Contacts of the helix formed by residues 395 - 416 (chain D) in PDB entry 4BGG
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 CYS 395 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D GLN* 3.0 21.0 + - + +
393D VAL 3.3 0.4 - - - -
394D ASP* 1.3 78.4 - - - +
396D PHE* 1.3 67.2 + - - +
397D ASP* 3.6 25.8 - - - -
398D SER* 3.1 32.6 + - - +
399D TYR* 3.7 8.6 - - - -
401D ARG* 4.9 6.1 - - - -
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Residues in contact with PHE 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ALA* 3.6 40.2 - - + -
332D ILE 3.9 4.5 - - - -
333D ALA* 3.9 9.2 - - + -
359D VAL* 3.7 32.3 - - + -
361D HIS* 3.4 41.7 - + + +
368D LEU* 3.6 24.4 - - + +
394D ASP 3.9 3.0 + - - -
395D CYS* 1.3 72.4 - - - +
397D ASP* 1.3 65.2 + - - +
399D TYR* 3.0 20.9 + + - +
400D LYS* 3.6 36.0 + - + -
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Residues in contact with ASP 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D CYS* 3.2 13.2 - - - -
396D PHE* 1.3 80.7 - - - +
398D SER* 1.3 64.7 + - - +
400D LYS* 3.0 37.4 + - - +
401D ARG* 3.0 60.6 + - - +
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Residues in contact with SER 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D GLU* 4.7 1.4 - - - +
391D ILE* 3.9 19.5 - - - +
392D GLN* 2.9 39.1 + - - +
395D CYS* 3.1 17.9 + - - +
397D ASP* 1.3 77.5 - - - +
399D TYR* 1.3 63.7 + - - +
401D ARG* 3.4 13.5 + - - +
402D VAL* 3.2 28.2 + - - +
482D PRO* 6.0 1.8 - - - -
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Residues in contact with TYR 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D ALA* 3.7 21.7 - - + +
335D ARG* 4.1 36.6 - - + +
359D VAL* 4.0 15.0 - - + -
368D LEU* 4.5 6.7 - - + -
370D VAL* 4.1 23.7 - - + +
391D ILE* 4.4 19.3 - - + -
392D GLN 4.9 0.4 - - - -
393D VAL* 2.7 44.9 + - + +
395D CYS 3.7 15.0 - - - -
396D PHE* 3.0 15.0 + + - +
398D SER* 1.3 74.1 - - - +
400D LYS* 1.3 64.0 + - - +
402D VAL* 3.4 9.9 + - + +
403D ASP* 3.3 22.5 + - - +
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Residues in contact with LYS 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D HIS* 3.6 57.6 + - + +
331D ALA* 5.6 0.8 - - - +
333D ALA* 4.5 2.2 - - + -
396D PHE* 3.6 35.7 + - + +
397D ASP* 3.0 39.2 + - - +
399D TYR* 1.3 79.7 - - - +
401D ARG* 1.3 59.6 + - + +
403D ASP* 3.0 17.7 + - - +
404D ILE* 3.1 18.0 + - + +
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Residues in contact with ARG 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D GLU* 4.6 0.7 - - - +
392D GLN* 5.3 8.1 - - - +
395D CYS* 4.9 6.1 - - - -
397D ASP* 3.0 49.9 + - - +
398D SER* 3.8 10.4 + - - +
399D TYR 3.3 0.2 - - - -
400D LYS* 1.3 74.9 - - + +
402D VAL* 1.3 65.6 + - - +
404D ILE* 3.3 11.2 + - + +
405D TRP 3.2 13.9 + - - -
482D PRO* 3.4 36.6 + - + +
483D SER* 4.0 28.7 + - - +
485D ARG* 3.1 30.4 + - + +
486D LEU 5.9 0.9 - - - +
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Residues in contact with VAL 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D ARG* 5.0 15.3 - - + +
381D TYR 5.2 2.1 - - - +
382D MET* 6.1 1.1 - - - -
383D ALA* 4.3 12.1 - - + +
385D GLU* 3.8 16.6 - - - +
386D VAL* 3.8 19.1 - - + -
391D ILE* 3.8 21.3 - - + -
398D SER 3.2 15.5 + - - +
399D TYR* 3.5 13.7 - - + +
401D ARG* 1.3 76.7 - - - +
403D ASP* 1.3 65.9 + - - +
405D TRP* 3.5 4.9 + - - +
406D ALA* 3.3 19.6 + - - +
