Contacts of the helix formed by residues 113 - 137 (chain E) in PDB entry 1JTY
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 113 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E TYR* 3.7 17.7 + - - -
106E TYR 4.6 0.2 - - - +
107E TYR* 3.2 24.3 + - - +
108E LYS 5.7 0.2 - - - -
109E THR 3.1 19.5 - - - +
110E ASN* 3.4 7.1 + - - +
111E SER 2.6 10.3 + - - -
112E ILE* 1.3 74.2 - - - +
114E GLU* 1.3 64.1 + - - +
115E LYS 3.5 0.9 - - - +
116E MET* 3.3 5.6 - - - +
117E ASN* 2.7 45.3 + - - +
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Residues in contact with GLU 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ASN 3.3 10.5 + - - +
111E SER* 3.3 5.4 + - - +
113E ASN* 1.3 81.2 - - - +
115E LYS* 1.3 85.0 + - + +
117E ASN* 3.3 4.1 + - - +
118E LYS* 2.6 60.9 + - - +
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Residues in contact with LYS 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E LEU* 4.5 23.6 - - + -
55E ASN* 5.6 4.5 - - - +
111E SER* 3.5 31.0 - - - +
112E ILE* 5.2 2.2 - - - -
113E ASN 5.1 0.4 - - - +
114E GLU* 1.3 89.4 + - + +
116E MET* 1.3 57.5 + - - +
118E LYS* 2.5 40.7 + - + +
119E LEU* 2.7 21.1 + - + -
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Residues in contact with MET 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 5.0 5.6 - - + +
54E LEU* 3.3 34.3 - - + -
99E ILE* 4.3 8.1 - - + -
102E PHE* 3.5 33.0 - - + -
103E TYR* 3.5 32.5 - - + -
112E ILE* 4.0 10.7 - - - +
113E ASN* 3.3 21.0 - - - +
115E LYS* 1.3 77.6 - - - +
117E ASN* 1.3 59.3 + - - +
119E LEU* 3.2 9.2 + - + +
120E GLU* 2.8 55.1 + - - +
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Residues in contact with ASN 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLU* 5.8 1.6 + - - -
103E TYR* 4.6 12.7 + - - -
113E ASN* 2.7 38.7 + - - +
114E GLU* 3.7 7.0 - - - +
115E LYS 2.8 3.0 + - - -
116E MET* 1.3 78.0 - - - +
118E LYS* 1.3 60.0 + - + +
120E GLU* 3.3 7.1 + - - +
121E ASN* 2.8 45.0 + - - +
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Residues in contact with LYS 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLU* 2.6 60.6 + - + +
115E LYS* 2.5 24.7 + - + +
117E ASN* 1.3 73.3 - - + +
119E LEU* 1.3 59.3 + - + +
121E ASN* 3.2 10.5 - - - +
122E LYS* 3.1 26.3 + - - +
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Residues in contact with LEU 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E LEU* 5.1 7.2 - - + -
54E LEU* 3.9 42.6 - - + +
55E ASN* 4.4 18.4 - - - +
58E GLU* 3.6 35.0 - - + -
115E LYS* 2.7 21.2 + - + +
116E MET* 3.5 14.6 - - + +
118E LYS* 1.3 69.2 - - + +
120E GLU* 1.3 59.7 + - - +
121E ASN 2.5 17.5 + - - -
122E LYS* 2.7 20.0 + - + +
123E TYR* 3.1 23.4 + - + -
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Residues in contact with GLU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D GLU* 4.6 15.3 - - - +
54E LEU* 5.5 0.3 - - - +
92E TYR* 4.7 12.2 + - - +
99E ILE* 4.1 21.7 - - - +
103E TYR* 4.6 9.5 - - - +
116E MET* 2.8 52.8 + - - +
117E ASN* 3.4 9.9 - - - +
119E LEU* 1.3 75.9 - - - +
121E ASN* 1.3 59.8 + - - +
123E TYR* 4.2 17.9 - - - +
124E ILE* 3.2 20.8 + - - +
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Residues in contact with ASN 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ASN* 2.8 29.2 + - - +
