Contacts of the helix formed by residues 79 - 101 (chain B) in PDB entry 5LN3
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 MET 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 5.0 15.5 - - + -
20A GLY* 3.9 21.8 - - - +
21A ARG* 5.8 0.4 - - - -
28B ALA* 4.4 20.2 - - + +
76B TYR* 4.2 1.3 - - - -
78B GLY* 1.4 72.4 - - - -
80B GLY* 1.3 63.4 + - - +
81B PRO* 3.6 2.9 - - + -
82B ASP* 3.4 28.5 + - - +
83B TYR* 3.2 19.2 + - - +
128B ARG* 5.9 1.6 - - - +
131B GLY* 3.5 15.5 + - - +
132B VAL* 4.5 3.5 - - - +
415K GLU* 3.1 39.7 - - + +
416K PHE* 3.6 21.8 - - + -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.9 20.2 - - - -
78B GLY 3.7 1.0 + - - -
79B MET* 1.3 67.4 - - - +
81B PRO* 1.3 70.4 - - - +
83B TYR* 2.9 19.8 + - - +
84B ARG* 3.1 24.4 + - - +
416K PHE 3.4 12.5 + - - -
417K TYR* 5.3 4.3 - - - -
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Residues in contact with PRO 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLN* 3.9 21.4 - - + +
157A ALA* 3.9 18.4 - - + +
158A GLY* 3.8 25.6 - - - +
159A TYR* 4.6 9.2 - - + +
160A TYR* 6.5 0.2 - - + -
79B MET* 4.0 2.9 - - + -
80B GLY* 1.3 89.3 - - - +
82B ASP* 1.4 64.8 + - - +
84B ARG* 3.3 10.1 + - + +
85B VAL* 3.3 26.3 + - - +
415K GLU 4.8 9.9 - - - +
416K PHE 5.3 0.4 - - - +
417K TYR* 5.6 3.8 - - - -
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 5.3 3.8 - - - -
123A GLN* 3.1 22.8 + - - +
79B MET* 3.5 29.4 - - + +
80B GLY 3.1 0.6 - - - -
81B PRO* 1.4 78.8 - - - +
83B TYR* 1.4 54.8 + - - +
85B VAL* 3.5 2.1 + - - +
86B LEU* 2.8 35.0 + - - +
130B PHE* 3.8 30.0 - - + +
131B GLY* 3.4 23.6 + - - -
132B VAL* 4.7 7.4 - - + -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS 2.8 27.7 + - - -
66B GLU* 3.3 18.9 + - + +
74B LEU* 2.9 33.3 + - + +
75B VAL 4.5 0.9 - - - -
76B TYR* 3.4 54.7 - + + -
79B MET 3.2 9.2 + - - +
80B GLY 2.9 10.9 + - - +
82B ASP* 1.4 77.0 - - - +
84B ARG* 1.4 88.2 + - - +
86B LEU* 3.1 5.1 + - + -
87B VAL* 3.0 43.0 + - + +
132B VAL* 4.6 4.5 - - + +
134B LEU* 4.1 12.1 - - + -
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 5.4 12.1 - - + +
120A ASP* 4.7 11.2 - - - +
160A TYR* 3.9 30.7 + - + +
62B VAL* 3.9 24.1 - - - +
63B HIS* 3.0 40.8 + - - +
64B LYS* 5.0 1.4 - - - +
66B GLU* 4.5 14.5 + - - +
76B TYR* 4.5 11.1 + - - -
80B GLY* 3.1 18.0 + - - +
81B PRO* 3.3 10.0 + - + +
83B TYR* 1.4 97.8 - - - +
85B VAL* 1.4 62.0 + - - +
87B VAL* 3.3 6.8 + - - +
88B HIS* 3.1 20.5 + - - +
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Residues in contact with VAL 85 (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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120A ASP* 3.6 32.1 - - + +
123A GLN* 3.7 25.4 - - + +
124A VAL* 5.5 2.5 - - + -
81B PRO 3.3 13.5 + - - +
82B ASP 3.8 2.7 - - - +
84B ARG* 1.4 71.9 - - - +
86B LEU* 1.3 67.0 + - - +
88B HIS* 3.2 15.7 + - + +
89B ARG* 3.3 50.4 + - + +
130B PHE* 3.7 12.3 - - + -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 4.8 7.4 - - + -
82B ASP 2.8 19.1 + - - +
83B TYR* 3.1 7.8 + - + +
85B VAL* 1.3 77.3 - - - +
87B VAL* 1.3 68.3 + - + +
89B ARG* 3.4 6.4 + - + +
90B ALA* 3.3 20.3 + - + +
114B VAL* 4.7 26.7 - - + +
117B VAL* 5.0 15.5 - - + -
118B MET* 4.6 14.4 - - + -
130B PHE* 3.8 27.1 - - + -
132B VAL* 4.7 3.4 - - + -
134B LEU* 3.8 38.4 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 4.1 26.5 - - + +
