Contacts of the helix formed by residues 187 - 220 (chain M) in PDB entry 2QJK
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 ASP 187 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M VAL* 4.4 8.8 - - - +
151M TRP* 3.6 16.8 - - - -
181M LEU 5.7 0.4 - - - +
185M ALA* 3.1 11.1 + - + +
186M VAL* 1.3 74.4 - - - +
188M ASN* 1.3 83.4 + - - +
189M ALA* 3.4 6.1 - - + +
190M THR* 3.0 11.9 + - - +
191M LEU 3.1 13.9 + - - -
69R GLY* 6.5 1.3 - - - -
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Residues in contact with ASN 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M PRO 5.1 0.2 - - - -
72M HIS* 3.2 29.7 + - - +
73M VAL* 2.9 53.0 + - + +
187M ASP* 1.3 82.2 + - - +
189M ALA* 1.3 70.6 + - - +
190M THR 2.6 4.0 + - - -
191M LEU* 2.6 15.9 + - - +
192M ASN* 2.8 29.6 + - - +
70P THR* 4.8 1.0 + - - -
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Residues in contact with ALA 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181M LEU 4.2 8.7 - - - +
182M GLY 4.2 10.1 - - - +
187M ASP* 3.4 4.4 - - + +
188M ASN* 1.3 80.4 - - - +
190M THR* 1.3 59.8 + - - +
192M ASN* 3.8 7.8 - - - +
193M ARG* 2.9 46.8 + - - +
67P MET 4.4 2.0 - - - +
68P HIS* 6.0 3.4 - - - +
41R SER* 5.4 6.3 - - - +
44R VAL* 5.6 5.2 - - + -
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Residues in contact with THR 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M TRP* 5.7 0.2 - - - -
159M ALA* 5.8 0.7 - - + -
163M THR* 4.8 0.7 - - + -
180M LEU 3.8 17.7 - - - +
181M LEU* 2.9 31.4 + - + -
186M VAL* 3.8 12.8 - - + -
187M ASP* 3.0 26.8 + - - -
188M ASN 2.6 4.4 + - - -
189M ALA* 1.3 72.6 - - - +
191M LEU* 1.3 66.5 + - - -
193M ARG* 2.9 25.7 - - - +
194M PHE* 3.0 36.1 + - + -
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Residues in contact with LEU 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M TYR* 3.6 19.1 - - - +
71M PRO* 4.4 2.5 - - + -
72M HIS 3.8 14.6 - - - +
73M VAL* 3.4 30.3 - - + +
76M ALA* 4.0 10.1 - - + -
148M VAL* 4.3 5.4 - - + -
149M LEU* 3.7 23.8 - - + -
151M TRP* 3.8 39.6 - - + -
187M ASP 3.1 4.4 + - - +
188M ASN* 2.6 14.6 + - - +
190M THR* 1.3 73.7 - - - +
192M ASN* 1.3 64.6 + - - +
194M PHE* 2.9 18.0 + - - +
195M PHE* 3.0 11.7 + - - +
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Residues in contact with ASN 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M PRO* 3.8 18.7 + - - +
188M ASN* 2.8 28.1 + - - +
189M ALA* 3.8 7.4 - - - +
191M LEU* 1.3 75.4 - - - +
193M ARG* 1.3 62.3 + - - +
195M PHE* 3.2 16.1 + - - +
196M SER 3.4 8.3 + - - -
66P ALA 3.0 22.1 + - - +
67P MET* 3.0 28.2 + - - +
68P HIS* 3.5 9.0 - - - +
69P TYR 3.2 21.1 + - - +
70P THR* 3.6 13.5 + - - -
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Residues in contact with ARG 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179M TRP 3.3 4.9 + - - -
180M LEU 3.0 21.6 + - - -
182M GLY* 3.3 19.3 + - - -
189M ALA* 2.9 27.8 + - - +
190M THR* 2.9 23.0 + - - +