118E LYS* 3.2 10.8 - - - +
119E LEU 2.5 6.3 + - - -
120E GLU* 1.3 78.2 + - - +
122E LYS* 1.3 68.3 + - - +
123E TYR 3.1 0.9 - - - -
124E ILE* 2.7 27.3 - - + +
125E ASP* 2.8 10.7 + - - +
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Residues in contact with LYS 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLU* 3.2 35.9 + - + +
61E TRP* 5.5 0.8 + - - -
62E GLN* 4.0 21.0 + - - +
118E LYS 3.1 12.0 + - - +
119E LEU* 2.7 16.6 + - + +
121E ASN* 1.3 74.3 - - - +
123E TYR* 1.3 66.4 + - - +
125E ASP* 3.0 22.9 + - - +
126E ALA* 3.7 2.8 + - - +
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Residues in contact with TYR 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LEU* 3.8 7.6 + - + +
57E GLU* 4.1 1.6 - - - +
58E GLU* 2.9 53.8 + - + +
61E TRP* 3.6 30.5 + + - +
82E TYR* 4.1 9.4 + - - +
92E TYR* 3.3 75.4 - + + +
99E ILE* 5.7 1.1 - - + -
119E LEU* 3.1 34.9 + - + +
120E GLU* 4.2 10.3 - - - +
122E LYS* 1.3 80.9 - - - +
124E ILE* 1.3 62.5 + - - +
126E ALA* 3.2 20.6 + - - +
127E TYR* 4.7 0.9 - - - -
153E ALA* 5.9 0.4 - - - -
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Residues in contact with ILE 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E GLU 3.2 19.0 + - - +
121E ASN* 2.7 33.8 - - + +
123E TYR* 1.3 74.3 - - - +
125E ASP* 1.3 54.6 + - - +
126E ALA 2.7 16.9 + - - -
127E TYR* 3.0 15.5 + - - +
128E HIS* 3.4 6.7 + - + +
146E ASN* 4.5 4.7 - - - +
149E SER* 3.0 20.9 - - - +
150E LYS* 3.0 48.5 - - + +
153E ALA* 4.3 15.3 - - + -
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Residues in contact with ASP 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ASN 2.8 12.1 + - - +
122E LYS* 3.0 18.0 + - - +
124E ILE* 1.3 76.5 - - - +
126E ALA* 1.3 65.0 + - - +
128E HIS* 3.5 26.9 - - - +
129E VAL* 3.0 31.7 + - - +
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Residues in contact with ALA 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E TRP* 4.6 4.9 - - + +
65E TRP* 4.7 12.1 + - + +
82E TYR* 3.4 35.4 - - + +
122E LYS 3.7 2.5 + - - +
123E TYR 3.2 16.6 + - - +
124E ILE 2.7 1.2 + - - -
125E ASP* 1.3 81.2 - - - +
127E TYR* 1.3 63.4 + - + +
129E VAL* 3.3 5.8 + - - +
130E ILE* 3.2 24.7 + - - +
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Residues in contact with TYR 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E PHE* 3.5 26.0 - + - -
82E TYR* 2.8 40.6 - + - -
83E ASN* 2.6 33.7 + - - -
93E TYR* 4.4 1.7 + - - -
123E TYR 5.1 0.7 - - - -
124E ILE* 3.0 10.7 + - - +
126E ALA* 1.3 83.2 - - + +
128E HIS* 1.3 52.9 + - - +
130E ILE* 3.1 10.3 + - + +
131E PHE* 2.7 50.7 + + + -
149E SER* 3.7 15.0 - - - -
152E ALA* 3.5 19.5 - - + -
153E ALA* 3.7 28.7 - - + -
156E VAL* 3.1 17.6 - - + +
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Residues in contact with HIS 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ILE* 3.4 3.9 + - + +
125E ASP* 3.4 32.1 + - - +
127E TYR* 1.3 78.5 - - - +
129E VAL* 1.3 54.4 + - - +
131E PHE* 3.2 1.0 + - - +
132E LYS* 2.8 34.8 + - + +
145E VAL* 3.3 21.6 - - + +
146E ASN* 3.2 33.5 + - - +
149E SER* 3.2 17.7 + - - +
902E SO4 3.3 32.3 + - - -
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E ASN* 5.8 0.2 - - - +
125E ASP* 3.0 31.8 + - - +
126E ALA* 3.6 6.1 - - - +
128E HIS* 1.3 76.7 + - - +
130E ILE* 1.3 61.6 + - + +
