - - +
322H GLN* 4.2 6.1 - - - +
324H GLU* 1.3 73.6 - - - +
326H LEU* 1.3 64.3 + - - +
328H PHE* 3.3 14.5 + - + +
329H GLU* 3.1 42.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 326 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322H GLN 3.0 18.5 + - - +
323H ILE* 3.5 7.6 - - + +
324H GLU 3.2 0.4 - - - -
325H GLU* 1.3 76.0 - - - +
327H MET* 1.3 63.2 + - - +
329H GLU* 3.3 19.6 + - - +
330H LEU* 3.1 39.8 + - + +
375H LEU* 3.8 25.4 - - + -
435H SER* 4.0 7.4 - - - -
436H LEU* 3.8 48.2 - - + +
439H LEU* 4.1 20.0 - - + -
----------------------------------------------------------
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Residues in contact with MET 327 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H ILE* 2.8 20.9 + - - +
324H GLU* 3.4 18.2 - - - +
325H GLU 3.2 0.2 - - - -
326H LEU* 1.3 77.2 - - - +
328H PHE* 1.3 64.9 + - + +
329H GLU 3.4 0.3 + - - -
330H LEU* 3.5 6.3 + - - +
365H ILE* 5.0 13.0 - - + -
372H ARG* 2.8 48.5 + - + +
375H LEU* 3.5 29.6 - - + +
376H GLY* 3.8 30.1 - - - +
379H ARG* 4.5 24.5 - - - +
----------------------------------------------------------
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Residues in contact with PHE 328 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G ARG* 4.8 25.6 - - + -
185G SER* 3.7 25.9 - - - +
188G GLN* 5.7 5.4 - - - -
189G LYS* 4.0 1.9 + - - -
192G ARG* 5.7 0.2 - - - -
1004G SO4 4.5 12.8 - - - -
324H GLU 3.3 11.5 + - - +
325H GLU* 3.3 18.6 + - - +
326H LEU 3.3 0.4 - - - -
327H MET* 1.3 82.6 - - + +
329H GLU* 1.3 62.5 + - - +
331H SER* 4.2 0.7 + - - -
372H ARG* 3.1 31.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 329 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G LYS* 2.9 29.6 + - - +
192G ARG* 2.8 47.2 + - - +
223G ALA* 5.6 0.3 - - - +
325H GLU* 3.1 31.1 + - - +
326H LEU* 3.7 15.0 - - - +
327H MET 3.2 0.4 - - - -
328H PHE* 1.3 78.1 - - - +
330H LEU* 1.3 64.7 + - + +
331H SER* 2.9 7.1 + - - -
332H MET* 4.2 4.2 - - - +
435H SER* 3.1 33.8 + - - -
----------------------------------------------------------
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Residues in contact with LEU 330 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H LEU* 3.1 36.3 + - + +
327H MET 3.5 4.6 + - - +
329H GLU* 1.3 77.3 - - + +
331H SER* 1.3 59.6 + - - +
332H MET* 3.4 28.5 + - + +
369H GLU* 5.3 0.5 - - - +
371H TYR* 4.0 28.4 + - + +
372H ARG* 3.6 18.5 + - - +
375H LEU* 3.9 24.5 - - + -
419H CYS* 5.2 3.1 - - + -
423H LEU* 4.4 22.2 - - + -
431H ILE* 4.4 14.1 - - + +
436H LEU* 4.9 10.1 - - + -
----------------------------------------------------------
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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