192M ASN* 1.3 79.1 - - - +
194M PHE* 1.3 72.1 + - + +
196M SER* 3.5 2.6 + - - -
197M LEU* 3.1 29.4 + - + +
67P MET* 3.7 32.6 + - + +
68P HIS* 4.2 18.9 - - - -
38R MET* 3.0 70.2 + - + +
39R ASN 5.0 1.0 + - - -
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Residues in contact with PHE 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M PHE* 3.6 35.7 - + - -
145M MET* 3.7 23.0 - - + +
148M VAL* 3.7 27.6 - - + -
149M LEU* 4.6 8.3 - - + -
159M ALA* 4.5 5.6 - - + -
163M THR* 4.4 13.0 - - + -
180M LEU* 4.5 7.2 - - + -
190M THR* 3.0 38.1 + - + +
191M LEU* 2.9 10.9 + - - +
193M ARG* 1.3 86.9 - - + +
195M PHE* 1.3 56.3 + - - +
197M LEU* 3.1 2.7 + - + +
198M HIS* 2.5 39.7 + - - +
503M SMA 3.7 23.8 - - + -
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Residues in contact with PHE 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M ALA* 4.4 22.0 - - + -
69M TYR* 3.6 33.4 - + - -
71M PRO* 3.7 30.5 - - + -
149M LEU* 4.0 18.9 - - + +
191M LEU 3.0 8.2 + - - +
192M ASN* 3.2 10.7 + - - +
194M PHE* 1.3 77.4 - - - +
196M SER* 1.3 66.6 + - - +
198M HIS* 3.8 2.4 - - + +
199M TYR* 3.0 36.7 + + - +
502M HEM 3.7 20.4 - - + -
66P ALA 5.3 2.5 - - - -
195P PHE* 2.9 44.4 - + - -
199P TYR* 5.7 0.4 - + - -
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Residues in contact with SER 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192M ASN 3.4 2.6 + - - -
193M ARG 3.6 8.3 - - - -
194M PHE 3.3 0.4 - - - -
195M PHE* 1.3 83.6 - - - +
197M LEU* 1.3 61.6 + - - +
199M TYR* 3.6 1.0 - - - +
200M LEU* 3.2 10.0 + - - +
63P ILE* 2.8 31.9 + - - +
66P ALA* 3.3 19.6 - - - +
67P MET* 3.7 22.2 - - - -
199P TYR* 3.0 30.4 + - - -
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Residues in contact with LEU 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M MET* 3.6 17.9 - - + -
193M ARG* 3.1 22.6 + - + +
194M PHE* 3.1 1.8 + - + +
196M SER* 1.3 75.4 - - - +
198M HIS* 1.3 65.0 + - - +
199M TYR 3.0 2.4 + - - -
200M LEU* 3.2 21.2 + - + +
201M LEU* 3.0 33.6 + - + +
503M SMA 4.0 25.4 - - + -
63P ILE* 4.8 2.0 - - + -
67P MET* 3.4 27.1 - - + -
38R MET* 5.1 7.6 - - + -
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Residues in contact with HIS 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M THR* 3.4 23.0 + - + +
145M MET* 4.2 13.4 - - + -
146M GLY* 3.5 19.3 + - - -
149M LEU* 3.6 17.9 - - + -
194M PHE 2.5 22.5 + - - +
195M PHE* 3.2 4.5 + + + +
197M LEU* 1.3 72.1 - - - +
199M TYR* 1.3 56.7 + - - +
202M PRO* 3.0 25.7 - - - +
502M HEM 2.0 96.1 + + + -
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Residues in contact with TYR 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M ILE* 3.7 14.0 - - + +
66M ALA* 4.2 4.9 - - + -
195M PHE* 3.0 27.6 + + + +
196M SER* 3.6 9.4 - - - +
198M HIS* 1.3 77.1 - - - +
200M LEU* 1.3 64.8 + - - +
202M PRO* 3.0 15.1 - - - +
203M PHE* 3.6 29.2 - + - -
502M HEM 3.5 39.5 - - + +
195P PHE* 5.7 0.2 - + - -
196P SER* 2.7 42.4 + - - -
