Contacts of the helix formed by residues 216 - 252 (chain E) in PDB entry 4KNF
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 TYR 216 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E ALA 3.7 21.5 - - - +
207E GLY* 2.8 13.2 + - - -
210E MET* 4.5 26.1 - - + +
211E GLY* 4.8 20.9 + - - -
212E GLY 5.5 2.9 - - - -
215E VAL* 1.3 77.9 - - - +
217E ALA* 1.3 63.1 + - - +
218E SER 3.3 3.6 + - - -
219E ASN* 3.4 21.9 + - - +
220E LEU* 3.3 20.3 + - - +
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Residues in contact with ALA 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E TRP* 4.4 14.6 - - + -
87E GLY 5.7 0.9 - - - +
89E THR* 3.7 19.5 - - - +
215E VAL* 3.1 20.1 + - + +
216E TYR* 1.3 74.7 - - - +
218E SER* 1.3 62.1 + - - +
220E LEU* 3.6 4.9 - - - +
221E ASN* 3.0 31.9 + - - -
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Residues in contact with SER 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E THR* 6.3 0.4 - - - -
29E VAL* 3.8 24.9 - - - +
83E TRP* 4.5 7.0 - - - -
216E TYR 3.3 1.0 - - - -
217E ALA* 1.3 75.3 - - - +
219E ASN* 1.3 70.7 + - - +
221E ASN* 3.1 4.0 + - - +
222E LEU* 2.9 34.1 + - - +
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Residues in contact with ASN 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E ALA* 4.4 12.6 - - + +
216E TYR* 3.4 28.5 + - + +
218E SER* 1.3 79.8 - - - +
220E LEU* 1.3 62.2 + - - +
222E LEU* 3.9 10.9 - - - +
223E ILE* 2.9 43.0 + - + +
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Residues in contact with LEU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E THR* 4.1 24.5 - - + +
142E GLU* 4.1 3.4 - - - +
203E GLY 3.8 22.7 - - - +
207E GLY* 4.3 6.9 - - - -
208E TYR* 3.6 38.8 - - + +
215E VAL* 4.4 12.8 - - + -
216E TYR 3.3 9.6 + - - +
217E ALA 3.6 7.4 - - - +
218E SER 3.1 0.2 - - - -
219E ASN* 1.3 77.3 - - - +
221E ASN* 1.3 62.8 + - - +
223E ILE* 3.1 4.3 + - - +
224E TYR* 2.9 74.8 + - + +
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Residues in contact with ASN 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 4.2 17.5 - - + -
33E PHE* 4.0 12.1 - - + -
83E TRP* 3.7 15.8 - - - -
89E THR* 3.2 37.6 + - - +
90E PRO* 4.2 2.5 - - - +
94E ARG* 3.1 25.2 + - - +
217E ALA 3.0 21.6 + - - +
218E SER 3.1 4.0 + - - +
220E LEU* 1.3 82.8 - - - +
222E LEU* 1.3 58.3 + - - +
224E TYR* 3.5 3.1 + - - +
225E ASN* 2.9 38.9 + - - +
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Residues in contact with LEU 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E THR* 4.2 17.7 - - + +
29E VAL* 3.8 26.2 - - + +
32E SER* 3.5 32.8 + - - +
218E SER* 2.9 40.9 + - - +
219E ASN* 3.9 12.1 - - - +
221E ASN* 1.3 74.9 - - - +
223E ILE* 1.3 64.8 + - + +
225E ASN* 3.5 2.1 + - - +
226E LEU* 3.1 23.4 + - - +
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Residues in contact with ILE 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ILE* 3.3 34.7 - - + +
202E ALA* 4.3 6.5 - - + +
203E GLY* 3.4 17.5 - - - +
206E ALA* 3.7 28.0 - - + -
219E ASN* 2.9 31.4 + - + +
220E LEU 3.1 2.9 + - - +
222E LEU* 1.3 78.7 - - + +
224E TYR* 1.3 58.9 + - + +
226E LEU* 3.2 10.8 + - + +
227E ALA* 2.8 26.2 + - - +
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Residues in contact with TYR 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ARG* 3.4 36.1 - - + +
98E TRP* 3.4 33.9 - + + -
142E GLU* 2.5 31.8 + - - -
200E TYR* 3.4 32.4 - + - -
203E GLY* 3.9 3.4 - - - -
204E TYR* 3.6 24.4 - - - +
220E LEU* 2.9 42.7 + - + +
221E ASN* 3.9 3.4 - - - +
223E ILE* 1.3 75.7 - - - +
225E ASN* 1.3 59.2 + - - +
227E ALA* 3.1 5.7 + - - +
228E ASP* 2.8 33.8 + - - +
301E RET 3.8 6.0 - - + +
