Contacts of the helix formed by residues 168 - 200 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A THR* 4.0 0.4 - - - +
147A ARG* 4.3 15.7 - - - +
166A PHE* 4.2 9.7 - - + +
167A LEU* 1.3 84.8 - - + +
169A TRP* 1.3 57.9 + - - +
170A ASP* 3.4 12.6 - - - +
171A GLU* 3.1 37.9 + - - +
172A ALA 2.8 29.8 + - - -
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Residues in contact with TRP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLN* 3.6 11.0 - - - +
108A GLY* 3.8 23.6 - - - -
109A LEU* 3.5 38.1 - - + +
112A GLN* 3.6 36.1 - - - +
122A TYR* 4.0 16.8 - + - -
124A LYS* 4.1 16.2 - - + -
144A THR* 3.1 32.8 + - + -
145A GLY* 4.0 10.7 - - - +
168A PRO* 1.3 73.0 - - - +
170A ASP* 1.3 70.0 + - - +
172A ALA* 3.4 6.2 + - - +
173A LEU* 3.1 39.0 + - + +
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLN* 5.6 3.9 + - - +
168A PRO* 3.6 21.7 - - - +
169A TRP* 1.3 80.8 - - - +
171A GLU* 1.3 78.0 + - - +
173A LEU* 3.6 1.9 + - - +
174A ALA* 3.3 21.9 + - - +
202B LEU* 5.6 0.2 - - - -
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 3.9 18.5 - - + +
168A PRO* 3.1 32.9 + - + +
170A ASP* 1.3 92.2 + - - +
172A ALA* 1.3 53.7 + - - +
174A ALA* 3.4 0.7 + - - +
175A PHE* 2.7 38.9 + - - +
201B GLY 5.4 2.5 - - - +
202B LEU* 3.7 29.4 - - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A MSE 4.3 4.0 - - + -
142A ILE* 4.2 16.8 - - + +
144A THR* 3.5 37.9 - - + -
167A LEU* 3.7 19.0 - - + +
168A PRO 2.8 15.1 + - - +
169A TRP 4.0 1.1 - - - +
170A ASP 3.3 0.4 + - - -
171A GLU* 1.3 72.5 - - - +
173A LEU* 1.3 59.0 + - - +
175A PHE* 3.7 1.9 - - - +
176A ALA* 2.9 29.9 + - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN 6.0 1.8 - - - +
105A GLN* 3.5 38.4 - - + +
124A LYS* 3.5 29.6 - - + +
126A MSE 4.1 9.6 - - - -
144A THR* 5.4 0.4 - - + -
169A TRP* 3.1 49.5 + - + +
170A ASP 4.4 0.9 - - - +
171A GLU 3.4 0.2 - - - -
172A ALA* 1.3 78.3 - - + +
174A ALA* 1.3 64.4 + - - +
176A ALA* 3.4 5.9 + - + +
177A THR* 3.0 29.8 + - - +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ASP 3.3 17.2 + - - +
171A GLU 3.8 2.5 - - - +
173A LEU* 1.3 76.7 - - - +
175A PHE* 1.3 63.7 + - - +
177A THR* 3.2 8.0 + - - -
178A VAL* 3.1 26.3 + - - +
200B PHE* 3.4 46.6 - - + +
202B LEU* 4.0 10.8 - - + -
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Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ILE* 3.7 29.4 - - + -
165A VAL* 5.2 1.1 - - + -
167A LEU* 3.9 21.5 - - + -
171A GLU 2.7 22.3 + - - +
172A ALA 3.7 2.2 - - - +
174A ALA* 1.3 75.3 - - - +
176A ALA* 1.3 55.4 + - - +
178A VAL* 3.4 6.8 + - + +
179A LEU* 2.9 39.5 + - + +
202B LEU* 3.8 11.4 - - + +
207B THR* 4.0 20.6 - - + -
210B LEU* 3.5 45.3 - - + -
211B LEU* 3.8 31.4 - - + -
214B THR* 4.0 14.1 - - + -
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A MSE 3.6 28.7 - - + -
142A ILE* 4.2 17.5 - - + -
172A ALA 2.9 17.3 + - - +
173A LEU* 3.7 5.2 - - + +
175A PHE* 1.3 76.6 - - - +
177A THR* 1.3 61.5 + - - +
179A LEU* 3.5 1.5 + - - +
180A HIS* 2.7 40.4 + - + +
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU 3.0 15.0 + - - -
174A ALA* 3.5 11.4 - - - -
175A PHE 3.2 0.2 - - - -
176A ALA* 1.3 78.2 - - - +
178A VAL* 1.3 57.3 + - - +
180A HIS* 3.4 1.0 + - - +
181A ALA* 3.0 27.5 + - - +
200B PHE* 4.6 6.5 - - + -
252B ILE* 3.8 24.1 - - + +
255B SER* 4.1 25.3 + - - -
256B LEU* 3.8 25.1 - - + -
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Residues in contact with VAL 178 (chain A).
