Contacts of the helix formed by residues 198 - 227 (chain B) in PDB entry 1S5E
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 THR 198 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PRO 4.5 5.3 + - - -
186B GLY* 5.5 2.6 - - - -
199B CYS* 1.3 66.3 + - - +
200B ASP* 3.5 11.0 - - + +
201B GLU* 3.1 50.5 + - + +
202B LYS* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE 3.9 12.6 - - - -
169B PRO* 3.4 43.5 - - + +
185B PRO 4.0 9.1 + - - -
186B GLY* 3.6 11.1 + - - +
187B CYS* 2.1 49.3 - - - -
198B THR* 1.3 71.9 + - - +
200B ASP* 1.3 60.2 + - - +
202B LYS* 3.1 4.7 + - - +
203B THR* 2.9 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN* 4.8 7.3 + - - +
166B GLY 4.5 5.2 - - - +
167B PHE 4.2 5.9 - - - +
168B PRO* 4.1 10.4 - - - +
169B PRO* 4.1 21.7 - - - +
198B THR* 3.3 9.4 - - + +
199B CYS* 1.3 80.4 - - - +
201B GLU* 1.3 58.8 + - + +
203B THR* 3.6 8.9 + - - +
204B GLN* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B THR* 3.1 40.3 + - + +
200B ASP* 1.3 73.4 - - + +
202B LYS* 1.3 59.1 + - - +
204B GLN* 3.3 7.2 + - + +
205B SER* 3.0 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PRO* 4.0 11.4 - - + -
185B PRO* 4.0 24.2 - - + +
198B THR 3.0 11.7 + - - +
199B CYS 3.7 6.3 - - - +
201B GLU* 1.3 74.4 - - - +
203B THR* 1.3 65.9 + - - +
205B SER* 3.3 8.8 + - - +
206B LEU* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE 4.0 12.8 - - - +
40B ASN* 4.0 14.6 - - - +
163B GLY 4.8 2.7 + - - -
164B LEU* 4.3 11.2 - - + +
166B GLY* 3.9 32.1 + - - +
174B TRP* 4.7 1.2 - - - -
184B PRO* 3.9 15.9 - - - +
187B CYS* 4.5 3.3 - - - -
199B CYS* 2.9 20.6 + - - -
200B ASP* 3.6 10.7 + - - +
202B LYS* 1.3 78.4 - - - +
204B GLN* 1.3 62.5 + - - +
206B LEU* 3.4 8.9 + - - +
207B GLY* 3.1 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY 3.7 2.6 + - - -
35B THR* 4.3 6.9 + - - +
37B MET 2.9 23.3 + - - -
38B ASN* 3.6 13.4 - - - +
39B ILE* 2.9 35.0 + - - +
200B ASP 3.1 14.7 + - - +
201B GLU* 3.6 7.6 - - - +
202B LYS 3.2 0.2 - - - -
203B THR* 1.3 77.9 - - + +
205B SER* 1.3 65.8 + - - +
207B GLY* 3.2 2.9 + - - -
208B VAL* 3.0 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU 3.0 15.5 + - - -
202B LYS* 3.3 13.2 + - - +
204B GLN* 1.3 76.7 - - - +
206B LEU* 1.3 62.1 + - - +
208B VAL* 3.4 8.9 + - - +
209B LYS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLY* 4.1 11.2 - - - +
164B LEU* 3.7 13.7 - - + +
182B HIS 5.8 0.7 - - - +
184B PRO* 3.9 33.4 - - + -
185B PRO* 5.2 3.6 - - + -
202B LYS* 2.9 24.1 + - + +
203B THR* 3.7 4.5 - - - +
205B SER* 1.3 80.0 + - - +
207B GLY* 1.3 56.1 + - - +
209B LYS* 3.4 16.2 + - + +
210B PHE* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.8 24.8 - - - +
116B LEU* 4.0 4.3 - - - +
164B LEU* 3.5 14.7 - - - +
203B THR 3.1 13.6 + - - -
204B GLN 3.2 3.3 + - - -
206B LEU* 1.3 74.7 - - - +
208B VAL* 1.3 59.9 + - - +
210B PHE* 3.3 5.1 + - - +
211B LEU* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 3.9 31.0 - - + +
