Contacts of the helix formed by residues 67 - 92 (chain B) in PDB entry 5DTM
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 SER 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TRP* 3.8 2.2 - - - -
64B ASP* 3.1 29.4 + - - +
65B THR 3.4 0.4 - - - -
66B LYS* 1.3 79.2 - - - +
68B PHE* 1.3 63.6 + - - +
69B GLU* 3.6 11.1 + - - +
70B SER* 3.2 22.3 + - - -
71B MET* 3.1 22.5 + - - +
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Residues in contact with PHE 68 (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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4B LYS 3.8 12.8 - - - -
5B LEU* 4.7 11.7 - - + -
6B GLU 3.6 24.0 - - - -
7B LEU* 3.8 11.2 - - + -
22B TRP* 3.5 64.3 - + + +
66B LYS 4.2 0.2 + - - -
67B SER* 1.3 71.7 + - - +
69B GLU* 1.3 79.0 + - - +
71B MET* 3.4 0.5 + - - -
72B GLN* 2.9 68.1 + - - +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 3.3 9.0 + - - +
68B PHE* 1.3 98.4 + - + +
70B SER* 1.3 56.6 + - - +
72B GLN* 3.5 11.5 + - - +
73B ARG* 3.0 39.5 + - - +
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 5.4 1.0 - - - +
63B TYR* 3.6 9.7 - - - +
64B ASP* 2.9 41.3 + - - +
67B SER* 3.2 16.4 + - - -
69B GLU* 1.3 77.7 - - - +
71B MET* 1.3 57.6 + - - +
73B ARG* 3.4 27.3 + - - +
74B LEU* 3.1 27.7 + - - +
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.8 18.8 - - + -
22B TRP* 4.0 8.1 - - + -
24B LEU* 4.4 4.7 - - + -
34B ALA* 3.9 34.8 - - + +
37B ILE* 4.0 15.7 - - + -
38B ILE* 4.3 3.1 - - + -
63B TYR* 4.8 4.3 - - - -
64B ASP 3.7 10.8 - - - +
65B THR* 3.8 33.7 - - - +
67B SER 3.1 18.6 + - - +
68B PHE 3.9 2.5 - - - +
70B SER* 1.3 73.2 - - - +
72B GLN* 1.3 59.3 + - - +
74B LEU* 3.4 29.5 + - + +
75B CYS* 3.0 33.3 + - - -
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LYS 5.1 2.6 + - - -
6B GLU 4.9 3.2 + - - +
7B LEU* 3.7 16.5 - - + +
68B PHE* 2.9 49.8 + - + +
69B GLU* 3.8 11.4 - - - +
71B MET* 1.3 74.5 - - - +
73B ARG* 1.4 58.2 + - - +
75B CYS* 3.3 4.1 + - + +
76B ASP* 2.8 34.0 + - + +
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Residues in contact with ARG 73 (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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58B TYR* 5.7 4.7 - - - -
59B VAL* 4.1 19.8 - - + +
62B ASP 5.4 5.1 + - - -
69B GLU* 3.0 33.1 + - - +
70B SER* 3.7 26.1 + - - +
71B MET 3.3 0.2 - - - -
72B GLN* 1.4 75.1 + - - +
74B LEU* 1.3 59.0 + - - +
76B ASP* 3.3 7.2 + - + +
77B LYS* 2.9 49.8 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.4 2.5 - - + -
38B ILE* 3.6 28.0 - - + -
41B ILE* 3.9 17.0 - - + -
55B MET* 4.1 1.7 - - + +
59B VAL* 3.7 36.1 - - + +
60B LEU* 3.5 29.6 - - + -
63B TYR* 5.0 7.0 - - + -
70B SER 3.1 14.6 + - - +
71B MET* 3.5 30.1 - - + +
73B ARG* 1.3 76.8 - - - +
75B CYS* 1.3 61.3 + - - +
77B LYS* 3.4 2.8 + - - +
78B TYR* 3.2 21.1 + - - +
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Residues in contact with CYS 75 (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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7B LEU* 4.2 24.0 - - + -
8B ARG 3.7 18.6 - - - +
9B LEU* 3.7 24.2 - - + -
37B ILE* 3.7 20.9 - - - -
41B ILE* 4.6 0.4 - - - -
71B MET* 3.0 21.2 + - - +
72B GLN* 3.8 6.5 - - - +
74B LEU* 1.3 76.2 - - - +
76B ASP* 1.3 51.9 + - - +
78B TYR* 3.3 4.8 + - - +
79B ASN* 2.8 41.8 + - - +
