Contacts of the helix formed by residues 97 - 120 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLY 5.6 1.2 + - - -
94C HIS 3.3 24.0 + - - -
95C ILE* 3.2 18.2 + - + +
97C ASN* 3.8 4.0 - - - +
91D PHE* 5.4 0.8 - - + +
92D GLY* 3.1 36.8 + - - +
93D ASP* 4.3 1.0 - - - +
94D HIS* 3.5 28.9 + - - +
96D ASN* 1.3 75.3 - - - +
98D GLU* 1.3 64.6 + - - +
99D ASN 3.2 1.3 - - - -
100D CYS* 3.2 11.7 + - + +
101D TRP* 3.2 21.3 + - - +
150D LEU* 4.0 20.1 - - + +
154D PHE* 5.3 0.9 - - - -
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE* 5.3 6.3 - - + +
96D ASN* 3.6 3.2 - - + +
97D ASN* 1.3 77.2 - - - +
99D ASN* 1.3 57.7 + - - +
100D CYS 3.0 5.6 + - - -
101D TRP* 3.3 8.5 + - - +
102D GLN* 3.2 24.9 + - - +
157D ARG* 5.4 11.6 + - - +
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Residues in contact with ASN 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ASN* 4.5 11.1 + - + +
97D ASN 3.2 0.6 - - - -
98D GLU* 1.3 76.8 - - - +
100D CYS* 1.3 61.8 + - - +
102D GLN* 4.6 4.9 - - - +
103D PRO* 3.4 19.3 - - - +
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Residues in contact with CYS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLY 5.0 2.5 - - - +
91D PHE* 3.6 27.5 - - + +
93D ASP* 4.0 7.2 - - - -
94D HIS* 3.7 32.3 - - - -
96D ASN 4.6 1.6 - - - -
97D ASN* 3.2 21.0 + - - +
98D GLU 3.0 0.6 - - - -
99D ASN* 1.3 83.3 - - - +
101D TRP* 1.3 58.3 - - - +
102D GLN 3.2 4.9 - - - -
103D PRO* 3.4 12.4 - - - +
104D ILE* 4.3 13.9 - - - +
154D PHE* 4.4 4.4 - - - -
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Residues in contact with TRP 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ASN 3.2 13.1 + - - +
98D GLU* 3.3 6.9 + - - +
100D CYS* 1.3 76.0 - - - +
102D GLN* 1.3 60.6 + - - +
104D ILE* 4.4 2.9 - - - +
105D MET* 3.1 30.0 + - + +
154D PHE* 3.5 36.9 - - + -
157D ARG* 4.0 23.0 + - - +
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Residues in contact with GLN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLU 3.2 14.9 + - - +
99D ASN* 4.6 4.9 - - - -
101D TRP* 1.3 75.0 - - - +
103D PRO* 1.4 73.4 - - + +
104D ILE 3.2 2.0 + - - -
105D MET* 3.3 6.4 + - - +
106D LYS* 3.0 24.0 + - - +
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Residues in contact with PRO 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ILE* 3.8 15.9 - - + +
89D PRO* 6.2 3.8 - - + -
99D ASN 3.4 23.8 - - - +
100D CYS* 3.4 13.7 - - - +
102D GLN* 1.4 92.5 - - + +
104D ILE* 1.3 58.2 + - + +
106D LYS* 3.5 7.9 + - + +
107D PHE* 3.1 25.6 + - - +
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MET* 3.9 24.2 - - + -
29D VAL* 3.9 26.5 - - + -
67D ILE* 4.6 6.3 - - + -
88D THR* 3.9 24.2 - - + +
89D PRO* 4.7 8.5 - - + +
91D PHE* 4.6 7.6 - - + -
100D CYS 4.3 10.1 - - - +
101D TRP 4.1 6.0 + - - +
102D GLN 3.2 0.8 - - - -
103D PRO* 1.3 76.4 - - + +
105D MET* 1.3 65.5 + - + +
106D LYS 3.1 0.2 - - - -
107D PHE* 3.3 6.9 + - - +
108D ILE* 3.1 23.5 + - + +
154D PHE* 4.1 20.6 - - + -
