Contacts of the helix formed by residues 97 - 120 (chain A) in PDB entry 5CYP
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 ASN 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 5.4 0.9 - - + -
92A GLY* 3.2 38.7 + - - +
94A HIS* 3.6 25.7 + - - +
96A ASN* 1.3 74.6 - - - +
98A GLU* 1.3 65.6 + - - +
99A ASN 3.2 1.8 - - - -
100A CYS* 3.1 23.5 + - + +
101A TRP* 3.1 14.7 + - - +
150A LEU* 4.0 19.6 - - + +
154A PHE* 5.3 0.9 - - - -
92B GLY 5.8 0.4 + - - -
94B HIS 3.5 17.0 + - - -
95B ILE* 3.3 25.1 + - + +
97B ASN* 3.9 3.0 - - - +
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Residues in contact with GLU 98 (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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96A ASN* 3.6 4.5 - - + +
97A ASN* 1.3 76.8 - - - +
99A ASN* 1.3 62.3 + - - +
100A CYS 3.0 4.6 + - - -
101A TRP* 3.3 8.0 + - - +
102A GLN* 3.3 23.0 + - - +
157A ARG* 5.0 13.4 + - - +
95B ILE* 4.1 13.2 - - + +
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASN* 4.5 17.3 + - - +
97A ASN 3.2 0.6 - - - -
98A GLU* 1.3 79.0 - - - +
100A CYS* 1.3 60.8 + - - +
102A GLN* 4.6 5.3 - - - +
103A PRO* 3.4 21.3 - - - +
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Residues in contact with CYS 100 (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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90A GLY 5.2 2.2 - - - +
91A PHE* 3.6 26.8 - - + +
93A ASP* 4.1 6.5 - - - -
94A HIS* 3.7 30.7 - - - -
96A ASN 4.6 1.8 - - - -
97A ASN* 3.1 24.3 + - - +
98A GLU 3.0 0.6 - - - -
99A ASN* 1.3 82.8 - - - +
101A TRP* 1.3 59.1 + - - +
102A GLN 3.2 4.9 - - - -
103A PRO* 3.4 12.3 - - - +
104A ILE* 4.4 13.7 - - - +
154A PHE* 4.4 4.8 - - - -
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Residues in contact with TRP 101 (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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97A ASN 3.1 12.7 + - - +
98A GLU* 3.3 3.8 + - - +
100A CYS* 1.3 76.0 - - - +
102A GLN* 1.3 58.0 + - - +
103A PRO 3.8 0.2 - - - -
104A ILE* 4.4 3.1 - - - +
105A MET* 3.1 29.5 + - + +
154A PHE* 3.6 35.3 - - + -
157A ARG* 3.1 31.6 + - - +
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Residues in contact with GLN 102 (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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98A GLU 3.3 14.8 + - - +
99A ASN* 4.6 5.6 - - - +
101A TRP* 1.3 75.3 - - - +
103A PRO* 1.4 72.2 - - + +
104A ILE 3.2 2.2 + - - -
105A MET* 3.2 6.5 + - - +
106A LYS* 3.1 22.5 + - - +
157A ARG* 5.5 0.9 - - - +
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Residues in contact with PRO 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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67A ILE* 3.8 16.0 - - + +
89A PRO* 6.2 3.6 - - + -
99A ASN 3.4 22.4 - - - +
100A CYS* 3.4 14.1 - - - +
102A GLN* 1.4 92.2 - - + +
104A ILE* 1.3 60.3 + - + +
106A LYS* 3.6 8.0 + - + +
107A PHE* 3.3 21.0 + - - +
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Residues in contact with ILE 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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27A MET* 3.9 25.4 - - + -
29A VAL* 3.9 26.0 - - + -
67A ILE* 4.7 6.5 - - + -
88A THR* 4.0 24.7 - - + +
89A PRO* 4.9 6.5 - - + +
91A PHE* 4.6 9.0 - - + -
100A CYS 4.4 9.0 - - - +
101A TRP 4.2 5.1 + - - +
102A GLN 3.2 0.8 - - - -
103A PRO* 1.3 76.9 - - + +
105A MET* 1.3 66.8 + - - +
