Contacts of the helix formed by residues 334 - 356 (chain D) in PDB entry 3M0V
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 ASP 334 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D THR* 1.3 71.6 - - - +
335D PRO* 1.3 66.4 - - - +
336D ILE* 3.0 10.9 + - - +
337D GLU* 2.9 40.0 + - + +
338D SER* 3.1 11.4 + - - -
406D TYR* 2.9 27.0 + - - -
412D ARG* 2.8 41.0 + - - +
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Residues in contact with PRO 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLY 3.4 14.8 - - - +
59D VAL 3.1 25.4 - - - +
60D GLY* 3.6 23.8 - - - +
61D THR* 3.8 15.9 - - - +
74D GLU* 5.2 1.8 - - - +
330D HIS* 4.0 17.9 - - + +
333D THR 3.1 10.3 - - - +
334D ASP* 1.3 87.3 - - - +
336D ILE* 1.3 54.6 + - - +
338D SER* 3.4 1.7 + - - -
339D LEU* 2.9 37.3 + - - +
412D ARG* 4.3 8.5 - - - +
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Residues in contact with ILE 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D VAL* 5.0 6.5 - - + +
84D ASP* 3.7 30.3 - - + +
87D VAL* 4.1 7.4 - - + -
88D ILE* 3.9 25.1 - - + +
334D ASP* 3.0 7.6 + - - +
335D PRO* 1.3 76.9 - - - +
337D GLU* 1.3 58.2 + - - +
339D LEU* 3.4 2.3 + - - +
340D ILE* 2.9 40.1 + - + +
406D TYR* 3.5 28.7 - - + +
411D TYR* 3.7 24.9 - - + -
412D ARG* 3.5 22.4 - - - +
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Residues in contact with GLU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.6 25.6 - - + +
334D ASP* 2.9 25.8 + - + +
336D ILE* 1.3 74.8 - - - +
338D SER* 1.3 63.9 + - - +
340D ILE* 3.2 10.2 + - - +
341D ASN* 3.0 22.2 + - - +
403D VAL* 4.0 14.9 - - + +
406D TYR* 3.4 29.0 - - + -
407D ARG* 2.8 56.2 + - - +
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Residues in contact with SER 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.6 7.4 - - - +
293D ASP* 2.7 27.6 + - - +
330D HIS* 3.2 26.0 - - - -
333D THR* 2.6 30.9 + - - +
334D ASP 3.1 6.2 + - - -
335D PRO 3.8 3.1 - - - -
337D GLU* 1.3 77.2 - - - +
339D LEU* 1.3 55.0 + - - +
341D ASN* 3.4 1.4 + - - +
342D SER* 2.7 38.4 + - - -
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Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 4.7 7.0 - - + -
55D PRO* 4.1 13.7 - - + +
58D GLY 3.6 24.2 - - - +
59D VAL* 4.2 13.2 - - + +
88D ILE* 3.5 36.1 - - + +
95D THR* 5.3 0.2 - - - +
326D ILE* 4.0 31.3 - - + +
328D GLN* 4.2 1.3 - - - +
330D HIS* 3.4 24.0 - - + +
335D PRO 2.9 19.2 + - - +
336D ILE 3.8 0.2 - - - +
338D SER* 1.3 76.0 - - - +
340D ILE* 1.3 62.7 + - - +
342D SER* 3.9 2.3 - - - -
343D ALA* 3.0 25.6 + - - +
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Residues in contact with ILE 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D VAL* 5.1 0.2 - - + -
88D ILE* 4.2 16.2 - - + -
91D LEU* 4.1 27.4 - - + -
92D THR* 3.8 18.7 - - + +
336D ILE* 2.9 32.3 + - + +
337D GLU* 3.2 11.6 + - - +
339D LEU* 1.3 78.5 - - - +
341D ASN* 1.3 69.2 + - - +
343D ALA* 3.4 2.8 + - - +
344D ASN* 3.1 33.6 + - - +
402D PRO* 3.4 30.1 - - + +
403D VAL* 3.8 6.7 - - + +
406D TYR* 4.4 11.0 - - + -
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Residues in contact with ASN 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.5 36.3 - - + +
372A MET* 5.9 0.2 - - - -
375A GLU* 4.6 21.0 + - - +
293D ASP* 5.5 2.5 - - + +
337D GLU 3.0 11.3 + - - +
338D SER* 4.1 2.7 - - - +
340D ILE* 1.3 76.0 - - - +
342D SER* 1.3 60.7 + - - +
344D ASN* 3.4 17.7 - - - +
345D GLU* 2.9 28.8 + - - +
348D ARG* 5.8 0.2 + - - -
