Contacts of the helix formed by residues 152 - 188 (chain B) in PDB entry 5AQP
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 SER 152 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B SER 3.4 7.1 + - - -
151B ASN* 1.3 75.7 - - - +
153B PRO* 1.4 70.0 - - - +
154B GLN* 3.3 15.9 + - - -
155B GLU* 3.3 29.1 + - - +
156B GLU* 3.6 12.9 + - - +
230B PHE* 3.7 19.7 - - - -
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Residues in contact with PRO 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASN 4.7 1.1 - - - +
152B SER* 1.4 83.8 - - - +
154B GLN* 1.3 75.2 - - - +
156B GLU* 3.1 27.8 + - + +
157B VAL* 3.6 3.6 + - - +
190D PHE* 3.5 27.1 - - + -
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B SER* 3.4 14.3 - - - +
153B PRO* 1.3 93.5 - - - +
155B GLU* 1.4 59.9 + - - +
157B VAL* 3.2 19.6 + - - +
158B GLU* 3.6 10.2 + - - +
230B PHE* 4.0 14.8 - - + -
188D GLN 2.8 27.8 + - - -
189D GLY* 3.3 31.2 - - - +
190D PHE* 3.8 34.8 - - + -
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASN* 5.1 10.0 + - - -
152B SER* 3.3 24.0 + - - +
154B GLN* 1.4 74.5 - - - +
156B GLU* 1.4 60.2 + - - +
158B GLU* 3.1 3.9 + - - +
159B LEU* 2.9 37.0 + - + +
229B ASN 4.5 2.3 - - - +
230B PHE* 3.4 43.0 - - + -
231B LYS 4.4 0.9 + - - -
232B ASP* 3.3 18.3 + - - +
233B SER* 2.8 44.1 + - - +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASN* 5.7 5.0 + - - +
152B SER 3.6 10.1 + - - +
153B PRO* 3.1 20.2 + - + +
155B GLU* 1.4 78.0 - - - +
157B VAL* 1.3 54.9 + - + +
159B LEU* 3.5 22.3 + - - +
160B LYS* 3.0 29.8 + - - +
163B LYS* 5.7 2.8 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO 4.1 2.5 - - - +
154B GLN 3.2 8.5 + - - +
155B GLU 3.2 0.2 - - - -
156B GLU* 1.3 77.0 - - + +
158B GLU* 1.3 68.0 + - - +
160B LYS* 3.4 6.7 + - - +
161B LYS* 3.2 41.5 + - + +
190D PHE* 3.7 35.2 - - + -
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLN 3.6 9.9 + - - +
155B GLU* 3.1 4.7 + - - +
157B VAL* 1.3 80.4 - - - +
159B LEU* 1.3 60.4 + - - +
161B LYS* 2.9 42.6 + - - +
162B LEU* 3.0 32.5 + - + +
224B LEU* 3.8 14.0 - - + +
225B ILE 5.1 4.5 + - - +
226B LEU* 3.7 26.2 - - + +
230B PHE* 4.3 11.9 - - + -
233B SER* 3.8 16.4 - - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU* 2.9 31.9 + - + +
156B GLU* 3.8 28.5 - - - +
158B GLU* 1.3 75.1 - - - +
160B LYS* 1.4 56.3 + - - +
162B LEU* 3.4 5.7 + - - +
163B LYS* 3.0 43.9 + - - +
232B ASP* 4.0 15.0 - - + +
233B SER* 3.6 31.6 - - - +
236B LYS* 3.8 26.2 - - + +
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU 3.0 18.4 + - - +
157B VAL* 3.8 6.7 - - - +
158B GLU 3.3 0.2 - - - -
159B LEU* 1.4 73.5 - - - +
161B LYS* 1.3 63.0 + - + +
163B LYS* 3.2 12.8 + - + +
164B HIS* 3.1 36.9 + - + +
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Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 3.2 25.7 + - + +
158B GLU* 2.9 46.3 + - - +
160B LYS* 1.3 73.0 - - - +
162B LEU* 1.4 57.3 + - - +
