Contacts of the helix formed by residues 307 - 337 (chain H) in PDB entry 2VIG
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 307 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E GLN* 3.7 15.7 - - - +
501G FAD 3.5 57.7 - - + +
299H ALA* 5.1 9.2 - - + +
300H PHE* 5.2 9.2 - - + -
303H PRO 4.7 2.9 - - - +
304H LEU* 3.0 29.8 + - + +
306H LYS* 1.3 77.9 - - + +
308H GLN* 1.3 66.9 + - - +
310H ILE* 3.1 16.8 + - + +
311H GLN* 3.0 22.5 + - - +
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Residues in contact with GLN 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E LEU* 3.7 11.9 - - - +
308E GLN* 3.3 24.3 + - + +
309E VAL* 3.2 40.7 + - + +
400F LEU* 4.2 18.2 - - + +
501F FAD 2.9 35.3 + - - -
306H LYS 3.6 5.6 + - - +
307H LEU* 1.3 71.1 - - - +
309H VAL* 1.3 57.5 + - - +
311H GLN* 3.1 12.9 + - - +
312H PHE* 2.9 36.6 + - + -
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Residues in contact with VAL 309 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E GLN* 3.1 32.2 + - + +
309E VAL* 4.8 4.5 - - + +
312E PHE* 3.2 55.9 - - + -
396G GLU* 4.0 16.8 - - + -
501G FAD 4.2 8.1 - - + +
308H GLN* 1.3 74.8 - - - +
310H ILE* 1.3 58.0 + - + +
312H PHE* 3.4 8.5 + - - +
313H LYS* 2.9 37.6 + - + +
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Residues in contact with ILE 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501G FAD 4.0 33.2 - - - +
294H ALA* 4.1 20.4 - - + -
304H LEU* 3.2 39.5 - - + +
305H THR* 4.3 1.8 - - - +
307H LEU* 3.1 20.9 + - + +
309H VAL* 1.3 71.8 - - - +
311H GLN* 1.3 66.3 + - - +
313H LYS* 3.2 14.9 + - + +
314H LEU* 3.0 33.8 + - + +
366H ILE* 4.0 23.3 - - + -
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Residues in contact with GLN 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F LEU* 3.4 23.6 - - + +
403F ALA* 3.4 30.5 - - + +
404F GLY 5.5 0.6 + - - -
407F LEU* 5.0 9.2 - - + -
305H THR* 2.9 30.8 + - - +
306H LYS* 3.8 18.6 + - - +
307H LEU 3.0 11.1 + - - +
308H GLN* 3.4 14.9 - - - +
310H ILE* 1.3 77.6 - - - +
312H PHE* 1.3 61.2 + - + +
314H LEU* 3.4 6.6 + - - +
315H ALA* 2.9 24.9 + - - +
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Residues in contact with PHE 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E VAL* 3.5 35.0 - - + -
313E LYS* 5.7 2.5 - - - -
396F GLU* 3.7 42.2 - - + -
399F ARG* 3.7 31.9 - - + -
400F LEU* 3.8 27.6 - - + -
501F FAD 5.1 0.4 - + - -
308H GLN 2.9 16.3 + - - +
309H VAL* 3.4 11.0 - - - +
311H GLN* 1.3 75.0 - - - +
313H LYS* 1.3 65.3 + - - +
315H ALA* 3.4 4.9 + - - +
316H ASP* 3.0 35.0 + - - +
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Residues in contact with LYS 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E PHE* 6.1 0.2 - - - -
396G GLU* 2.7 45.2 + - - +
399G ARG* 6.0 0.4 - - - +
501G FAD 4.9 0.7 - - - -
309H VAL* 2.9 26.3 + - + +
310H ILE* 3.2 16.1 + - + +
312H PHE* 1.3 75.1 - - - +
314H LEU* 1.3 58.8 + - - +
316H ASP* 3.6 6.0 - - - +
317H MET* 3.0 35.9 + - - +
362H GLN* 2.7 35.5 + - - +
365H GLN* 4.4 5.3 - - + +
366H ILE* 3.9 31.6 - - + -
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Residues in contact with LEU 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F ALA* 5.5 2.7 - - + -
406F LEU* 3.7 20.2 - - + +
407F LEU* 4.3 10.1 - - + -
287H LEU* 4.1 7.0 - - + +
290H ALA* 4.2 8.1 - - + -
291H VAL* 3.8 30.1 - - + +