106A LYS 3.2 0.2 - - - -
107A PHE* 3.3 6.5 + - - +
108A ILE* 3.2 30.6 + - + +
154A PHE* 4.2 22.4 - - + -
158A LEU* 4.5 8.7 - - + -
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Residues in contact with MET 105 (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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101A TRP 3.1 21.3 + - - +
102A GLN* 3.2 7.1 + - - +
104A ILE* 1.3 77.9 - - + +
106A LYS* 1.3 61.0 + - - +
108A ILE* 3.6 5.1 + - + +
109A ASN* 2.9 43.7 + - - +
154A PHE* 5.8 2.9 - - + -
157A ARG* 4.3 30.7 - - + +
158A LEU* 4.0 26.2 - - - -
161A VAL* 3.7 34.5 - - + -
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Residues in contact with LYS 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 GLN 3.1 16.2 + - - +
103A PRO* 3.8 8.1 - - + +
105A MET* 1.3 76.2 - - - +
107A PHE* 1.3 59.4 + - - +
109A ASN* 3.4 4.9 + - - +
110A ASP* 2.9 57.2 + - - +
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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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27A MET* 3.4 30.5 - - + -
67A ILE* 3.9 30.7 - - + -
69A SER* 3.8 21.3 - - - -
86A ILE* 3.8 20.9 - - + -
103A PRO 3.3 11.9 + - - +
104A ILE* 3.3 8.3 + - - +
106A LYS* 1.3 78.9 - - - +
108A ILE* 1.3 62.1 + - - +
110A ASP* 3.4 6.1 + - - -
111A GLN* 3.1 62.8 + - + +
131A THR 5.3 1.1 - - - -
133A VAL* 4.4 2.0 - - + -
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Residues in contact with ILE 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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27A MET* 4.3 19.1 - - + -
104A ILE* 3.2 22.8 + - + +
105A MET* 3.8 7.2 - - + +
106A LYS 3.3 0.2 - - - -
107A PHE* 1.3 79.8 - - - +
109A ASN* 1.3 65.3 + - - +
111A GLN* 3.3 9.2 + - - +
112A TYR* 3.2 45.8 + - + +
133A VAL* 4.3 17.1 + - + -
158A LEU* 3.7 30.5 - - + -
161A VAL* 4.3 22.4 - - + +
162A VAL* 4.5 11.7 - - + -
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Residues in contact with ASN 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 MET* 2.9 36.1 + - - +
106A LYS* 4.0 5.0 - - - +
108A ILE* 1.3 77.7 - - - +
110A ASP* 1.3 56.9 + - - +
112A TYR* 3.2 16.1 + - - +
113A GLU* 2.7 34.5 + - - +
161A VAL* 4.8 10.1 - - - +
285A TYR* 3.5 29.8 + - + +
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Residues in contact with ASP 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 LYS* 2.9 53.6 + - - +
107A PHE* 3.7 7.7 + - + +
108A ILE 3.3 0.2 - - - -
109A ASN* 1.3 75.8 - - - +
111A GLN* 1.3 65.9 + - - +
113A GLU* 3.1 10.5 + - - +
114A LYS* 2.7 42.1 + - + +
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Residues in contact with GLN 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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107A PHE* 3.1 58.1 + - + +
108A ILE* 3.6 7.6 - - - +
109A ASN 3.3 0.2 - - - -
110A ASP* 1.3 84.0 - - - +
112A TYR* 1.3 62.1 + - - +
114A LYS* 3.7 22.0 + - - +
115A TYR* 3.1 25.1 + - - +
131A THR* 2.7 53.6 + - - +
132A ARG* 3.6 16.8 - - - +
133A VAL* 4.6 2.7 - - + +
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Residues in contact with TYR 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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108A ILE* 3.2 28.3 + - + -
109A ASN* 3.2 23.7 + - - +
111A GLN* 1.3 75.4 - - - +
113A GLU* 1.3 61.0 + - - +
116A LEU* 3.3 8.1 + - - +
132A ARG* 3.7 29.4 - - + -
133A VAL 3.9 14.9 + - - -
161A VAL* 2.8 32.6 + - + -
