Contacts of the helix formed by residues 102 - 129 (chain C) in PDB entry 2WP9
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 THR 102 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B MET* 3.4 4.4 - - - +
213B VAL* 5.3 0.2 - - - -
221B ASN* 3.8 6.3 - - - +
224B ARG* 3.5 26.0 - - - +
100C GLU* 3.5 19.3 - - + +
101C GLU* 1.3 83.5 - - - +
103C PHE* 1.3 64.4 + - - +
104C GLU* 3.7 8.7 + - - +
105C ALA* 3.1 22.9 + - - +
106C GLY 3.0 17.3 + - - -
108C ARG* 4.5 1.7 + - - -
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 4.1 22.0 - - + +
213B VAL* 3.9 24.8 - - + +
214B SER* 3.6 39.5 - - - +
21C PRO* 4.1 24.2 - - + -
23C THR* 4.3 10.3 - - + -
101C GLU 3.9 0.2 + - - -
102C THR* 1.3 72.8 - - - +
104C GLU* 1.3 67.9 + - - +
106C GLY* 3.2 1.6 + - - -
107C LYS* 2.9 64.0 + - + +
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C THR* 3.3 7.3 + - - +
103C PHE* 1.3 82.3 - - + +
105C ALA* 1.3 65.5 + - - +
107C LYS* 2.9 44.3 + - - +
108C ARG* 3.0 31.0 + - - +
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C MET* 4.9 0.2 - - - -
99C LEU* 6.2 0.4 - - + -
100C GLU* 3.6 37.9 - - + +
102C THR* 3.1 16.6 + - - +
104C GLU* 1.3 78.7 - - - +
106C GLY* 1.3 56.8 + - - +
108C ARG* 3.1 25.4 + - - +
109C SER* 3.0 32.1 + - - -
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Residues in contact with GLY 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 4.1 16.2 - - - -
23C THR* 3.6 7.2 - - - +
90C ARG* 2.7 32.5 + - - -
94C MET* 4.1 4.2 - - - +
102C THR 3.0 13.9 + - - -
103C PHE 3.5 4.0 - - - -
104C GLU 3.1 0.2 - - - -
105C ALA* 1.3 78.0 - - - +
107C LYS* 1.3 59.9 - - - +
109C SER* 3.8 2.7 - - - -
110C ALA* 3.2 10.6 + - - +
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Residues in contact with LYS 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PRO* 6.2 0.2 - - + -
22C ILE* 3.7 27.8 - - + +
23C THR* 4.6 0.7 - - + -
103C PHE* 2.9 52.1 + - + +
104C GLU* 2.9 36.6 + - - +
106C GLY* 1.3 72.9 - - - +
108C ARG* 1.3 66.4 + - - +
110C ALA* 3.3 3.8 + - - +
111C LYS* 3.1 38.5 + - - +
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLU* 5.0 6.9 + - - -
102C THR* 4.5 1.6 + - - -
104C GLU* 3.0 28.1 + - - +
105C ALA* 3.1 37.9 - - - +
107C LYS* 1.3 75.5 - - + +
109C SER* 1.3 58.4 + - - +
111C LYS* 3.1 10.2 + - - +
112C ILE* 2.9 40.9 + - + +
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Residues in contact with SER 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ARG* 2.7 33.8 + - - -
94C MET* 3.8 5.9 - - - +
99C LEU* 3.8 27.4 - - - -
105C ALA 3.0 18.2 + - - -
106C GLY* 3.8 2.1 - - - -
107C LYS 3.2 0.2 - - - -
108C ARG* 1.3 73.6 - - - +
110C ALA* 1.3 65.0 + - - +
112C ILE* 3.6 9.7 + - - +
113C SER* 2.9 29.5 + - - -
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 4.3 20.2 - - + -
23C THR* 4.7 1.8 - - - -
26C ALA* 4.2 19.7 - - + -
90C ARG* 3.8 16.6 - - - +
106C GLY 3.2 15.3 + - - +
107C LYS 3.6 4.0 - - - +
109C SER* 1.3 82.6 + - - +
111C LYS* 1.3 57.0 + - - +