199P TYR* 3.3 50.5 - + + -
200P LEU* 3.7 6.6 - - - +
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Residues in contact with LEU 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M SER 3.2 12.9 + - - +
197M LEU* 3.2 17.2 + - + +
199M TYR* 1.3 79.9 - - - +
201M LEU* 1.3 68.6 + - + +
203M PHE* 3.0 20.6 + - + +
204M VAL* 3.5 18.4 + - + -
63P ILE* 3.2 44.4 - - + -
199P TYR* 3.5 11.2 + - - +
203P PHE* 3.8 21.1 - - + -
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Residues in contact with LEU 201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M ALA* 3.8 12.6 - - + +
141M ALA* 3.7 16.2 - - + -
142M THR* 3.3 37.9 - - - +
145M MET* 3.7 13.7 - - + -
197M LEU* 3.0 21.3 + - + +
198M HIS 4.7 0.2 - - - +
200M LEU* 1.3 75.3 - - + +
202M PRO* 1.3 73.4 - - + +
204M VAL* 2.7 35.0 + - + +
205M ILE* 2.7 14.4 + - + +
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Residues in contact with PRO 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M LEU* 4.5 4.8 - - + +
59M ILE* 4.3 15.7 - - + +
142M THR* 4.0 11.0 - - + -
198M HIS 3.0 28.7 - - - +
199M TYR 3.0 13.2 - - - +
201M LEU* 1.3 83.1 - - + +
203M PHE* 1.3 57.5 + - + +
205M ILE* 3.0 14.6 + - + +
206M ALA* 2.7 29.0 + - - +
502M HEM 3.7 45.1 - - + -
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Residues in contact with PHE 203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M ILE* 4.6 25.1 - - + -
63M ILE* 4.9 0.7 - - + -
199M TYR* 3.6 33.7 - + - -
200M LEU* 3.0 15.4 + - + +
202M PRO* 1.3 73.6 - - + +
204M VAL* 1.3 67.9 + - + +
206M ALA* 3.1 10.5 + - + +
207M ALA* 2.8 23.0 + - - +
502M HEM 5.5 3.4 - - + -
200P LEU* 3.9 24.9 - - + -
203P PHE* 3.3 59.5 - + + -
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Residues in contact with VAL 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M ALA* 5.8 2.9 - - + -
200M LEU* 3.7 26.7 - - + +
201M LEU* 2.7 35.8 + - + +
203M PHE* 1.3 72.6 - - + +
205M ILE* 1.3 64.6 + - + +
207M ALA* 3.0 12.2 + - + +
208M LEU* 2.9 35.4 + - + +
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Residues in contact with ILE 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M LEU* 4.1 13.7 - - + -
104M PHE* 5.3 0.7 - - + -
135M ILE* 4.4 8.3 - - + -
138M ALA* 3.9 15.9 - - + -
139M MET* 3.9 27.6 - - + +
142M THR* 3.9 19.5 - - - +
201M LEU 2.7 17.6 + - - +
202M PRO* 3.1 10.3 - - + +
204M VAL* 1.3 76.2 - - + +
206M ALA* 1.3 65.3 + - - +
208M LEU* 2.8 22.5 + - - +
209M VAL* 2.8 30.7 + - + +
501M HEM 4.2 12.1 - - + -
502M HEM 4.0 18.4 - - + -
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Residues in contact with ALA 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M LEU* 3.7 21.7 - - + +
59M ILE* 4.9 6.5 - - + -
202M PRO 2.7 15.5 + - - +
203M PHE* 3.1 17.0 - - + +
205M ILE* 1.3 73.0 - - - +
207M ALA* 1.3 63.3 + - - +
209M VAL* 3.2 4.7 + - - +
210M ALA* 3.0 20.6 + - - +
505M ANJ 4.2 22.4 - - + +
