Contacts of the helix formed by residues 92 - 115 (chain A) in PDB entry 1ORR
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 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A THR* 2.6 19.9 + - + +
89A SER 3.6 2.7 - - - -
91A ASP* 1.3 78.4 - - + +
93A PRO* 1.3 65.7 - - - +
94A CYS* 4.0 2.3 + - - +
95A MET* 3.3 43.2 + - + +
96A ASP* 3.2 16.6 + - - +
63B ASN* 2.9 23.7 + - - +
64B ASP* 5.4 1.2 + - - -
67B ARG* 3.3 38.2 + - - +
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Residues in contact with PRO 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER 3.2 17.4 - - - +
90A ILE 3.7 5.2 - - - +
91A ASP 3.6 7.0 - - - +
92A ASN* 1.3 85.6 - - - +
94A CYS* 1.3 64.0 + - + +
96A ASP* 3.3 6.6 + - + +
97A PHE* 2.9 25.5 + - - +
164A PRO* 4.1 17.1 - - + +
67B ARG* 5.5 0.2 - - - +
105C LEU* 5.8 1.2 - - - +
109C GLU* 3.6 19.5 - - - +
112C ARG* 3.9 16.4 - - - +
175C TYR* 5.1 2.5 + - + -
179C TYR* 3.5 18.4 - - + +
183C PHE* 3.9 14.8 - - + -
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Residues in contact with CYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 3.3 1.7 - - - +
93A PRO* 1.3 80.5 - - - +
95A MET* 1.3 62.3 + - - +
97A PHE* 3.3 8.4 + - - +
98A GLU* 3.0 50.1 + - - +
63B ASN* 3.7 32.3 - - - +
62C LYS* 4.8 19.5 - - - +
105C LEU* 6.4 0.9 - - - -
109C GLU* 4.0 22.1 + - + +
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Residues in contact with MET 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 4.1 13.2 - - - +
83A GLN* 4.1 11.2 - - + -
88A THR* 3.5 30.7 - - + -
92A ASN* 3.3 37.4 + - + +
94A CYS* 1.3 78.0 - - - +
96A ASP* 1.3 62.7 + - - +
98A GLU* 3.3 10.4 + - - +
99A ILE* 3.0 44.2 + - + +
63B ASN* 3.8 5.3 - - - +
64B ASP* 4.4 11.7 - - - +
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLN* 2.7 35.7 + - + +
89A SER* 3.6 21.7 - - - -
92A ASN 3.2 11.0 + - - +
93A PRO* 3.6 8.2 - - + +
94A CYS 3.2 0.2 - - - -
95A MET* 1.3 82.5 - - - +
97A PHE* 1.3 57.0 + - - +
100A ASN* 2.9 47.3 + - - +
164A PRO* 2.9 19.9 - - - +
165A TYR* 3.8 3.2 - - - -
168A SER* 2.6 25.2 + - - -
175C TYR* 4.2 1.2 + - - -
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO 2.9 17.6 + - - +
94A CYS* 3.6 7.6 - - - +
96A ASP* 1.3 78.8 - - - +
98A GLU* 1.3 71.7 + - + +
101A VAL* 2.8 48.5 + - + +
102A GLY* 3.1 8.3 + - - -
168A SER* 4.2 2.7 - - - -
97C PHE* 3.8 23.8 - + - -
101C VAL* 3.5 28.3 - - + -
102C GLY* 4.6 12.1 - - - -
105C LEU* 4.1 25.8 - - + -
175C TYR* 3.6 32.1 - + + +
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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
----------------------------------------------------------
60A ARG* 3.7 29.4 + - + +
94A CYS* 3.0 41.7 + - - +
95A MET* 3.7 7.7 - - - +
97A PHE* 1.3 87.7 - - + +
99A ILE* 1.3 58.6 + - - +
102A GLY* 3.2 9.1 - - - +
103A GLY 2.8 24.6 + - - -
61B ASN* 3.0 32.8 + - - +
63B ASN* 4.7 2.9 + - - +
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.8 17.6 - - + +
60A ARG* 3.6 27.6 - - + +
79A HIS* 5.5 0.7 + - - -
81A ALA 5.0 2.6 - - - +
82A GLY* 3.6 30.7 - - - +
83A GLN* 3.7 17.7 - - + +
95A MET* 3.0 40.0 + - + +
96A ASP 4.2 1.3 - - - +
98A GLU* 1.3 76.9 - - - +
100A ASN* 1.3 60.5 + - - +
103A GLY* 3.1 23.0 + - - -
104A THR* 4.0 1.2 + - - -
1200A NAD 3.9 22.2 - - - +