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Residues in contact with ASN 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 4.5 1.4 + - - +
32E SER* 2.8 37.4 + - - +
33E PHE* 3.6 26.1 - - - +
36E VAL* 3.8 19.5 - - + +
76E TYR* 3.4 16.6 + - - -
94E ARG* 2.9 25.5 + - - -
221E ASN* 2.9 29.8 + - - +
222E LEU 3.9 2.5 - - - +
224E TYR* 1.3 73.1 - - - +
226E LEU* 1.3 65.1 + - - +
228E ASP* 3.6 1.9 + - - +
229E PHE* 3.2 23.4 + - - +
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Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ILE* 4.5 18.6 - - + -
222E LEU 3.1 17.6 + - - +
223E ILE* 3.4 10.1 - - + +
225E ASN* 1.3 76.9 - - - +
227E ALA* 1.3 58.8 + - - +
229E PHE* 3.4 11.2 + - + +
230E VAL* 3.0 44.1 + - + +
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Residues in contact with ALA 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ILE* 3.7 24.0 - - + -
200E TYR* 3.4 35.0 - - + +
223E ILE 2.8 17.1 + - - +
224E TYR* 3.1 7.6 + - - +
226E LEU* 1.3 78.0 - - - +
228E ASP* 1.3 56.8 + - - +
230E VAL 3.5 0.3 + - - -
231E ASN* 2.8 38.9 + - - +
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Residues in contact with ASP 228 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E MET* 3.5 16.2 - - + +
76E TYR* 2.5 36.5 + - - +
94E ARG* 3.1 16.3 + - - -
97E ASN* 4.5 2.2 + - - -
98E TRP* 3.2 22.2 + - - -
200E TYR* 2.7 25.5 + - - -
224E TYR 2.8 10.7 + - - +
225E ASN 4.0 0.9 - - - +
226E LEU 3.4 0.2 - - - -
227E ALA* 1.3 75.4 - - - +
229E PHE* 1.3 56.9 + - - +
232E LYS* 2.9 51.0 + - - +
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Residues in contact with PHE 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU 6.1 0.7 - - - -
36E VAL* 4.9 17.9 - - + -
39E GLY* 5.3 5.2 - - - -
40E MET* 4.3 1.8 - - - +
225E ASN 3.2 18.2 + - - +
226E LEU* 3.6 12.3 - - + +
227E ALA 3.3 0.2 - - - -
228E ASP* 1.3 74.3 - - - +
230E VAL* 1.3 67.1 + - + +
233E ILE* 3.1 46.5 + - + +
234E LEU* 3.0 56.0 + - + -
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Residues in contact with VAL 230 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ILE* 4.5 10.8 - - + +
196E GLY* 4.7 4.0 - - - -
199E ILE* 4.2 25.4 - - + -
226E LEU* 3.0 37.0 + - + +
227E ALA 4.0 2.5 - - - +
229E PHE* 1.3 77.5 - - + +
231E ASN* 1.3 67.4 + - - +
234E LEU* 3.1 43.7 - - + +
235E PHE* 3.1 10.7 + - - +
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Residues in contact with ASN 231 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E LEU* 4.5 11.5 - - - +
192E ILE* 3.4 8.7 - - - +
196E GLY* 3.0 46.1 + - - -
197E TRP* 3.2 23.4 - - + +
200E TYR* 3.5 22.6 - - + +
227E ALA* 2.8 32.3 + - - +
230E VAL* 1.3 84.0 - - - +
232E LYS* 1.3 60.6 + - - +
235E PHE* 3.3 25.3 - - - +
301E RET 4.7 4.7 - - + -
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Residues in contact with LYS 232 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E MET* 4.0 9.0 - - + -
47E PHE* 4.3 2.1 - - - -
65E SER* 5.3 1.6 - - - +
68E ILE* 3.5 25.9 - - + +
69E THR* 4.1 12.8 - - + +
72E ALA* 3.9 19.5 - - + -
97E ASN* 4.3 14.1 - - - +
101E THR* 3.0 19.7 + - - -
105E LEU* 5.9 2.0 - - + -
228E ASP* 2.9 42.9 + - - +
231E ASN* 1.3 78.8 - - - +
233E ILE* 1.3 63.6 + - - +
236E GLY* 3.3 18.7 + - - -
301E RET 1.3 72.4 - - + +
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Residues in contact with ILE 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 4.5 1.8 - - - +
39E GLY* 3.5 29.6 - - - +
40E MET* 3.8 30.7 - - + +
43E ALA* 3.9 22.9 - - + -
47E PHE* 3.8 4.1 - - - -
69E THR* 4.2 4.7 - - + -
229E PHE* 3.1 47.9 + - + +
232E LYS* 1.3 74.8 - - - +
234E LEU* 1.3 63.1 + - + +
236E GLY 3.6 0.3 + - - -
237E LEU* 3.0 39.7 + - + +
