Contacts of the helix formed by residues 102 - 128 (chain A) in PDB entry 1O5L
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 ARG 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU 5.2 0.2 - - - -
100A LYS 4.3 0.8 - - - -
101A ASP* 1.3 71.2 + - - +
103A GLU* 1.3 60.0 + - - +
105A LEU* 3.2 10.9 + - + +
106A LEU* 2.8 51.7 + - + +
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.1 44.3 + - + +
101A ASP* 3.2 9.0 + - - +
102A ARG* 1.3 79.8 - - - +
104A LEU* 1.3 55.0 + - - +
106A LEU* 3.9 8.1 - - - +
107A PHE* 3.0 28.6 + - - +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.8 15.3 - - + -
3A LEU* 4.1 24.9 - - + -
6A LEU* 4.2 25.6 - - + -
94A PHE* 4.6 13.2 - - + -
97A LEU* 3.7 39.5 - - + +
98A LEU* 3.9 12.8 - - + +
101A ASP* 3.3 27.7 + - + +
102A ARG 3.2 0.4 - - - -
103A GLU* 1.3 76.2 - - - +
105A LEU* 1.3 61.2 + - - +
107A PHE* 3.2 7.0 + - + +
108A PHE* 2.8 32.8 + - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.7 43.7 - - + +
99A MET* 5.9 0.9 - - - -
101A ASP 3.1 13.4 + - - +
102A ARG* 3.5 15.0 - - + +
104A LEU* 1.3 75.8 - - - +
106A LEU* 1.3 59.1 + - + +
108A PHE* 3.4 1.6 + - + +
109A LEU* 2.9 63.3 + - + +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ARG* 2.8 45.1 + - + +
103A GLU* 3.9 7.2 - - - +
105A LEU* 1.3 76.0 - - + +
107A PHE* 1.3 56.9 + - - +
109A LEU* 3.9 10.2 - - + +
110A LYS* 2.9 32.0 + - - +
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Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.5 40.4 - - + -
3A LEU* 3.8 36.3 - - + -
59A VAL 5.4 3.1 - - - -
60A GLN* 6.2 1.1 - - - -
61A ILE* 4.4 14.1 - - + -
103A GLU 3.0 20.0 + - - +
104A LEU* 3.2 7.4 + - + +
106A LEU* 1.3 75.0 - - - +
108A PHE* 1.3 60.1 + - + +
110A LYS* 3.3 13.2 + - + +
111A ASP* 2.9 40.4 + - + +
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 3.7 26.2 - - + -
64A SER* 4.0 17.9 - - - -
67A ILE* 4.3 8.1 - - + -
68A PHE* 3.8 37.0 - + - -
94A PHE* 3.9 18.2 - + + -
98A LEU* 4.0 23.8 - - + -
104A LEU* 2.8 21.1 + - + +
105A LEU* 3.7 3.6 - - + +
107A PHE* 1.3 76.0 - - + +
109A LEU* 1.3 79.2 + - + +
111A ASP* 3.2 5.2 + - + +
112A VAL* 3.1 47.2 + - + +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 2.9 52.4 + - + +
106A LEU* 4.0 11.2 - - + +
108A PHE* 1.3 84.2 - - + +
110A LYS* 1.3 55.5 + - - +
112A VAL* 3.5 6.0 + - + +
113A SER* 2.7 40.3 + - - +
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU 2.9 19.5 + - - +
107A PHE* 3.3 11.7 - - + +
109A LEU* 1.3 75.3 - - - +
111A ASP* 1.3 59.3 + - - +
113A SER* 3.9 4.3 - - - -
114A GLU* 3.0 47.9 + - + +
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 5.4 5.7 - - - +
61A ILE* 5.0 14.0 + - + +
64A SER* 2.4 36.9 + - - +
107A PHE* 2.9 34.4 + - + +
108A PHE* 3.2 13.0 + - + +
110A LYS* 1.3 73.8 - - - +
112A VAL* 1.3 63.6 + - + +
114A GLU* 4.0 3.5 - - - +
115A HIS* 2.9 49.3 + - - -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 3.6 33.9 - - - +
65A GLY* 4.0 16.4 - - - +
108A PHE* 3.1 33.5 + - + +
109A LEU* 3.9 6.7 - - + +
111A ASP* 1.3 75.7 - - - +
113A SER* 1.3 59.8 + - - +
115A HIS* 3.4 5.3 + - - +
116A PHE* 3.0 28.2 + - + +
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 2.7 24.9 + - - +
110A LYS* 4.0 4.9 - - - -
112A VAL* 1.3 76.6 - - - +
114A GLU* 1.3 61.1 + - - +
116A PHE* 3.3 10.2 + - - +
117A ARG* 2.9 30.4 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS* 3.0 37.7 + - + +
111A ASP* 4.0 4.3 - - - +
113A SER* 1.3 75.3 - - - +
115A HIS* 1.3 66.4 + - + +
117A ARG* 2.9 45.0 + - - +
118A VAL* 3.2 29.8 + - + +
