Contacts of the helix formed by residues 334 - 356 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A THR* 1.3 73.2 + - - +
335A PRO* 1.3 67.8 - - - +
336A ILE* 2.9 13.7 + - - +
337A GLU* 2.9 38.8 + - + +
338A SER* 3.1 10.6 + - - -
406A TYR* 2.8 26.2 + - - -
412A ARG* 2.8 40.6 + - - +
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Residues in contact with PRO 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY 3.5 14.4 - - - +
59A VAL* 3.0 28.9 - - - +
60A GLY* 3.7 18.8 - - - +
61A THR* 3.7 15.9 - - - +
74A GLU* 5.2 2.5 - - - +
330A HIS* 4.0 16.6 + - + +
333A THR 3.1 9.4 - - - +
334A ASP* 1.3 87.4 - - - +
336A ILE* 1.3 56.0 + - + +
338A SER* 3.4 1.4 + - - -
339A LEU* 2.9 36.3 + - - +
412A ARG* 4.2 8.7 - - - +
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 4.8 6.3 - - + -
84A ASP* 3.8 31.6 - - + +
87A VAL* 4.0 10.8 - - + -
88A ILE* 4.1 16.9 - - + +
334A ASP* 2.9 8.6 + - - +
335A PRO* 1.3 76.9 - - + +
337A GLU* 1.3 57.9 + - - +
339A LEU* 3.5 2.1 + - - +
340A ILE* 3.0 46.9 + - + +
406A TYR* 3.5 28.7 - - + +
411A TYR* 3.6 26.9 - - + -
412A ARG* 3.5 22.0 - - - +
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Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A THR* 5.8 0.2 - - - -
334A ASP* 2.9 24.4 + - + +
336A ILE* 1.3 75.4 - - - +
338A SER* 1.3 64.4 + - - +
340A ILE* 3.3 8.9 + - - +
341A ASN* 3.0 22.0 + - - +
403A VAL* 3.9 13.6 - - + +
406A TYR* 3.3 30.3 - - + -
407A ARG* 2.7 56.4 + - - +
371D LEU* 3.6 24.3 - - + +
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASP* 2.7 27.7 + - - +
330A HIS* 3.2 28.0 - - - -
333A THR* 2.6 31.9 + - - +
334A ASP 3.1 6.0 + - - -
335A PRO 3.9 2.0 - - - -
337A GLU* 1.3 77.3 - - - +
339A LEU* 1.3 54.3 + - - +
341A ASN* 3.4 0.8 + - - +
342A SER* 2.6 38.5 + - - -
371D LEU* 3.6 7.8 - - - +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.6 15.9 - - + -
55A PRO* 4.0 14.6 - - + -
58A GLY 3.7 24.0 - - - +
59A VAL* 4.2 7.4 - - + -
88A ILE* 3.5 37.2 - - + +
326A ILE* 3.9 32.4 - - + +
328A GLN* 4.3 0.4 - - - +
330A HIS* 3.6 20.9 - - + +
335A PRO 2.9 18.7 + - - +
336A ILE* 3.9 0.7 - - - +
338A SER* 1.3 75.5 - - - +
340A ILE* 1.3 63.0 + - - +
342A SER* 3.8 2.9 - - - -
343A ALA* 3.0 26.0 + - - +
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.2 15.7 - - + -
91A LEU* 4.1 26.7 - - + -
92A THR* 3.6 19.4 - - + +
336A ILE* 3.0 42.1 + - + +
337A GLU* 3.4 9.9 - - - +
339A LEU* 1.3 78.8 - - - +
341A ASN* 1.3 68.4 + - - +
343A ALA* 3.4 2.4 + - - +
344A ASN* 3.1 32.8 + - - +
402A PRO* 3.3 31.4 - - + +
403A VAL* 4.0 5.2 - - + -
406A TYR* 4.5 10.1 - - + -
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Residues in contact with ASN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASP* 5.5 2.9 - - + +
337A GLU 3.0 8.4 + - - +
338A SER 4.2 2.5 - - - +
340A ILE* 1.3 78.3 - - - +
342A SER* 1.3 60.6 + - - +
344A ASN* 3.4 18.4 - - - +
345A GLU* 2.9 32.9 + - + +
402A PRO* 5.4 0.7 - - - +
403A VAL* 3.3 22.1 + - - +
371D LEU* 3.7 33.9 - - + +
372D MET* 5.9 0.2 - - - -
375D GLU* 4.5 22.3 + - - +