402D PRO* 5.5 1.2 - - - +
403D VAL* 3.4 21.9 - - - +
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Residues in contact with SER 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ASP* 3.4 17.2 - - - +
294D ALA* 4.0 7.5 - - - +
326D ILE* 4.2 9.4 - - - -
328D GLN* 3.0 37.7 + - - -
338D SER 2.7 23.8 + - - -
339D LEU* 3.9 4.5 - - - -
341D ASN* 1.3 73.8 - - - +
343D ALA* 1.3 66.8 + - - +
345D GLU* 3.1 8.0 + - - +
346D ILE* 3.0 26.7 + - - +
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Residues in contact with ALA 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D VAL* 4.2 12.2 - - + +
92D THR* 4.6 5.4 - - + +
94D ALA* 4.6 9.6 - - + +
95D THR* 3.7 28.5 - - + -
326D ILE* 4.0 9.6 - - + +
339D LEU 3.0 18.3 + - - +
340D ILE 3.6 4.7 - - - +
342D SER* 1.3 76.0 - - - +
344D ASN* 1.3 64.2 + - - +
346D ILE* 3.3 5.1 + - - +
347D ARG* 3.1 25.4 + - - +
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Residues in contact with ASN 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D THR* 3.7 22.4 + - - +
94D ALA* 5.6 1.8 - - - +
340D ILE* 3.1 23.4 + - - +
341D ASN* 3.4 23.5 - - - +
342D SER 3.1 0.2 - - - -
343D ALA* 1.3 78.0 - - - +
345D GLU* 1.3 57.4 + - - +
347D ARG* 3.2 10.4 + - - +
348D ARG* 2.8 39.3 + - - +
386D GLU* 5.8 0.7 - - - +
389D LEU* 3.6 6.5 - - + +
393D ARG* 3.3 32.0 + - - +
402D PRO* 4.0 7.8 - - - +
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Residues in contact with GLU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 3.7 25.7 + - - -
382A ARG* 5.0 3.6 + - - -
294D ALA 3.1 28.5 - - - +
295D GLY* 3.7 8.1 - - - -
299D PRO* 3.7 17.2 - - - +
302D LEU* 3.8 7.1 - - + +
341D ASN 2.9 16.2 + - - +
342D SER 3.1 3.8 + - - +
344D ASN* 1.3 74.0 - - - +
346D ILE* 1.3 60.8 + - - +
348D ARG* 2.9 41.5 + - - +
349D ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PHE* 3.6 18.8 - - + -
52D VAL* 4.0 9.4 - - + -
282D PHE* 3.6 39.0 - - + -
294D ALA* 4.1 14.8 - - + -
302D LEU* 4.3 10.1 - - + -
306D PHE* 3.4 27.3 - - + -
326D ILE* 3.6 25.4 - - + -
342D SER 3.0 13.7 + - - +
343D ALA* 3.6 7.0 - - - +
344D ASN 3.2 0.2 - - - -
345D GLU* 1.3 73.0 - - - +
347D ARG* 1.3 66.2 + - - +
349D ALA* 3.4 3.1 + - - +
350D TYR* 3.1 21.0 + - - +
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Residues in contact with ARG 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 3.0 33.9 + - + +
48D GLU* 3.3 22.6 + - - +
50D PHE* 2.9 42.5 + - + +
51D PHE* 3.7 2.2 - - - -
52D VAL* 6.3 0.7 - - + -
92D THR 3.8 15.0 + - - -
93D ARG* 3.1 23.6 + - - +
94D ALA* 3.2 18.1 - - + +
343D ALA 3.1 14.2 + - - +
344D ASN* 3.6 11.0 - - - +
346D ILE* 1.3 76.9 - - - +
348D ARG* 1.3 58.1 + - - +
350D TYR* 3.3 8.2 + - - +
351D ALA* 2.8 31.7 + - - +
389D LEU* 4.1 15.7 + - + +
392D ALA* 4.3 13.5 - - - +
393D ARG* 4.9 7.9 - - - +
396D THR* 5.4 1.0 + - - -
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Residues in contact with ARG 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ARG* 3.5 47.6 - - - +
341D ASN 5.8 0.2 + - - -
344D ASN* 2.8 24.4 + - - +
345D GLU* 2.9 38.2 + - - +
347D ARG* 1.3 76.5 - - - +
349D ALA* 1.3 61.6 + - - +
351D ALA* 3.3 2.9 + - - +
352D GLN* 3.0 45.1 + - - +
384D ASP* 4.6 1.4 + - - -
385D VAL* 3.6 16.5 - - + +
386D GLU* 3.0 40.8 + - - +
389D LEU* 3.6 19.1 - - + +
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Residues in contact with ALA 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D PRO 5.3 1.3 - - - +