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Residues in contact with ASP 76 (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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72B GLN* 2.8 21.3 + - + +
73B ARG* 3.6 8.7 - - + +
75B CYS* 1.3 72.7 - - - +
77B LYS* 1.3 60.3 + - + +
79B ASN* 3.3 10.5 + - - +
80B ARG* 2.7 75.7 + - - +
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Residues in contact with LYS 77 (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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55B MET* 3.7 21.9 - - + +
56B GLU* 3.0 37.8 + - + +
58B TYR* 3.9 21.9 + - - -
59B VAL* 4.0 19.7 - - + -
73B ARG* 2.9 35.8 + - - +
74B LEU 3.7 4.7 - - - +
76B ASP* 1.3 76.1 - - + +
78B TYR* 1.3 61.6 + - - +
80B ARG* 3.5 17.2 + - - +
81B ALA* 3.1 23.6 + - - +
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Residues in contact with TYR 78 (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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9B LEU* 3.8 21.1 - - + -
10B LYS 2.8 31.8 + - - -
12B PRO* 3.8 1.7 - - - +
41B ILE* 3.7 36.1 - - + -
44B VAL* 3.8 17.5 - - + +
45B CYS* 4.8 0.2 - - - -
51B LEU* 3.9 18.6 - - + -
55B MET* 3.8 18.5 - - + +
74B LEU 3.2 11.7 + - - +
75B CYS 3.6 4.7 - - - +
76B ASP 3.3 0.2 - - - -
77B LYS* 1.3 79.2 - - - +
79B ASN* 1.3 71.6 + - - +
81B ALA* 3.2 4.0 + - - +
82B ILE* 3.0 55.2 + - + +
208B TRP* 3.5 16.2 - + - -
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 2.8 29.9 + - - +
9B LEU* 3.6 0.9 - - - -
10B LYS* 2.9 47.4 + - + +
75B CYS* 2.8 25.6 + - - +
76B ASP* 3.3 11.5 + - - +
78B TYR* 1.3 82.4 - - - +
80B ARG* 1.4 55.8 + - - +
82B ILE* 3.4 7.1 + - - +
83B ASP* 3.0 34.1 + - - +
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Residues in contact with ARG 80 (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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56B GLU* 6.0 0.7 - - - -
76B ASP* 2.7 52.7 + - - +
77B LYS* 3.8 17.5 - - - +
79B ASN* 1.4 69.0 - - + +
81B ALA* 1.3 60.4 + - - +
83B ASP* 3.4 12.1 + - - +
84B SER* 3.0 31.9 + - - -
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Residues in contact with ALA 81 (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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51B LEU* 3.5 17.6 - - + +
54B ALA* 4.2 10.1 - - + -
55B MET* 3.7 33.4 - - + +
77B LYS 3.1 14.4 + - - +
78B TYR* 3.2 9.6 + - - +
80B ARG* 1.3 72.9 - - - +
82B ILE* 1.3 65.5 + - - +
84B SER* 3.2 5.1 + - - -
85B ILE* 3.1 26.7 + - - +
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Residues in contact with ILE 82 (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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10B LYS* 3.8 26.0 - - + +
11B SER 3.9 2.2 - - - +
12B PRO* 3.8 20.9 - - + -
48B ILE* 5.7 0.2 - - + -
51B LEU* 3.8 22.4 - - + -
78B TYR* 3.0 55.8 + - + +
79B ASN* 3.5 9.2 - - - +
81B ALA* 1.3 75.5 - - - +
83B ASP* 1.3 57.7 + - - +
85B ILE* 3.2 7.9 + - + +
86B HIS* 2.9 55.5 + - + +
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Residues in contact with ASP 83 (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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10B LYS* 2.9 36.8 + - - +
79B ASN 3.0 19.5 + - - +
80B ARG* 3.6 13.1 - - - +
82B ILE* 1.3 75.8 - - - +
84B SER* 1.4 58.1 + - - +
