Contacts of the helix formed by residues 360 - 388 (chain B) in PDB entry 6R7Z
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 TYR 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B SER 4.1 3.5 + - - +
357B VAL* 3.2 14.1 + - - +
359B LEU* 1.3 77.3 - - - +
361B VAL* 1.3 64.4 + - - +
362B PRO 3.6 0.2 - - - -
363B SER* 3.8 4.8 + - - +
364B ILE* 3.3 21.5 + - - +
435B THR* 4.7 19.9 - - - -
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B VAL 3.7 5.1 + - - +
358B LEU* 3.5 13.4 + - - +
359B LEU 3.3 0.2 - - - -
360B TYR* 1.3 76.7 - - - +
362B PRO* 1.4 66.4 - - + +
364B ILE* 3.0 8.6 + - - +
365B ILE* 2.8 28.2 + - - +
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Residues in contact with PRO 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.4 20.8 - - + +
339B MET* 5.1 13.5 - - + +
340B GLU* 5.0 7.9 - - + +
343B ALA* 4.8 16.4 - - + -
358B LEU 3.3 16.4 - - - +
359B LEU* 3.6 12.3 - - - +
361B VAL* 1.4 88.8 - - + +
363B SER* 1.3 57.3 + - - +
365B ILE* 3.7 9.1 - - + +
366B TYR* 2.8 28.4 + - - +
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Residues in contact with SER 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.4 27.0 - - - -
359B LEU 4.9 4.3 - - - -
360B TYR* 3.8 8.5 + - - -
361B VAL 3.2 0.6 - - - -
362B PRO* 1.3 81.0 - - - +
364B ILE* 1.3 58.8 + - - +
366B TYR* 3.4 3.4 + - - +
367B ALA* 2.9 27.7 + - - +
432B SER* 5.4 5.8 - - - -
435B THR* 4.7 18.4 - - - -
436B LEU* 5.1 12.8 - - - +
439B THR* 5.7 1.3 - - - -
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B TYR 3.3 13.3 + - - +
361B VAL* 3.0 11.8 + - - +
363B SER* 1.3 77.8 - - - +
365B ILE* 1.3 60.3 + - - +
367B ALA* 3.2 7.3 + - - +
368B ILE* 2.9 28.4 + - - +
439B THR* 4.6 17.0 - - - -
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Residues in contact with ILE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B VAL 2.8 15.2 + - - +
362B PRO* 3.7 9.9 - - + +
364B ILE* 1.3 77.1 - - - +
366B TYR* 1.3 57.9 + - - +
368B ILE* 3.3 6.9 + - - +
369B VAL* 2.9 27.7 + - - +
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Residues in contact with TYR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.7 31.4 - - + -
362B PRO 2.8 21.7 + - - +
363B SER* 3.7 5.4 - - - +
365B ILE* 1.3 72.9 - - - +
367B ALA* 1.3 53.8 + - - +
369B VAL* 3.6 7.1 - - - +
370B ILE* 2.7 34.1 + - - +
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B SER 2.9 17.9 + - - +
364B ILE* 3.5 8.7 - - - +
366B TYR* 1.3 75.6 - - - +
368B ILE* 1.3 60.1 + - - +
370B ILE* 3.2 8.6 + - - +
371B GLU* 2.8 29.1 + - - +
436B LEU* 5.1 4.9 - - + +
439B THR* 4.5 17.0 - - - +
440B SER* 4.7 15.5 - - - +
443B LEU* 5.7 5.0 - - + +
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ILE 2.9 15.4 + - - +
365B ILE* 3.7 8.1 - - - +
367B ALA* 1.3 76.5 - - - +
369B VAL* 1.3 58.9 + - - +
371B GLU* 3.3 6.6 + - - +
372B ILE* 2.8 28.5 + - - +
443B LEU* 5.9 3.8 - - - -
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 6.5 0.9 - - + -
365B ILE 2.9 17.2 + - - +