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Residues in contact with SER 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASP* 3.4 16.9 - - - +
294A ALA* 3.9 8.4 - - - +
326A ILE* 4.3 6.1 - - - -
328A GLN* 3.0 35.9 + - - -
338A SER 2.6 24.8 + - - -
339A LEU* 3.8 4.9 - - - -
341A ASN* 1.3 74.9 - - - +
343A ALA* 1.3 65.9 + - - +
345A GLU* 3.1 7.5 + - - +
346A ILE* 3.0 29.6 + - - +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.2 11.4 - - + +
92A THR* 4.6 5.8 - - - +
94A ALA* 4.5 9.5 - - + +
95A THR* 3.8 28.0 - - + -
326A ILE* 4.0 10.6 - - + +
339A LEU 3.0 17.1 + - - +
340A ILE* 3.7 5.2 - - - +
342A SER* 1.3 76.2 - - - +
344A ASN* 1.3 65.5 + - - +
346A ILE* 3.3 4.2 + - - +
347A ARG* 3.1 26.6 + - - +
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Residues in contact with ASN 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.8 21.0 + - - +
94A ALA* 5.6 1.8 - - - +
340A ILE* 3.1 20.6 + - - +
341A ASN* 3.4 24.3 - - + +
343A ALA* 1.3 79.1 - - - +
345A GLU* 1.3 56.6 - - - +
347A ARG* 3.2 7.7 + - - +
348A ARG* 2.8 42.4 + - - +
386A GLU* 5.7 0.2 - - - +
389A LEU* 3.5 9.3 - - + +
393A ARG* 3.4 30.2 + - - +
402A PRO* 3.9 14.7 - - - +
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA 3.2 30.3 - - - +
295A GLY* 4.2 9.5 - - - +
296A ALA* 5.8 0.2 - - - -
299A PRO* 4.6 7.6 - - - +
302A LEU* 3.9 7.1 - - + +
341A ASN* 2.9 17.3 + - + +
342A SER 3.1 6.7 + - - +
344A ASN* 1.3 75.6 - - - +
346A ILE* 1.3 57.4 + - - +
348A ARG* 2.6 45.9 + - - +
349A ALA* 3.0 29.1 + - - +
375D GLU* 5.6 0.2 - - - +
378D LYS* 3.9 21.4 + - - +
382D ARG* 4.4 7.3 + - - -
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Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.6 18.8 - - + -
52A VAL* 4.1 7.4 - - + -
282A PHE* 3.6 31.9 - - + -
294A ALA* 3.9 15.0 - - + -
302A LEU* 4.3 9.2 - - + -
306A PHE* 3.5 29.2 - - + -
326A ILE* 3.5 33.2 - - + -
342A SER 3.0 15.0 + - - +
343A ALA* 3.6 7.4 - - - +
345A GLU* 1.3 73.1 - - - +
347A ARG* 1.3 64.7 + - - +
349A ALA 3.4 1.0 + - - -
350A TYR* 3.0 22.0 + - - +
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.1 26.9 + - + +
48A GLU* 3.2 28.5 + - - +
50A PHE* 2.9 43.7 + - + +
51A PHE* 3.8 2.2 - - - -
52A VAL* 6.3 0.4 - - + -
92A THR 3.8 15.4 + - - -
93A ARG* 3.1 23.0 + - - +
94A ALA* 3.3 19.1 - - + +
343A ALA 3.1 14.3 + - - +
344A ASN* 3.7 10.5 - - - +
346A ILE* 1.3 77.0 - - - +
348A ARG* 1.3 58.4 + - - +
350A TYR* 3.5 8.6 - - - +
351A ALA* 2.8 31.7 + - - +
389A LEU* 4.0 18.0 + - + +
392A ALA* 4.2 15.0 - - - +
393A ARG* 4.9 6.5 - - - +
396A THR* 5.5 1.0 + - - -
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASN 5.7 0.2 + - - -
344A ASN* 2.8 25.1 + - - +
345A GLU* 2.6 44.6 + - - +
347A ARG* 1.3 76.1 - - - +
349A ALA* 1.3 62.7 + - - +
351A ALA* 3.3 2.4 + - - +
352A GLN* 3.0 43.6 + - - +
384A ASP* 4.6 1.0 + - - -
385A VAL* 3.5 17.2 - - + +
386A GLU* 2.9 42.6 + - - +
389A LEU* 3.7 18.3 - - + +
382D ARG* 3.6 39.1 - - - +
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PRO 5.2 1.3 - - - +