158D LEU* 4.4 17.0 - - + -
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Residues in contact with MET 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TRP* 3.1 21.5 + - + +
102D GLN* 3.3 6.7 + - - +
104D ILE* 1.3 76.9 - - + +
106D LYS* 1.3 61.1 + - - +
108D ILE* 3.5 5.6 + - + +
109D ASN* 3.0 41.1 + - - +
154D PHE* 5.8 2.0 - - + -
157D ARG* 4.3 30.1 - - + +
158D LEU* 3.8 28.5 - - - -
161D VAL* 3.7 33.7 - - + -
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Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLN 3.0 16.1 + - - +
103D PRO* 3.6 9.9 - - + +
104D ILE 3.1 0.2 - - - -
105D MET* 1.3 76.0 - - - +
107D PHE* 1.3 58.4 + - - +
109D ASN* 3.4 6.1 + - - +
110D ASP* 2.9 42.0 + - - +
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Residues in contact with PHE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MET* 3.4 30.3 - - + -
67D ILE* 3.9 31.9 - - + -
69D SER* 4.0 13.7 - - - -
86D ILE* 3.8 27.4 - - + -
103D PRO 3.1 14.9 + - - +
104D ILE* 3.6 8.1 - - - +
106D LYS* 1.3 75.8 - - - +
108D ILE* 1.3 62.5 + - - +
110D ASP* 3.3 6.8 + - + -
111D GLN* 3.1 63.7 + - + +
131D THR 5.2 0.7 - - - -
133D VAL* 4.1 3.8 - - + -
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Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MET* 4.1 14.6 - - + -
104D ILE* 3.1 21.8 + - + +
105D MET* 3.6 11.9 - - + +
106D LYS 3.2 0.2 - - - -
107D PHE* 1.3 78.9 - - - +
109D ASN* 1.3 65.6 + - - +
111D GLN* 3.3 5.9 + - - +
112D TYR* 3.2 45.2 + - + +
133D VAL* 3.6 38.2 + - + -
158D LEU* 4.8 10.1 - - + -
161D VAL* 4.2 23.6 - - + +
162D VAL* 4.5 11.2 - - + -
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Residues in contact with ASN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D MET* 3.0 33.3 + - - +
106D LYS* 4.0 5.2 - - - +
108D ILE* 1.3 83.8 - - - +
110D ASP* 1.3 63.2 + - - +
112D TYR* 3.3 8.7 + - - -
113D GLU* 2.8 30.0 + - - +
161D VAL* 5.1 8.5 - - - +
285D TYR* 3.5 32.4 + - + +
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LYS* 2.9 30.2 + - - +
107D PHE* 3.6 8.2 - - + +
108D ILE 3.2 0.2 - - - -
109D ASN* 1.3 80.6 - - - +
111D GLN* 1.3 67.0 + - - +
113D GLU* 3.6 8.2 - - - +
114D LYS* 2.8 29.1 + - - +
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Residues in contact with GLN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE* 3.1 60.0 + - + +
108D ILE* 3.7 7.2 - - - +
109D ASN 3.3 0.2 - - - -
110D ASP* 1.3 83.4 - - - +
112D TYR* 1.3 65.0 + - + +
114D LYS* 3.4 5.3 + - - +
115D TYR* 3.2 17.5 + - - +
131D THR* 2.8 54.1 + - - +
132D ARG* 3.6 23.3 - - - +
133D VAL* 4.5 4.0 - - + +
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Residues in contact with TYR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ILE* 3.2 27.4 + - + -
109D ASN* 3.7 10.3 - - - +
111D GLN* 1.3 77.1 - - - +
113D GLU* 1.3 58.1 + - - +
116D LEU* 3.3 25.6 + - - +
132D ARG* 3.5 39.5 - - + -
133D VAL 3.9 10.8 + - - -
161D VAL* 2.9 32.6 + - + -
