Contacts of the helix formed by residues 38 - 61 (chain B) in PDB entry 5FWP
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 ILE 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.5 33.0 - - + -
34B SER 5.5 0.2 - - - +
35B ASN* 3.3 42.6 - - + +
36B LYS* 3.9 2.7 - - - +
37B GLU* 1.3 78.4 - - + +
39B PHE* 1.3 65.7 + - - +
40B LEU 3.1 2.7 - - - -
41B ARG* 3.0 42.3 + - - +
42B GLU* 3.0 15.5 + - + +
135B SER* 5.0 3.6 - - - -
138B LEU* 4.3 5.8 - - + -
204B LYS* 5.1 0.4 - - - +
205B HIS* 4.3 11.9 - - - +
393B GLU* 3.4 27.6 - - + +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS 3.2 23.6 + - - +
37B GLU 3.1 6.4 - - - -
38B ILE* 1.3 77.7 - - - +
40B LEU* 1.3 90.3 + - + +
42B GLU* 4.0 0.7 - - - +
43B LEU* 3.1 34.8 + - + +
84B LEU* 4.1 5.4 - - + -
135B SER* 3.6 33.7 - - - +
136B ALA* 4.0 11.0 - - - -
139B VAL* 3.6 25.8 - - + -
140B ALA* 6.5 0.2 - - + -
183B LEU* 3.5 32.8 - - + -
185B LEU* 4.9 2.0 - - + -
192B TYR* 3.7 43.1 - + + -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU 3.3 5.5 + - - +
38B ILE 3.1 0.6 - - - -
39B PHE* 1.3 110.3 - - + +
41B ARG* 1.3 58.9 + - - +
43B LEU* 3.3 4.7 + - + +
44B ILE* 2.8 52.2 + - + +
75B ILE* 5.4 10.8 - - + -
84B LEU* 3.8 18.4 - - + -
86B LEU* 5.9 5.6 - - + -
183B LEU* 5.4 0.7 - - + -
192B TYR* 5.0 4.3 - - + -
198B VAL* 4.5 24.0 - - + +
201B VAL* 3.8 34.3 - - + -
202B VAL* 5.5 2.7 - - + +
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 5.3 3.2 - - - -
37B GLU 4.5 0.2 + - - -
38B ILE* 3.0 31.8 + - - +
40B LEU* 1.3 79.3 - - - +
42B GLU* 1.3 81.4 + - - +
44B ILE* 3.8 4.9 - - - +
45B SER* 2.6 46.9 + - - +
201B VAL* 4.8 2.5 - - + +
205B HIS* 3.3 63.3 + - + +
206B SER* 4.7 8.0 + - - +
360B VAL* 4.2 18.4 - - + -
361B PHE 4.9 1.1 + - - -
362B ILE* 6.4 0.4 - - - -
392B ARG* 4.5 16.1 - - - +
393B GLU* 2.8 37.3 + - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 5.4 5.8 - - + -
38B ILE* 3.0 15.8 + - + +
39B PHE 4.0 1.1 - - - +
41B ARG* 1.3 112.8 + - - +
43B LEU* 1.3 61.6 + - + +
45B SER* 3.6 6.6 + - - -
46B ASN* 3.0 33.6 + - - +
132B GLY* 3.5 22.2 - - - +
135B SER* 3.6 27.1 - - - +
392B ARG* 3.9 15.9 + - - +
1692B ATP 3.3 24.1 + - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.1 25.2 + - + +
40B LEU* 3.9 4.0 - - + +
42B GLU* 1.3 75.0 - - + +
44B ILE* 1.3 60.5 + - - +
46B ASN* 3.3 10.5 + - + +
47B ALA* 2.9 27.2 + - - +
86B LEU* 3.6 21.8 - - + -
88B ASP* 4.2 5.1 - - - +
133B PHE* 4.3 31.0 - - + +
135B SER* 5.7 0.9 - - - +
136B ALA* 4.4 10.3 - - + -
181B VAL* 4.2 21.8 - - + -
183B LEU* 3.9 35.9 - - + -
1692B ATP 6.4 0.7 - - + +
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 2.8 35.5 + - + +
41B ARG 3.9 2.2 - - - +
43B LEU* 1.3 72.5 - - - +
45B SER* 1.3 68.0 + - - +
47B ALA* 3.1 8.7 + - - +
48B SER* 2.9 20.6 + - - -
73B ILE* 3.6 21.9 - - + +
75B ILE* 4.3 19.5 - - + -
