Contacts of the helix formed by residues 91 - 112 (chain B) in PDB entry 1UDY
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 CYS 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE* 3.9 4.3 - - + +
39B ALA* 3.7 20.4 - - + -
87B LEU 3.3 5.0 + - - +
88B ALA 3.1 5.2 + - - -
90B GLY* 1.3 81.1 - - - +
92B THR* 1.3 58.2 + - - +
93B GLY* 3.0 20.9 - - - -
94B VAL* 3.6 27.5 - - + +
95B GLN* 3.1 26.5 + - - +
217B GLN* 6.1 0.2 - - - -
219B CYS* 4.5 6.1 - - - -
364B LYS* 3.3 29.8 - - - +
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Residues in contact with THR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA* 3.6 26.9 + - + +
91B CYS* 1.3 70.7 - - - +
93B GLY* 1.3 61.4 + - - +
95B GLN* 3.9 7.9 - - - -
96B THR* 2.6 35.3 + - - -
217B GLN* 3.4 9.7 + - - +
266B LEU* 3.8 27.1 - - + +
364B LYS* 4.8 1.4 - - - +
368B ASP* 3.3 30.3 + - - +
372B TYR* 3.4 28.4 - - + +
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B CYS* 3.0 12.5 - - - -
92B THR* 1.3 81.1 + - - +
94B VAL* 1.3 65.1 + - - +
96B THR* 3.8 0.3 - - - -
97B ALA* 3.4 13.9 + - - +
217B GLN* 3.9 27.5 - - - +
219B CYS* 3.7 12.9 - - - -
220B SER* 3.8 13.2 - - - -
364B LYS* 5.2 0.6 - - - +
368B ASP* 5.3 0.4 + - - -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 5.8 0.9 - - + -
35B ILE* 4.1 19.5 - - + -
39B ALA* 5.5 3.6 - - + -
42B TYR* 5.7 1.8 - - + -
49B PRO* 4.3 11.0 - - + -
52B LEU* 4.0 40.8 - - + -
53B LEU* 4.8 5.6 - - + -
91B CYS* 3.5 26.8 + - + +
93B GLY* 1.3 75.3 - - - +
95B GLN* 1.3 57.6 + - - +
97B ALA* 3.0 29.8 + - - +
98B ILE* 3.2 17.1 + - + +
219B CYS* 3.7 14.5 - - - -
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 6.1 0.6 - - - +
84B THR* 2.8 30.4 - - + +
87B LEU* 3.5 30.9 - - + +
88B ALA* 3.6 17.8 - - - +
91B CYS 3.1 16.6 + - - +
92B THR* 4.0 3.4 + - - +
94B VAL* 1.3 80.3 - - - +
96B THR* 1.3 72.1 + - - +
98B ILE* 3.1 13.5 + - - +
99B GLU* 2.9 42.7 + - + +
262B GLY* 4.7 1.2 - - - -
372B TYR* 4.0 15.0 + - - -
1400B CS8 4.2 8.2 - - - +
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR 2.6 24.2 + - - -
93B GLY* 3.8 4.3 - - - -
94B VAL 3.3 0.2 - - - -
95B GLN* 1.3 84.3 + - - +
97B ALA* 1.3 65.9 + - - +
99B GLU 4.4 0.7 - - - +
100B ALA* 2.9 23.0 + - - +
168B THR* 4.4 14.4 - - + +
217B GLN* 3.0 25.3 + - - +
220B SER* 4.4 6.1 - - - +
372B TYR* 4.3 0.2 + - - -
375B TYR* 3.4 14.5 + - + +
1399B FAD 5.8 0.9 - - + -
1400B CS8 3.5 30.0 - - + +
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B TYR* 4.3 14.4 - - + +
49B PRO* 5.4 3.6 - - + -
53B LEU* 4.0 18.2 - - + -
93B GLY 3.4 6.6 + - - +
94B VAL* 3.0 16.0 + - - +
96B THR* 1.3 79.2 - - - +
98B ILE* 1.3 64.7 - - - +
100B ALA* 3.4 4.8 + - - +
101B ASN* 3.7 4.0 + - - +
130B MET* 5.2 2.0 - - - +
168B THR* 4.7 3.1 - - - -
169B ASN* 3.0 38.2 - - - +
220B SER* 4.8 7.1 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 5.1 3.6 - - + -