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 3.1 12.9 + - - +
175A PHE* 3.5 19.5 - - + +
177A THR* 1.3 73.4 - - - +
179A LEU* 1.3 68.0 + - - +
181A ALA* 3.5 5.6 + - - -
182A HIS* 3.1 19.4 + - - +
193B ALA* 3.4 34.4 - - + +
196B ALA* 4.0 11.9 - - + -
197B GLY* 3.7 23.6 - - - +
200B PHE* 4.1 14.6 - - + -
202B LEU* 4.6 2.9 - - + -
207B THR* 5.1 2.0 - - + -
211B LEU* 3.9 17.2 - - + +
256B LEU* 4.4 4.0 - - + -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL* 3.9 36.1 - - + -
142A ILE* 3.9 18.6 - - + -
175A PHE* 2.9 29.3 + - + +
176A ALA 3.8 0.9 - - - +
178A VAL* 1.3 79.4 - - - +
180A HIS* 1.3 66.2 + - + +
182A HIS* 3.5 2.8 + - - +
183A ALA* 3.0 27.5 + - + +
211B LEU* 3.5 35.7 - - + +
214B THR* 3.9 14.8 - - + -
215B SER* 3.6 26.0 - - - +
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Residues in contact with HIS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A MSE 5.6 6.5 - - + -
127A ILE 4.9 3.2 + - - -
128A VAL* 4.1 28.1 - - + +
142A ILE* 5.4 0.9 - - + -
176A ALA* 2.7 39.2 + - + +
177A THR 4.1 0.4 - - - +
179A LEU* 1.3 91.8 - - + +
181A ALA* 1.3 62.0 + - - +
183A ALA* 4.2 4.5 - - + -
184A PHE* 2.8 63.2 + + + +
218B PHE* 5.0 8.0 - + - -
252B ILE* 3.7 21.3 - - + -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A THR 3.0 18.9 + - - +
178A VAL* 3.6 10.1 - - - +
180A HIS* 1.3 75.2 - - - +
182A HIS* 1.3 61.9 + - - +
185A ALA* 3.0 28.8 + - - +
193B ALA* 4.7 7.0 - - + -
252B ILE* 4.0 14.2 - - + +
256B LEU* 4.4 12.1 - - + -
266B PHE* 3.6 24.6 - - + -
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Residues in contact with HIS 182 (chain A).
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 3.1 8.4 + - - +
179A LEU 3.8 2.0 - - - +
181A ALA* 1.3 78.9 - - - +
183A ALA* 1.3 60.8 + - - +
185A ALA* 3.3 3.7 + - - +
186A ALA* 2.8 39.0 + - + +
223A LEU* 4.6 12.9 - - + +
186B ALA* 3.9 6.1 - - + -
189B THR* 3.0 31.2 + - - +
190B PHE* 3.5 32.4 + + + -
193B ALA* 3.6 24.5 - - + +
211B LEU* 3.7 17.0 - - + -
212B LEU* 5.6 1.0 - - - +
215B SER* 3.7 25.6 + - - -
219B VAL* 5.0 4.8 - - + +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL* 6.0 1.1 - - + -
179A LEU* 3.0 19.6 + - + +
180A HIS* 4.0 7.2 - - + +
182A HIS* 1.3 80.5 - - - +
184A PHE* 1.3 63.4 + - - +
186A ALA* 3.7 2.9 - - - +
187A MSE 3.3 25.0 + - - +
215B SER* 4.5 7.2 - - - -
218B PHE* 3.8 24.7 - - + -
219B VAL* 3.7 27.1 - - + +
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR* 3.6 23.1 - + - -
180A HIS* 2.8 54.4 + + + +
181A ALA 4.4 0.7 - - - +
183A ALA* 1.3 72.5 - - + +
185A ALA* 1.3 64.9 + - - +
187A MSE 3.3 20.0 + - - +
188A VAL* 3.1 27.9 + - - +
218B PHE* 4.0 15.5 - + - -
245B HIS* 3.8 11.7 - + - -
248B ALA* 4.8 9.6 - - + -
249B PHE* 3.2 43.5 - + + -
252B ILE* 3.9 14.8 - - + -
266B PHE* 4.6 4.5 - - + -
269B VAL* 4.7 0.9 - - - -
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ALA 3.0 21.4 + - - +
182A HIS 3.8 1.3 - - - +
184A PHE* 1.3 77.2 - - - +
186A ALA* 1.3 62.3 + - - +
188A VAL* 3.1 3.1 + - - +
189A THR* 2.9 28.1 + - - +
189B THR* 3.6 23.3 - - + -
192B GLU* 6.0 0.4 - - - +
265B VAL* 5.1 2.5 - - + -
266B PHE* 4.0 11.1 - - + -
269B VAL* 3.8 25.8 - - + +
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Residues in contact with ALA 186 (chain A).
