Contacts of the helix formed by residues 168 - 200 (chain B) in PDB entry 3L6D
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 PRO 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B THR* 3.3 0.7 - - - +
147B ARG* 4.1 17.0 - - - +
166B PHE* 4.2 8.9 - - + -
167B LEU* 1.3 88.8 - - + +
169B TRP* 1.3 67.0 + - - +
170B ASP 3.4 2.0 - - - +
171B GLU* 3.0 36.6 + - + +
172B ALA 2.9 17.7 + - - -
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Residues in contact with TRP 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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103B ASN* 5.2 0.9 - - - -
105B GLN* 4.1 10.5 + - - +
108B GLY* 3.7 41.7 - - - -
109B LEU* 3.8 32.5 - - + +
112B GLN* 3.9 24.7 - - - -
122B TYR* 4.0 15.0 - + - -
124B LYS* 4.0 20.6 - - + -
144B THR* 3.0 36.1 + - + -
145B GLY* 3.9 12.9 + - - +
168B PRO* 1.3 72.0 - - - +
170B ASP* 1.3 85.1 + - - +
172B ALA* 3.3 1.6 + - - +
173B LEU* 3.2 51.5 + - + +
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Residues in contact with ASP 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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105B GLN* 3.7 16.9 + - - +
109B LEU* 5.7 1.7 - - - +
168B PRO* 3.1 1.6 + - - +
169B TRP* 1.3 97.0 - - - +
171B GLU* 1.3 62.9 - - + +
173B LEU* 4.2 3.8 - - - +
174B ALA* 3.2 24.7 + - - +
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Residues in contact with GLU 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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201A GLY 5.3 4.7 - - - +
202A LEU* 3.9 26.8 - - + +
167B LEU* 4.1 16.6 - - + +
168B PRO* 3.0 36.8 + - + +
170B ASP* 1.3 78.0 - - + +
172B ALA* 1.3 59.7 + - - +
174B ALA* 3.8 0.5 - - - +
175B PHE* 2.8 34.3 + - - +
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Residues in contact with ALA 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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126B MSE 3.5 12.4 - - + +
142B ILE* 4.1 8.9 - - + +
143B HIS 4.5 0.2 - - - +
144B THR* 3.4 39.5 - - + +
167B LEU* 3.8 21.3 - - + +
168B PRO 2.9 7.6 + - - +
169B TRP 3.3 2.0 + - - +
171B GLU* 1.3 77.9 - - - +
173B LEU* 1.3 62.6 + - - +
175B PHE* 3.9 0.9 - - - +
176B ALA* 2.9 26.5 + - - +
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Residues in contact with LEU 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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105B GLN* 3.5 47.6 - - + +
124B LYS* 3.8 32.5 - - + -
126B MSE 3.9 11.4 - - + -
144B THR* 5.1 1.8 - - + -
169B TRP* 3.2 45.3 + - + +
170B ASP* 4.2 3.1 - - - +
172B ALA* 1.3 75.4 - - - +
174B ALA* 1.3 58.5 + - - +
176B ALA* 3.3 3.6 + - - +
177B THR* 2.9 33.8 + - - +
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Residues in contact with ALA 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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200A PHE* 3.6 46.2 - - + +
202A LEU* 4.1 11.0 - - + -
170B ASP 3.2 17.8 + - - +
171B GLU 3.8 2.7 - - - +
173B LEU* 1.3 75.1 - - - +
175B PHE* 1.3 68.8 + - - +
177B THR* 3.1 6.7 + - - -
178B VAL* 3.0 27.9 + - - +
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Residues in contact with PHE 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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202A LEU* 3.8 11.4 - - + +