113C SER* 3.1 8.4 + - - -
114C PHE* 2.9 33.4 + - + -
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Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.5 28.3 - - + -
107C LYS* 3.1 25.3 + - - +
108C ARG* 3.5 10.3 - - - +
110C ALA* 1.3 75.5 - - - +
112C ILE* 1.3 65.9 + - + +
114C PHE* 3.0 12.2 + - + +
115C VAL* 3.0 26.5 + - + +
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ARG* 2.9 29.4 + - + +
109C SER* 4.0 7.4 - - - +
111C LYS* 1.3 76.2 - - + +
113C SER* 1.3 58.0 + - - +
115C VAL* 3.3 8.7 + - + +
116C ILE* 2.9 48.1 + - + +
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Residues in contact with SER 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C VAL* 4.0 18.1 - - - +
87C VAL* 4.0 22.7 - - - +
90C ARG* 3.7 21.3 - - - +
109C SER 2.9 20.0 + - - -
110C ALA* 3.2 12.3 - - - -
111C LYS 3.1 0.2 - - - -
112C ILE* 1.3 75.8 - - - +
114C PHE* 1.3 67.9 + - - +
116C ILE* 3.4 3.2 + - - +
117C THR* 2.9 28.3 + - - -
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.5 35.0 - - + -
25C ILE* 5.0 5.6 - - + -
26C ALA* 3.9 29.8 - - + -
29C LEU* 4.9 8.1 - - + -
83C TYR* 3.5 38.4 - + - -
87C VAL* 5.0 2.5 - - + -
110C ALA* 2.9 19.5 + - + -
111C LYS* 3.0 8.9 + - + +
113C SER* 1.3 76.2 - - - +
115C VAL* 1.3 66.1 + - + +
117C THR* 2.9 8.5 + - - -
118C VAL* 2.9 29.1 + - + +
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LYS* 3.0 15.9 + - + +
112C ILE* 3.6 11.7 - - + +
114C PHE* 1.3 78.5 - - + +
116C ILE* 1.3 68.0 + - + +
118C VAL* 3.1 15.1 + - - +
119C VAL* 3.1 23.2 + - + +
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Residues in contact with ILE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C VAL* 4.2 29.2 - - + -
112C ILE* 2.9 42.2 + - + +
113C SER* 3.8 3.6 - - - +
115C VAL* 1.3 76.6 - - + +
117C THR* 1.3 57.6 + - - +
119C VAL* 3.5 8.2 + - + +
120C LEU* 3.0 34.5 + - + +
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C THR* 4.4 15.7 - - + +
82C ALA* 4.7 2.6 - - + +
83C TYR* 3.9 53.1 - - + +
86C VAL* 4.0 13.0 - - - +
87C VAL* 5.1 0.9 - - - +
113C SER 2.9 16.2 + - - -
114C PHE* 2.9 11.2 + - - -
116C ILE* 1.3 74.1 - - - +
118C VAL* 1.3 62.6 + - + +
120C LEU* 3.2 6.7 + - - +
121C SER* 2.7 27.8 + - - -
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Residues in contact with VAL 118 (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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114C PHE* 2.9 19.0 + - + +
115C VAL* 3.6 10.1 - - - +
117C THR* 1.3 77.3 - - + +
119C VAL* 1.3 65.2 + - + +
121C SER* 3.1 10.2 + - - -
122C LEU* 3.1 35.7 + - + +
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Residues in contact with VAL 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C VAL* 3.1 23.9 + - + +
116C ILE* 3.6 10.3 - - + +
118C VAL* 1.3 79.3 - - + +
120C LEU* 1.3 64.9 + - + +
122C LEU* 3.1 12.8 + - + +
123C LEU* 3.0 38.5 + - + +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ALA* 3.9 30.5 - - + -
85C VAL* 6.5 0.4 - - + -
