Contacts of the helix formed by residues 310 - 332 (chain A) in PDB entry 1JDN
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 ASN 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 2.9 41.0 + - - +
26A ARG* 5.0 2.2 - - - +
247A PHE* 3.3 16.8 - - + +
248A ASN* 4.0 7.9 - - - +
249A SER* 4.6 9.2 - - - -
307A ASP* 4.9 10.2 + - + +
309A VAL* 1.3 75.8 - - - +
311A MET* 1.3 66.1 + - - +
312A PHE* 2.6 39.5 + - - +
313A VAL* 2.9 18.9 + - - +
314A GLU* 3.1 27.1 + - - +
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Residues in contact with MET 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA* 4.1 1.7 - - - +
115A LEU* 4.4 4.7 - - + -
133A ALA* 3.7 18.5 - - + +
134A PRO* 3.6 37.0 - - + +
247A PHE* 3.1 58.2 + - + -
279A LEU* 3.9 24.7 - - + +
310A ASN* 1.3 74.5 - - - +
312A PHE* 1.3 85.1 + - + +
314A GLU* 3.9 4.9 - - - +
315A GLY* 2.9 24.8 + - - -
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.9 19.5 - - + -
22A PHE* 3.7 44.2 - + + -
27A VAL* 4.9 1.1 - - + -
90A VAL* 4.1 16.2 - - + -
112A ALA* 3.5 31.2 - - + -
115A LEU* 4.3 6.5 - - + -
247A PHE* 3.5 42.8 - + + -
310A ASN* 2.6 19.4 + - - +
311A MET* 1.3 92.7 - - + +
313A VAL* 1.3 65.1 + - - +
315A GLY* 3.0 9.5 + - - -
316A PHE* 3.0 25.8 + - + -
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU 4.5 4.9 - - - +
26A ARG* 3.3 28.3 - - + +
27A VAL* 4.5 8.7 - - + +
30A ALA* 3.3 36.7 - - + +
290A PHE* 3.9 14.9 - - + -
294A VAL* 4.3 4.5 - - + -
308A TYR 3.5 24.2 - - - +
309A VAL* 4.3 2.0 - - - -
310A ASN* 2.9 34.5 + - - +
312A PHE* 1.3 77.1 - - - +
314A GLU* 1.3 62.2 + - - +
316A PHE* 3.8 1.2 + - - +
317A HIS 3.6 7.6 + - - -
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASN* 5.6 0.5 - - - +
279A LEU* 4.4 7.3 - - - +
287A PHE* 3.3 25.2 - - + -
290A PHE* 4.4 11.9 - - + -
309A VAL* 4.2 10.8 - - + +
310A ASN* 3.1 21.7 + - - +
311A MET* 4.1 3.5 - - - +
313A VAL* 1.3 75.0 - - - +
315A GLY* 1.3 66.7 + - - +
317A HIS* 3.4 2.6 + - - +
318A ASP* 3.1 28.8 + - - +
355A ILE* 4.1 13.9 - - + -
356A ALA* 3.6 16.6 - - + +
1B NAG 2.7 35.3 - - - +
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Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA* 4.2 9.2 - - - -
132A VAL* 3.3 28.4 - - - +
133A ALA* 5.7 1.1 - - - -
311A MET 2.9 18.3 + - - -
312A PHE 3.0 4.2 + - - -
314A GLU* 1.3 77.6 - - - +
316A PHE* 1.3 56.8 + - - +
318A ASP* 3.1 4.5 + - - -
319A ALA* 2.8 24.9 + - - +
367A ARG* 5.9 2.0 - - - -
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.8 27.8 - - + -
22A PHE* 4.9 0.4 - - + -
27A VAL* 3.5 35.0 - - + -
31A ILE* 3.8 14.0 - - + +
87A LEU* 4.2 20.2 - - + +
88A GLY* 3.8 23.8 - - - -
90A VAL* 3.8 18.6 - - + -
110A LEU 4.0 2.2 - - - -
111A SER* 4.0 4.0 - - - -
112A ALA* 3.6 35.0 - - + -
312A PHE* 3.0 25.2 + - + +
313A VAL 4.5 1.8 - - - +
315A GLY* 1.3 72.3 - - - +
317A HIS* 1.3 68.1 + - - +
319A ALA* 3.2 15.0 + - + +
320A ILE* 3.4 16.6 + - - +
