Contacts of the helix formed by residues 100 - 122 (chain G) in PDB entry 5Y39
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 GLY 100 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G THR 3.6 4.2 + - - -
99G VAL* 1.3 80.5 - - - +
101G PHE* 1.3 65.3 + - - -
103G MET* 3.2 6.4 + - - +
104G LEU* 3.1 18.4 + - - +
112J ASN* 3.1 37.1 - - - +
113J LEU 4.8 3.7 + - - -
114J GLY* 5.5 1.6 - - - -
121J ASP* 3.7 4.5 - - - -
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Residues in contact with PHE 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G LEU* 4.0 28.9 - - + +
74G MET 3.5 21.8 - - - -
75G ASP* 3.5 26.9 - - + -
80G ARG* 3.4 51.4 - - + +
99G VAL 3.6 1.2 + - - -
100G GLY* 1.3 68.8 - - - -
102G GLY* 1.3 61.4 + - - +
104G LEU* 3.7 17.8 - - + +
105G LYS* 2.9 32.7 + - - +
70H SER* 5.5 0.7 - - - -
72H ILE* 4.8 16.6 - - + -
111J LEU* 3.8 22.2 - - + +
112J ASN 3.2 4.5 + - - +
121J ASP* 4.5 3.6 + - - -
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Residues in contact with GLY 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G PHE* 1.3 72.8 - - - +
103G MET* 1.3 55.1 + - - -
105G LYS* 3.5 1.6 + - - +
106G ALA* 2.9 30.7 + - - +
107J ASP* 3.8 11.4 - - - +
111J LEU* 3.5 24.9 - - - +
112J ASN 2.7 20.1 + - - -
113J LEU* 3.6 10.5 - - - +
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Residues in contact with MET 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F LEU* 4.2 13.2 - - + -
145F GLN* 5.3 6.7 - - - +
17G GLY 6.2 0.2 - - - +
99G VAL* 4.1 12.1 - - + -
100G GLY 3.2 11.2 + - - +
102G GLY* 1.3 71.9 - - - +
104G LEU* 1.3 61.4 + - - +
106G ALA* 3.3 6.6 + - - -
107G LYS* 2.9 56.9 + - + +
83J MET 5.3 1.6 - - - +
84J GLU* 3.7 33.9 - - + -
87J LEU* 3.7 17.3 - - + -
112J ASN 3.3 4.2 + - - -
113J LEU* 3.5 38.8 - - + +
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Residues in contact with LEU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G VAL* 4.7 2.0 - - + -
73G LEU* 4.3 2.0 - - + -
80G ARG* 3.8 38.8 - - + -
81G VAL 3.9 12.3 - - - +
82G ALA* 3.9 8.7 - - + -
93G MET* 3.7 44.1 - - + +
95G ALA* 4.4 18.4 - - + -
99G VAL* 4.1 8.4 - - + +
100G GLY 3.1 13.6 + - - +
101G PHE* 3.7 19.7 - - + +
103G MET* 1.3 75.5 - - - +
105G LYS* 1.3 57.7 + - - +
107G LYS* 3.8 4.5 - - - +
108G ALA* 3.0 29.3 + - - +
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Residues in contact with LYS 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G PHE* 3.6 45.5 - - + +
73G LEU* 4.4 8.0 - - + +
101G PHE 2.9 17.2 + - - +
102G GLY* 3.9 3.4 - - - +
104G LEU* 1.3 75.2 - - - +
106G ALA* 1.3 58.8 + - - +
108G ALA* 3.5 1.2 + - - +
109G GLN* 2.9 60.4 + - - +
74H TYR* 3.5 32.6 - - + +
107J ASP* 5.3 4.0 - - - +
109J GLN* 4.1 9.9 + - - -
111J LEU* 4.3 17.3 - - + -
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Residues in contact with ALA 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F GLN* 3.8 17.4 + - - +
102G GLY 2.9 19.3 + - - +
103G MET* 3.7 10.3 - - - +
105G LYS* 1.3 76.0 - - - +
107G LYS* 1.3 57.0 + - - +
109G GLN* 3.5 10.6 + - - +
110G ALA* 3.0 29.3 + - - +
113J LEU* 4.6 9.9 - - + -
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Residues in contact with LYS 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F GLN* 4.7 2.2 - - - +