86B LEU* 4.8 9.9 - - + -
202B VAL* 5.1 8.5 - - + -
206B SER* 3.8 23.1 - - - +
209B ILE* 4.2 10.3 - - + -
213B ILE* 3.6 30.5 - - + -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 2.6 38.5 + - - +
42B GLU* 3.6 9.7 + - - -
44B ILE* 1.3 72.9 - - - +
46B ASN* 1.3 62.2 + - - +
48B SER* 2.7 24.0 + - - -
49B ASP* 2.9 20.4 + - - +
126B ILE* 4.0 27.4 - - - +
209B ILE* 5.3 6.6 - - - +
360B VAL* 4.8 7.5 - - - +
1692B ATP 5.9 1.6 - - - -
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Residues in contact with ASN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 3.0 20.2 + - - +
43B LEU* 3.5 14.0 - - + +
45B SER* 1.3 74.4 - - - +
47B ALA* 1.3 66.7 + - - +
49B ASP* 3.3 11.4 + - - +
50B ALA* 3.1 21.7 + - - +
126B ILE* 6.0 0.2 - - - +
132B GLY 4.7 0.4 - - - -
133B PHE* 4.4 14.5 - - - +
1692B ATP 2.7 55.0 + - + +
1693B MG 1.5 29.8 - - - -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU 2.9 10.6 + - - +
44B ILE* 3.1 10.1 + - - +
46B ASN* 1.3 77.1 - - - +
48B SER* 1.3 56.2 + - - +
50B ALA* 3.1 5.5 + - - +
51B LEU* 2.9 32.1 + - + +
73B ILE* 3.6 20.0 - - + -
88B ASP* 3.3 32.5 - - + +
90B GLY* 5.1 0.3 - - - -
1692B ATP 3.7 11.8 + - - -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE 2.9 11.5 + - - -
45B SER* 2.7 24.1 + - - -
47B ALA* 1.3 72.3 - - - +
49B ASP* 1.3 62.1 + - - +
51B LEU* 3.3 12.0 + - - +
52B ASP* 2.9 35.7 + - - -
73B ILE* 4.0 2.0 - - - +
209B ILE* 4.1 23.9 - - - +
211B TYR* 3.6 16.1 - - - -
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER 2.9 21.7 + - - +
46B ASN* 3.4 21.3 - - - +
47B ALA 3.2 0.2 - - - -
48B SER* 1.3 78.5 + - - +
50B ALA* 1.3 57.0 + - - +
52B ASP* 3.1 2.8 + - - +
53B LYS* 2.8 29.7 + - - +
110B THR* 4.4 8.0 + - - +
124B SER 4.9 0.5 - - - +
125B MET* 3.3 33.8 - - - +
126B ILE* 2.8 48.0 + - - +
1693B MG 4.0 1.7 - - - -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN 3.1 6.3 + - - +
47B ALA 3.1 7.6 + - - +
49B ASP* 1.3 75.6 - - - +
51B LEU* 1.3 59.5 + - - +
53B LYS* 3.1 17.8 + - + +
54B ILE* 3.0 30.8 + - - +
90B GLY* 3.7 13.1 - - - -
91B ILE 4.0 2.2 + - - +
1692B ATP 3.3 44.6 - - + +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 2.9 16.8 + - + +
48B SER* 3.6 3.1 - - - +
49B ASP 3.2 0.2 - - - -
50B ALA* 1.3 76.1 - - - +
52B ASP* 1.3 58.6 + - - +
54B ILE* 3.3 6.5 + - - +
55B ARG* 3.1 21.8 + - - +
71B LEU* 3.7 14.7 - - + +
72B LYS 3.6 16.4 - - - +
73B ILE* 3.8 22.7 - - + -
88B ASP 5.9 0.2 - - - -
89B THR* 3.0 45.1 - - - +
90B GLY 4.9 0.2 - - - +
211B TYR* 3.4 57.1 + - + -
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Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 2.9 17.6 + - - +
49B ASP* 3.4 9.9 - - - +
51B LEU* 1.3 74.2 - - - +
53B LYS* 1.3 64.0 + - - +
55B ARG* 3.3 8.2 + - - +
56B TYR* 2.9 25.1 + - - +
123B ILE* 3.8 15.6 - - + +
124B SER 3.3 25.0 + - - +
125B MET* 3.7 15.6 - - + +