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* 2.8 38.9 + - + +
183A ALA* 3.7 5.2 - - - +
184A PHE 3.3 0.2 - - - -
185A ALA* 1.3 71.9 - - - +
187A MSE 1.3 61.5 + - - +
189A THR* 2.7 26.5 + - - -
190A PHE* 3.2 8.1 + - - +
182B HIS* 4.0 4.5 - - + -
186B ALA* 4.8 11.0 - - + +
189B THR* 4.1 7.0 + - - +
219B VAL* 4.2 16.6 - - + -
223B LEU* 4.6 2.6 - - + +
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Residues in contact with MSE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR* 3.6 21.1 - - + +
183A ALA 3.3 12.4 + - - +
184A PHE* 3.5 31.6 - - + +
185A ALA 3.3 0.2 - - - -
186A ALA* 1.3 78.0 - - - +
188A VAL* 1.3 58.0 + - + +
190A PHE* 3.1 8.0 + - - +
191A PHE* 3.0 44.4 + - + -
218B PHE* 4.7 7.4 - - - -
219B VAL* 4.9 6.9 - - + +
222B ALA* 3.8 33.4 - - + +
223B LEU* 4.0 16.6 - - + +
249B PHE* 5.9 1.3 - - + -
286B ILE* 3.9 33.4 - - + -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE 3.1 15.0 + - - +
185A ALA 3.1 5.1 + - - +
187A MSE 1.3 74.5 - - + +
189A THR* 1.3 60.9 + - - +
191A PHE* 3.1 20.1 + - + +
192A GLU* 2.8 31.0 + - + +
265A VAL* 4.1 12.1 - - + -
249B PHE* 4.2 7.0 - - + -
269B VAL* 3.9 35.2 - - + +
272B VAL* 4.2 23.3 - - + -
273B VAL* 4.0 16.8 - - + -
286B ILE* 5.5 1.8 - - + -
289B THR* 4.8 2.7 - - + +
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Residues in contact with THR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ALA 2.9 21.3 + - - +
186A ALA* 2.7 19.4 + - - -
188A VAL* 1.3 75.8 - - - +
190A PHE* 1.3 57.4 + - - +
192A GLU* 3.4 7.4 + - - +
193A ALA* 3.0 29.5 + - - +
265A VAL* 3.8 17.9 - - + +
182B HIS* 3.0 22.1 + - - +
185B ALA* 3.7 32.5 - - + -
186B ALA 4.1 1.9 + - - -
189B THR* 3.8 19.5 - - + -
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Residues in contact with PHE 190 (chain A).
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 3.2 0.6 + - - +
187A MSE 3.1 11.3 + - - +
189A THR* 1.3 79.2 + - - +
191A PHE* 1.4 77.1 + + - +
193A ALA* 3.2 2.1 + - - +
194A VAL* 3.0 41.9 + - + +
208A ALA 3.4 27.8 - - - -
211A LEU* 4.1 11.4 - - + -
212A LEU* 3.8 22.2 - - + -
182B HIS* 3.6 33.9 - + + -
223B LEU* 3.6 32.3 - - + -
226B ALA* 4.9 3.4 - - + -
227B VAL* 3.7 22.2 - - + -
230B LEU* 4.4 11.7 - - + -
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A MSE 3.0 44.1 + - + -
188A VAL* 3.1 15.9 + - + +
190A PHE* 1.4 85.0 - + - +
192A GLU* 1.3 56.6 + - - +
194A VAL* 3.9 3.0 - - - +
195A GLY* 2.9 26.7 + - - -
222B ALA 5.8 0.2 - - - -
223B LEU* 5.3 1.3 - - + -
226B ALA* 3.6 30.3 - - + -
230B LEU* 5.4 1.6 - - + -
286B ILE* 3.7 24.0 - - + -
287B ALA* 3.9 17.9 - - + -
289B THR* 3.7 24.9 - - + -
290B THR* 3.4 35.3 + - - +
293B PHE* 3.9 6.0 - - - -
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 2.8 20.5 + - + +
189A THR* 3.7 7.0 - - - +
191A PHE* 1.3 73.2 - - - +
193A ALA* 1.3 58.2 + - - +
195A GLY* 3.3 0.9 + - - -
196A ALA* 2.8 28.6 + - - +
263A THR* 3.4 31.4 - - + +
264A PRO* 3.1 14.9 - - - +
265A VAL* 2.8 34.7 + - + +
266A PHE* 2.8 28.8 + - - +
293B PHE* 3.6 28.3 - - + -
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Residues in contact with ALA 193 (chain A).
