Contacts of the helix formed by residues 159 - 184 (chain E) in PDB entry 5JRE
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 159 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E TRP* 3.8 19.0 - - + -
113E PHE* 3.6 14.3 - - - -
158E LYS* 1.3 75.4 - - - +
160E PHE* 1.3 66.2 + - - +
161E ASP* 2.9 31.8 + - - +
162E LEU* 3.0 21.9 + - + +
163E ARG* 2.9 24.0 + - - +
12F TYR* 3.0 9.3 + - - +
16F GLU* 3.1 16.3 + - - +
19F LYS* 4.2 14.8 - - - +
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Residues in contact with PHE 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E LYS 3.4 4.7 + - - -
159E ASN* 1.3 74.8 - - - +
161E ASP* 1.3 74.7 + - - +
163E ARG* 3.3 26.1 + - + +
164E ARG* 3.1 55.7 + - + +
78G ILE* 5.9 7.0 - - + -
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Residues in contact with ASP 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E PHE* 3.8 20.7 - - + -
159E ASN* 2.9 12.9 + - - +
160E PHE* 1.3 85.0 - - - +
162E LEU* 1.3 63.5 + - - +
164E ARG* 3.1 32.3 + - - +
165E LYS* 3.2 29.8 + - - +
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Residues in contact with LEU 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TRP* 5.0 2.5 - - + -
112E LEU* 3.9 18.4 - - + +
113E PHE* 3.6 53.8 - - + +
116E GLY* 6.0 0.4 - - - -
157E LEU* 3.7 30.2 - - + +
159E ASN* 3.0 28.9 + - + +
161E ASP* 1.3 74.7 - - - +
163E ARG* 1.3 63.9 + - - +
165E LYS* 3.1 20.3 + - + +
166E LEU 3.3 8.7 + - - -
12F TYR* 3.6 32.1 - - + +
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Residues in contact with ARG 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E LEU* 3.2 38.1 - - + +
158E LYS 3.9 12.3 + - - -
159E ASN 2.9 19.5 + - - +
160E PHE* 3.7 24.9 - - + +
162E LEU* 1.3 75.2 - - - +
164E ARG* 1.3 61.6 + - - +
166E LEU* 3.3 27.7 + - + +
167E ASP* 3.4 13.6 + - - +
27G ILE* 4.1 28.5 + - - +
30G SER* 3.8 27.5 + - - -
34G LYS* 5.2 4.7 - - - +
78G ILE* 5.7 10.5 - - - +
82G GLU* 5.0 1.4 + - - -
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Residues in contact with ARG 164 (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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160E PHE* 3.1 48.5 + - + +
161E ASP* 3.1 39.0 + - - +
162E LEU 3.2 0.2 - - - -
163E ARG* 1.3 73.8 - - - +
165E LYS* 1.3 60.0 + - + +
167E ASP* 3.2 15.0 + - - +
168E TYR* 3.0 25.7 + - - +
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Residues in contact with LYS 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E GLN* 3.8 6.4 - - - +
113E PHE* 3.7 51.6 - - - +
116E GLY* 3.7 26.9 - - - +
117E ASP* 3.1 24.2 + - - +
152E LEU* 5.6 1.6 - - + -
161E ASP* 3.2 15.6 + - - +
162E LEU* 3.1 16.4 + - + +
164E ARG* 1.3 76.3 - - + +
166E LEU* 1.3 57.4 + - - +
168E TYR* 3.2 12.1 + - + +
169E VAL* 2.9 34.4 + - - +
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Residues in contact with LEU 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E TYR* 3.5 28.4 - - + +
152E LEU* 3.5 36.3 - - + +
153E LEU* 3.6 28.3 - - + +
157E LEU* 4.4 8.5 - - + -
162E LEU 3.3 8.2 + - - +
163E ARG* 3.3 18.3 + - + +
165E LYS* 1.3 79.3 - - - +
167E ASP* 1.3 61.0 + - - +
169E VAL* 3.3 8.6 + - - +
170E SER 3.2 16.8 + - - -
34G LYS* 3.6 37.2 - - + -
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Residues in contact with ASP 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E TYR* 5.4 0.6 + - - -
163E ARG 3.4 12.0 + - - +
164E ARG* 3.2 16.2 + - - +
166E LEU* 1.3 73.5 - - - +
168E TYR* 1.3 65.9 + - - +
170E SER* 3.2 9.4 + - - -
171E ASN* 3.0 32.0 + - - +
34G LYS* 3.1 33.6 + - - -