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Residues in contact with LEU 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E PHE* 3.0 41.3 + - + +
230E VAL* 3.1 38.1 - - + +
233E ILE* 1.3 74.9 - - + +
235E PHE* 1.3 65.2 + - - +
237E LEU* 3.0 31.5 + - + +
238E ILE* 3.0 20.5 + - + +
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Residues in contact with PHE 235 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E SER* 6.0 0.7 - - - -
105E LEU* 3.6 34.3 - - + -
108E GLU* 4.4 9.9 - - + -
109E PHE* 4.0 22.7 - + - -
112E ILE* 4.5 5.8 - - + -
188E ALA* 3.8 27.8 - - + -
189E MET* 4.3 4.7 - - - -
192E ILE* 3.6 37.7 - - + +
230E VAL 3.1 10.0 + - - +
231E ASN 3.3 19.1 - - - +
232E LYS 4.3 0.6 + - - -
234E LEU* 1.3 73.3 - - - +
236E GLY* 1.3 64.4 + - - +
238E ILE* 3.0 25.4 + - + +
239E ILE* 3.2 35.4 + - + +
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Residues in contact with GLY 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E PHE* 3.3 24.4 - - - -
62E LEU* 5.1 0.5 - - - +
65E SER* 4.0 16.4 + - - -
232E LYS 3.3 14.6 + - - -
234E LEU 3.2 0.6 - - - -
235E PHE* 1.3 80.3 - - - +
237E LEU* 1.3 56.1 - - - +
238E ILE 3.2 0.3 + - - -
239E ILE* 3.2 6.8 + - - +
240E TRP* 2.9 27.9 + - - +
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Residues in contact with LEU 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ALA* 6.4 0.9 - - + -
46E PHE* 4.0 33.2 - - + -
47E PHE* 3.5 11.4 - - + -
233E ILE* 3.0 26.4 + - + +
234E LEU* 3.0 28.1 + - + +
236E GLY* 1.3 75.8 - - - +
238E ILE* 1.3 57.1 + - + +
240E TRP* 3.3 17.5 + - + -
241E ASN* 2.9 26.0 + - - +
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Residues in contact with ILE 238 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E ALA* 3.9 23.8 - - + -
191E MET* 4.1 25.6 - - + -
192E ILE* 5.6 1.3 - - + -
234E LEU* 3.0 16.9 + - + +
235E PHE* 3.0 20.4 + - + +
237E LEU* 1.3 76.3 - - + +
239E ILE* 1.3 64.2 + - - +
241E ASN* 3.1 7.9 + - - +
242E VAL* 3.0 31.7 + - + +
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Residues in contact with ILE 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E TRP* 4.7 12.2 - - + -
61E SER* 4.2 26.2 - - - +
62E LEU* 4.4 10.3 - - + -
65E SER* 5.1 2.5 - - - +
108E GLU* 4.7 11.9 - - - +
112E ILE* 4.3 8.3 - - + -
185E ALA* 4.0 32.5 - - + +
188E ALA* 4.7 4.3 - - + -
235E PHE* 3.2 41.5 + - + +
236E GLY* 3.7 8.5 - - - +
238E ILE* 1.3 75.4 - - + +
240E TRP* 1.3 66.9 + - - +
241E ASN 3.1 0.3 + - - -
242E VAL* 3.2 7.7 + - + +
243E ALA* 2.9 21.7 + - - +
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Residues in contact with TRP 240 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 4.1 16.4 - - + -
111A LEU* 6.0 5.6 - - + -
46E PHE* 3.3 38.0 - + - -
47E PHE* 4.2 9.0 - + + -
50E GLU* 3.2 37.3 + - + +
62E LEU* 3.8 28.7 - - + +
236E GLY 2.9 16.5 + - - +
237E LEU* 3.3 18.6 - - + +
239E ILE* 1.3 78.3 - - - +
241E ASN* 1.3 97.0 + - + +
243E ALA* 3.3 3.1 + - - +
244E VAL* 3.0 59.9 + - + +
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Residues in contact with ASN 241 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E LEU 2.9 14.1 + - - +
238E ILE* 3.3 11.9 - - + +
239E ILE 3.1 0.2 - - - -
240E TRP* 1.3 98.0 - - + +
242E VAL* 1.3 67.8 + - + +
243E ALA 3.1 1.1 - - - -
244E VAL* 3.3 7.3 + - - +
245E LYS* 3.1 56.7 + - - +
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Residues in contact with VAL 242 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E TRP* 4.0 12.3 - - + -
181E ALA* 3.4 39.4 - - + +
184E SER* 4.0 20.0 - - - -
185E ALA* 4.3 10.3 - - + +
238E ILE* 3.0 27.2 + - + +
239E ILE* 3.6 8.7 - - - +
241E ASN* 1.3 75.8 - - + +
243E ALA* 1.3 56.9 + - - +