35B ILE* 6.0 0.2 - - + -
53B LEU* 3.7 12.3 - - + -
56B ALA* 3.9 15.3 - - + -
61B LEU 3.9 17.0 - - - +
62B MET* 3.5 38.7 - - + +
63B ASN 5.5 0.7 - - - +
87B LEU* 3.6 31.2 - - + -
94B VAL* 3.2 17.2 + - + +
95B GLN* 3.1 10.2 + - - +
97B ALA* 1.3 77.5 - - - +
99B GLU* 1.3 66.6 + - + +
101B ASN* 3.1 28.8 - - - +
102B THR* 3.9 5.8 + - + +
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 5.5 2.1 - - - +
80B SER* 4.0 10.0 + - - -
84B THR* 3.3 20.0 + - + +
87B LEU* 6.1 0.6 - - + +
95B GLN* 2.9 39.5 + - - +
96B THR 3.4 0.2 + - - -
98B ILE* 1.3 75.2 - - + +
100B ALA* 1.3 62.2 + - - +
101B ASN 2.8 6.8 + - - -
102B THR* 3.0 34.9 + - - +
103B LEU* 3.1 33.7 + - + +
258B PRO* 4.2 17.4 - - + +
259B VAL* 6.0 0.2 - - - +
1400B CS8 3.4 30.7 - - + +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR 2.9 17.0 + - - +
98B ILE 3.3 0.4 - - - -
99B GLU* 1.3 75.8 - - - +
101B ASN* 1.3 62.0 + - - +
103B LEU* 3.8 8.5 - - - +
104B GLY* 3.3 13.5 + - - -
131B CYS 3.7 10.9 - - - +
132B ALA* 4.4 3.8 - - - -
133B TYR* 4.7 2.5 + - + +
168B THR* 3.5 33.0 - - + +
169B ASN* 3.5 17.5 - - + +
1399B FAD 5.3 1.6 - - - +
1400B CS8 3.9 9.1 - - + +
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Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B MET* 4.0 15.3 - - + +
63B ASN* 2.7 29.3 + - - +
97B ALA 3.7 2.8 + - - -
98B ILE* 3.1 16.3 + - - +
99B GLU 2.8 1.4 - - - -
100B ALA* 1.3 76.8 - - - +
102B THR* 1.3 62.1 + - + +
103B LEU 3.0 1.1 - - - -
104B GLY 2.9 18.5 + - - -
105B GLN* 3.0 13.5 + - - +
124B MET* 4.2 1.2 - - - +
129B LEU 3.4 18.8 + - - -
130B MET* 3.3 13.4 - - - +
131B CYS* 2.8 42.7 + - - +
169B ASN* 4.2 1.6 - - - +
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASN* 4.6 15.7 - - - +
64B THR* 4.8 13.5 - - + +
65B HIS* 4.8 12.3 - - + -
80B SER* 5.7 1.3 + - - +
98B ILE* 4.2 10.8 - - + +
99B GLU* 3.0 34.3 + - - +
101B ASN* 1.3 74.8 - - - +
103B LEU* 1.3 61.9 + - - +
105B GLN* 3.7 19.3 - - - +
106B VAL* 2.9 39.7 + - - +
255B THR* 5.9 1.4 - - - -
258B PRO* 6.1 0.3 - - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 3.1 37.8 + - - +
100B ALA* 3.8 8.1 - - - +
101B ASN 3.0 0.8 - - - -
102B THR* 1.3 82.9 + - - +
104B GLY* 1.3 60.4 + - - +
106B VAL* 4.9 2.7 - - - -
107B PRO* 3.0 20.1 - - - +
133B TYR* 3.4 30.7 - - + -
251B THR* 4.6 4.5 - - + +
252B PHE* 6.2 0.2 - - + -
255B THR* 4.0 25.8 - - + +
259B VAL* 5.1 0.9 - - + -
376B GLU* 3.2 26.5 - - - +
1400B CS8 3.3 43.7 - - + -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ALA 3.3 5.8 + - - -
101B ASN 2.9 7.4 + - - -
103B LEU* 1.3 79.6 - - - +
105B GLN* 1.3 59.7 + - - +
107B PRO* 3.3 12.2 - - - +
108B LEU* 4.5 1.6 + - - +
131B CYS* 4.1 8.7 - - - -
132B ALA 4.2 20.0 - - - -
133B TYR* 4.4 3.3 - - - +
175B TRP* 3.2 24.3 - - - -
177B PHE* 3.9 8.9 - - - +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASN* 2.7 39.3 + - - +
65B HIS* 5.1 3.0 - - + +