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Residues in contact with TYR 168 (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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116E GLY 3.7 23.8 - - - -
117E ASP* 4.3 16.7 + - - -
119E ALA* 4.5 3.1 - - + -
120E GLY* 3.2 37.8 - - - -
164E ARG 3.0 13.4 + - - +
165E LYS* 3.2 12.6 - - + +
167E ASP* 1.3 76.3 - - - +
169E VAL* 1.3 64.9 + - - +
171E ASN* 3.1 13.5 + - + +
172E ILE* 2.9 43.5 + - + +
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Residues in contact with VAL 169 (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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116E GLY* 4.4 10.3 - - - +
119E ALA* 4.0 27.6 - - + -
145E LEU* 4.0 13.0 - - + +
148E LEU* 4.7 9.2 - - + -
149E TYR* 4.0 30.7 - - + +
152E LEU* 4.3 20.6 - - + -
165E LYS 2.9 19.0 + - - +
166E LEU 3.5 8.1 - - - +
167E ASP 3.3 0.2 - - - -
168E TYR* 1.3 74.5 - - + +
170E SER* 1.3 65.6 + - - +
172E ILE* 3.2 3.8 + - - +
173E ILE* 3.0 26.6 + - + +
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Residues in contact with SER 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E TYR* 3.8 26.7 + - - -
166E LEU 3.2 3.9 + - - -
167E ASP* 3.2 12.5 + - - -
169E VAL* 1.3 79.9 - - - +
171E ASN* 1.3 63.1 + - - +
173E ILE* 3.4 14.3 + - - +
174E ASN* 3.2 30.7 + - - +
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Residues in contact with ASN 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E ASP* 3.0 24.0 + - - +
168E TYR* 3.5 13.2 - - + +
170E SER* 1.3 76.6 + - - +
172E ILE* 1.3 66.6 + - + +
174E ASN* 3.2 15.6 + - - +
175E LYS* 3.1 26.8 + - + +
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Residues in contact with ILE 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ALA* 3.5 33.9 - - + +
120E GLY* 4.2 7.0 - - - -
123E LEU* 3.8 32.5 - - + +
145E LEU* 3.7 18.4 - - + -
168E TYR* 2.9 45.9 + - + +
169E VAL 3.2 7.6 + - - +
171E ASN* 1.3 77.9 - - + +
173E ILE* 1.3 62.8 + - - +
175E LYS* 3.1 11.4 + - + +
176E LEU* 3.0 21.0 + - + +
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Residues in contact with ILE 173 (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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142E LYS* 4.6 6.7 - - + +
145E LEU* 3.7 46.7 - - + +
146E GLU* 3.9 27.4 - - + +
149E TYR* 4.2 10.3 - - + -
169E VAL* 3.0 28.1 + - + +
170E SER* 3.6 11.4 - - - +
171E ASN 3.3 0.2 - - - -
172E ILE* 1.3 77.4 - - - +
174E ASN* 1.3 58.8 + - - +
176E LEU* 3.3 9.0 + - - +
177E ILE* 2.9 46.0 + - + +
38G TYR* 6.3 0.2 - - + -
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Residues in contact with ASN 174 (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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170E SER* 3.2 21.9 + - - +
171E ASN* 3.5 17.3 + - - +
172E ILE 3.2 0.4 - - - -
173E ILE* 1.3 79.6 - - - +
175E LYS* 1.3 61.7 + - + +
177E ILE* 3.4 16.5 + - - +
178E GLU* 3.1 22.7 + - - +
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Residues in contact with LYS 175 (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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178B GLU* 4.7 15.0 - - - +
123E LEU* 4.3 22.7 - - + -
171E ASN* 3.1 17.4 + - + +
172E ILE* 3.1 11.4 + - + +
174E ASN* 1.3 71.7 - - + +
176E LEU* 1.3 67.1 + - - +
178E GLU* 3.2 15.0 - - - +
179E PHE* 3.0 38.6 + - + -
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Residues in contact with LEU 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ILE* 5.6 0.4 - - + -
123E LEU* 3.9 18.1 - - + +
126E SER* 3.9 25.4 - - - +
130E LEU* 4.7 7.6 - - + -
138E ALA* 3.8 21.5 - - + +
141E ALA* 3.9 10.8 - - + -
142E LYS* 3.5 37.2 - - + +
145E LEU* 4.0 17.0 - - + -