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Residues in contact with ALA 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203M PHE 2.8 14.8 + - - +
204M VAL* 3.1 15.5 - - + +
206M ALA* 1.3 73.2 - - - +
208M LEU* 1.3 66.6 + - + +
210M ALA* 3.0 24.2 - - - +
211M ILE* 3.3 9.4 + - - +
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Residues in contact with LEU 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M VAL* 4.0 12.0 - - + +
134M LEU* 3.9 35.7 - - + +
135M ILE* 3.8 22.2 - - + +
138M ALA* 5.2 4.7 - - + -
204M VAL* 2.9 28.1 + - + +
205M ILE* 2.8 16.2 + - - +
207M ALA* 1.3 72.7 - - + +
209M VAL* 1.3 52.5 + - - +
211M ILE* 2.8 23.7 + - + +
212M HIS* 2.7 34.0 + - - +
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Residues in contact with VAL 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M ALA* 6.0 0.4 - - - -
55M LEU* 3.9 10.8 - - + -
135M ILE* 4.0 3.6 - - + +
205M ILE* 2.8 34.4 + - + +
206M ALA* 3.3 7.4 - - - +
208M LEU* 1.3 72.0 - - - +
210M ALA* 1.3 66.5 + - - +
212M HIS* 3.2 10.1 - - + +
213M ILE* 3.0 31.2 + - + +
501M HEM 3.6 52.3 - - + -
505M ANJ 4.0 23.6 - - + +
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Residues in contact with ALA 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M ALA 3.0 10.1 + - - +
207M ALA* 3.0 16.0 + - - +
208M LEU 3.0 0.2 - - - -
209M VAL* 1.3 73.9 - - - +
211M ILE* 1.3 57.1 + - + +
213M ILE* 2.7 30.7 + - - +
214M TRP* 2.8 12.7 + - - +
505M ANJ 4.6 10.5 + - + -
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Residues in contact with ILE 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M VAL* 4.2 18.8 - - + -
207M ALA 3.9 11.7 - - - +
208M LEU* 2.8 25.0 + - + +
210M ALA* 1.3 78.4 - - + +
212M HIS* 1.3 52.8 + - - +
214M TRP* 3.3 17.4 - - + +
215M ALA* 2.7 35.1 + - + +
23P LEU* 3.9 27.6 - - + -
25P ILE* 4.6 16.4 - - + -
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Residues in contact with HIS 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M THR* 3.6 30.3 + - + +
131M VAL* 4.0 11.4 - - + +
132M GLY* 3.9 6.5 + - - -
135M ILE* 4.1 5.2 - - + -
208M LEU 2.7 14.8 + - - +
209M VAL* 3.2 16.4 - - + +
210M ALA 3.0 0.2 + - - -
211M ILE* 1.3 73.9 - - - +
213M ILE* 1.3 63.7 + - - +
215M ALA* 3.2 6.4 + - - +
216M PHE* 3.0 24.4 + + - +
501M HEM 2.0 101.5 + + + -
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Residues in contact with ILE 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M THR* 5.6 2.2 - - + -
209M VAL* 3.0 16.3 + - + +
210M ALA* 2.7 12.8 + - - +
212M HIS* 1.3 70.3 - - + +
214M TRP* 1.3 66.4 + - - +
216M PHE* 3.2 23.6 + - + -
217M HIS* 2.9 55.5 + - + +
501M HEM 5.4 1.8 - - + -
505M ANJ 3.0 70.2 - - + +
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Residues in contact with TRP 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210M ALA 2.8 11.7 + - - +
211M ILE* 3.3 21.3 - - + +
213M ILE* 1.3 77.0 - - - +
215M ALA* 1.3 61.1 + - - +
217M HIS* 3.3 7.2 + - + +
218M SER* 2.8 39.2 + - - -
23P LEU* 3.5 16.4 - - + -