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Residues in contact with ASP 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D LEU* 3.9 11.1 - - + +
320D HIS* 2.9 26.6 + - + +
333D ALA* 3.5 2.6 - - - -
334D HIS* 2.8 33.2 + - - +
335D ARG* 2.8 30.8 + - - -
336D ASP 4.5 0.7 + - - -
337D LEU* 3.7 8.6 + - + +
399D TYR 3.3 10.7 + - - +
400D LYS 3.0 10.9 + - - +
402D VAL* 1.3 79.0 - - - +
404D ILE* 1.3 60.0 + - - +
406D ALA* 3.3 6.8 + - - +
407D PHE* 2.9 27.9 + - - +
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Residues in contact with ILE 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D LEU* 4.3 11.2 - - + -
320D HIS* 4.4 3.8 - - + -
400D LYS* 3.1 17.2 + - + +
401D ARG* 3.6 11.7 - - + +
402D VAL 3.2 0.4 - - - -
403D ASP* 1.3 76.0 - - - +
405D TRP* 1.3 65.9 + - - +
407D PHE* 3.2 5.1 + - + +
408D GLY 3.1 17.8 + - - -
477D CYS* 3.5 33.4 - - + +
485D ARG* 4.2 8.5 - - + -
486D LEU 3.4 22.9 - - - +
487D THR* 3.9 2.2 - - - -
488D ALA* 3.5 39.0 - - + +
491D ILE* 4.1 9.4 - - + -
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Residues in contact with TRP 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D ARG 5.3 0.2 + - - -
381D TYR 3.2 23.1 + - - -
382D MET 3.3 13.8 + - - -
383D ALA* 3.6 19.3 - - + -
384D PRO* 3.5 32.1 - - + -
401D ARG 3.2 8.7 + - - +
402D VAL 3.6 8.5 - - - +
404D ILE* 1.3 78.6 - - - +
406D ALA* 1.3 63.6 + - - +
408D GLY* 3.2 11.6 + - - -
409D LEU* 3.4 26.0 + - + +
431D PHE* 4.6 17.5 - + - -
448D VAL* 4.1 13.2 - - + -
453D GLN 5.0 0.4 - - - -
454D ARG* 3.6 32.1 - - - -
455D PRO* 6.2 0.2 - - + -
477D CYS 3.6 11.8 + - - +
478D TRP* 3.4 50.1 + + + -
485D ARG* 4.0 10.1 - - - +
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Residues in contact with ALA 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D LEU* 3.6 33.2 - - + +
381D TYR* 4.1 21.2 - - + +
402D VAL 3.3 9.4 + - - +
403D ASP* 3.3 9.7 + - - +
404D ILE 3.3 0.6 - - - -
405D TRP* 1.3 84.2 - - - +
407D PHE* 1.3 63.9 + - - +
409D LEU* 3.1 6.6 + - - +
410D VAL* 3.1 26.3 + - - +
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Residues in contact with PHE 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D VAL* 4.2 7.6 - - + -
312D ILE* 3.5 40.6 - - + -
313D ALA* 4.0 15.9 - - + -
316D LEU* 4.2 13.5 - - + -
337D LEU* 4.0 12.7 - - + +
403D ASP 2.9 18.0 + - - +
404D ILE* 3.2 8.9 + - - +
406D ALA* 1.3 75.4 - - - +
408D GLY* 1.3 59.3 + - - +
410D VAL* 3.1 10.0 + - + +
411D LEU* 2.9 55.4 + - + +
477D CYS* 4.2 2.9 - - - -
491D ILE* 3.5 47.6 - - + -
495D LEU* 4.6 3.1 - - + -
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Residues in contact with GLY 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D ILE 3.1 10.3 + - - -
405D TRP 3.2 4.4 + - - -
407D PHE* 1.3 78.6 - - - +
409D LEU* 1.3 60.4 + - - +
411D LEU* 3.3 10.2 - - - +
412D TRP 3.1 17.0 + - - -
474D MET* 3.8 4.0 - - - +
477D CYS* 3.9 19.7 - - - -
478D TRP* 3.6 24.2 - - - -
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Residues in contact with LEU 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D ARG 3.9 7.6 - - - +
381D TYR* 3.8 40.2 - - + -
405D TRP* 3.4 35.9 + - + +
406D ALA* 3.1 7.7 + - - +
408D GLY* 1.3 75.9 - - - +
410D VAL* 1.3 58.8 + - - +
412D TRP* 3.2 9.2 + - - +
413D GLU* 3.0 30.9 + - - +
430D PRO* 3.9 16.3 - - + +
431D PHE* 4.1 11.0 - - + -
455D PRO* 3.7 30.5 - - + -
478D TRP* 3.6 12.3 - - + +