164B HIS* 3.3 11.7 + - - +
165B LEU* 3.0 35.2 + - + +
224B LEU* 4.0 21.0 - - + +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU* 3.0 21.6 + - + +
159B LEU* 3.7 2.0 - - - +
161B LYS* 1.4 72.8 - - - +
163B LYS* 1.3 54.3 + - - +
165B LEU* 3.1 10.3 + - + +
166B GLU* 2.7 39.0 + - - +
221B ILE* 5.1 2.7 - - + -
224B LEU* 3.8 24.7 - - + -
226B LEU* 4.6 5.4 - - + -
233B SER* 3.6 38.6 - - - +
236B LYS* 3.7 21.3 - - + -
237B ARG* 3.8 28.3 - - + +
240B LEU* 4.0 15.9 - - + +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU* 5.7 3.2 + - - -
159B LEU* 3.0 29.2 + - - +
160B LYS* 3.2 12.5 + - - +
162B LEU* 1.3 72.1 - - - +
164B HIS* 1.3 60.5 + - - +
166B GLU* 3.4 20.3 + - - +
167B LYS* 3.0 32.9 + - + +
236B LYS* 4.3 18.8 - - - +
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Residues in contact with HIS 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LYS* 3.1 32.4 + - + -
161B LYS* 3.4 11.5 + - - +
163B LYS* 1.3 75.3 - - - +
165B LEU* 1.3 59.7 + - + +
167B LYS* 3.4 8.7 + - + +
168B SER* 3.1 30.5 + - - -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 3.0 23.8 + - + +
162B LEU* 3.1 12.5 + - + +
164B HIS* 1.3 74.9 - - + +
166B GLU* 1.4 56.4 + - - +
168B SER* 3.1 8.0 + - - +
169B VAL* 2.9 31.2 + - - +
217B ILE* 4.3 22.7 - - + +
220B GLU* 3.9 40.2 - - + +
221B ILE* 3.9 27.6 - - + +
224B LEU* 4.5 12.6 - - + -
240B LEU* 3.7 15.3 - - + -
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU 2.7 19.4 + - - +
163B LYS* 3.5 17.2 - - - +
165B LEU* 1.4 70.1 - - - +
167B LYS* 1.4 58.4 + - + +
169B VAL* 3.4 3.5 + - - +
170B GLU* 3.0 26.2 + - - +
236B LYS* 3.3 48.3 + - + +
240B LEU* 3.8 29.6 - - + +
243B LYS* 5.3 2.8 + - - -
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 3.0 17.8 + - + +
164B HIS* 3.7 12.1 - - + +
165B LEU 3.3 0.2 - - - -
166B GLU* 1.4 73.0 - - + +
168B SER* 1.3 64.4 + - - +
170B GLU* 3.3 9.5 + - - +
171B LYS* 3.1 27.2 + - - +
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B HIS 3.1 15.6 + - - -
165B LEU* 3.4 11.5 - - - +
167B LYS* 1.3 73.2 - - - +
169B VAL* 1.3 63.7 + - - +
171B LYS* 3.3 9.6 + - - +
172B ILE* 3.2 28.9 + - - +
217B ILE* 3.8 21.9 - - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU 2.9 18.7 + - - +
166B GLU 3.6 7.6 - - - +
167B LYS 3.3 0.2 - - - -
168B SER* 1.3 74.8 - - - +
170B GLU* 1.4 52.4 + - - +
172B ILE* 3.1 10.6 + - - +
173B ALA* 2.8 32.1 + - - +
214B PHE* 4.1 4.4 - - + -
217B ILE* 3.6 28.5 - - + -
240B LEU* 3.7 19.5 - - + -
243B LYS* 4.4 9.6 - - + +
244B VAL* 3.6 23.3 - - + -
247B PHE* 3.9 26.9 - - + -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLU 3.0 14.4 + - - +
167B LYS* 3.3 12.8 + - - +
169B VAL* 1.4 75.0 - - - +
171B LYS* 1.3 55.8 + - + +
173B ALA* 3.3 9.6 + - - +
174B ASP* 3.0 36.0 + - - +
243B LYS* 5.0 8.9 - - - +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LYS* 3.1 17.8 + - + +
168B SER* 3.6 11.9 - - - +
169B VAL 3.3 0.2 - - - -