132E LYS* 3.7 5.8 - - - +
133E GLU* 2.8 55.5 + - + +
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Residues in contact with ILE 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E TRP* 4.2 14.1 - - + +
75E ASN* 3.2 29.8 - - + +
78E LYS* 3.4 49.8 - - + +
79E PHE* 3.5 21.3 - - + +
82E TYR* 4.6 8.3 - - + -
126E ALA 3.2 12.0 + - - +
127E TYR* 3.1 12.5 + - + +
129E VAL* 1.3 81.5 - - + +
131E PHE* 1.3 64.9 + - + +
134E GLY 3.1 12.6 + - - -
140E TRP* 3.1 20.0 - - + -
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Residues in contact with PHE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E PHE* 3.8 26.9 - + - -
127E TYR* 2.7 36.6 + - + +
128E HIS 3.7 2.7 - - - +
130E ILE* 1.3 74.1 - - + +
132E LYS* 1.3 66.8 + - - +
134E GLY 3.1 0.7 + - - -
135E ASN* 2.8 22.2 + - - +
140E TRP* 2.9 20.8 + + - -
142E ILE* 3.3 28.3 - - + -
145E VAL* 4.0 7.9 - - + -
148E VAL* 3.8 10.8 - - + -
149E SER* 3.2 33.0 - - - -
152E ALA* 4.1 1.8 - - + -
182E PHE* 3.8 22.7 - + - -
183E LEU* 4.3 7.9 - - + -
186E LEU* 4.3 16.6 - - + -
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Residues in contact with LYS 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E HIS* 2.8 24.7 + - - +
129E VAL* 3.7 4.5 - - - +
131E PHE* 1.3 73.2 - - - +
133E GLU* 1.3 68.8 + - - +
135E ASN* 2.9 37.3 - - - +
136E LEU* 3.6 17.8 + - + +
145E VAL* 4.3 4.3 - - + +
902E SO4 3.1 46.1 + - - +
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Residues in contact with GLU 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E ASN* 3.2 19.7 - - - +
129E VAL* 2.8 35.6 + - + +
132E LYS* 1.3 82.9 - - - +
134E GLY* 1.3 60.0 + - - +
136E LEU* 2.8 21.7 - - + +
137E ASN* 2.5 39.0 + - - +
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Residues in contact with GLY 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E ASN* 3.6 9.5 - - - -
130E ILE 3.1 5.1 + - - -
131E PHE 3.1 3.6 + - - -
133E GLU* 1.3 78.3 - - - +
135E ASN* 1.3 67.1 + - - +
137E ASN* 3.1 12.1 + - - -
139E GLU* 2.9 25.2 + - - -
140E TRP* 3.3 28.6 + - - -
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Residues in contact with ASN 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PHE 2.8 9.4 + - - -
132E LYS* 2.9 20.8 + - + +
134E GLY* 1.3 81.4 - - - +
136E LEU* 1.3 59.9 + - + +
138E GLY* 2.9 12.0 + - - -
140E TRP* 3.0 17.1 - - - +
141E SER* 3.6 6.4 + - - -
142E ILE* 3.0 35.2 + - - +
145E VAL* 3.3 31.5 - - - +
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Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LYS* 3.8 20.4 - - + +
133E GLU* 2.8 36.6 - - + +
135E ASN* 1.3 73.4 - - + +
137E ASN* 1.3 72.8 + - - +
138E GLY* 2.5 18.0 + - - -
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Residues in contact with ASN 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E ASN* 3.4 13.7 - - - +
133E GLU* 2.5 41.8 + - - +
134E GLY* 3.1 11.2 + - - +
136E LEU* 1.3 87.2 - - - +
138E GLY* 1.3 51.4 + - - +
139E GLU* 2.8 30.9 + - + +
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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
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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) + - + + + + + -
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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