172E ILE 3.0 10.8 + - - +
173E ILE* 3.3 10.7 + - - +
175E LYS* 1.3 74.2 - - - +
177E ILE* 1.3 66.6 + - - +
179E PHE* 3.1 7.7 + - + +
180E ILE* 2.9 31.3 + - + +
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Residues in contact with ILE 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LYS* 3.4 34.8 - - + -
146E GLU* 4.9 1.3 - - - +
173E ILE* 2.9 33.4 + - + +
174E ASN* 3.6 16.2 - - - +
176E LEU* 1.3 75.2 - - - +
178E GLU* 1.3 58.7 + - - +
180E ILE* 3.2 10.0 + - - +
181E ILE* 2.9 47.0 + - + +
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Residues in contact with GLU 178 (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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178B GLU* 4.6 5.4 - - - +
182D TRP* 4.2 16.8 - - - -
174E ASN 3.1 14.0 + - - +
175E LYS* 3.2 17.3 - - - +
177E ILE* 1.3 77.4 - - - +
179E PHE* 1.3 77.9 + - - +
181E ILE* 3.2 11.4 + - - +
182E TRP* 3.0 56.3 + - + +
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Residues in contact with PHE 179 (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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174B ASN 5.9 0.2 - - - -
177B ILE* 5.7 0.9 - - + -
178B GLU* 3.8 35.2 - - + -
181B ILE* 4.0 32.1 - - + -
123E LEU* 3.7 25.8 - - + -
127E SER* 3.5 24.5 - - - -
130E LEU* 3.6 24.0 - - + -
175E LYS* 3.0 28.8 + - + -
176E LEU* 3.1 7.6 + - + +
178E GLU* 1.3 93.9 - - - +
180E ILE* 1.3 58.1 + - - +
182E TRP* 3.4 8.9 + + - +
183E LYS* 3.0 32.7 + - - +
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Residues in contact with ILE 180 (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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130E LEU* 5.3 1.1 - - + -
135E ILE* 4.8 5.6 - - + -
138E ALA* 3.7 42.8 - - + +
139E LYS* 4.0 28.3 - - + +
142E LYS* 4.1 22.9 - - + -
176E LEU* 2.9 23.1 + - + +
177E ILE* 3.5 7.4 - - - +
179E PHE* 1.3 74.6 - - - +
181E ILE* 1.3 61.9 + - + +
183E LYS* 5.0 2.0 - - - -
184E SER* 2.9 48.2 + - - +
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Residues in contact with ILE 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E ILE* 2.9 35.6 + - + +
178E GLU* 3.2 11.2 + - - +
180E ILE* 1.3 78.9 - - + +
182E TRP* 1.3 72.8 + - + +
184E SER* 3.8 12.0 + - - -
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Residues in contact with TRP 182 (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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178B GLU 6.1 0.2 - - - -
181B ILE* 4.6 19.1 - - + +
182B TRP* 3.6 43.9 - + + +
182D TRP* 4.4 13.0 - + - -
178E GLU* 3.0 55.8 + - + +
179E PHE* 3.5 14.8 - + - +
180E ILE 3.3 0.2 - - - -
181E ILE* 1.3 86.5 - - + +
183E LYS* 1.3 61.6 + - + +
184E SER 3.7 3.5 + - - -
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Residues in contact with LYS 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 4.4 35.4 + - + +
183B LYS 5.6 4.2 + - - -
130E LEU* 3.9 46.2 + - + +
131E ILE* 4.9 8.2 + - - +
133E GLY* 5.4 4.8 - - - -
135E ILE* 3.1 26.1 - - + +
179E PHE 3.0 16.3 + - - +
180E ILE* 4.4 1.1 - - - +
182E TRP* 1.3 78.2 - - + +
184E SER* 1.3 62.1 + - - +
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Residues in contact with SER 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E ILE* 3.6 25.5 - - - +
139E LYS* 3.8 17.3 + - - -
180E ILE* 2.9 24.3 + - - +
181E ILE* 4.3 11.9 - - - -
182E TRP 3.5 3.3 - - - -
183E LYS* 1.3 80.3 - - - +
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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) + - + + + + + -
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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