170B GLU* 1.3 75.1 - - + +
172B ILE* 1.3 61.7 + - + +
174B ASP* 3.4 12.5 + - - +
175B GLN* 3.4 27.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 3.2 19.0 + - - +
169B VAL* 3.1 5.9 + - - +
171B LYS* 1.3 73.4 - - + +
173B ALA* 1.3 64.4 + - - +
175B GLN* 3.1 17.1 + - - +
176B LEU* 3.1 20.1 + - - +
210B THR* 3.6 29.1 - - + +
213B GLN* 3.7 38.1 - - + +
214B PHE* 3.6 26.0 - - + +
217B ILE* 3.7 30.5 - - + -
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL 2.8 20.0 + - - +
170B GLU* 3.4 11.2 - - - +
172B ILE* 1.3 72.8 - - - +
174B ASP* 1.4 56.5 + - - +
176B LEU* 3.4 7.5 + - - +
177B GLU* 2.9 27.0 + - - +
214B PHE* 3.9 8.8 - - - -
243B LYS* 5.4 0.9 - - - +
247B PHE* 3.6 36.8 - - + -
----------------------------------------------------------
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Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLU* 3.0 23.4 + - - +
171B LYS* 3.6 13.3 - - - +
172B ILE 3.3 0.2 - - - -
173B ALA* 1.4 72.2 - - - +
175B GLN* 1.3 60.5 + - + +
177B GLU* 3.3 9.0 + - - +
178B GLU* 3.0 28.9 + - - +
----------------------------------------------------------
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Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LYS* 3.4 18.1 + - - +
172B ILE* 3.1 15.9 + - - +
174B ASP* 1.3 75.8 - - + +
176B LEU* 1.4 56.4 + - - +
178B GLU* 3.4 7.4 + - - +
179B LEU* 3.0 32.3 + - + +
206B ARG* 5.1 1.2 + - - -
210B THR* 4.0 12.5 + - - +
213B GLN* 3.0 38.1 + - - +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE 3.1 10.8 + - - +
173B ALA* 3.5 9.4 - - - +
174B ASP 3.3 0.2 - - - -
175B GLN* 1.4 74.1 - - - +
177B GLU* 1.4 59.2 + - - +
179B LEU* 3.1 17.4 + - + +
180B ASN* 2.8 47.6 + - - +
207B VAL* 6.3 1.3 - - + -
210B THR* 4.3 10.2 - - + +
214B PHE* 4.5 2.9 - - + -
247B PHE* 3.8 42.4 - - + +
250B GLU* 4.0 17.7 - - + +
251B CYS* 4.0 28.7 - - - +
254B VAL* 4.9 7.0 - - + -
----------------------------------------------------------
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ALA 2.9 17.0 + - - +
174B ASP* 3.3 11.4 + - - +
176B LEU* 1.4 75.0 - - - +
178B GLU* 1.4 56.4 + - - +
180B ASN* 3.3 17.2 + - - +
181B LYS* 3.1 53.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASP 3.0 16.7 + - - +
175B GLN* 3.7 7.4 - - - +
176B LEU 3.3 0.2 - - - -
177B GLU* 1.4 73.1 - - - +
179B LEU* 1.4 59.6 + - - +
181B LYS* 3.3 30.0 + - - +
182B GLU* 2.9 57.4 + - - +
206B ARG* 4.4 5.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLN* 3.0 16.5 + - + +
176B LEU* 3.4 17.7 - - + +
178B GLU* 1.4 75.0 - - - +
180B ASN* 1.4 57.6 + - - +
182B GLU* 3.3 3.9 + - - +
183B LEU* 2.9 34.9 + - + +
203B LEU* 3.8 36.7 - - + +
206B ARG* 3.7 47.5 - - + +
207B VAL* 3.7 18.8 - - + +
210B THR* 3.7 24.7 - - - +
254B VAL* 5.8 1.8 - - + -
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 2.8 32.8 + - - +
177B GLU* 3.6 21.6 + - - +
179B LEU* 1.4 76.6 - - - +
181B LYS* 1.4 56.3 + - - +