162D VAL* 4.4 1.6 - - + +
277D THR* 3.8 16.0 - - + +
281D HIS* 3.4 27.5 - - + +
282D PHE* 3.6 20.6 - + + -
285D TYR* 3.5 38.6 - + + -
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ASN 2.8 17.2 + - - +
110D ASP* 3.6 11.2 - - - +
111D GLN 3.1 0.2 - - - -
112D TYR* 1.3 75.6 - - - +
114D LYS* 1.3 59.5 + - - +
115D TYR 3.2 1.8 - - - -
116D LEU* 3.1 11.1 + - - +
117D GLN* 2.8 38.1 + - + +
285D TYR* 2.4 32.8 + - - +
289D ARG* 4.8 3.5 - - - +
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ASP 2.8 17.7 + - - +
111D GLN* 3.4 10.1 + - - +
113D GLU* 1.3 77.1 - - - +
115D TYR* 1.3 58.0 + - - +
117D GLN* 3.8 5.0 + - - +
118D GLU* 3.2 33.4 + - - +
131D THR* 4.5 9.9 - - - +
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Residues in contact with TYR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D GLN 3.2 15.7 + - - +
112D TYR 4.1 0.2 - - - +
113D GLU 3.2 0.6 - - - -
114D LYS* 1.3 77.1 - - - +
116D LEU* 1.3 59.9 + - - +
118D GLU* 3.5 3.6 + - - +
119D GLU* 3.2 42.6 + - - +
128D ILE* 3.6 42.5 + - + +
129D PRO 4.0 8.1 - - - -
130D ASP* 3.9 29.7 + - + -
131D THR* 4.9 1.5 + - - +
132D ARG* 3.8 38.6 + - + -
282D PHE* 3.6 20.4 - + + -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D TYR 3.3 15.7 + - - +
113D GLU* 3.1 12.9 + - - +
115D TYR* 1.3 76.9 - - - +
117D GLN* 1.3 56.5 + - - +
118D GLU 3.1 4.7 - - - -
119D GLU* 4.0 11.2 - - + +
120D VAL* 3.2 31.5 + - + +
282D PHE* 4.4 5.6 - - + -
285D TYR* 4.1 12.8 - - + -
286D ARG* 3.6 37.7 - - + -
289D ARG* 3.9 27.8 - - + -
290D LEU* 3.9 25.1 - - + -
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Residues in contact with GLN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D GLU* 2.8 25.6 + - + +
114D LYS* 4.3 6.1 - - - +
116D LEU* 1.3 76.9 - - - +
118D GLU* 1.3 62.0 + - + +
120D VAL* 4.5 3.9 - - - +
121D ASN* 3.8 16.6 + - - +
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS* 3.2 21.0 + - - +
115D TYR 3.5 5.8 + - - +
116D LEU 3.1 0.4 - - - -
117D GLN* 1.3 81.6 - - + +
119D GLU* 1.3 57.1 + - - +
121D ASN* 3.8 9.0 + - - +
124D ARG* 2.4 48.5 + - - +
127D ARG 4.9 0.7 - - - +
128D ILE* 3.8 21.4 - - + +
129D PRO* 3.7 30.0 - - - +
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Residues in contact with GLU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D TYR* 3.2 35.8 + - - +
116D LEU* 3.3 9.8 + - + +
118D GLU* 1.3 76.5 - - - +
120D VAL* 1.3 64.5 + - - +
121D ASN 3.1 9.3 + - - +
124D ARG* 4.0 9.7 + - - +
128D ILE* 3.6 17.7 - - + +
282D PHE* 3.5 18.6 - - - -
286D ARG* 2.9 36.5 + - - -
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 3.2 18.4 + - + +
117D GLN* 5.1 3.4 - - - +
119D GLU* 1.3 79.4 - - - +
121D ASN* 1.3 61.2 + - - +
122D ILE* 3.4 5.2 + - - +
290D LEU* 5.9 8.3 - - + -
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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
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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