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Residues in contact with HIS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.6 18.5 + - - +
31A ILE* 4.7 0.2 - - - +
33A TYR* 3.5 33.9 - + - -
34A ALA* 3.4 20.2 - - + +
37A SER* 4.6 3.4 + - - -
286A GLU* 5.4 2.0 + - - -
290A PHE* 3.5 22.4 - + + -
313A VAL 3.6 8.7 + - - +
314A GLU 3.4 8.2 + - - +
315A GLY 3.2 0.6 - - - -
316A PHE* 1.3 78.5 - - - +
318A ASP* 1.3 74.3 + - - +
320A ILE* 3.2 16.6 + - - +
321A LEU* 3.5 34.9 + - + +
355A ILE* 3.2 26.8 - - + +
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 4.5 9.9 - - + -
314A GLU* 3.1 13.3 + - - +
315A GLY* 3.1 9.7 + - - +
317A HIS* 1.3 91.7 + - - +
319A ALA* 1.3 58.3 + - - +
320A ILE 3.3 0.2 - - - -
321A LEU* 3.5 5.8 + - - +
322A LEU* 3.0 27.7 + - - +
352A PHE* 3.5 14.6 - - + -
354A GLY* 3.4 22.5 - - - -
355A ILE* 3.0 21.4 + - - +
356A ALA* 4.8 2.1 + - - +
357A GLY 4.7 1.2 - - - +
359A VAL* 3.8 13.1 - - + +
367A ARG* 4.9 6.0 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.8 8.4 - - + +
110A LEU* 3.5 26.3 - - + +
111A SER 6.0 0.2 - - - -
132A VAL* 3.9 24.0 - - + -
315A GLY 2.8 18.9 + - - +
316A PHE* 3.6 21.1 - - + +
317A HIS 3.2 0.4 - - - -
318A ASP* 1.3 71.9 - - - +
320A ILE* 1.3 61.6 + - - +
322A LEU* 3.4 0.8 + - - -
323A TYR* 3.0 26.7 + - - +
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Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.4 3.1 - - + -
31A ILE* 4.1 17.3 - - + +
34A ALA* 3.6 25.1 - - + -
35A LEU* 4.1 27.4 - - + -
38A VAL* 3.8 19.3 - - + -
54A PHE* 5.1 8.7 - - + -
85A LEU* 4.8 10.1 - - + -
87A LEU* 3.8 23.6 - - + -
316A PHE 3.4 11.4 + - - +
317A HIS 3.2 8.9 + - - +
319A ALA* 1.3 75.0 - - - +
321A LEU* 1.3 67.7 + - - +
323A TYR* 3.1 15.9 + - + +
324A VAL* 3.1 16.8 + - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 4.5 5.4 - - + -
37A SER* 4.5 6.3 - - - +
38A VAL* 3.5 26.5 - - + -
317A HIS* 3.5 38.1 - - + +
318A ASP* 3.5 9.3 + - - +
319A ALA 3.4 0.2 - - - -
320A ILE* 1.3 75.7 - - - +
322A LEU* 1.3 64.6 + - - +
324A VAL* 3.3 6.6 + - - +
325A LEU* 2.9 34.1 + - + +
352A PHE* 4.0 15.0 - - + -
353A GLU 4.1 20.2 - - - +
354A GLY* 4.6 1.6 - - - -
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.0 13.5 - - + -
130A THR* 4.2 5.4 - - - +
132A VAL* 4.1 15.7 - - + -
318A ASP 3.0 16.8 + - - +
319A ALA 3.7 4.9 - - - +
321A LEU* 1.3 76.4 - - - +
323A TYR* 1.3 62.8 + - - +
325A LEU* 3.5 4.1 + - + +
326A ALA* 3.1 22.5 + - - +
347A THR* 2.9 41.1 - - - +
350A ARG* 4.0 23.6 - - + -
352A PHE* 3.8 24.7 - - + -
359A VAL* 5.7 0.2 - - + -
361A ILE* 4.1 22.0 - - + -
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Residues in contact with TYR 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.8 26.5 - - + +
54A PHE* 4.4 18.6 - + - -
84A ASP* 3.6 15.2 + - - +
85A LEU* 4.0 28.5 - - + -
108A PRO* 4.1 11.4 - - + -
110A LEU* 4.7 10.1 - - + -
319A ALA 3.0 14.4 + - - +
320A ILE* 3.1 11.2 + - + +
322A LEU* 1.3 76.3 - - - +
324A VAL* 1.3 60.5 + - - +
326A ALA* 3.1 6.3 + - - +
327A LEU* 2.8 47.6 + - + +