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Residues in contact with ASN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA 4.5 1.4 - - - +
82A GLY* 3.2 10.2 - - - -
83A GLN* 2.9 38.4 + - - +
96A ASP* 2.9 34.1 + - - +
99A ILE* 1.3 75.5 - - - +
101A VAL* 1.3 57.7 + - - +
104A THR* 2.6 30.2 + - - -
122A TYR* 4.3 2.1 + - - +
165A TYR* 4.1 0.6 - - - -
168A SER* 3.0 35.1 + - - +
169A LYS* 3.6 23.5 + - + +
172A ALA* 3.6 5.9 - - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 2.8 39.7 + - + +
100A ASN* 1.3 72.2 - - - +
102A GLY* 1.3 66.1 + - - +
104A THR 3.2 0.9 + - - -
105A LEU* 2.9 38.1 + - + +
168A SER* 3.4 35.7 - - - +
171A ALA* 4.1 20.4 - - + -
172A ALA* 4.7 3.1 - - - +
175A TYR* 4.9 1.6 - - + -
97C PHE* 3.3 31.2 - - + -
101C VAL* 4.9 1.1 - - + -
175C TYR* 4.2 1.1 - - + +
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 5.1 1.6 - - - -
97A PHE* 3.1 9.9 + - - -
98A GLU* 3.2 12.1 - - - -
101A VAL* 1.3 79.4 - - - +
103A GLY* 1.3 62.0 + - - +
105A LEU* 3.4 2.7 + - - +
106A ASN* 2.9 33.5 + - - +
97C PHE* 4.5 14.3 - - - -
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.3 41.9 + - - +
79A HIS* 4.3 0.7 - - - -
98A GLU 2.8 11.6 + - - -
99A ILE 3.1 14.3 + - - -
102A GLY* 1.3 76.0 - - - +
104A THR* 1.3 61.0 + - - +
106A ASN* 3.3 3.5 + - - +
107A LEU* 3.2 19.9 + - - +
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Residues in contact with THR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.0 23.7 + - + -
81A ALA 5.5 0.2 + - - -
99A ILE 4.0 0.5 + - - -
100A ASN* 2.6 26.2 + - - -
101A VAL 3.2 3.1 + - - -
103A GLY* 1.3 72.8 - - - +
105A LEU* 1.3 62.8 + - + +
107A LEU* 3.2 3.4 + - - +
108A LEU* 2.8 38.3 + - + +
122A TYR* 3.8 5.0 - - + -
172A ALA* 3.7 24.8 - - + +
176A MET* 3.4 34.1 - - + -
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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
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62A LYS* 5.5 0.4 - - - -
101A VAL* 2.9 40.8 + - + +
102A GLY* 3.8 5.4 - - - +
104A THR* 1.3 83.2 - - + +
106A ASN* 1.3 62.2 + - - +
108A LEU* 4.3 6.7 - - + -
109A GLU* 2.8 35.1 + - + +
172A ALA* 5.2 1.8 - - - -
175A TYR* 3.7 53.8 - - + -
179A TYR* 4.2 16.2 - - + +
93C PRO 6.0 0.9 - - - +
97C PHE* 4.0 28.3 - - + -
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Residues in contact with ASN 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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59A ILE 2.9 21.8 + - - +
60A ARG* 3.0 23.8 + - - +
61A ASN 3.7 0.2 - - - -
62A LYS* 3.5 39.8 + - + +
65A VAL* 3.8 19.2 - - + +
66A THR* 5.0 2.4 + - - -
102A GLY* 2.9 23.0 + - - +
103A GLY 3.5 7.4 - - - +
104A THR 3.3 0.2 - - - -
105A LEU* 1.3 76.2 - - - +
107A LEU* 1.3 63.0 + - - +
109A GLU* 3.9 4.5 - - - +
110A ALA* 3.1 23.9 + - - +
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Residues in contact with LEU 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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5A LEU* 4.6 4.7 - - + -
7A THR* 4.9 5.6 - - + -
59A ILE* 5.1 2.2 - - + -
65A VAL* 3.7 14.3 - - + +
68A LEU* 5.6 0.9 - - + -
69A ILE* 3.8 29.4 - - + -
77A CYS* 4.0 20.2 - - + -
79A HIS* 3.6 43.3 - - + +
103A GLY 3.2 10.8 + - - +
104A THR* 3.2 6.5 + - - +
106A ASN* 1.3 80.8 - - - +
108A LEU* 1.4 57.3 + - - +