67B PRO 5.0 1.1 - - - +
68B ILE* 4.1 17.3 - - + +
74B LEU* 4.4 15.3 - - + -
83B TYR* 3.0 43.4 + - + +
84B ARG* 3.5 10.1 - - - +
86B LEU* 1.3 78.5 - - + +
88B HIS* 1.4 54.9 + - - +
90B ALA* 3.9 1.8 - - - +
91B ARG* 2.9 50.7 + - + +
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Residues in contact with HIS 88 (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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1082 LEU* 5.3 12.5 - - + +
1122 SER* 5.9 2.5 - - - -
120A ASP* 5.7 9.4 - - - +
84B ARG 3.1 12.8 + - - +
85B VAL* 3.2 12.9 + - + +
87B VAL* 1.4 72.6 - - - +
89B ARG* 1.4 70.1 + - + +
91B ARG* 3.4 37.2 + - - +
92B LYS* 3.1 35.2 + - + +
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Residues in contact with ARG 89 (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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124A VAL* 4.3 11.3 - - - +
127A GLN* 3.6 23.0 + - - -
85B VAL* 3.3 36.5 + - + +
86B LEU* 4.1 7.4 - - + +
87B VAL 3.4 0.2 - - - -
88B HIS* 1.4 82.4 - - + +
90B ALA* 1.4 56.8 + - - +
92B LYS* 3.2 9.1 + - - +
93B LEU* 3.1 37.7 + - + +
117B VAL* 4.6 14.6 - - + -
121B TYR* 3.4 26.9 + - - -
130B PHE* 4.1 8.8 - - - -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 4.3 15.9 - - + -
74B LEU* 5.8 2.0 - - + -
86B LEU* 3.3 16.5 + - + +
87B VAL 3.9 2.5 - - - +
89B ARG* 1.4 74.0 - - - +
91B ARG* 1.3 57.0 + - - +
92B LYS 3.1 0.2 - - - -
93B LEU* 3.1 11.2 + - - +
94B ALA* 2.7 36.2 + - - +
110B LEU* 5.0 7.0 - - + -
113B ARG* 5.0 3.1 + - + -
114B VAL* 4.3 23.8 - - + -
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Residues in contact with ARG 91 (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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1082 LEU* 3.3 32.7 + - + +
1112 LEU* 3.7 26.8 - - - +
1122 SER* 3.4 28.7 - - - +
116A LYS* 5.2 11.5 - - - +
67B PRO 4.2 9.2 - - - -
68B ILE* 4.1 22.4 - - + +
87B VAL* 2.9 31.5 + - + +
88B HIS* 3.4 39.6 + - - +
90B ALA* 1.3 73.6 - - - +
92B LYS* 1.3 67.9 + - - +
94B ALA* 4.1 0.5 - - - +
95B GLN* 3.4 39.6 + - - +
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Residues in contact with LYS 92 (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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1082 LEU* 4.0 28.4 - - + +
88B HIS* 3.1 26.4 + - + +
89B ARG* 3.4 11.9 - - - +
91B ARG* 1.3 79.1 - - - +
93B LEU* 1.4 57.9 + - + +
95B GLN* 3.5 2.3 + - - +
96B GLN* 3.1 30.5 + - + +
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Residues in contact with LEU 93 (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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89B ARG* 3.1 24.2 + - + +
90B ALA* 3.6 9.9 - - - +
92B LYS* 1.4 75.6 - - + +
94B ALA* 1.4 64.2 + - - +
96B GLN* 3.5 23.2 + - + +
97B TYR* 3.1 21.3 + - - +
113B ARG* 3.4 35.8 + - + +
117B VAL* 5.2 14.4 - - + -
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Residues in contact with ALA 94 (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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68B ILE* 4.1 13.0 - - + -
69B THR* 3.8 26.4 - - + +
90B ALA 2.7 20.5 + - - +
91B ARG 4.1 2.7 - - - +
92B LYS 3.4 0.2 - - - -
93B LEU* 1.4 72.2 - - - +
95B GLN* 1.4 62.0 + - - +
98B TYR* 3.3 28.1 + - - +
105B ILE* 4.4 5.6 - - + +
110B LEU* 4.4 1.1 - - + -
113B ARG* 3.5 22.6 - - - +