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 3.0 16.8 + - - +
190A PHE 3.2 2.2 + - - +
192A GLU* 1.3 79.1 - - - +
194A VAL* 1.3 57.5 + - - +
196A ALA* 3.2 8.6 + - - +
197A GLY* 2.9 24.8 + - - -
211A LEU* 3.7 10.3 - - + -
263A THR* 6.2 0.2 - - - -
178B VAL* 3.5 34.0 - - - +
181B ALA* 5.0 4.5 - - + -
182B HIS* 3.6 18.6 - - + +
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 3.0 45.2 + - + +
191A PHE* 3.9 4.5 - - - +
193A ALA* 1.3 74.6 - - - +
195A GLY* 1.3 62.8 + - - +
197A GLY* 3.1 3.1 + - - -
198A ASP* 3.0 21.7 + - - +
204A VAL* 3.8 21.3 - - + +
207A THR* 5.2 6.2 - - - +
208A ALA* 4.0 15.7 - - + +
211A LEU* 3.8 19.3 - - + -
178B VAL* 5.9 0.2 - - - -
230B LEU* 4.1 11.4 - - + -
290B THR* 3.6 21.3 - - + -
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE 2.9 16.4 + - - -
192A GLU 3.7 2.9 - - - -
194A VAL* 1.3 78.2 - - - +
196A ALA* 1.3 60.0 + - - +
198A ASP* 3.3 16.9 + - - +
199A ARG* 3.3 16.7 + - - +
290B THR* 4.1 12.9 - - - +
293B PHE* 4.0 24.8 - - - +
294B ALA* 5.8 0.2 - - - -
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Residues in contact with ALA 196 (chain A).
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 2.8 17.1 + - - +
193A ALA* 3.2 11.9 + - - +
195A GLY* 1.3 70.9 - - - +
197A GLY* 1.3 63.5 + - - +
199A ARG* 2.9 15.2 + - - +
200A PHE* 3.2 18.6 + - + -
256A LEU* 4.1 19.3 - - + -
261A VAL* 4.2 13.4 - - + +
263A THR* 4.3 11.9 - - + -
178B VAL* 3.8 14.1 - - + -
293B PHE* 4.9 1.0 - - - +
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Residues in contact with GLY 197 (chain A).
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 2.9 14.3 + - - -
194A VAL* 3.1 4.9 + - - -
196A ALA* 1.3 75.9 - - - +
198A ASP* 1.3 61.8 + - - +
200A PHE* 2.9 15.9 + - - +
201A GLY 3.3 0.2 + - - -
202A LEU* 3.0 37.8 + - - +
207A THR* 5.1 3.6 - - - -
178B VAL* 3.8 15.2 - - - +
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL 3.0 11.8 + - - +
195A GLY* 3.4 12.3 - - - +
196A ALA 3.2 0.4 - - - -
197A GLY* 1.3 74.1 - - - +
199A ARG* 1.3 66.8 + - - +
201A GLY* 3.0 18.7 + - - -
202A LEU 3.4 14.3 + - - +
203A PRO* 5.3 2.1 - - - +
204A VAL* 4.1 21.5 + - + +
294B ALA* 4.4 18.0 - - - +
295B ARG* 4.9 1.4 + - - +
296B GLU* 4.5 12.5 - - - +
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY 3.3 10.7 + - - +
196A ALA* 2.9 10.9 + - - +
198A ASP* 1.3 86.7 - - - +
200A PHE* 1.3 59.0 + - - +
201A GLY 3.2 2.0 + - - -
259A GLN* 2.8 21.9 + - + +
260A GLY 4.5 10.7 + - - -
261A VAL* 3.7 24.9 - - + -
262A TRP* 4.5 18.8 - - - +
293B PHE* 2.9 30.7 + - - +
294B ALA 4.4 2.0 + - - -
295B ARG* 3.4 42.2 - - + +
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Residues in contact with PHE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ALA 3.2 23.4 + - - -
197A GLY 2.9 9.2 + - - +
199A ARG* 1.3 77.5 - - - +
201A GLY* 1.3 59.5 + - - +
202A LEU* 3.4 7.4 + - + +
255A SER* 4.0 17.5 - - - -
256A LEU* 4.0 18.4 - - + -
259A GLN* 3.6 45.5 - - + +
261A VAL* 4.5 2.7 - - + -
105B GLN* 6.2 0.2 - - - -
174B ALA* 3.6 33.3 - - + +
177B THR* 4.7 9.9 - - + -
178B VAL* 3.9 25.6 - - + -
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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