Contacts of the helix formed by residues 66 - 88 (chain C) in PDB entry 3DOY
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 PRO 66 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 4.6 9.2 - - + -
55C PHE* 5.2 0.4 - - + -
58C HIS* 3.8 29.8 - - + +
64C ILE 3.2 3.8 - - - +
65C PHE* 1.3 97.8 - - + +
67C GLY* 1.3 66.1 + - - +
68C VAL* 4.2 5.8 - - + -
69C LEU* 2.9 38.2 + - + +
70C ILE* 3.2 11.3 + - - +
1003C CL 4.2 0.2 - - + -
27D MET* 3.6 34.3 - - + -
72D GLU* 5.2 1.6 - - - +
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE 3.4 2.2 + - - -
66C PRO* 1.3 71.0 - - - +
68C VAL* 1.3 61.8 - - - +
70C ILE* 3.1 19.2 + - - +
71C VAL* 3.3 7.1 + - - +
109C PHE* 3.2 42.4 - - - -
1003C CL 3.2 22.8 - - - +
72D GLU* 5.5 0.4 + - - -
101D PHE* 5.2 0.7 - - - -
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PRO* 4.2 11.0 - - + -
67C GLY* 1.3 75.2 - - - +
69C LEU* 1.3 66.3 + - + +
70C ILE 3.3 0.2 - - - -
71C VAL* 3.5 8.3 + - - +
72C GLU* 3.1 18.9 + - - +
109C PHE* 5.0 0.4 - - - -
27D MET* 4.8 0.7 - - + -
68D VAL* 3.5 48.3 - - + +
69D LEU* 4.5 7.2 - - + -
71D VAL* 4.6 2.9 - - + -
72D GLU* 3.6 36.8 + - + +
101D PHE* 3.7 21.0 - - + -
104D ILE* 4.4 10.3 - - + -
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C MET* 4.5 15.9 - - - -
29C LEU* 3.7 25.4 - - + +
54C VAL* 3.9 22.2 - - + -
65C PHE* 3.8 26.3 - - + -
66C PRO* 2.9 41.0 + - + +
68C VAL* 1.3 83.8 - - + +
70C ILE* 1.3 60.3 + - - +
71C VAL 3.2 0.4 - - - -
72C GLU* 3.5 4.7 - - + +
73C GLY* 3.0 22.7 + - - -
121C TYR* 4.6 1.0 + - - -
27D MET* 5.0 3.8 - - - -
68D VAL* 4.4 16.2 - - + -
69D LEU* 4.6 9.4 - - + -
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Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE* 3.8 20.4 - - + +
66C PRO 3.2 9.4 + - - +
67C GLY* 3.1 21.0 + - - +
69C LEU* 1.3 77.3 - - - +
71C VAL* 1.3 64.1 + - + +
73C GLY 3.2 1.2 + - - -
74C MET* 3.0 26.1 + - + +
109C PHE* 4.4 13.0 - - + -
111C ILE 5.4 0.9 - - - +
113C VAL* 3.4 30.7 - - + +
119C LEU* 4.0 15.3 - - + -
121C TYR* 3.6 3.2 - - + -
139C ALA* 3.5 31.0 - - + -
146C VAL* 4.7 6.3 - - + -
147C ALA* 4.3 9.9 - - + -
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY 3.3 12.5 + - - +
68C VAL* 3.7 10.3 - - - +
69C LEU 3.2 0.2 - - - -
70C ILE* 1.3 79.1 - - + +
72C GLU* 1.3 56.6 + - - +
74C MET* 3.2 11.0 + - - +
75C ALA* 2.8 26.8 + - + +
104C ILE* 4.0 22.2 - - + -
107C VAL* 4.0 31.0 - - + -
109C PHE* 4.1 6.3 - - + -
149C ALA* 4.6 8.1 - - + -
151C LEU* 3.9 26.4 - - + +
68D VAL* 4.7 4.5 - - + -
104D ILE* 5.2 4.3 - - + -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C HIS* 3.5 17.2 + - - -
27C MET* 3.8 17.8 - - + +
29C LEU* 3.5 15.5 - - + -
68C VAL 3.1 15.2 + - - +
69C LEU* 3.5 10.1 - - + +
70C ILE 3.2 0.4 - - - -
71C VAL* 1.3 74.9 - - - +
73C GLY* 1.3 60.1 + - - +
75C ALA* 3.1 10.9 + - - +
76C GLN* 2.7 58.9 + - - +
3002C 2BE 5.6 0.3 - - - +
58D HIS* 4.6 5.2 + - - -
66D PRO* 5.4 1.4 - - - +
67D GLY 5.8 0.7 + - - -
68D VAL* 3.7 24.5 - - + +
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Residues in contact with GLY 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 4.0 13.9 - - - +