110A ALA* 3.2 2.5 + - - +
111A VAL* 2.9 36.9 + - + +
120A ILE* 4.4 15.3 - - + -
176A MET* 4.7 3.4 - - + -
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Residues in contact with LEU 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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104A THR* 2.8 35.5 + - + +
105A LEU* 3.8 8.1 - - + +
107A LEU* 1.4 73.2 - - - +
109A GLU* 1.3 56.7 + - - +
111A VAL* 3.3 3.6 + - - +
112A ARG* 2.8 32.6 + - - +
120A ILE* 4.2 9.6 - - + -
175A TYR* 4.0 38.1 - - + +
176A MET* 3.9 26.7 - - + +
179A TYR* 3.7 40.4 - - + -
185A LEU* 4.1 11.0 - - + +
187A THR* 4.4 3.6 - - + -
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Residues in contact with GLU 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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62A LYS* 3.7 24.9 + - - +
105A LEU* 2.8 28.0 + - + +
106A ASN 3.9 1.8 - - - +
108A LEU* 1.3 72.3 - - - +
110A ALA* 1.3 58.0 + - - +
112A ARG* 3.0 40.5 + - - -
113A GLN* 2.9 47.4 + - - +
179A TYR* 2.6 28.4 + - - +
93C PRO* 3.6 5.0 - - - +
94C CYS* 4.0 22.9 + - + +
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Residues in contact with ALA 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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65A VAL* 4.5 1.1 - - + +
66A THR* 4.1 23.3 - - - +
69A ILE* 3.7 28.9 - - + +
106A ASN 3.1 19.5 + - - +
107A LEU* 3.7 4.0 - - - +
109A GLU* 1.3 73.2 - - - +
111A VAL* 1.3 62.9 + - - +
114A TYR* 2.9 44.4 + - + +
115A ASN 3.7 0.3 + - - -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.2 22.7 - - + -
77A CYS* 6.3 0.4 - - + -
107A LEU* 2.9 23.9 + - + +
108A LEU 3.9 2.7 - - - +
110A ALA* 1.3 77.2 - - - +
112A ARG* 1.3 60.4 + - - +
115A ASN* 2.8 43.1 + - - +
116A SER* 2.8 17.0 + - - -
118A CYS* 4.0 27.8 - - + +
120A ILE* 4.2 19.1 - - + -
185A LEU* 3.9 18.8 - - + -
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Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU 2.8 18.8 + - - +
109A GLU* 3.0 42.4 + - - +
111A VAL* 1.3 81.0 - - - +
113A GLN* 1.3 81.4 + - - +
116A SER* 3.8 12.1 - - - -
179A TYR* 4.0 8.1 - - + -
183A PHE* 3.4 52.2 - - + -
185A LEU* 4.2 14.6 - - + +
90C ILE 5.0 1.6 + - - -
91C ASP 5.2 4.4 + - - -
93C PRO* 3.6 21.5 - - - +
67D ARG* 6.0 1.2 - - - +
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 5.4 5.5 - - - +
109A GLU* 2.9 35.4 + - - +
110A ALA* 5.2 0.2 - - - +
112A ARG* 1.3 106.3 + - - +
114A TYR* 1.3 94.9 + - + +
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.7 26.1 - - + +
69A ILE* 4.7 3.8 - - + -
70A THR* 3.6 32.3 - - + -
73A MET* 3.4 19.2 - - - +
110A ALA* 2.9 21.3 + - + +
113A GLN* 1.3 113.8 + - + +
115A ASN* 1.3 62.3 + - - +
116A SER 3.9 0.7 - - - -
114D TYR* 3.5 22.8 + + - -
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 3.7 20.2 - - + +
73A MET* 3.3 25.2 - - - +
74A PRO* 2.8 50.3 + - - +
110A ALA 3.7 0.8 + - - -
111A VAL* 2.8 21.8 + - - +
114A TYR* 1.3 75.9 - - - +
116A SER* 1.3 61.5 - - - +
117A ASN* 3.0 11.3 + - - +
118A CYS* 3.1 20.3 + - - +
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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
------------------------------------------------------------
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