207A THR* 4.1 19.3 - - + -
210A LEU* 3.6 46.0 - - + -
211A LEU* 3.4 37.5 - - + -
214A THR* 4.0 15.9 - - + -
142B ILE* 3.7 27.6 - - + -
165B VAL* 5.2 1.8 - - + -
167B LEU* 3.9 22.4 - - + -
171B GLU 2.8 23.1 + - - +
172B ALA 3.9 2.2 - - - +
174B ALA* 1.3 75.3 - - - +
176B ALA* 1.3 56.9 + - - +
178B VAL* 3.5 2.4 - - + +
179B LEU* 2.8 37.0 + - + +
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Residues in contact with ALA 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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126B MSE 4.1 18.2 - - + -
142B ILE* 4.0 22.7 - - + -
172B ALA 2.9 18.5 + - - +
173B LEU* 3.7 4.3 - - - +
175B PHE* 1.3 77.7 - - - +
177B THR* 1.3 63.1 + - - +
179B LEU* 4.3 1.1 - - - -
180B HIS* 2.8 40.7 + - + +
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Residues in contact with THR 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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200A PHE* 4.7 6.6 - - + -
252A ILE* 3.8 26.0 - - + +
255A SER* 3.9 32.0 + - - +
256A LEU* 4.1 18.4 - - + -
173B LEU* 2.9 19.4 + - - +
174B ALA* 3.1 7.6 + - - -
176B ALA* 1.3 77.9 - - - +
178B VAL* 1.3 58.6 + - - +
180B HIS* 3.9 1.0 - - - +
181B ALA* 2.9 26.3 + - - +
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Residues in contact with VAL 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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193A ALA* 3.5 30.1 - - + +
194A VAL* 5.9 0.2 - - - -
196A ALA* 3.8 13.5 - - + -
197A GLY* 3.8 27.8 - - - +
200A PHE* 3.9 19.3 - - + -
202A LEU* 4.5 4.0 - - + -
207A THR* 5.1 2.2 - - + -
211A LEU* 3.8 16.4 - - + -
256A LEU* 4.5 3.4 - - + -
174B ALA 3.0 14.8 + - - +
175B PHE* 3.5 14.8 - - + +
177B THR* 1.3 73.1 - - - +
179B LEU* 1.3 67.7 + - - +
181B ALA* 3.6 6.5 - - - +
182B HIS* 3.1 18.5 + - - +
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Residues in contact with LEU 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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211A LEU* 3.3 31.2 - - + +
214A THR* 3.8 26.7 - - + -
215A SER* 3.5 35.4 - - - +
128B VAL* 3.9 28.5 - - + -
142B ILE* 4.0 13.2 - - + -
175B PHE* 2.8 24.3 + - + +
176B ALA 3.9 1.8 - - - +
178B VAL* 1.3 79.4 - - - +
180B HIS* 1.3 65.6 + - + +
182B HIS* 3.4 2.3 + - - +
183B ALA* 3.0 26.8 + - + +
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Residues in contact with HIS 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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218A PHE* 5.0 8.0 - + - -
252A ILE* 3.7 22.0 - - + -
126B MSE 5.5 6.7 - - + -
127B ILE 4.9 3.9 + - - -
128B VAL* 4.1 28.5 - - + +
142B ILE* 5.3 1.1 - - + -
176B ALA* 2.8 39.7 + - + +
177B THR 4.1 0.7 - - - +
179B LEU* 1.3 90.5 - - + +
181B ALA* 1.3 66.8 + - - +
183B ALA* 4.3 3.8 - - + +
184B PHE* 2.9 55.7 + + + +
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Residues in contact with ALA 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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192A GLU* 6.0 0.2 - - - +
193A ALA* 5.0 6.1 - - + -
252A ILE* 4.0 10.6 - - + +
256A LEU* 4.4 10.3 - - + -
263A THR* 6.1 0.9 - - + -
266A PHE* 3.5 31.1 - - + -