366B TYR* 3.7 8.1 - - - +
368B ILE* 1.3 73.4 - - - +
370B ILE* 1.3 56.6 + - - +
372B ILE* 3.3 7.9 + - - +
373B MET* 2.7 35.9 + - - +
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TYR 2.7 21.4 + - - +
367B ALA* 3.4 9.6 - - - +
369B VAL* 1.3 74.3 - - - +
371B GLU* 1.3 57.0 + - - +
373B MET* 3.6 4.9 - - - +
374B ASN* 2.8 32.4 + - - +
407B PHE* 5.3 0.5 - - - -
411B ASN* 4.8 24.7 - - + +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ALA 2.8 16.9 + - - +
368B ILE* 3.9 6.3 - - - +
370B ILE* 1.3 76.3 - - - +
372B ILE* 1.3 59.3 + - - +
374B ASN* 4.1 7.2 - - - +
375B ARG* 3.8 17.7 + - - +
443B LEU* 5.3 13.0 - - + +
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Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ILE 2.8 16.9 + - - +
369B VAL* 3.6 7.9 - - - +
370B ILE 3.1 0.4 - - - -
371B GLU* 1.3 79.1 - - - +
373B MET* 1.3 58.7 + - - +
375B ARG* 3.2 5.7 + - - +
376B LEU* 2.9 29.7 + - - +
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Residues in contact with MET 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER* 6.4 0.4 - - - -
369B VAL 2.7 20.9 + - - +
370B ILE* 3.8 6.3 - - - +
372B ILE* 1.3 74.3 - - - +
374B ASN* 1.3 58.0 + - - +
376B LEU* 3.8 7.3 - - - +
377B TYR* 2.8 31.7 + - - +
407B PHE* 3.4 18.5 - - + -
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Residues in contact with ASN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE 2.8 22.3 + - - +
371B GLU* 4.4 6.5 - - - +
372B ILE 3.2 0.2 - - - -
373B MET* 1.3 73.3 - - - +
375B ARG* 1.3 57.6 + - - +
377B TYR* 3.8 1.6 - - - +
378B ARG* 2.9 27.7 + - - +
407B PHE* 3.6 17.8 - - + -
408B ASN* 6.2 4.3 - - + -
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Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU 3.8 13.1 + - - +
372B ILE* 3.2 7.7 + - - +
374B ASN* 1.3 77.1 - - - +
376B LEU* 1.3 65.6 + - - +
378B ARG* 3.2 9.0 + - - +
379B TYR* 3.2 34.3 + - + -
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE 2.9 17.3 + - - +
373B MET* 3.8 9.2 - - - +
375B ARG* 1.3 76.6 - - - +
377B TYR* 1.3 62.4 + - - +
379B TYR* 3.4 10.5 + - - +
380B ALA* 3.1 21.0 + - - +
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Residues in contact with TYR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B CYS* 5.8 5.2 - - + -
373B MET 2.8 22.5 + - - +
374B ASN 3.9 1.6 - - - +
376B LEU* 1.3 71.3 - - - +
378B ARG* 1.3 55.6 + - - +
380B ALA* 3.6 7.2 - - - +
381B ALA* 2.7 38.7 + - + +
407B PHE* 3.6 34.5 - - + -
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Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASN 2.9 18.1 + - - +
375B ARG* 3.4 11.2 - - - +
376B LEU 3.2 0.4 - - - -
377B TYR* 1.3 77.9 - - - +
379B TYR* 1.3 62.2 + - + +
381B ALA* 4.2 3.4 - - - +
382B GLU* 3.0 30.3 + - - +
404B VAL* 6.4 2.2 - - + -
495B PHE* 6.1 4.9 - - + -
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Residues in contact with TYR 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ARG* 3.2 19.5 + - + -
376B LEU* 3.8 9.2 - - - +