294H ALA* 4.5 4.7 - - + -
305H THR* 4.1 19.7 - - + -
310H ILE* 3.0 34.5 + - + +
311H GLN* 3.7 7.2 - - - +
313H LYS* 1.3 73.7 - - - +
315H ALA* 1.3 63.5 + - - +
317H MET* 3.4 11.3 + - - +
318H ALA 3.0 18.9 + - - -
366H ILE* 3.8 22.9 - - + -
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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
----------------------------------------------------------
350F LEU* 6.3 0.4 - - - -
399F ARG* 3.4 38.4 - - + +
402F ILE* 3.5 27.6 - - + +
403F ALA* 3.9 4.6 - - - +
406F LEU* 4.7 0.6 - - - +
311H GLN 2.9 17.8 + - - +
312H PHE 3.9 3.4 - - - +
314H LEU* 1.3 72.7 - - - +
316H ASP* 1.3 57.7 + - - +
318H ALA* 3.4 3.7 + - - +
319H LEU* 2.9 30.9 + - - +
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Residues in contact with ASP 316 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F LEU* 4.9 3.1 - - - +
399F ARG* 2.9 41.9 + - - +
312H PHE* 3.0 26.0 + - - +
313H LYS* 3.6 5.8 - - - +
315H ALA* 1.3 73.4 - - - +
317H MET* 1.3 61.1 + - + +
319H LEU* 3.5 7.7 + - - +
320H ALA* 3.0 31.1 + - - +
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Residues in contact with MET 317 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H LEU* 3.9 23.3 - - + -
290H ALA* 4.2 15.3 - - + -
313H LYS 3.0 24.4 + - - +
314H LEU* 3.5 12.8 - - - +
316H ASP* 1.3 74.5 - - + +
318H ALA* 1.3 66.4 + - - +
320H ALA 3.4 0.2 + - - -
321H LEU* 3.0 20.0 + - - +
359H ILE* 3.5 63.9 - - + +
362H GLN* 3.9 22.7 - - + -
363H ALA* 4.1 8.5 - - + +
366H ILE* 4.0 10.3 - - - -
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Residues in contact with ALA 318 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F MET* 3.8 18.6 - - + -
402F ILE* 4.7 2.0 - - + -
406F LEU* 3.8 30.7 - - + -
287H LEU* 4.1 13.3 - - + +
314H LEU 3.0 16.6 + - - +
315H ALA* 3.8 4.3 - - - +
317H MET* 1.3 73.7 - - - +
319H LEU* 1.3 58.2 + - - +
321H LEU* 3.3 2.2 + - - +
322H GLU* 2.9 38.7 + - - +
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Residues in contact with LEU 319 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F LEU* 3.3 34.3 - - + -
347F MET* 3.7 38.3 - - + +
350F LEU* 3.8 35.4 - - + -
351F ALA* 4.3 9.4 - - + +
354F GLU* 5.8 1.3 - - - +
399F ARG* 5.7 1.1 - - - +
402F ILE* 4.9 1.3 - - + -
315H ALA 2.9 18.7 + - - +
316H ASP* 3.8 9.9 - - - +
318H ALA* 1.3 73.2 - - - +
320H ALA* 1.3 59.6 + - - +
323H SER* 2.9 38.0 + - - +
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Residues in contact with ALA 320 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H ASP 3.0 17.9 + - - +
317H MET* 3.8 4.0 - - - +
319H LEU* 1.3 75.0 - - - +
321H LEU* 1.3 63.0 + - - +
323H SER* 3.7 4.6 - - - -
324H ALA* 3.0 25.5 + - - +
355H ALA* 4.1 24.2 - - + +
358H ALA* 6.0 3.4 - - + -
359H ILE* 4.1 7.2 - - + -
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Residues in contact with LEU 321 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H LEU* 3.9 32.5 - - + +
283H ALA* 3.9 15.3 - - + +
284H GLN* 3.5 42.6 - - - +
287H LEU* 3.8 18.8 - - + -
317H MET 3.0 16.6 + - - +
318H ALA* 3.6 4.5 - - - +
320H ALA* 1.3 74.3 - - - +
322H GLU* 1.3 62.5 + - + +
324H ALA* 3.2 4.4 + - + +
325H ARG* 2.9 45.1 + - - +
355H ALA* 5.0 1.3 - - + -
359H ILE* 3.9 8.4 - - + +
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Residues in contact with GLU 322 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F LEU* 4.6 2.5 - - + -