177B THR 2.9 18.0 + - - +
178B VAL* 3.6 9.6 - - - +
179B LEU 3.3 0.2 - - - -
180B HIS* 1.3 75.5 - - - +
182B HIS* 1.3 57.8 + - - +
185B ALA* 2.9 34.2 + - - +
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Residues in contact with HIS 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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186A ALA* 4.0 5.6 - - + -
189A THR* 3.0 30.4 + - - +
190A PHE* 3.5 40.0 + + + -
193A ALA* 3.6 25.0 - - + +
211A LEU* 4.6 7.4 - - + -
212A LEU* 5.4 1.0 - - - +
215A SER* 3.5 27.2 + - - -
219A VAL* 5.0 4.0 - - - +
178B VAL 3.1 10.8 + - - +
179B LEU* 3.8 3.1 - - - +
181B ALA* 1.3 77.3 - - - +
183B ALA* 1.3 59.8 + - - +
185B ALA* 3.4 2.8 + - - -
186B ALA* 2.8 38.5 + - + +
223B LEU* 4.5 13.7 - - + +
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Residues in contact with ALA 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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215A SER* 4.4 7.9 - - - -
218A PHE* 3.8 26.0 - - + -
219A VAL* 3.7 26.8 - - + +
128B VAL* 6.0 0.4 - - + -
179B LEU* 3.0 19.6 + - + +
180B HIS* 4.1 6.3 - - + +
182B HIS* 1.3 78.2 - - - +
184B PHE* 1.3 64.1 + - + +
186B ALA* 3.5 3.1 + - - +
187B MSE 3.2 27.6 + - - +
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Residues in contact with PHE 184 (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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218A PHE* 4.0 16.6 - + - -
245A HIS* 3.9 20.4 - + - -
248A ALA* 4.9 9.9 - - + -
249A PHE* 3.3 39.6 - + + -
252A ILE* 3.8 18.6 - - + -
266A PHE* 4.4 5.2 - - + -
269A VAL* 4.7 1.1 - - - -
130B TYR* 3.9 12.3 - + - -
180B HIS* 2.9 54.5 + + + +
183B ALA* 1.3 75.3 - - + +
185B ALA* 1.3 65.8 + - - +
187B MSE 3.3 18.6 + - - +
188B VAL* 3.0 27.5 + - - +
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Residues in contact with ALA 185 (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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189A THR* 3.7 25.8 - - + -
192A GLU* 5.9 0.7 - - - +
265A VAL* 5.0 3.4 - - + -
266A PHE* 4.2 10.2 - - + +
269A VAL* 3.7 26.3 - - + +
181B ALA 2.9 21.7 + - - +
182B HIS* 4.5 0.2 - - - -
184B PHE* 1.3 78.4 - - - +
186B ALA* 1.3 56.3 - - - +
188B VAL* 3.1 2.8 + - - +
189B THR* 2.9 32.9 + - - +
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Residues in contact with ALA 186 (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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182A HIS* 3.9 5.1 - - + -
186A ALA* 4.8 9.9 - - + -
189A THR* 4.1 6.7 + - - +
219A VAL* 4.3 18.2 - - + -
223A LEU* 4.6 2.2 - - + +
182B HIS* 2.8 36.5 + - + +
183B ALA* 3.6 5.8 - - - +
185B ALA* 1.3 74.5 - - - +
187B MSE 1.3 62.1 + - - +
189B THR* 2.7 25.8 + - - -
190B PHE* 3.3 8.0 + - - +
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Residues in contact with MSE 187 (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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218A PHE* 4.7 7.4 - - - -
219A VAL* 5.1 7.2 - - + +
222A ALA* 3.8 31.9 - - + +
223A LEU* 3.9 17.9 - - + -
245A HIS* 4.8 1.3 - - + +
249A PHE* 6.2 0.7 - - + -
286A ILE* 3.9 28.3 - - + -
130B TYR* 3.7 19.5 - - + +
183B ALA 3.2 11.4 + - - +
184B PHE* 3.5 31.0 - - + +
185B ALA 3.3 0.2 - - - -
