Contacts of the helix formed by residues 159 - 183 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.0 8.5 + - - +
16A GLU* 3.2 16.5 + - - +
19A LYS* 4.3 13.9 - - - +
109B TRP* 3.9 18.6 - - + -
113B PHE* 3.6 11.2 - - - -
157B LEU* 4.7 0.2 - - - +
158B LYS* 1.3 75.0 - - - +
160B PHE* 1.3 66.1 + - - +
161B ASP* 3.0 32.2 + - - +
162B LEU* 3.0 26.1 + - + +
163B ARG* 2.9 24.4 + - - +
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B LYS 3.4 5.1 + - - -
159B ASN* 1.3 75.2 - - - +
161B ASP* 1.3 73.8 + - - +
163B ARG* 3.3 25.7 + - + +
164B ARG* 3.1 55.6 + - + +
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.8 20.5 - - + -
159B ASN* 3.0 12.4 + - - +
160B PHE* 1.3 86.0 - - - +
162B LEU* 1.3 63.9 + - - +
164B ARG* 3.1 32.5 + - - +
165B LYS* 3.2 29.8 + - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.6 31.6 - - + +
109B TRP* 4.9 3.8 - - + -
112B LEU* 3.9 18.2 - - + +
113B PHE* 3.7 54.3 - - + +
116B GLY* 6.0 0.2 - - - -
157B LEU* 3.7 31.0 - - + +
159B ASN* 3.0 28.2 + - + +
161B ASP* 1.3 73.9 - - - +
163B ARG* 1.3 63.7 + - - +
165B LYS* 3.1 21.2 + - + +
166B LEU 3.3 8.3 + - - -
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LEU* 3.2 36.3 - - + +
158B LYS 3.9 13.0 + - - -
159B ASN 2.9 18.8 + - - +
160B PHE* 3.7 24.5 - - + +
162B LEU* 1.3 75.6 - - - +
164B ARG* 1.3 63.2 + - - +
166B LEU* 3.3 27.6 - - + +
167B ASP* 3.4 13.4 + - - +
27E ILE* 4.0 29.2 - - - +
30E SER* 4.0 24.7 + - - -
34E LYS* 5.6 1.0 - - - +
78E ILE* 6.0 7.9 - - - +
82E GLU* 5.8 0.2 + - - -
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PHE* 3.1 47.6 + - + +
161B ASP* 3.1 38.6 + - - +
162B LEU 3.3 0.4 - - - -
163B ARG* 1.3 74.2 - - + +
165B LYS* 1.3 60.6 + - + +
167B ASP* 3.2 13.1 + - - +
168B TYR* 3.0 25.8 + - - +
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLN* 3.8 6.0 - - - +
113B PHE* 3.7 38.8 - - - +
116B GLY* 3.7 36.3 - - - +
117B ASP* 3.0 25.5 + - - +
152B LEU* 5.5 1.1 - - + -
161B ASP* 3.2 17.1 + - - +
162B LEU* 3.1 18.6 + - + +
164B ARG* 1.3 77.4 - - + +
166B LEU* 1.3 57.0 + - - +
168B TYR* 3.2 12.9 + - + +
169B VAL* 2.9 32.4 + - - +
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 3.5 26.6 - - + +
152B LEU* 3.5 37.6 - - + +
153B LEU* 3.6 38.6 - - + +
157B LEU* 4.4 8.5 - - + -
162B LEU 3.3 8.6 + - - +
163B ARG* 3.3 19.7 - - + +
165B LYS* 1.3 78.7 - - - +
167B ASP* 1.3 61.4 + - - +
169B VAL* 3.3 11.3 + - - +
170B SER 3.2 16.3 + - - -
34E LYS* 3.8 24.0 - - + -
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B TYR* 5.4 0.4 - - - -
163B ARG 3.4 13.2 + - - +
164B ARG* 3.2 17.0 + - - +
166B LEU* 1.3 74.9 - - - +
168B TYR* 1.3 65.9 + - - +
170B SER* 3.2 8.9 + - - -
171B ASN* 3.0 32.0 + - - +
34E LYS* 3.5 28.5 + - - -
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Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLY 3.7 23.8 - - - -
117B ASP* 4.3 16.0 + - - -
119B ALA* 4.5 4.7 - - + -
120B GLY* 3.2 37.6 - - - -
164B ARG 3.0 12.4 + - - +
165B LYS* 3.2 11.2 - - + +
167B ASP* 1.3 76.7 - - - +
169B VAL* 1.3 64.7 + - - +
171B ASN* 3.1 13.1 + - + +
172B ILE* 3.0 41.8 + - + +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLY 4.5 9.2 - - - +