14G ALA* 2.8 33.5 + - + +
16G THR* 2.8 18.0 + - - -
17G GLY 5.2 0.6 + - - -
19G VAL* 3.6 8.1 - - + +
93G MET* 3.4 23.1 - - + -
103G MET* 2.9 43.7 + - + +
104G LEU 3.8 0.2 - - - +
106G ALA* 1.3 74.6 - - - +
108G ALA* 1.3 60.2 + - - +
110G ALA* 3.4 6.9 + - - +
111G LEU* 3.0 34.2 + - - +
83J MET* 3.9 27.1 - - + -
84J GLU* 2.8 30.8 + - - +
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Residues in contact with ALA 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G PHE* 3.6 26.0 - - + -
82G ALA* 4.2 8.3 - - + -
84G THR* 4.8 3.6 - - + -
91G LEU* 3.6 12.6 - - + +
93G MET* 4.0 17.6 - - + -
104G LEU 3.0 19.2 + - - +
105G LYS 3.8 0.2 - - - +
107G LYS* 1.3 75.0 - - - +
109G GLN* 1.3 56.7 + - - +
111G LEU* 3.3 4.4 + - - +
112G VAL* 3.0 33.2 + - - +
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Residues in contact with GLN 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G PHE* 4.0 15.8 - - + -
105G LYS* 2.9 57.2 + - - +
106G ALA* 3.8 8.8 - - - +
108G ALA* 1.3 72.6 - - - +
110G ALA* 1.3 64.8 + - - +
112G VAL* 3.3 10.8 + - + +
113G GLN* 3.1 23.4 + - - +
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Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F GLN* 3.9 9.6 - - + +
106G ALA 3.0 18.3 + - - +
107G LYS 3.7 4.9 - - - +
109G GLN* 1.3 75.6 - - - +
111G LEU* 1.3 57.8 + - - +
113G GLN* 3.0 11.3 + - - +
114G TYR* 2.9 41.4 + - + +
83J MET* 3.7 27.1 - - + -
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Residues in contact with LEU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 3.9 20.4 - - + +
11G LEU* 3.7 22.0 - - + +
13G GLN* 4.3 4.7 - - + -
14G ALA* 3.9 24.2 - - + +
22G THR* 3.6 31.0 - - + -
91G LEU* 3.8 13.0 - - + -
93G MET* 5.2 2.0 - - - -
107G LYS 3.0 19.5 + - - +
108G ALA* 3.6 4.9 - - - +
109G GLN 3.3 0.2 - - - -
110G ALA* 1.3 73.2 - - - +
112G VAL* 1.3 64.6 + - - +
114G TYR* 3.3 19.4 + - + +
115G LEU* 3.0 32.2 + - + +
83J MET* 4.5 5.4 - - - -
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Residues in contact with VAL 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G THR* 3.7 18.4 - - + +
85G ARG 3.6 26.5 - - - +
86G VAL* 4.3 12.1 - - + -
91G LEU* 4.2 6.9 - - + +
108G ALA 3.0 22.2 + - - +
109G GLN* 3.3 12.5 + - + +
111G LEU* 1.3 74.5 - - - +
113G GLN* 1.3 61.6 + - - +
116G GLU* 3.0 59.0 + - - +
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Residues in contact with GLN 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 4.6 9.7 - - - +
98B THR* 4.1 23.0 - - - +
109G GLN 3.1 13.8 + - - +
110G ALA* 3.0 15.7 + - - +
112G VAL* 1.3 81.3 + - - +
114G TYR* 1.3 64.5 + - + +
115G LEU 3.3 1.0 + - - -
116G GLU* 4.0 11.5 + - - +
117G GLU* 5.0 3.1 + - - +
118G PRO* 5.9 0.3 - - - +
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Residues in contact with TYR 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E GLU* 4.8 13.9 - - - -
116E ARG* 5.3 9.9 - - - -
145F GLN* 4.3 12.8 - - - +
10G VAL* 3.9 24.3 - - + +
13G GLN* 3.3 26.9 - - - +
110G ALA* 2.9 45.6 + - + +
111G LEU* 3.3 10.9 + - + +
113G GLN* 1.3 77.9 - - + +
115G LEU* 1.3 59.1 + - - +
118G PRO* 4.4 12.7 - - - +
83J MET* 3.6 22.9 - - + +