183B LEU* 3.5 10.1 - - - +
184B THR* 3.0 32.4 + - - -
250B GLU* 3.8 21.4 + - - +
254B VAL* 3.5 27.0 - - - +
----------------------------------------------------------
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLU* 3.1 42.2 + - - +
178B GLU* 3.7 29.1 + - - +
180B ASN* 1.4 74.5 - - - +
182B GLU* 1.4 62.7 + - - +
184B THR* 3.6 7.4 + - - +
185B GLY* 3.2 18.2 + - - -
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 2.9 38.1 + - - +
179B LEU* 3.3 5.3 + - - +
181B LYS* 1.4 77.0 - - - +
183B LEU* 1.4 63.5 + - - +
185B GLY* 3.4 3.2 + - - -
186B ILE* 3.3 27.6 + - - +
203B LEU* 4.3 14.0 - - + +
206B ARG* 2.8 41.5 + - - -
----------------------------------------------------------
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 2.9 23.6 + - + +
180B ASN* 3.5 27.6 - - - +
182B GLU* 1.4 72.6 - - - +
184B THR* 1.4 67.5 + - - +
186B ILE* 3.5 3.4 + - - +
187B GLN* 3.1 31.8 + - + +
200B LEU* 4.2 15.7 - - + +
203B LEU* 3.8 22.1 - - + +
254B VAL* 3.8 31.6 - - + -
257B ASN* 6.5 0.9 - - + -
258B ILE* 5.7 2.7 - - + -
----------------------------------------------------------
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Residues in contact with THR 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASN 3.0 19.6 + - - -
181B LYS* 3.8 8.7 - - - +
183B LEU* 1.4 78.7 - - - +
185B GLY* 1.3 56.8 - - - +
187B GLN* 3.3 7.1 + - - +
188B GLN* 3.1 34.1 + - + +
----------------------------------------------------------
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LYS 3.2 13.6 + - - -
182B GLU* 3.4 4.9 + - - -
183B LEU 3.3 0.4 - - - -
184B THR* 1.3 74.4 - - - +
186B ILE* 1.3 62.6 + - - +
188B GLN* 3.7 2.3 - - - -
189B GLY* 3.2 22.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 3.3 16.2 + - + +
183B LEU 3.8 4.9 - - - +
185B GLY* 1.3 73.6 - - - +
187B GLN* 1.3 65.9 + - - +
189B GLY* 3.3 8.9 + - - -
191B LEU* 4.6 9.6 - - + +
196B GLN* 3.3 47.8 + - + +
199B ALA* 3.6 42.4 - - + +
200B LEU* 3.8 15.7 - - + +
203B LEU* 4.2 15.5 - - + -
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Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 3.1 20.0 + - + +
184B THR* 3.3 8.3 + - - +
186B ILE* 1.3 82.4 - - - +
188B GLN* 1.3 56.9 + - + +
189B GLY 3.4 0.2 - - - -
196B GLN* 3.6 15.7 + - - +
200B LEU* 5.6 7.2 - - + -
----------------------------------------------------------
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Residues in contact with GLN 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B THR* 3.1 18.4 + - + +
185B GLY* 3.7 4.6 - - - +
187B GLN* 1.3 75.1 - - + +
189B GLY* 1.3 60.5 + - - +
190B PHE* 5.7 0.9 - - - -
----------------------------------------------------------
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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
------------------------------------------------------------
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