245E LYS* 3.8 10.9 - - - +
246E GLU* 3.1 28.5 + - - +
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Residues in contact with ALA 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E VAL* 3.4 21.5 - - + -
58E TRP* 3.5 37.7 - - + -
62E LEU* 5.2 3.6 - - + -
239E ILE 2.9 16.0 + - - +
240E TRP* 3.6 5.2 - - - +
242E VAL* 1.3 78.5 - - - +
244E VAL* 1.3 57.2 + - - +
246E GLU* 4.0 0.5 - - - +
247E SER* 2.8 35.3 + - - -
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Residues in contact with VAL 244 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 5.8 0.2 - - - +
50E GLU* 5.0 0.2 - - - +
53E GLN* 4.1 24.2 - - + +
54E VAL* 3.8 14.1 - - + -
240E TRP* 3.0 55.7 + - + +
241E ASN* 3.3 15.8 + - - +
243E ALA* 1.3 73.1 - - - +
245E LYS* 1.3 70.6 + - + +
247E SER* 4.1 0.7 - - - -
248E SER* 3.0 27.0 + - - -
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Residues in contact with LYS 245 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E ASN* 3.1 51.2 + - - +
242E VAL* 3.8 10.0 - - - +
244E VAL* 1.3 77.5 - - + +
246E GLU* 1.3 58.9 + - - +
248E SER* 3.2 4.5 + - - -
249E ASN* 2.9 41.3 + - - +
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Residues in contact with GLU 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E SER* 4.7 0.5 + - - -
57E LYS* 2.7 33.7 + - - -
58E TRP* 3.0 20.4 + - - +
179E SER* 4.2 10.8 + - - +
180E PRO* 6.2 1.6 - - + -
181E ALA* 3.1 31.0 - - + -
242E VAL 3.1 16.6 + - - +
243E ALA 4.0 2.0 - - - +
245E LYS* 1.3 79.4 - - - +
247E SER* 1.3 60.6 + - - +
249E ASN* 3.5 6.4 + - - +
250E ALA* 3.0 30.6 + - - +
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Residues in contact with SER 247 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E GLN 3.9 8.1 - - - -
54E VAL* 3.3 12.1 - - - +
55E SER* 3.0 36.1 + - - -
58E TRP* 3.7 9.2 - - - -
243E ALA 2.8 24.3 + - - -
244E VAL 4.1 0.4 - - - -
246E GLU* 1.3 79.7 - - - +
248E SER* 1.3 61.2 + - - +
250E ALA* 3.6 6.9 + - - +
251E LYS* 3.4 35.0 + - - +
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Residues in contact with SER 248 (chain E).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E VAL 3.0 20.8 + - - -
245E LYS* 3.6 5.6 - - - -
247E SER* 1.3 75.3 - - - +
249E ASN* 1.3 66.3 + - - +
251E LYS* 3.9 7.6 + - - +
252E LEU* 3.4 27.3 + - - +
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Residues in contact with ASN 249 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E LYS* 2.9 25.8 + - - +
246E GLU* 3.9 6.3 - - - +
248E SER* 1.3 78.8 - - - +
250E ALA* 1.3 64.2 + - - +
251E LYS 3.2 0.2 - - - -
252E LEU* 3.0 34.3 + - - +
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Residues in contact with ALA 250 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E SER* 6.1 3.1 - - - +
57E LYS* 5.3 4.3 - - - +
246E GLU* 3.0 28.4 + - - +
247E SER* 3.7 9.2 - - - +
248E SER 3.4 0.2 - - - -
249E ASN* 1.3 77.4 - - - +
251E LYS* 1.3 62.6 + - + +
252E LEU 3.5 5.4 + - - +
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Residues in contact with LYS 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E ASP 5.6 2.6 + - - -
53E GLN 5.3 4.9 + - - -
54E VAL 5.1 3.2 + - - -
55E SER* 5.0 15.7 - - - +
247E SER* 3.4 29.8 + - - +
248E SER* 4.2 7.4 - - - +
249E ASN 3.2 0.8 - - - -
250E ALA* 1.3 79.5 - - + +
252E LEU* 1.3 66.3 + - + +
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Residues in contact with LEU 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E SER* 3.4 19.0 + - - +
249E ASN* 3.0 28.3 + - - +
250E ALA 3.9 4.5 - - - +
251E LYS* 1.3 84.0 - - + +
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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