30C VAL* 3.8 2.6 - - - +
69C LEU 3.0 11.6 + - - -
70C ILE 3.2 0.4 + - - -
72C GLU* 1.3 77.2 - - - +
74C MET* 1.3 57.7 + - - +
76C GLN* 3.4 5.5 + - - +
77C SER* 3.0 31.2 + - - -
121C TYR* 3.4 31.6 - - - -
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Residues in contact with MET 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.0 23.4 + - + +
71C VAL* 3.4 15.5 - - + +
72C GLU 3.1 0.2 - - - -
73C GLY* 1.3 75.1 - - - +
75C ALA* 1.3 58.9 + - - +
77C SER 3.2 1.6 + - - -
78C GLY 2.9 23.9 + - - -
121C TYR* 3.5 18.6 - - + -
123C LEU* 3.2 30.3 - - + +
137C GLY* 3.5 11.7 - - - +
138C THR* 3.5 40.2 - - - +
139C ALA* 4.2 14.1 - - + -
147C ALA* 5.2 1.8 - - - -
148C GLU* 4.6 3.6 - - - -
149C ALA* 4.1 24.2 - - + +
151C LEU* 4.0 9.2 - - + -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C VAL* 2.8 14.7 + - + +
72C GLU* 3.1 16.4 + - - +
74C MET* 1.3 75.6 - - - +
76C GLN* 1.3 57.1 + - - +
78C GLY 3.1 1.3 + - - +
79C GLY 2.8 25.1 + - - -
101C PHE* 3.0 41.4 - - + -
104C ILE* 6.2 1.6 - - + -
151C LEU* 3.4 20.6 - - + +
3002C 2BE 5.3 0.2 - - + -
68D VAL* 6.2 1.1 - - + -
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Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 4.2 12.7 - - + +
23C HIS* 3.3 26.1 - - + +
27C MET 2.7 25.2 + - - -
28C LEU* 3.7 7.7 - - - +
29C LEU* 2.7 30.6 + - - +
30C VAL* 3.7 13.9 - - + +
72C GLU* 2.7 48.8 + - - +
73C GLY 3.6 5.2 - - - +
75C ALA* 1.3 75.9 - - - +
77C SER* 1.3 63.0 + - - +
79C GLY* 3.1 2.4 + - - -
80C PHE* 2.9 23.4 + - - +
3002C 2BE 4.0 7.4 - - + -
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Residues in contact with SER 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 4.0 9.2 - - - +
42C ILE* 3.4 29.7 - - - +
44C ALA* 4.1 7.4 - - - +
73C GLY 3.0 14.8 + - - -
74C MET 3.2 8.3 + - - -
76C GLN* 1.3 75.7 - - - +
78C GLY* 1.3 62.6 + - - +
80C PHE* 3.2 3.9 + - - -
81C LEU* 3.0 18.7 + - - +
121C TYR* 3.3 22.9 - - - +
123C LEU* 3.5 16.8 - - - -
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Residues in contact with GLY 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C MET 2.9 14.8 + - - -
75C ALA 3.6 3.6 - - - -
77C SER* 1.3 75.4 - - - +
79C GLY* 1.3 57.6 + - - +
81C LEU* 3.1 8.3 + - - +
82C ALA* 2.9 29.9 + - - +
101C PHE* 4.9 2.0 - - - -
123C LEU* 4.3 3.3 - - - +
135C VAL* 4.5 29.2 - - - -
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Residues in contact with GLY 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 4.7 0.2 - - - -
75C ALA 2.8 13.2 + - - -
76C GLN 3.1 5.1 + - - -
78C GLY* 1.3 77.2 - - - +
80C PHE* 1.3 60.9 + - - +
82C ALA* 3.5 3.9 + - - +
83C PHE* 3.0 25.5 + - - +
99C VAL* 4.5 16.6 - - - +
101C PHE* 4.3 2.1 - - - -
3002C 2BE 3.7 25.1 + - - -
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Residues in contact with PHE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.8 31.4 - + + -
16C HIS 4.7 0.2 - - - -
17C ILE* 4.3 19.5 - - + -
20C ILE* 3.6 38.6 - - + -
21C LEU* 4.3 20.5 - - + +
33C ILE* 4.1 19.7 - - + -
36C LEU* 4.0 13.7 - - + -
42C ILE* 4.0 16.6 - - + -
76C GLN 2.9 11.9 + - - +
77C SER* 3.2 9.2 + - - +