337A LYS* 4.0 16.3 - - - +
343A ILE* 3.6 42.7 - - + +
347A THR* 5.2 0.4 - - - -
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.5 31.6 - - + -
48A LEU 3.7 27.8 - - - +
49A PRO* 4.1 14.6 - - + -
54A PHE* 4.2 18.4 - - + -
320A ILE* 3.1 12.0 + - + +
321A LEU* 3.6 8.5 - - - +
323A TYR* 1.3 80.5 - - + +
325A LEU* 1.3 74.3 + - + +
326A ALA 3.0 0.3 + - - -
327A LEU* 3.0 9.7 + - + +
328A HIS* 3.0 26.9 + - + +
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 2.9 29.9 + - + +
322A LEU* 3.7 7.9 - - - +
324A VAL* 1.3 82.0 - - + +
326A ALA* 1.3 64.2 + - - +
328A HIS* 3.6 7.1 - - - +
329A GLU* 3.4 19.6 + - - +
350A ARG* 4.4 25.2 + - - +
351A THR 5.2 0.4 - - - +
352A PHE* 3.7 40.8 - - + -
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 3.1 15.0 + - + +
323A TYR* 3.4 8.5 - - - +
325A LEU* 1.3 74.3 - - - +
327A LEU* 1.3 66.9 + - - +
329A GLU* 2.9 16.0 + - - +
330A VAL* 2.9 18.1 + - - +
343A ILE* 3.5 33.0 - - + +
346A GLN* 3.9 21.5 - - + +
347A THR* 4.2 5.6 - - - +
350A ARG* 4.7 1.3 - - - +
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.2 19.7 - - + -
49A PRO* 5.1 19.1 - - + -
50A PRO* 5.9 0.7 - - + -
52A THR* 6.0 0.9 - - + -
54A PHE* 6.0 0.9 - - + -
323A TYR* 2.8 47.7 + - + +
324A VAL* 3.4 7.0 - - + +
326A ALA* 1.3 71.4 - - - +
328A HIS* 1.3 64.8 + - - +
330A VAL* 2.9 9.8 + - + +
331A LEU* 2.9 52.3 + - + +
336A SER 4.9 0.4 - - - -
337A LYS* 4.0 26.0 - - + -
343A ILE* 4.4 8.2 - - + +
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.5 43.1 + - + +
49A PRO* 5.9 3.8 - - + -
324A VAL* 3.0 15.0 + - + +
325A LEU* 3.6 13.0 - - - +
327A LEU* 1.3 77.1 - - - +
329A GLU* 1.3 70.0 + - - +
331A LEU* 3.7 11.4 - - - +
332A ARG* 3.3 40.1 + - + +
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU 3.4 9.2 + - - +
326A ALA* 2.9 11.0 + - - +
328A HIS* 1.3 88.9 - - - +
330A VAL* 1.3 61.4 + - - +
332A ARG* 3.5 33.1 + - - +
333A ALA* 3.6 17.2 + - - +
346A GLN* 3.6 36.6 + - + +
350A ARG* 4.6 11.9 + - - +
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA 2.9 22.2 - - - +
327A LEU* 2.9 6.2 + - + +
329A GLU* 1.3 76.2 - - - +
331A LEU* 1.3 70.7 + - + +
333A ALA* 3.0 15.0 + - - +
334A GLY 3.3 0.2 + - - -
335A TYR* 3.1 45.9 + - + -
336A SER 4.4 9.2 - - - +
342A LYS* 3.9 20.6 - - + +
343A ILE* 3.7 29.8 - - + -
346A GLN* 3.9 13.0 - - + -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 5.8 1.1 - - + -
50A PRO* 4.3 28.7 - - + -
327A LEU* 2.9 50.7 + - + +
328A HIS* 3.7 9.6 - - - +
330A VAL* 1.3 75.2 - - + +
332A ARG* 1.3 56.0 + - + +
334A GLY* 2.6 30.3 + - - -
335A TYR 3.4 19.2 - - - +
336A SER* 4.2 8.7 - - - -
337A LYS 4.4 1.1 - - - +
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Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS* 3.3 36.7 + - + +
329A GLU* 3.5 28.0 + - - +
331A LEU* 1.3 79.3 - - + +
333A ALA* 1.3 58.5 + - - +
334A GLY* 3.2 1.0 + - - -
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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