211B TYR* 2.6 32.4 + - - -
359B ARG* 5.3 5.2 + - - -
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASP* 2.8 19.6 + - - +
50B ALA* 3.1 20.5 + - + +
52B ASP* 1.3 75.8 - - - +
54B ILE* 1.3 62.8 + - - +
56B TYR 3.4 0.2 + - - -
57B GLU* 3.0 28.9 + - - +
91B ILE* 3.6 22.0 - - + -
109B GLY* 4.2 13.3 + - - -
110B THR* 4.3 13.5 + - - +
113B PHE* 3.4 40.6 - - + -
125B MET* 3.4 15.9 - - + +
1692B ATP 3.6 34.8 + - + -
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA 3.0 13.6 + - - +
51B LEU* 3.4 6.1 - - + +
53B LYS* 1.3 74.0 - - - +
55B ARG* 1.3 57.1 + - - +
57B GLU* 3.1 4.2 + - - +
58B SER* 2.8 32.7 + - - -
64B LYS* 5.3 4.1 - - + +
65B LEU* 3.5 17.9 - - + -
71B LEU* 3.3 20.6 - - + -
89B THR 3.0 28.9 - - - +
90B GLY* 3.4 13.2 - - - -
91B ILE* 3.5 24.5 - - + +
177B ARG* 3.5 29.6 - - - +
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU 3.1 11.3 + - - +
52B ASP* 3.5 10.1 - - - +
54B ILE* 1.3 80.0 - - - +
56B TYR* 1.3 62.7 + - - +
58B SER* 2.6 24.2 + - - +
59B LEU* 3.0 30.9 + - + +
71B LEU* 4.3 11.0 - - + -
122B ASP* 2.8 45.0 + - - -
123B ILE* 3.3 19.7 - - - +
211B TYR* 3.8 17.7 - - - +
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP 2.9 16.3 + - - +
53B LYS 3.7 3.4 - - - +
55B ARG* 1.3 75.7 - - - +
57B GLU* 1.3 76.4 + - - +
59B LEU* 3.1 34.9 + - + +
60B THR* 3.6 21.4 + - + +
113B PHE* 3.6 23.8 - + + -
116B ALA* 3.9 22.3 + - + -
117B LEU* 3.5 20.8 - - + -
119B ALA* 4.5 7.4 - - - +
120B GLY 3.9 12.4 + - - -
121B ALA* 3.6 21.1 - - + -
123B ILE* 3.7 19.5 - - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS 3.0 21.1 + - - +
54B ILE* 3.7 5.4 - - - +
56B TYR* 1.3 90.3 - - - +
58B SER* 1.3 56.8 + - - +
60B THR* 2.7 26.1 + - - -
61B ASP 2.9 9.2 + - - -
64B LYS* 2.7 48.0 + - + +
91B ILE* 4.0 13.9 - - + -
113B PHE* 3.3 27.1 - - + -
116B ALA* 5.5 2.8 - - - +
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 2.8 16.6 + - - -
55B ARG* 2.6 24.6 + - - +
57B GLU* 1.3 70.9 - - - +
59B LEU* 1.3 65.2 + - - +
61B ASP 3.5 10.1 - - - -
62B PRO* 3.1 28.3 - - - +
64B LYS* 4.5 3.3 - - - +
65B LEU* 3.5 41.1 - - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 3.0 45.7 + - + +
56B TYR* 3.1 34.5 + - + +
58B SER* 1.3 78.2 + - - +
60B THR* 1.3 61.8 + - + +
62B PRO* 4.9 2.1 - - - +
121B ALA* 6.3 0.4 - - - -
122B ASP* 4.3 8.5 - - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 3.9 29.8 - - + +
57B GLU* 2.7 20.4 + - - -
59B LEU* 1.3 81.2 - - + +
61B ASP* 1.3 62.8 + - - +
62B PRO* 3.9 4.4 - - - +
64B LYS* 3.9 11.8 + - - -
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU 2.9 4.9 + - - -
58B SER* 3.4 6.9 - - - -
60B THR* 1.3 82.1 - - - +
62B PRO* 1.3 60.7 - - - +
63B SER* 2.6 33.1 + - - -
64B LYS* 3.0 51.8 + - - +
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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