79C GLY* 1.3 76.4 - - - +
81C LEU* 1.3 60.6 + - - +
83C PHE* 4.0 3.1 - - - +
84C THR* 2.8 53.9 + - + +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.4 26.5 - - + -
37C GLN 3.7 14.1 - - - +
38C ALA* 4.8 0.2 - - - -
39C ASN 4.4 1.3 - - - +
40C GLN 4.3 0.4 - - - +
41C LYS* 3.6 34.1 - - - +
42C ILE* 4.0 13.2 - - + -
77C SER 3.0 12.8 + - - +
78C GLY* 3.3 7.4 - - - +
80C PHE* 1.3 73.8 - - - +
82C ALA* 1.3 68.0 + - - +
84C THR* 3.0 6.1 + - - +
85C SER* 2.9 36.3 + - - +
123C LEU 4.3 4.5 - - - +
124C GLU* 4.7 1.8 - - - -
125C VAL* 3.9 26.5 - - + +
133C TRP* 5.5 0.4 - - + -
135C VAL* 5.0 6.7 - - + -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLY 2.9 15.4 + - - +
79C GLY* 3.8 7.0 - - - +
81C LEU* 1.3 75.4 - - - +
83C PHE* 1.3 64.0 + - - +
85C SER* 3.0 18.0 + - - -
86C LEU* 3.2 14.8 + - - +
99C VAL* 5.5 3.4 - - + -
133C TRP* 3.7 41.7 - - + -
155C ILE* 3.9 14.8 - - + -
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Residues in contact with PHE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 3.6 39.0 - - + -
79C GLY 3.0 15.2 + - - +
80C PHE 4.0 2.5 - - - +
82C ALA* 1.3 79.5 - - - +
84C THR* 1.3 65.8 + - + +
86C LEU* 3.1 5.7 + - - +
87C TRP* 3.0 56.1 + + + -
88C GLY 3.4 20.9 - - - -
90C ASP 3.6 6.5 - - - -
93C ILE* 3.9 8.5 - - + -
94C ALA* 3.4 36.8 - - + -
97C LYS* 3.8 19.7 - - + -
99C VAL* 5.5 2.9 - - + -
155C ILE* 4.6 3.9 - - + +
3002C 2BE 4.9 12.3 - - + -
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Residues in contact with THR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 4.9 4.9 - - + -
20C ILE* 4.9 1.8 - - + -
36C LEU* 3.3 25.2 - - + +
38C ALA* 5.9 0.5 - - - -
80C PHE* 2.8 55.5 + - + +
81C LEU* 3.0 9.4 + - - +
83C PHE* 1.3 80.6 - - + +
85C SER* 1.3 59.3 + - - +
88C GLY* 2.7 48.0 + - - +
89C PHE* 4.8 3.8 - - - +
2004C BEN 3.1 12.4 + - - -
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA* 3.7 5.4 - - - +
39C ASN* 2.8 42.4 + - - +
81C LEU* 2.9 22.4 + - - +
82C ALA 3.0 10.5 + - - -
84C THR* 1.3 79.2 + - - +
86C LEU* 1.3 58.3 - - - +
133C TRP* 3.6 20.6 - - - -
2004C BEN 3.4 24.7 + - - -
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN* 4.9 3.1 - - - +
82C ALA 3.2 4.5 + - - +
83C PHE 3.1 2.5 + - - +
85C SER* 1.3 84.8 - - - +
87C TRP* 1.3 98.7 + - + +
128C HIS* 4.2 9.0 - - + -
130C GLY 6.0 0.7 - - - +
133C TRP* 3.0 37.5 - - + +
155C ILE* 3.5 33.0 - - + -
2004C BEN 3.5 9.8 - - - -
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Residues in contact with TRP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 3.0 47.7 + + + +
86C LEU* 1.3 116.8 + - + +
88C GLY* 1.3 66.3 + - - +
89C PHE 3.8 0.2 + - - -
90C ASP* 3.7 12.3 - - + +
93C ILE* 3.6 38.0 - - + +
97C LYS* 3.6 36.5 - - + +
131C MET* 6.1 2.5 - - + -
155C ILE* 4.2 18.2 - - + -
2004C BEN 3.6 16.8 - - - -
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 3.4 16.1 - - - -
84C THR* 2.7 40.9 + - - +
87C TRP* 1.3 76.0 - - - +
89C PHE* 1.3 57.4 + - - -
90C ASP 3.0 7.4 + - - -
2004C BEN 3.6 25.3 - - - -
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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