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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
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1042 SER* 3.5 12.0 - - - +
1072 GLU* 3.2 26.0 - - - +
1082 LEU* 3.2 44.5 + - - +
1112 LEU* 3.9 13.7 - - - +
68B ILE 4.8 6.0 + - - +
69B THR* 5.2 5.2 - - + -
91B ARG* 3.4 37.9 + - - +
92B LYS 4.0 2.2 - - - +
93B LEU 3.4 0.2 - - - -
94B ALA* 1.4 73.7 - - - +
96B GLN* 1.4 69.5 + - - +
98B TYR 3.4 1.3 + - - -
99B LEU* 3.1 37.8 + - + +
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Residues in contact with GLN 96 (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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1042 SER* 5.3 6.1 - - - -
92B LYS* 3.1 21.5 + - + +
93B LEU* 3.5 36.2 + - + +
95B GLN* 1.4 79.7 - - - +
97B TYR* 1.4 92.8 + - - +
99B LEU* 3.2 10.6 + - - +
100B VAL* 3.3 23.0 + - - +
113B ARG* 5.1 1.4 - - - +
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Residues in contact with TYR 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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743 TYR* 3.5 34.1 - + - -
773 LYS* 5.1 12.5 + - - +
93B LEU 3.1 4.7 + - - +
96B GLN* 1.4 97.3 - - - +
98B TYR* 1.3 96.6 - + + +
99B LEU 3.5 2.1 + - - -
100B VAL* 3.6 19.7 + - + +
101B TYR* 3.7 16.7 - + - -
109B GLN* 5.5 5.8 + - - -
113B ARG* 3.4 29.4 - - - +
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Residues in contact with TYR 98 (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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743 TYR* 3.9 16.7 + - - -
94B ALA 3.3 20.8 + - - +
95B GLN* 3.5 4.9 - - - -
96B GLN 3.3 0.2 - - - -
97B TYR* 1.3 111.4 - + + +
99B LEU* 1.3 65.6 + - - +
101B TYR* 3.3 14.0 - - + +
102B GLN* 5.0 1.4 - - - -
103B GLU* 3.7 33.9 - - + +
104B PRO* 5.5 0.2 - - + -
105B ILE* 4.0 31.0 - - + +
106B PRO* 3.5 30.2 - - + +
109B GLN* 3.7 20.9 - - + +
113B ARG* 3.7 15.5 - - - -
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Residues in contact with LEU 99 (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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1002 GLN* 2.8 28.8 - - + +
1032 SER* 4.7 6.5 - - - +
1042 SER* 2.9 45.3 - - - +
1072 GLU* 3.9 21.3 - - - +
95B GLN* 3.1 28.4 + - + +
96B GLN 3.2 3.3 + - - +
98B TYR* 1.3 83.1 - - - +
100B VAL* 1.4 54.2 + - - +
101B TYR 3.1 3.8 - - - -
102B GLN* 2.7 35.0 + - - +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002 GLN* 3.5 20.8 + - - +
893 SER* 5.3 2.1 - - - -
933 ASN* 3.3 44.5 + - + +
96B GLN* 3.3 24.6 + - - +
97B TYR* 3.6 13.2 - - + +
99B LEU* 1.4 64.3 - - - +
101B TYR* 1.4 74.9 + - + +
102B GLN* 4.0 2.4 + - - +
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703 ARG* 6.0 0.5 - - - -
743 TYR* 3.7 31.3 - + - -
863 THR* 5.0 4.3 - - + -
893 SER* 4.0 19.3 - - - -
903 MET* 3.5 36.2 - - + +
933 ASN* 3.7 22.5 + - - -
97B TYR* 3.7 31.2 + + - +
98B TYR* 3.3 9.0 - - + +
99B LEU* 3.1 23.4 - - - -
100B VAL* 1.4 85.9 - - + +
102B GLN* 1.4 64.5 + - - +
103B GLU* 3.6 30.1 - - + +
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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
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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) + - + + + + + -
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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