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Residues in contact with VAL 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D LEU* 4.1 17.5 - - + -
309D VAL* 6.3 0.2 - - + -
312D ILE* 4.2 12.3 - - + -
337D LEU* 5.0 2.9 - - + -
338D LYS* 4.0 14.4 - - - +
339D SER* 4.0 19.3 - - - +
342D ILE* 4.0 22.4 - - + -
381D TYR* 4.0 2.2 - - + -
406D ALA 3.1 15.0 + - - +
407D PHE* 3.1 11.6 + - + +
409D LEU* 1.3 73.0 - - - +
411D LEU* 1.3 67.1 + - - +
413D GLU* 3.1 21.1 + - + +
414D VAL* 3.0 23.1 + - + +
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D VAL* 3.5 33.8 - - + +
407D PHE* 2.9 45.6 + - + +
408D GLY* 3.3 12.6 - - - +
410D VAL* 1.3 78.8 - - - +
412D TRP* 1.3 55.5 + - - +
414D VAL* 3.3 5.6 + - - +
415D ALA* 3.0 31.1 + - - +
470D LEU* 4.2 24.9 - - + +
473D LEU* 4.2 28.0 - - + -
474D MET* 3.9 16.6 - - + +
477D CYS* 4.9 1.1 - - - -
495D LEU* 5.5 1.3 - - + -
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Residues in contact with TRP 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D GLY 3.1 6.7 + - - +
409D LEU* 3.2 9.6 + - - +
411D LEU* 1.3 75.2 - - - +
413D GLU* 1.3 86.6 + - + +
415D ALA* 4.0 2.0 - - - +
416D ARG* 3.3 58.5 + - - +
428D LYS 3.6 20.9 - - - -
429D PRO 3.8 0.7 - - - -
430D PRO* 3.7 24.9 - - + -
431D PHE 5.0 1.3 - - - -
432D TYR* 3.9 29.4 - + - -
455D PRO* 3.5 26.6 - - + +
456D ASN* 3.0 29.3 + - + -
458D PRO* 5.1 0.4 - - - +
461D TRP* 4.0 11.9 - + - -
474D MET* 3.3 39.4 - - + -
478D TRP* 4.2 4.5 - + + -
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Residues in contact with GLU 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D LEU* 4.2 8.3 - - + +
339D SER* 2.7 24.4 + - - -
381D TYR* 2.4 36.2 + - - -
409D LEU 3.0 12.8 + - - +
410D VAL* 3.3 17.7 - - + +
412D TRP* 1.3 86.4 - - + +
414D VAL* 1.3 62.7 + - + +
416D ARG* 3.7 13.4 - - - +
417D ARG* 3.9 10.6 - - - +
427D TYR* 2.5 37.1 + - + -
428D LYS 3.9 12.3 - - - +
430D PRO* 3.7 17.1 - - + +
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Residues in contact with VAL 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D LEU* 3.9 28.9 - - + -
295D LEU* 4.0 15.3 - - + -
300D LEU* 3.8 24.0 - - + +
305D CYS* 4.0 11.2 - - - +
308D ILE* 4.1 16.4 - - + -
309D VAL* 3.9 23.6 - - + -
312D ILE* 5.2 0.4 - - + -
410D VAL* 3.0 22.1 + - + +
411D LEU 3.8 3.8 - - - +
413D GLU* 1.3 75.9 - - - +
415D ALA* 1.3 57.8 + - - +
417D ARG* 3.0 25.5 + - - +
418D MET* 3.7 3.5 + - - +
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Residues in contact with ALA 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D CYS* 4.5 9.0 - - - -
411D LEU 3.0 16.9 + - - +
412D TRP* 3.4 0.6 + - - +
414D VAL* 1.3 74.3 - - - +
416D ARG* 1.3 64.7 + - - +
418D MET* 3.1 20.1 + - - +
461D TRP* 3.8 24.4 + - + -
467D LEU* 3.6 27.4 - - + +
470D LEU* 4.4 16.6 - - + -
474D MET* 5.1 1.1 - - - -
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Residues in contact with ARG 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D TRP* 3.3 56.2 + - + +
413D GLU 3.7 11.0 - - - +
415D ALA* 1.3 78.1 - - - +
417D ARG* 1.3 57.9 + - + +
418D MET 3.3 2.2 + - - +
424D VAL* 3.4 4.0 - - - +
425D GLU* 3.2 50.2 + - + +
426D ASP* 2.9 32.2 + - - +
427D TYR* 5.9 0.2 - - - -
428D LYS* 3.4 33.2 - - - +
432D TYR* 4.3 13.9 + - - -
456D ASN 5.6 0.8 + - - -
458D PRO* 5.5 8.2 - - + +
460D ARG* 5.4 1.4 + - - +
461D TRP* 3.8 21.0 - - + +
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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