162A VAL* 4.2 2.3 - - - +
277A THR* 4.0 7.2 - - + +
281A HIS* 3.6 25.4 - - + +
282A PHE* 3.3 44.5 - + + -
285A TYR* 3.4 35.0 - + + -
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Residues in contact with GLU 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 ASN 2.7 13.7 + - - +
110A ASP* 3.3 14.4 - - - +
112A TYR* 1.3 71.5 - - - +
114A LYS* 1.3 61.0 + - + +
115A TYR 3.2 1.6 - - - -
116A LEU* 3.2 10.6 + - - +
117A GLN* 3.0 35.1 + - + +
285A TYR* 2.5 35.4 + - - +
289A ARG* 5.2 4.2 - - - +
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Residues in contact with LYS 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 ASP* 2.7 26.4 + - + +
111A GLN* 3.7 31.8 + - - +
113A GLU* 1.3 76.3 - - + +
115A TYR* 1.3 59.4 + - - +
117A GLN* 3.8 5.4 + - - +
118A GLU* 3.5 27.7 + - - +
131A THR* 4.4 17.2 + - - +
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Residues in contact with TYR 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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111A GLN 3.1 17.3 + - - +
114A LYS* 1.3 76.9 - - - +
116A LEU* 1.3 63.4 + - - +
118A GLU* 3.5 3.8 + - - +
119A GLU* 3.3 36.4 + - - +
128A ILE* 3.6 46.1 + - + +
129A PRO 3.8 9.0 - - - -
130A ASP* 3.8 31.7 + - + +
131A THR* 4.8 1.8 - - - +
132A ARG* 3.7 46.1 + - + -
282A PHE* 3.9 14.4 - + + -
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Residues in contact with LEU 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 TYR 3.3 16.8 + - - +
113A GLU* 3.2 11.7 + - - +
115A TYR* 1.3 77.3 - - - +
117A GLN* 1.3 56.3 + - - +
118A GLU 3.1 4.9 - - - -
119A GLU* 4.0 12.1 - - + +
120A VAL* 3.1 31.5 + - + +
282A PHE* 4.1 8.9 - - + -
285A TYR* 4.2 17.9 - - + -
286A ARG* 3.5 43.7 - - + +
289A ARG* 4.5 19.1 - - + +
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Residues in contact with GLN 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 GLU* 3.0 23.1 + - + +
114A LYS* 4.2 7.2 - - - +
115A TYR 3.4 0.2 - - - -
116A LEU* 1.3 76.9 - - - +
118A GLU* 1.3 60.3 + - + +
120A VAL* 3.7 13.0 - - + +
121A ASN* 3.4 20.1 + - - +
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Residues in contact with GLU 118 (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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114A LYS* 3.5 14.3 + - - +
115A TYR 3.5 3.7 + - - +
116A LEU 3.1 0.4 - - - -
117A GLN* 1.3 80.9 - - + +
119A GLU* 1.3 58.8 + - - +
120A VAL 3.4 0.4 - - - -
121A ASN* 3.5 18.5 + - - +
124A ARG* 2.4 48.7 + - - +
127A ARG 4.7 0.9 - - - +
128A ILE* 3.8 19.2 - - + +
129A PRO* 3.7 33.9 - - - +
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Residues in contact with GLU 119 (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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115A TYR* 3.3 25.0 + - + +
116A LEU* 3.3 11.3 + - + +
118A GLU* 1.3 76.4 - - - +
120A VAL* 1.3 58.9 + - - +
121A ASN 3.1 6.6 + - - -
122A ILE* 5.6 0.3 - - - -
124A ARG* 4.1 13.6 + - - +
128A ILE* 3.5 20.8 - - + +
282A PHE* 3.6 24.3 - - - -
283A GLU* 5.4 0.7 - - - +
286A ARG* 2.8 32.0 + - - +
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Residues in contact with VAL 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 LEU* 3.1 18.8 + - + +
117A GLN* 3.7 17.9 - - + +
119A GLU* 1.3 75.0 - - - +
121A ASN* 1.3 62.2 + - - +
122A ILE* 2.9 13.8 + - - +
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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