86B HIS* 3.4 9.5 + - - +
87B GLN* 3.0 33.8 + - + +
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Residues in contact with SER 84 (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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54B ALA* 4.5 14.0 - - - +
80B ARG* 3.0 15.8 + - - +
81B ALA* 3.2 9.2 + - - -
83B ASP* 1.4 74.8 - - - +
85B ILE* 1.3 59.3 + - - +
87B GLN* 3.2 9.5 + - - +
88B LEU* 3.0 27.5 + - - +
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Residues in contact with ILE 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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12B PRO* 5.4 0.7 - - + +
48B ILE* 5.1 3.1 - - + -
50B ASP* 3.2 46.7 - - + +
51B LEU* 3.8 15.9 - - + +
54B ALA* 3.5 20.6 - - + -
81B ALA 3.1 12.5 + - - +
82B ILE* 3.8 11.7 - - + +
84B SER* 1.3 74.7 - - - +
86B HIS* 1.3 68.9 + - + +
88B LEU* 3.3 11.5 + - + +
89B TRP* 2.9 66.5 + - + +
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Residues in contact with HIS 86 (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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11B SER 3.5 14.4 - - - -
12B PRO* 2.8 25.7 + - - +
13B VAL* 4.6 0.8 - - - -
14B GLY* 4.1 14.1 + - - -
82B ILE* 2.9 41.4 + - + +
83B ASP* 3.8 9.3 + - - +
85B ILE* 1.3 82.3 - - + +
87B GLN* 1.3 56.5 + - - +
89B TRP* 3.5 22.4 + + - +
90B LYS* 3.1 35.3 + - - +
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Residues in contact with GLN 87 (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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83B ASP* 3.0 20.9 + - + +
84B SER* 3.2 11.2 + - - +
86B HIS* 1.3 74.8 - - + +
88B LEU* 1.3 64.9 + - - +
90B LYS* 3.2 35.2 + - - +
91B GLY* 3.0 21.5 + - - -
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Residues in contact with LEU 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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50B ASP* 3.8 35.9 - - + +
84B SER 3.0 12.9 + - - +
85B ILE* 3.5 14.6 - - + +
87B GLN* 1.3 75.4 - - - +
89B TRP* 1.3 65.1 + - + +
91B GLY* 3.6 2.2 + - - -
92B THR* 3.1 31.5 + - - -
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Residues in contact with TRP 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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12B PRO 3.7 20.2 - - - -
13B VAL* 5.7 3.8 - - + -
48B ILE* 3.7 40.6 - - + -
50B ASP* 3.6 20.5 + - - -
85B ILE* 2.9 37.0 + - + +
86B HIS* 3.9 18.2 - + - +
87B GLN 3.3 0.2 - - - -
88B LEU* 1.3 86.0 - - + +
90B LYS* 1.3 59.5 + - - +
92B THR* 3.2 24.8 - - - +
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 3.1 19.6 + - - +
87B GLN* 3.2 40.9 + - - +
89B TRP* 1.3 79.6 - - - +
91B GLY* 1.4 62.3 + - - +
92B THR 3.2 6.8 + - - +
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLN 3.0 10.3 + - - -
88B LEU* 3.8 4.7 - - - -
90B LYS* 1.4 77.9 - - - +
92B THR* 1.3 55.4 + - - +
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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 LEU* 3.1 22.1 + - - -
89B TRP* 3.2 21.3 - - - +
90B LYS 3.2 5.2 - - - +
91B GLY* 1.3 78.7 - - - +
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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) + - + + + + + -
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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