302D LEU* 3.8 24.9 - - + +
303D PHE* 3.9 13.4 - - + +
306D PHE* 3.7 23.6 - - + +
345D GLU* 3.0 14.8 + - - +
346D ILE 3.9 1.6 - - - +
348D ARG* 1.3 73.3 - - - +
350D TYR* 1.3 65.4 + - - +
352D GLN* 3.4 11.7 + - - +
353D ALA* 3.0 23.9 + - - +
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Residues in contact with TYR 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LYS* 3.8 33.3 + - - +
47D VAL* 4.3 7.4 - - + -
50D PHE* 3.7 45.5 - + + -
306D PHE* 3.9 28.4 - + + -
310D VAL* 4.5 11.4 - - + -
313D GLU* 5.6 2.5 + - - -
346D ILE 3.1 17.5 + - - +
347D ARG* 3.5 7.4 - - - +
348D ARG 3.3 0.2 - - - -
349D ALA* 1.3 76.9 - - - +
351D ALA* 1.3 63.9 + - - +
353D ALA* 3.1 5.4 + - - +
354D LEU* 3.0 55.9 + - + +
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Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D VAL* 4.4 6.5 - - + +
47D VAL* 3.8 25.8 - - + -
347D ARG 2.8 17.7 + - - +
348D ARG 3.6 4.0 - - - +
350D TYR* 1.3 77.6 - - - +
352D GLN* 1.3 62.2 + - - +
354D LEU* 3.1 18.3 + - - +
355D LEU* 3.4 17.2 + - - +
385D VAL* 3.9 22.4 - - + -
388D ILE* 5.1 0.9 - - + -
389D LEU* 4.1 5.6 - - + -
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Residues in contact with GLN 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D PHE* 3.7 15.5 - - + +
348D ARG* 3.0 38.7 + - - +
349D ALA* 3.9 9.6 - - - +
350D TYR 3.3 0.2 - - - -
351D ALA* 1.3 76.0 - - - +
353D ALA* 1.3 63.5 + - - +
355D LEU* 3.0 18.0 + - - +
380D ALA* 3.3 35.5 - - - +
381D TYR* 3.1 43.8 + - - -
383D THR 3.1 18.3 + - - +
384D ASP* 5.1 0.8 - - - +
385D VAL* 3.9 11.4 - - + +
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Residues in contact with ALA 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D PHE* 3.6 11.8 - - + -
306D PHE* 3.7 21.3 - - + +
307D ASN* 4.1 6.7 - - - +
310D VAL* 3.6 23.2 - - + +
349D ALA 3.0 15.4 + - - +
350D TYR 3.1 9.8 + - - +
352D GLN* 1.3 78.5 - - - +
354D LEU* 1.3 61.0 + - - +
355D LEU 3.3 0.9 + - - -
356D VAL* 3.3 9.8 + - - +
358D ARG* 3.1 22.2 + - - +
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Residues in contact with LEU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 5.9 1.0 - - - +
43D VAL* 4.4 27.9 - - + +
46D LYS* 3.7 46.9 - - + +
47D VAL* 4.7 0.4 - - + -
310D VAL* 4.1 19.7 - - + -
313D GLU* 5.4 5.2 - - - +
350D TYR* 3.0 50.5 + - + +
351D ALA* 3.1 10.5 + - - +
353D ALA* 1.3 76.5 - - - +
355D LEU* 1.3 62.0 + - - +
356D VAL 3.3 5.1 + - - +
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Residues in contact with LEU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.9 27.4 - - + -
36D ARG* 4.3 7.6 + - - +
38D VAL* 4.2 18.9 - - + +
43D VAL* 3.9 29.8 - - + -
351D ALA 3.4 12.3 - - - +
352D GLN* 3.0 9.8 + - - +
354D LEU* 1.3 77.6 - - - +
356D VAL* 1.3 63.9 + - - +
357D ASP* 3.2 4.5 + - - +
380D ALA* 3.9 14.9 - - + +
383D THR* 3.6 40.2 - - + +
385D VAL* 3.8 15.7 - - + -
388D ILE* 5.3 0.7 - - + -
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Residues in contact with VAL 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D PHE* 4.0 9.9 - - + -
307D ASN* 4.0 2.0 - - - +
352D GLN 3.6 0.6 + - - +
353D ALA* 3.6 10.3 - - - +
354D LEU 3.3 6.0 - - - +
355D LEU* 1.3 77.5 - - - +
357D ASP* 1.3 70.1 + - - +
358D ARG* 2.9 51.9 + - - +
361D LEU* 4.0 19.1 - - + -
376D THR* 4.6 7.0 - - + +
377D LEU* 3.8 21.1 - - + -
380D ALA* 3.6 22.0 - - + -
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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