186B ALA* 1.3 77.7 - - - +
188B VAL* 1.3 63.2 + - + +
190B PHE* 3.1 8.0 + - - +
191B PHE* 3.1 43.8 + - + -
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Residues in contact with VAL 188 (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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249A PHE* 4.1 7.0 - - + -
269A VAL* 3.6 34.1 - - + -
272A VAL* 4.0 26.2 - - + -
273A VAL* 4.0 17.5 - - + -
286A ILE* 5.6 1.6 - - + -
289A THR* 4.9 2.9 - - + +
184B PHE 3.0 16.3 + - - +
185B ALA 3.1 4.0 + - - +
187B MSE 1.3 74.9 - - + +
189B THR* 1.3 59.2 + - - +
191B PHE* 3.1 18.8 + - + -
192B GLU* 2.8 29.0 + - + +
265B VAL* 4.1 12.1 - - + -
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Residues in contact with THR 189 (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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182A HIS* 3.0 22.9 + - - +
185A ALA* 3.6 32.5 - - + -
186A ALA 4.1 2.1 + - - -
189A THR* 3.8 16.8 - - + -
185B ALA 2.9 19.2 + - - +
186B ALA* 2.7 21.1 + - - -
188B VAL* 1.3 75.4 - - - +
190B PHE* 1.3 60.6 + - - +
192B GLU* 3.5 7.7 + - - +
193B ALA* 3.1 25.1 + - - +
265B VAL* 3.7 22.0 - - + -
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Residues in contact with PHE 190 (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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182A HIS* 3.6 34.8 - + + -
223A LEU* 3.7 31.6 - - + -
226A ALA* 5.0 1.6 - - + -
227A VAL* 3.7 22.0 - - + -
230A LEU* 4.5 10.8 - - + -
186B ALA 3.9 0.7 - - - +
187B MSE 3.1 9.3 + - - +
188B VAL 3.1 0.6 - - - -
189B THR* 1.3 79.9 + - - +
191B PHE* 1.3 78.6 + + - +
193B ALA* 3.2 1.9 + - - +
194B VAL* 3.0 43.4 + - + +
208B ALA 3.5 19.7 - - - -
211B LEU* 4.1 12.1 - - + -
212B LEU* 3.8 30.1 - - + -
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Residues in contact with PHE 191 (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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222A ALA 5.8 0.4 - - - -
223A LEU* 5.3 2.0 - - + -
226A ALA* 3.7 30.5 - - + -
230A LEU* 5.1 1.6 - - + -
286A ILE* 3.6 25.8 - - + -
287A ALA* 3.9 17.9 - - + -
289A THR* 3.7 25.8 - - + -
290A THR* 3.6 33.5 + - - +
293A PHE* 3.9 5.4 - - - -
187B MSE 3.1 44.8 + - + -
188B VAL* 3.1 15.7 + - + +
190B PHE* 1.3 85.6 - + - +
192B GLU* 1.3 58.3 + - - +
194B VAL* 3.9 2.1 - - - +
195B GLY* 2.9 27.7 + - - -
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Residues in contact with GLU 192 (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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293A PHE* 3.6 32.3 - - + -
188B VAL 2.8 20.1 + - - +
189B THR* 3.8 7.8 - - - +
191B PHE* 1.3 74.6 - - - +
193B ALA* 1.3 57.5 + - - +
195B GLY* 3.4 0.9 + - - -
196B ALA* 2.9 28.9 + - - +
263B THR* 3.4 26.8 - - + +
264B PRO* 3.2 13.9 - - - +
265B VAL* 2.8 36.6 + - + +
266B PHE* 2.8 29.5 + - - +
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Residues in contact with ALA 193 (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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178A VAL* 3.4 37.0 - - - +
181A ALA* 4.7 5.6 - - + -
182A HIS* 3.6 19.1 - - + +
189B THR 3.1 17.5 + - - +
190B PHE 3.9 1.8 - - - +
192B GLU* 1.3 72.5 - - - +
194B VAL* 1.3 60.8 + - - +
196B ALA* 3.2 8.6 + - - +