24P PRO* 4.0 24.5 - - + +
25P ILE* 3.3 47.6 - - + -
28P LEU* 3.7 32.8 - - + -
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Residues in contact with ALA 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M VAL* 4.7 5.2 - - + -
128M THR* 3.8 26.6 + - - +
131M VAL* 5.7 0.9 - - + -
211M ILE* 2.7 21.2 + - + +
212M HIS* 3.4 5.2 - - - +
214M TRP* 1.3 70.2 - - - +
216M PHE* 1.3 58.6 + - - +
217M HIS 3.0 4.9 - - - -
218M SER* 3.0 18.4 + - - -
219M THR* 3.5 15.9 + - - +
22P ARG 3.9 1.9 - - - +
23P LEU* 3.6 27.1 - - + -
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Residues in contact with PHE 216 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M THR* 3.8 7.6 + - + +
212M HIS* 3.0 28.7 + + - +
213M ILE* 3.2 35.4 - - + -
215M ALA* 1.3 76.9 - - - +
217M HIS* 1.3 75.9 + + - +
218M SER 3.3 0.2 - - - -
219M THR* 4.0 7.6 - - - -
220M GLY* 3.3 26.5 + - - -
221M ASN* 3.1 29.0 + - - -
501M HEM 3.4 68.6 - + + +
505M ANJ 3.3 25.1 - - - -
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Residues in contact with HIS 217 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLY 4.9 6.2 + - - -
31M ASP 4.6 2.0 + - - -
32M THR* 3.2 44.1 + - + +
35M ILE* 3.8 42.4 - - + +
213M ILE* 2.9 46.1 + - + +
214M TRP* 3.5 10.5 - - + +
215M ALA 3.0 0.2 - - - -
216M PHE* 1.3 98.8 - + - +
218M SER* 1.3 61.3 + - - +
219M THR 3.3 1.6 + - - -
220M GLY* 3.8 5.0 + - - -
221M ASN* 5.7 0.2 + - - -
505M ANJ 3.8 10.7 + - - -
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Residues in contact with SER 218 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLY* 4.6 11.6 + - - +
214M TRP* 2.8 33.2 + - - -
215M ALA 3.0 4.8 + - - -
217M HIS* 1.3 78.9 - - - +
219M THR* 1.3 60.1 + - - +
220M GLY 3.7 0.2 - - - -
21P SER 4.5 6.8 - - - +
22P ARG 3.1 26.5 + - - +
23P LEU* 4.3 0.7 - - - +
24P PRO* 3.9 13.9 - - - +
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Residues in contact with THR 219 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLY 5.5 1.8 - - - -
4M ILE* 5.4 0.7 - - - -
124M PRO* 4.3 35.2 - - + +
125M ARG* 4.1 9.6 + - - +
128M THR* 4.8 1.8 + - - +
215M ALA 3.7 10.7 + - - +
216M PHE* 3.9 6.8 + - - -
217M HIS 3.3 0.2 - - - -
218M SER* 1.3 82.6 - - - +
220M GLY* 1.3 73.1 + - - +
228M GLU* 4.2 5.4 - - - +
231M ARG* 3.5 23.4 + - - +
501M HEM 4.0 4.9 + - - -
21P SER 4.5 3.6 - - - +
22P ARG* 3.7 28.3 - - + +
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Residues in contact with GLY 220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLY 5.5 0.6 - - - +
4M ILE* 4.3 21.0 - - - +
35M ILE* 4.8 8.1 - - - -
36M PRO 6.0 0.4 - - - -
125M ARG* 3.6 5.5 + - - -
216M PHE 3.3 12.4 + - - -
217M HIS 3.8 6.1 + - - -
218M SER 3.7 1.2 - - - -
219M THR* 1.3 94.3 + - - +
221M ASN* 1.3 66.8 + - - +
228M GLU* 5.6 0.2 - - - -
231M ARG* 4.9 1.6 - - - -
501M HEM 3.5 6.2 - - - +
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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