330F ARG* 2.9 39.1 + - - +
343F LYS* 2.7 31.7 + - - -
347F MET* 3.5 23.1 - - - +
406F LEU* 4.9 2.6 - - - +
318H ALA* 2.9 25.5 + - - +
319H LEU 4.2 1.6 - - - +
321H LEU* 1.3 73.9 - - + +
323H SER* 1.3 63.0 + - - +
325H ARG* 3.3 12.0 + - - +
326H LEU* 3.2 27.8 + - - +
503H EDO 3.6 19.5 - - - +
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Residues in contact with SER 323 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F SER* 3.3 21.5 + - - +
326F LEU* 5.2 0.5 - - - +
327F LEU* 3.1 34.5 - - - +
351F ALA* 5.2 0.2 - - - +
319H LEU* 2.9 27.8 + - - +
320H ALA* 3.7 5.8 - - - -
322H GLU* 1.3 77.4 - - - +
324H ALA* 1.3 61.4 + - - +
326H LEU* 3.4 6.1 + - - +
327H LEU* 3.2 24.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 324 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H LEU* 3.6 19.3 - - + -
320H ALA 3.0 18.4 + - - +
321H LEU* 3.2 2.4 + - - +
323H SER* 1.3 76.0 - - - +
325H ARG* 1.3 58.0 + - - +
327H LEU* 3.3 5.5 + - - +
328H THR* 2.9 31.0 + - - -
348H ALA* 4.9 1.0 - - - +
351H ALA* 4.1 16.2 - - + +
352H ALA* 3.7 26.9 - - - +
355H ALA* 4.6 2.9 - - + -
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Residues in contact with ARG 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLU* 2.8 37.5 + - - -
280H LEU* 3.5 18.0 - - + +
284H GLN* 2.9 24.4 + - - +
321H LEU* 2.9 28.4 + - - +
322H GLU* 3.7 20.7 - - - +
324H ALA* 1.3 76.8 - - - +
326H LEU* 1.3 55.6 - - - +
328H THR* 3.1 3.3 + - - -
329H TRP* 2.8 66.8 + - + +
503H EDO 3.0 32.0 + - - +
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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
----------------------------------------------------------
323F SER 5.4 0.2 - - - +
326F LEU* 3.6 46.7 - - + +
327F LEU* 3.8 25.6 - - + +
330F ARG* 4.1 20.0 - - + +
322H GLU 3.2 15.6 + - - +
323H SER* 3.8 6.3 - - - +
324H ALA 3.4 0.2 - - - -
325H ARG* 1.3 75.3 - - - +
327H LEU* 1.3 57.8 + - - +
329H TRP* 3.9 12.9 - - + +
330H ARG* 3.0 28.9 + - - +
503H EDO 3.4 28.9 - - - -
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Residues in contact with LEU 327 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F LEU* 3.4 33.9 - - + -
323F SER* 3.8 26.5 - - - +
326F LEU* 3.7 16.2 - - + -
323H SER 3.2 15.1 + - - +
324H ALA* 3.5 7.2 - - - +
326H LEU* 1.3 74.6 - - - +
328H THR* 1.3 63.0 + - - +
330H ARG* 3.5 31.9 + - - +
331H ALA* 3.2 18.0 + - - +
344H GLU 4.2 2.8 - - - +
347H MET* 4.1 5.8 - - + +
348H ALA* 3.6 19.0 - - - +
351H ALA* 3.4 23.1 - - + -
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Residues in contact with THR 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ALA* 4.4 7.6 - - + -
273H ILE* 4.0 12.7 - - + +
276H ALA* 3.5 26.6 - - + +
277H SER* 3.6 24.2 - - - +
280H LEU* 3.6 18.2 - - + +
324H ALA 2.9 15.3 + - - -
325H ARG 3.1 7.6 + - - -
327H LEU* 1.3 78.7 - - - +
329H TRP* 1.3 64.5 + - + +
331H ALA* 3.2 4.0 + - - +
332H ALA* 3.0 20.8 + - - +
348H ALA* 3.5 11.8 + - + +
352H ALA* 4.6 0.2 - - - +
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Residues in contact with TRP 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU* 3.4 42.0 - - + -
42H LEU* 6.1 2.9 - - + -
96H LEU* 3.6 23.8 - - + +
99H ALA* 4.5 12.9 - - + +
100H ILE* 4.2 18.8 - - + +
103H GLU* 4.9 6.4 + - - -
280H LEU* 5.2 2.0 - - + +
325H ARG* 2.8 51.6 + - + +
326H LEU* 4.0 11.7 - - + +