197B GLY* 2.9 24.4 + - - -
211B LEU* 4.1 7.0 - - + -
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Residues in contact with VAL 194 (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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230A LEU* 4.2 6.3 - - + -
290A THR* 3.9 8.1 - - + +
190B PHE* 3.0 49.8 + - + +
191B PHE* 3.9 4.9 - - - +
193B ALA* 1.3 77.0 - - - +
195B GLY* 1.3 62.6 + - - +
197B GLY* 3.1 12.3 + - - +
198B ASP 3.2 8.3 + - - -
202B LEU 4.9 0.7 - - - +
204B VAL* 3.5 43.0 - - + +
207B THR* 5.3 5.9 - - + +
208B ALA* 4.1 15.0 - - + +
211B LEU* 4.1 14.6 - - + -
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Residues in contact with GLY 195 (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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290A THR* 3.9 23.3 - - - +
293A PHE* 3.9 17.5 - - - +
294A ALA* 5.6 0.4 - - - -
191B PHE 2.9 17.9 + - - -
192B GLU 3.8 1.3 - - - -
194B VAL* 1.3 76.2 - - - +
196B ALA* 1.3 61.1 + - - +
198B ASP* 3.2 23.3 + - - +
199B ARG* 3.6 7.4 + - - +
204B VAL* 4.9 0.2 - - - -
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Residues in contact with ALA 196 (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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178A VAL* 4.0 11.0 - - + -
293A PHE* 4.6 2.1 - - - +
192B GLU 2.9 18.8 + - - +
193B ALA* 3.2 9.2 + - - +
195B GLY* 1.3 73.3 - - - +
197B GLY* 1.3 64.4 + - - +
199B ARG* 3.1 14.5 + - - +
200B PHE* 3.1 19.2 + - - -
256B LEU* 4.3 16.8 - - + -
261B VAL* 4.0 20.4 - - + +
262B TRP 5.9 0.2 - - - +
263B THR* 4.5 6.5 - - + -
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Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 3.7 14.7 - - - +
193B ALA 2.9 14.4 + - - -
194B VAL* 3.1 6.6 + - - -
196B ALA* 1.3 76.5 - - - +
198B ASP* 1.3 55.4 + - - +
200B PHE* 2.9 22.8 + - - +
202B LEU* 3.0 37.1 + - - +
207B THR* 5.4 3.1 - - - -
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Residues in contact with ASP 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA* 3.9 27.0 - - + +
194B VAL 3.2 5.1 + - - -
195B GLY* 3.2 13.7 + - - +
197B GLY* 1.3 76.0 - - - +
199B ARG* 1.3 61.7 + - - +
201B GLY* 2.9 20.8 + - - -
202B LEU 3.4 12.7 + - - +
203B PRO* 5.2 2.6 - - - +
204B VAL* 4.1 25.2 + - + +
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 2.7 33.1 + - - +
294A ALA 3.0 22.2 + - - +
195B GLY 3.6 4.6 + - - +
196B ALA* 3.1 4.6 + - - +
198B ASP* 1.3 84.3 - - - +
200B PHE* 1.3 53.1 + - - +
201B GLY 3.3 0.6 + - - -
259B GLN* 2.6 35.6 + - + +
260B GLY 3.8 15.0 + - - -
261B VAL* 3.4 36.5 - - + +
262B TRP* 3.4 31.1 + - - +
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Residues in contact with PHE 200 (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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174A ALA* 3.4 36.2 - - + +
177A THR* 4.6 9.4 - - + -
178A VAL* 4.1 12.6 - - + -
196B ALA 3.1 24.6 + - - -
197B GLY* 2.9 10.2 + - - +
199B ARG* 1.3 79.0 - - - +
201B GLY* 1.3 57.5 + - - +
202B LEU* 3.7 8.5 + - + +
255B SER* 3.8 17.9 - - - -
256B LEU* 3.8 26.5 - - + -
259B GLN* 3.7 45.1 - - + +
261B VAL* 4.5 2.0 - - + -
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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