302A LEU* 3.7 31.4 - - + -
303A PHE* 3.9 18.5 - - + +
306A PHE* 3.7 14.8 - - + +
345A GLU 3.0 12.0 + - - +
346A ILE 3.8 1.1 - - - +
348A ARG* 1.3 76.7 - - - +
350A TYR* 1.3 62.9 + - - +
352A GLN* 3.4 13.0 + - - +
353A ALA* 3.0 23.4 + - - +
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Residues in contact with TYR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.4 43.8 + - - +
47A VAL* 4.2 7.2 - - + -
50A PHE* 3.7 46.2 - + + -
306A PHE* 3.9 29.5 - + + -
310A VAL* 4.4 11.2 - - + -
313A GLU* 6.1 0.4 - - - -
346A ILE 3.0 17.5 + - - +
347A ARG* 3.5 8.5 - - - +
349A ALA* 1.3 77.7 - - - +
351A ALA* 1.3 63.6 + - - +
353A ALA* 3.1 5.2 + - - +
354A LEU* 3.0 50.2 + - + +
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 4.3 6.7 - - + +
47A VAL* 3.8 25.6 - - + -
347A ARG 2.8 18.2 + - - +
348A ARG 3.7 4.3 - - - +
350A TYR* 1.3 75.6 - - - +
352A GLN* 1.3 63.1 + - - +
354A LEU* 3.1 18.3 + - - +
355A LEU* 3.2 18.2 + - - +
385A VAL* 4.1 22.0 - - + -
388A ILE* 5.0 1.6 - - + -
389A LEU* 4.3 4.7 - - + -
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Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 3.6 14.9 - - + +
348A ARG* 3.0 36.8 + - - +
349A ALA* 3.8 10.7 - - - +
351A ALA* 1.3 73.2 - - - +
353A ALA* 1.3 66.7 + - - +
355A LEU* 3.0 18.1 + - - +
380A ALA* 3.3 35.2 - - - +
381A TYR* 3.0 45.7 + - - -
383A THR 3.1 13.7 + - - -
384A ASP* 5.2 0.6 - - - +
385A VAL* 4.0 14.7 - - + +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 3.6 11.2 - - + -
306A PHE* 3.7 23.3 - - + +
307A ASN* 4.0 5.8 - - - +
310A VAL* 3.6 23.5 - - + +
349A ALA 3.0 14.3 + - - +
350A TYR 3.1 9.2 + - - +
352A GLN* 1.3 76.4 - - - +
354A LEU* 1.3 60.6 + - - +
355A LEU 3.4 0.5 + - - -
356A VAL* 3.4 10.5 + - - +
358A ARG* 2.9 23.2 + - - +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 5.9 0.7 - - - +
43A VAL* 4.2 29.3 - - + +
46A LYS* 3.8 38.6 - - + +
47A VAL* 4.5 0.7 - - + -
310A VAL* 4.1 19.5 - - + -
313A GLU* 5.3 1.1 - - - +
350A TYR* 3.0 57.8 + - + +
351A ALA* 3.3 9.4 - - - +
352A GLN 3.1 0.2 - - - -
353A ALA* 1.3 77.9 - - - +
355A LEU* 1.3 59.5 + - - +
356A VAL 3.5 5.0 + - - +
358A ARG* 5.9 0.2 + - - -
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.1 18.8 - - + -
36A ARG* 4.5 8.5 + - - +
38A VAL* 4.0 28.5 - - + +
43A VAL* 3.9 30.5 - - + -
351A ALA 3.4 11.9 - - - +
352A GLN* 3.0 9.6 + - - +
354A LEU* 1.3 75.9 - - - +
356A VAL* 1.3 64.3 + - - +
357A ASP* 3.3 3.8 + - - +
380A ALA* 3.9 16.0 - - + +
383A THR* 3.7 36.6 - - + +
385A VAL* 3.7 19.5 - - + -
388A ILE* 5.1 1.1 - - + -
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 4.0 17.3 - - + -
307A ASN* 4.1 4.0 - - - +
352A GLN 3.9 2.9 - - - +
353A ALA 3.5 15.7 - - - +
354A LEU 3.3 6.6 - - - +
355A LEU* 1.3 76.5 - - - +
357A ASP* 1.3 68.9 + - - +
358A ARG* 2.9 42.3 + - - +
361A LEU* 4.1 9.2 - - + -
376A THR* 4.4 8.1 - - + +
377A LEU* 4.0 22.2 - - + -
380A ALA* 3.6 21.5 - - + -
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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