378B ARG* 1.3 79.8 - - + +
380B ALA* 1.3 58.5 + - - +
382B GLU* 3.5 5.9 + - + +
383B PHE* 3.0 29.1 + - - +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU 3.1 17.0 + - - +
377B TYR* 3.3 7.6 + - - +
379B TYR* 1.3 77.5 - - - +
381B ALA* 1.3 57.4 + - - +
383B PHE* 3.5 5.6 + - - +
384B LEU* 2.9 30.2 + - - +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 2.7 22.3 + - + +
378B ARG* 4.2 4.5 - - - +
380B ALA* 1.3 70.3 - - - +
382B GLU* 1.3 61.4 + - - +
384B LEU* 4.1 5.1 - - - +
385B THR* 2.9 34.0 + - - -
400B LEU* 5.5 9.0 - - + +
403B LYS* 4.5 22.7 - - + -
404B VAL* 5.5 7.0 - - + +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ARG 3.0 19.7 + - - +
379B TYR* 3.8 7.4 - - + +
381B ALA* 1.3 77.4 - - - +
383B PHE* 1.3 57.0 + - - +
385B THR* 4.4 2.4 - - - -
386B SER* 2.9 31.9 + - - -
396B TYR* 4.6 10.3 + - - +
400B LEU* 6.2 2.2 - - - -
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Residues in contact with PHE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TYR 3.0 18.9 + - - +
380B ALA* 3.8 6.3 - - - +
382B GLU* 1.3 77.3 - - - +
384B LEU* 1.3 56.9 + - - +
386B SER* 3.5 3.7 + - - -
387B TRP* 3.1 29.6 + - - +
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B SER* 5.2 19.8 - - - -
321B PHE* 5.9 5.8 - - + -
380B ALA 2.9 19.9 + - - +
381B ALA* 4.1 5.4 - - - +
382B GLU 3.3 0.2 - - - -
383B PHE* 1.3 77.6 - - - +
385B THR* 1.3 59.7 + - - +
387B TRP* 3.8 12.0 + - + +
388B GLU* 3.8 17.8 + - - +
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Residues in contact with THR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ALA 2.9 18.0 + - - -
382B GLU* 4.4 1.8 - - - -
384B LEU* 1.3 77.5 - - - +
386B SER* 1.3 58.6 + - - +
387B TRP 3.1 5.2 + - - -
388B GLU* 3.7 13.1 + - - +
389B ASN 4.4 2.9 + - - -
390B HIS* 4.8 5.0 + - - +
396B TYR* 3.7 30.3 - - - -
399B HIS* 5.4 6.7 - - - -
400B LEU* 4.7 18.6 - - - -
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLY 4.8 9.2 - - - +
289B HIS* 5.7 2.6 + - - -
382B GLU 2.9 20.2 + - - -
383B PHE* 3.8 3.6 - - - -
385B THR* 1.3 76.7 - - - +
387B TRP* 1.3 60.0 + - - +
388B GLU 3.5 0.4 - - - -
389B ASN* 4.2 5.5 + - - -
396B TYR* 3.9 17.2 - - - -
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Residues in contact with TRP 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B HIS* 6.2 0.5 - - - -
313B ARG* 3.6 39.8 - - + +
317B VAL* 4.4 12.8 - - + -
383B PHE 3.1 18.0 + - - +
384B LEU* 3.8 11.9 + - + +
385B THR 3.1 0.8 - - - -
386B SER* 1.3 77.6 - - - +
388B GLU* 1.3 63.6 + - + +
389B ASN* 3.2 9.0 + - - +
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Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ARG* 3.8 30.4 - - - +
313B ARG* 4.9 12.3 - - + +
314B ILE* 5.2 9.2 - - + +
384B LEU 3.8 13.2 + - - +
385B THR* 3.7 9.0 + - - +
386B SER 3.5 0.6 - - - -
387B TRP* 1.3 82.4 - - + +
389B ASN* 1.3 69.6 + - - +
390B HIS* 3.5 4.4 - - + +
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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