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Residues in contact with LEU 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LEU* 4.1 30.5 - - + +
10G VAL* 3.7 27.8 - - + -
11G LEU* 4.0 15.7 - - + -
24G LEU* 3.8 27.4 - - + -
86G VAL* 4.0 9.0 - - + -
91G LEU* 4.5 10.5 - - + -
111G LEU* 3.0 21.0 + - + +
114G TYR* 1.3 79.6 - - - +
116G GLU* 1.3 64.4 + - - +
117G GLU 3.5 2.0 - - - -
118G PRO* 3.3 15.8 - - + +
119G LEU* 3.4 30.1 + - + +
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Residues in contact with GLU 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 4.8 17.1 + - - +
85G ARG* 5.2 1.0 - - - +
86G VAL* 3.9 9.9 - - + -
87G ALA* 3.1 30.7 + - - +
112G VAL* 3.0 39.0 + - - +
113G GLN* 4.0 9.6 + - - +
114G TYR 3.9 0.8 - - - -
115G LEU* 1.3 75.7 - - - +
117G GLU* 1.3 58.6 + - - +
119G LEU* 3.3 3.6 + - - +
120G THR* 2.8 42.0 + - - +
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Residues in contact with GLU 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY* 5.0 1.1 - - - +
18B GLY* 3.9 29.8 + - - +
19B VAL 4.8 1.4 - - - +
20B GLN* 2.8 42.9 + - - +
37B TYR* 4.7 3.8 - - - -
96B LYS* 3.2 26.3 - - + +
98B THR* 6.1 0.7 - - - +
113G GLN 5.0 4.2 + - - +
116G GLU* 1.3 78.8 - - - +
118G PRO* 1.4 72.5 - - + +
120G THR* 3.3 8.4 + - - +
121G GLN* 3.2 28.1 + - - +
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Residues in contact with PRO 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LEU* 6.0 4.9 - - + -
113G GLN 5.9 0.2 - - - +
114G TYR 4.4 11.4 - - - +
115G LEU* 3.3 14.8 - - + +
117G GLU* 1.4 96.6 - - + +
119G LEU* 1.3 63.4 + - + +
121G GLN* 3.1 35.3 - - + +
122G VAL* 4.1 3.6 + - - +
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Residues in contact with LEU 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LEU* 3.9 29.8 - - + -
24G LEU* 4.4 12.6 - - + -
86G VAL* 3.6 28.0 - - + +
87G ALA* 4.1 14.0 - - + +
88G ASN* 4.7 4.7 - - - +
89G LEU* 4.3 20.8 - - + +
115G LEU* 3.4 33.6 + - + +
116G GLU 3.3 6.5 + - - +
118G PRO* 1.3 75.1 - - + +
120G THR* 1.3 64.3 + - - +
122G VAL* 3.4 21.3 + - - +
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Residues in contact with THR 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 4.2 17.5 - - - +
37B TYR* 5.6 0.4 - - + +
96B LYS* 5.8 3.1 - - + -
87G ALA* 3.8 17.2 - - - +
116G GLU* 2.8 26.9 + - - +
117G GLU* 3.5 13.9 - - - +
119G LEU* 1.3 74.0 - - - +
121G GLN* 1.3 67.4 + - - +
122G VAL 3.0 8.3 + - - -
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Residues in contact with GLN 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN 4.6 2.2 + - - -
20B GLN* 4.9 0.9 + - - -
37B TYR* 3.0 72.9 + - + +
38B GLY 4.9 3.8 + - - -
117G GLU* 3.2 19.9 + - - +
118G PRO* 3.1 24.9 - - + +
120G THR* 1.3 76.5 - - - +
122G VAL* 1.3 67.6 + - + +
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Residues in contact with VAL 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ASN* 5.6 6.3 + - - -
118G PRO 4.9 2.7 - - - +
119G LEU* 3.4 19.0 + - - +
120G THR* 3.1 6.0 - - - -
121G GLN* 1.3 94.3 - - + +
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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
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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