119B ALA* 4.0 28.3 - - + +
145B LEU* 4.0 21.5 - - + +
148B LEU* 4.7 9.9 - - + -
149B TYR* 4.0 20.9 - - + +
152B LEU* 4.3 20.2 - - + -
165B LYS 2.9 19.7 + - - +
166B LEU* 3.5 8.3 - - - +
168B TYR* 1.3 74.6 - - + +
170B SER* 1.3 63.0 + - - +
172B ILE* 3.1 4.3 + - - +
173B ILE* 3.0 27.7 + - + +
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B TYR* 3.8 26.5 + - - -
166B LEU 3.2 4.8 + - - -
167B ASP* 3.4 12.3 - - - -
169B VAL* 1.3 79.8 - - - +
171B ASN* 1.3 64.4 + - - +
173B ILE* 3.4 14.1 + - - +
174B ASN* 3.2 29.5 + - - +
124E ARG* 6.0 0.2 + - - -
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Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ASP* 3.0 23.5 + - - +
168B TYR* 3.1 13.4 + - + +
170B SER* 1.3 76.7 + - - +
172B ILE* 1.3 67.5 - - + +
174B ASN* 3.2 15.6 + - - +
175B LYS* 3.1 26.7 + - + +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ALA* 3.5 35.7 - - + +
120B GLY* 4.2 7.6 - - - -
123B LEU* 3.8 32.3 - - + +
145B LEU* 3.7 18.2 - - + -
168B TYR* 3.0 44.4 + - + +
169B VAL 3.1 6.7 + - - +
171B ASN* 1.3 77.8 - - + +
173B ILE* 1.3 64.1 + - - +
175B LYS* 3.1 11.6 + - + +
176B LEU* 3.0 21.0 + - + +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LYS* 4.6 6.3 - - + +
145B LEU* 3.7 46.0 - - + +
146B GLU* 3.9 27.1 - - + +
149B TYR* 4.2 10.3 - - + -
169B VAL* 3.0 26.6 + - + +
170B SER* 3.6 10.8 - - - +
171B ASN 3.2 0.2 - - - -
172B ILE* 1.3 76.5 - - - +
174B ASN* 1.3 58.3 + - - +
176B LEU* 3.3 7.9 + - - +
177B ILE* 2.9 46.1 + - + +
38E TYR* 6.4 0.2 - - + -
124E ARG* 4.7 10.5 - - - +
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Residues in contact with ASN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B SER* 3.2 21.0 + - - +
171B ASN* 3.5 17.1 + - - +
172B ILE 3.2 0.4 - - - -
173B ILE* 1.3 77.7 - - - +
175B LYS* 1.3 62.0 + - + +
177B ILE* 3.4 8.6 + - - +
178B GLU* 3.1 22.6 + - - +
120E GLY 5.8 2.0 + - - -
123E LEU* 6.2 4.1 - - + +
124E ARG* 3.6 29.1 + - - +
179E PHE* 5.9 0.5 - - - -
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 4.3 24.5 - - + -
171B ASN* 3.1 16.4 + - + +
172B ILE* 3.1 11.3 + - + +
174B ASN* 1.3 71.9 - - + +
176B LEU* 1.3 66.1 + - - +
178B GLU* 3.3 14.8 - - - +
179B PHE* 3.0 41.1 + - + -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 4.0 18.8 - - + +
126B SER* 3.9 24.7 - - - +
138B ALA* 3.8 21.8 - - + +
141B ALA* 3.9 10.8 - - + -
142B LYS* 3.6 36.8 - - + +
145B LEU* 4.0 17.5 - - + -
172B ILE 3.0 10.5 + - - +
173B ILE* 3.5 9.9 - - - +
175B LYS* 1.3 75.1 - - - +
177B ILE* 1.3 67.0 + - - +
179B PHE* 3.1 14.0 + - + +
180B ILE* 2.9 31.8 + - + +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LYS* 3.4 33.2 - - + -
173B ILE* 2.9 30.4 + - + +
174B ASN* 3.6 8.5 - - - +
175B LYS 3.4 0.2 - - - -
176B LEU* 1.3 75.5 - - - +
178B GLU* 1.3 58.7 + - - +
180B ILE* 3.2 9.3 + - - +
181B ILE* 2.9 39.1 + - + +
124E ARG* 3.5 33.7 - - - +
127E SER* 3.7 31.4 - - - +
128E GLU* 4.4 2.5 - - - +
131E ILE* 5.1 5.6 - - + -
179E PHE* 5.7 1.1 - - + -
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Residues in contact with GLU 178 (chain B).