328H THR* 1.3 76.5 - - + +
330H ARG* 1.3 66.6 + - - +
332H ALA* 3.3 4.9 + - - +
333H MET* 2.9 38.7 + - - +
503H EDO 4.0 21.5 - - - -
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Residues in contact with ARG 330 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F GLU* 2.9 38.5 + - - +
326F LEU* 4.2 28.5 - - + +
326H LEU 3.0 18.7 + - - +
327H LEU* 3.6 23.0 + - - +
328H THR 3.3 0.2 - - - -
329H TRP* 1.3 77.7 - - - +
331H ALA* 1.3 60.3 + - - +
333H MET* 3.3 6.9 + - - +
334H LEU* 3.0 37.5 + - + +
343H LYS* 4.9 0.6 - - - +
344H GLU* 3.6 30.1 + - - +
347H MET* 3.3 21.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 331 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H ILE* 3.9 15.7 - - + +
327H LEU 3.2 9.9 + - - +
328H THR 3.2 6.9 + - - +
330H ARG* 1.3 75.3 - - - +
332H ALA* 1.3 63.6 + - - +
334H LEU* 3.4 5.0 + - - +
335H LYS* 3.1 23.9 + - - +
341H PHE* 3.8 5.3 - - - +
344H GLU* 3.7 18.1 - - + +
345H ALA* 3.6 34.1 - - + +
348H ALA* 4.6 2.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 332 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H TYR* 3.8 12.4 - - - +
96H LEU* 3.8 28.7 - - + +
99H ALA* 4.5 3.4 - - + -
273H ILE* 4.1 17.3 - - + +
328H THR 3.0 12.7 + - - +
329H TRP* 3.5 12.6 - - - +
331H ALA* 1.3 77.9 - - - +
333H MET* 1.3 57.8 + - - +
335H LYS* 3.4 3.3 + - - +
336H ASP* 3.0 33.1 + - - +
----------------------------------------------------------
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Residues in contact with MET 333 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H LEU* 4.4 30.5 - - + -
329H TRP* 2.9 31.1 + - - +
330H ARG* 3.8 6.1 - - - +
332H ALA* 1.3 72.4 - - - +
334H LEU* 1.3 61.6 + - + +
336H ASP* 3.6 7.6 - - + +
337H ASN* 2.8 44.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 334 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H ARG* 3.0 32.7 + - + +
331H ALA 3.7 4.0 - - - +
332H ALA 3.3 0.2 - - - -
333H MET* 1.3 77.0 - - + +
335H LYS* 1.3 61.9 + - - +
337H ASN* 3.0 10.1 + - - -
339H LYS* 2.9 49.4 + - + +
340H PRO 3.7 15.7 - - - +
341H PHE* 3.8 2.7 - - + -
344H GLU* 3.3 45.3 - - + +
----------------------------------------------------------
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Residues in contact with LYS 335 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ASP* 3.8 13.5 + - - -
95H TYR* 3.4 46.6 - - + -
270H MET* 3.8 24.6 - - + -
273H ILE* 4.7 1.8 - - + -
331H ALA 3.1 11.1 + - - +
332H ALA* 3.6 7.4 - - - +
334H LEU* 1.3 79.5 - - - +
336H ASP* 1.3 64.2 + - - +
338H LYS* 3.0 14.7 + - - +
339H LYS 4.3 1.3 - - - -
341H PHE* 3.5 47.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP 336 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ASP* 5.0 1.7 - - - +
94H ASP* 3.3 23.3 - - + +
95H TYR* 2.8 28.8 + - - +
96H LEU* 3.0 28.2 + - - +
332H ALA 3.0 18.4 + - - +
333H MET* 3.6 8.9 - - - +
335H LYS* 1.3 77.4 - - - +
337H ASN* 1.3 64.1 + - - +
338H LYS* 3.3 2.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 337 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H MET* 2.8 36.6 + - - +
334H LEU* 3.0 3.3 + - - +
336H ASP* 1.3 83.1 - - - +
338H LYS* 1.3 67.4 + - - +
339H LYS* 3.0 23.1 + - + +
----------------------------------------------------------
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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