86C VAL* 4.0 22.0 - - + -
116C ILE* 3.0 24.2 + - + +
117C THR 3.7 6.3 - - - +
119C VAL* 1.3 77.6 - - + +
121C SER* 1.3 52.6 + - - +
123C LEU* 3.2 23.0 + - + +
124C ALA* 2.7 35.6 + - - +
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TRP* 3.1 29.5 + - - -
79C THR* 2.7 38.4 + - - +
82C ALA* 5.2 0.8 - - - +
117C THR* 2.7 17.5 + - - -
118C VAL* 3.1 13.9 + - - -
120C LEU* 1.3 72.7 - - - +
122C LEU* 1.3 59.7 + - - +
124C ALA* 3.5 4.3 - - - +
125C GLY 2.9 19.6 + - - -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TRP* 6.1 0.7 - - - +
118C VAL* 3.1 29.1 + - + +
119C VAL* 3.1 12.4 + - + +
121C SER* 1.3 77.0 - - - +
123C LEU* 1.3 56.3 + - + +
124C ALA 2.9 1.3 - - - -
125C GLY* 2.8 4.5 + - - +
126C VAL* 2.7 40.5 + - + +
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Residues in contact with LEU 123 (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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119C VAL* 3.0 26.8 + - + +
120C LEU* 3.6 30.1 - - + +
122C LEU* 1.3 76.8 - - + +
124C ALA* 1.3 55.5 + - - +
126C VAL* 3.9 12.1 - - + +
127C LEU* 3.1 29.1 + - - +
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TRP* 4.4 8.1 - - + -
78C LEU* 3.9 33.2 - - + -
79C THR* 4.9 1.8 - - - +
120C LEU 2.7 17.2 + - - +
121C SER* 3.5 10.3 - - - +
123C LEU* 1.3 75.2 - - - +
125C GLY* 1.3 65.6 + - - +
127C LEU* 3.1 7.1 + - - +
128C VAL* 3.1 28.8 + - - +
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Residues in contact with GLY 125 (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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75C TRP* 3.7 19.5 - - - -
121C SER 2.9 10.1 + - - -
122C LEU* 2.8 12.9 + - - -
124C ALA* 1.3 71.6 - - - +
126C VAL* 1.3 61.7 + - - +
128C VAL* 3.3 6.3 + - - +
129C TRP* 3.2 27.1 + - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 2.7 23.3 + - + +
123C LEU* 3.9 13.0 - - + +
125C GLY* 1.3 71.5 - - - +
127C LEU* 1.3 63.0 + - - +
128C VAL 2.8 6.9 + - - -
129C TRP* 3.1 19.7 + - - +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 5.0 9.2 - - + -
123C LEU 3.1 17.2 + - - +
124C ALA* 3.1 8.3 + - - +
126C VAL* 1.3 80.9 - - - +
128C VAL* 1.3 68.1 + - + +
129C TRP 5.0 1.3 - - - +
34D VAL* 6.4 3.6 - - + -
37D PHE* 4.0 50.5 - - + +
38D ALA* 5.0 5.8 - - + +
43D LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C MET* 4.5 16.4 - - + +
71C LYS* 2.6 68.0 + - + +
74C MET* 4.0 13.7 - - + -
75C TRP* 4.8 7.4 - - + +
78C LEU* 4.0 24.2 - - + -
124C ALA 3.1 16.9 + - - +
125C GLY* 3.3 5.6 + - - +
126C VAL 2.9 1.4 - - - -
127C LEU* 1.3 86.3 - - + +
129C TRP* 1.3 52.5 - - - +
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Residues in contact with TRP 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PHE* 6.2 7.0 - + - -
71C LYS* 3.1 28.9 - - + +
125C GLY 3.2 16.0 + - - +
126C VAL* 3.1 13.0 + - - +
127C LEU 5.0 1.0 - - - +
128C VAL* 1.3 77.9 - - - +
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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