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Residues in contact with HIS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 4.9 12.8 + - - -
61A ILE 5.8 2.7 - - - -
64A SER* 4.1 4.9 + - - +
65A GLY* 5.9 4.3 - - - +
111A ASP* 2.9 51.4 + - - +
112A VAL* 3.8 5.6 - - - +
114A GLU* 1.3 75.3 - - + +
116A PHE* 1.3 66.6 + - - +
118A VAL* 3.6 7.7 + - + +
119A VAL* 3.3 24.2 + - - +
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.0 19.9 + - + +
113A SER* 3.5 11.0 - - - +
114A GLU 3.3 0.2 - - - -
115A HIS* 1.3 75.4 - - - +
117A ARG* 1.3 68.0 + - - +
119A VAL* 3.0 15.8 - - + +
120A SER* 2.9 37.4 + - - -
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Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER 2.9 17.5 + - - +
114A GLU* 2.9 39.1 + - - +
115A HIS 3.4 0.2 - - - -
116A PHE* 1.3 78.9 - - + +
118A VAL* 1.3 77.5 + - - +
120A SER* 3.4 5.8 + - - -
121A GLU* 3.0 75.2 + - + +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLU* 3.2 17.8 + - - +
115A HIS* 3.9 8.5 - - + +
116A PHE 3.2 0.2 - - - -
117A ARG* 1.3 101.4 - - - +
119A VAL* 1.3 63.9 + - + +
121A GLU* 4.1 4.1 - - - +
122A LYS* 3.2 26.4 + - + +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A HIS 3.3 14.0 + - - +
116A PHE* 3.0 31.6 - - + +
118A VAL* 1.3 81.8 - - + +
120A SER* 1.3 57.9 + - - +
122A LYS* 3.5 8.1 + - + +
123A LEU* 2.9 33.6 + - + +
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 2.9 36.7 + - - -
117A ARG* 3.7 6.3 - - - -
119A VAL* 1.3 78.4 - - - +
121A GLU* 1.3 57.0 + - - +
123A LEU* 3.4 8.7 + - - +
124A PHE* 3.0 49.1 + - - -
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ARG* 3.0 59.7 + - + +
118A VAL* 4.1 4.1 - - - +
120A SER* 1.3 73.6 - - - +
122A LYS* 1.3 64.9 + - - +
124A PHE* 3.4 10.7 + - + +
125A PHE* 3.0 49.5 + - + -
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A VAL* 3.2 21.1 + - + +
119A VAL* 3.7 8.7 - - + +
121A GLU* 1.3 75.5 - - - +
123A LEU* 1.3 62.2 + - - +
125A PHE* 3.3 11.2 + - - +
126A LEU* 3.1 45.5 + - + +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 2.9 23.0 + - + +
120A SER* 3.6 7.9 - - - +
121A GLU 3.3 0.2 - - - -
122A LYS* 1.3 76.5 - - - +
124A PHE* 1.3 55.5 + - + +
126A LEU* 3.6 7.3 + - + -
127A THR* 2.7 50.5 + - + +
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER* 3.0 39.0 + - - +
121A GLU* 3.7 10.5 - - + +
123A LEU* 1.3 73.9 - - - +
125A PHE* 1.3 63.0 + - + +
127A THR* 3.2 5.2 + - - -
128A THR* 2.7 54.3 + - + +
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU* 3.0 47.6 + - + +
122A LYS* 3.3 8.9 + - - +
124A PHE* 1.3 80.3 - - + +
126A LEU* 1.3 65.6 + - + +
127A THR 3.6 0.7 + - - -
128A THR* 4.1 8.6 + - - -
129A LYS* 4.5 6.8 + - - +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 3.1 42.1 + - + +
123A LEU* 4.1 8.3 - - + +
124A PHE 3.2 0.4 - - - -
125A PHE* 1.3 82.2 - - + +
127A THR* 1.3 62.1 + - + +
128A THR 3.8 0.2 - - - -
129A LYS* 4.4 8.3 + - - +
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 2.7 41.3 + - + +
124A PHE* 3.2 8.7 + - - -
126A LEU* 1.3 83.7 - - + +
128A THR* 1.3 65.5 + - - +
129A LYS* 3.6 22.4 + - - +
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 2.7 45.5 + - + +
125A PHE* 4.1 8.2 + - - +
126A LEU 3.8 0.2 - - - -
127A THR* 1.3 84.3 - - - +
129A LYS* 1.3 73.0 + - - +
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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
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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