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 3.1 13.4 + - - +
175B LYS* 3.3 18.2 - - - +
177B ILE* 1.3 76.7 - - - +
179B PHE* 1.3 72.3 + - - +
181B ILE* 3.3 4.3 + - - +
182B TRP* 3.0 22.3 + - - +
178D GLU* 5.7 0.3 - - - +
182D TRP* 2.9 36.6 + - + -
175E LYS* 4.7 14.9 - - - +
178E GLU* 4.6 5.4 - - - +
179E PHE* 3.8 34.2 - - + -
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 3.7 24.7 - - + -
127B SER* 3.5 26.9 - - - -
130B LEU* 3.6 33.5 - - + +
175B LYS* 3.0 30.5 + - + -
176B LEU* 3.1 13.2 + - + +
178B GLU* 1.3 97.1 - - - +
180B ILE* 1.3 63.2 + - + +
182B TRP* 3.4 16.8 + - - +
183B LYS* 3.5 8.5 + - - +
178D GLU* 3.9 33.2 - - + -
181D ILE* 5.3 9.9 - - + -
182D TRP* 4.5 8.1 - + - -
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 5.6 0.9 - - + -
135B ILE* 3.7 10.0 - - + +
138B ALA* 3.7 42.8 - - + +
139B LYS* 4.0 36.1 - - + +
142B LYS* 4.1 21.8 - - + -
176B LEU* 2.9 24.7 + - + +
177B ILE* 3.5 7.9 - - - +
178B GLU 3.1 0.2 - - - -
179B PHE* 1.3 75.1 - - + +
181B ILE* 1.3 65.3 + - - +
183B LYS 3.0 24.9 + - - -
131E ILE* 5.2 13.9 - - + -
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ILE* 2.9 35.3 + - + +
178B GLU* 3.3 7.2 + - - +
180B ILE* 1.3 74.7 - - - +
182B TRP* 1.3 69.6 + - - +
183B LYS 3.0 5.7 + - - +
127E SER* 4.2 13.7 - - - +
130E LEU* 4.6 10.3 - - + -
131E ILE* 4.7 13.0 - - + -
179E PHE* 4.0 48.0 - - + -
182E TRP* 4.6 14.3 - - + +
183E LYS* 4.4 35.3 - - + +
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Residues in contact with TRP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 4.4 10.3 - - + -
178B GLU 3.0 10.0 + - - +
179B PHE* 3.6 12.6 - - - +
180B ILE 3.3 0.2 - - - -
181B ILE* 1.3 79.2 - - - +
183B LYS* 1.3 77.9 + - + +
181D ILE* 3.1 45.3 - - + -
182D TRP* 3.1 56.9 + + + -
184D SER* 3.6 21.1 - - - -
182E TRP* 3.6 42.0 - + - +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 4.6 8.7 - - + -
133B GLY* 6.5 0.7 - - - -
135B ILE* 3.5 33.6 - - + +
179B PHE 3.5 3.8 + - - +
180B ILE 3.0 19.1 + - - -
181B ILE 3.8 4.1 - - - +
182B TRP* 1.3 103.5 - - + +
183E LYS* 5.6 3.6 + - - -
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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