66B ILE* 3.6 32.3 - - + +
101B ASN* 3.0 16.1 + - - +
102B THR* 3.7 17.4 - - - +
104B GLY* 1.3 75.2 - - - +
106B VAL* 1.3 55.8 + - + +
107B PRO* 3.2 2.9 - - - -
108B LEU* 2.7 30.0 + - - +
109B ILE* 2.9 20.0 + - + +
121B LEU* 4.7 5.3 - - + +
124B MET* 3.9 14.2 - - + +
131B CYS* 3.7 9.6 - - - -
175B TRP* 3.8 13.9 - - + -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS* 4.0 24.0 - - + +
102B THR* 2.9 35.2 + - - +
103B LEU* 4.9 0.9 - - - -
105B GLN* 1.3 71.1 - - - +
107B PRO* 1.3 66.2 - - + +
108B LEU 3.0 0.2 + - - -
109B ILE* 3.0 8.2 + - + -
110B ILE* 2.8 52.9 + - + +
251B THR* 3.9 25.8 - - + -
254B LYS* 4.3 20.2 - - + -
255B THR* 5.8 4.9 - - - +
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Residues in contact with PRO 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU 3.0 24.5 - - - +
104B GLY 3.3 7.9 - - - +
105B GLN 3.3 4.3 - - - -
106B VAL* 1.3 92.5 - - + +
108B LEU* 1.3 53.6 + - - +
110B ILE* 4.1 3.6 - - + -
111B GLY* 3.1 23.1 + - - -
133B TYR* 4.0 9.2 - - + -
177B PHE* 3.4 40.6 - - + -
238B LEU* 3.7 8.8 - - - +
247B ILE* 3.6 19.3 - - + +
251B THR* 3.7 15.7 - - + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLY 4.5 2.6 + - - +
105B GLN* 2.7 20.0 + - - +
107B PRO* 1.3 73.7 - - - +
109B ILE* 1.3 63.3 + - - +
110B ILE 3.3 0.2 - - - -
112B GLY* 2.7 27.0 + - - +
116B GLN* 3.6 13.2 - - + +
117B GLN* 3.0 55.2 - - + +
120B TYR* 4.9 2.7 - - + -
121B LEU* 3.3 22.4 - - + -
175B TRP* 4.8 9.0 - - + -
177B PHE* 5.8 2.7 - - + -
198B ILE* 4.0 26.0 - - + -
238B LEU* 3.3 24.2 - - + -
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS* 3.3 55.2 - - + +
66B ILE* 4.2 3.4 - - - +
67B PRO* 4.0 17.7 - - + -
105B GLN* 2.9 22.6 + - + +
106B VAL* 3.6 9.6 - - - +
108B LEU* 1.3 76.5 - - - +
110B ILE* 1.3 66.5 + - + +
112B GLY 4.6 0.2 - - - +
117B GLN* 3.0 22.6 - - - +
121B LEU* 3.8 17.2 - - + +
254B LYS* 5.0 5.8 - - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B HIS* 6.2 0.2 - - - +
106B VAL* 2.8 33.0 + - + +
107B PRO* 4.1 4.7 - - + +
109B ILE* 1.3 77.1 - - + +
111B GLY* 1.3 64.8 + - - +
239B THR* 4.9 1.4 - - - +
246B LYS 5.3 0.2 - - - +
247B ILE* 3.6 28.0 - - + +
250B GLY* 3.9 10.8 - - - +
251B THR* 3.9 23.6 - - - +
254B LYS* 3.7 29.6 - - + +
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO 3.1 18.1 + - - -
110B ILE* 1.3 84.1 - - - +
112B GLY* 1.3 61.1 + - - +
113B ASN 4.1 0.3 + - - -
238B LEU* 4.1 4.5 - - - -
239B THR* 2.6 45.0 + - - +
247B ILE* 4.5 8.3 - - - -
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO 3.8 1.8 + - - -
108B LEU* 2.7 27.7 + - - -
109B ILE 4.6 0.3 - - - +
110B ILE 5.3 0.3 - - - -
111B GLY* 1.3 73.8 - - - -
113B ASN* 1.3 62.8 + - - -
116B GLN* 3.1 13.9 - - - -
117B GLN* 2.8 23.4 - - - +
238B LEU* 3.9 9.0 - - - -
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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