34B GLY* 3.9 17.0 + - - +
35B THR* 4.0 18.8 - - + +
39B ILE* 3.8 6.2 - - + +
204B GLN* 3.0 41.8 + - + +
205B SER* 3.7 10.1 - - - +
207B GLY* 1.3 75.0 - - - +
209B LYS* 1.3 58.4 + - - +
211B LEU* 3.3 3.5 + - - +
212B ASP* 2.8 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B SER 2.9 18.1 + - - +
206B LEU* 3.6 17.3 - - + +
208B VAL* 1.3 77.8 - - - +
210B PHE* 1.3 63.3 + - - +
212B ASP* 3.3 10.1 + - + +
213B GLU* 3.0 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO 3.4 25.8 - - - -
93B ASN* 4.3 9.2 - - + -
95B PHE* 3.8 22.0 - + - -
116B LEU* 3.7 27.4 - - + -
160B ASP* 4.9 13.9 - - + -
164B LEU* 4.0 16.6 - - + -
206B LEU 3.0 17.4 + - - +
207B GLY* 3.6 7.9 - - - +
208B VAL 3.2 0.2 - - - -
209B LYS* 1.3 78.2 - - - +
211B LEU* 1.3 60.6 + - - +
213B GLU* 3.7 11.6 - - - +
214B TYR* 2.9 41.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN* 4.8 2.5 - - - +
30B TYR* 4.1 11.9 - - + +
34B GLY* 3.9 16.8 - - - +
37B MET* 3.8 29.2 - - + -
39B ILE* 4.5 2.9 - - + -
116B LEU* 3.7 27.1 - - + +
117B GLY* 3.9 12.8 - - - +
207B GLY 3.0 16.5 + - - +
208B VAL* 3.8 4.9 - - - +
210B PHE* 1.3 78.1 - - - +
212B ASP* 1.3 58.6 + - - +
214B TYR* 4.3 5.2 - - + -
215B GLN* 2.8 67.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 2.8 50.9 + - - +
34B GLY 4.9 1.7 + - - -
208B VAL* 2.8 28.2 + - - +
209B LYS* 3.4 12.4 - - + +
211B LEU* 1.3 71.7 - - - +
213B GLU* 1.3 65.0 + - + +
215B GLN* 3.6 12.8 + - - +
216B SER* 3.2 25.0 + - - -
79K GLU* 4.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS* 3.0 49.8 + - + +
210B PHE* 3.7 11.1 - - - +
212B ASP* 1.3 80.5 - - + +
214B TYR* 1.3 62.8 + - - +
216B SER* 3.4 17.8 + - - -
217B LYS* 3.5 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.4 17.5 - - - -
91B ALA* 3.4 24.3 - - - +
92B PRO* 4.1 18.6 - - + +
93B ASN* 3.6 49.2 + - + -
120B PRO* 4.9 1.8 - - + -
123B GLN* 4.1 2.9 + - - -
149B TYR* 5.3 5.1 + - - -
150B TYR* 4.4 7.8 + - - -
153B LEU* 5.1 2.4 - - - +
210B PHE* 2.9 31.7 + + + +
211B LEU* 3.8 8.7 - - + +
213B GLU* 1.3 72.1 - - - +
215B GLN* 1.3 64.8 + - - +
216B SER 3.1 1.8 - - - -
217B LYS* 3.0 33.4 + - + +
218B VAL* 3.1 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 2.7 46.2 + - + -
31B PHE* 3.6 25.2 - - + +
32B ASP 3.3 18.2 + - - +
33B ARG* 4.9 4.9 - - - -
34B GLY 5.1 0.2 + - - -
211B LEU* 2.8 50.2 + - + +
212B ASP* 3.8 14.3 - - - +
214B TYR* 1.3 73.1 - - - +
216B SER* 1.3 56.8 + - - +
218B VAL* 3.3 4.5 + - - -
219B LYS* 2.9 37.8 + - - +
79K GLU* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASP 3.2 13.4 + - - -
213B GLU* 3.4 13.6 - - - -
214B TYR 3.1 0.8 - - - -
215B GLN* 1.3 77.9 - - - +
217B LYS* 1.3 58.0 + - - +
219B LYS* 3.6 0.8 + - - +
220B ARG* 3.1 27.9 + - - +
23K LYS* 4.4 9.0 - - - +
78K THR 3.6 5.5 - - - +
79K GLU* 2.3 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 3.9 17.5 + - - +
213B GLU* 3.7 20.0 - - - +
214B TYR* 3.0 25.6 + - + +
216B SER* 1.3 76.1 - - - +
218B VAL* 1.3 66.0 + - + +
220B ARG* 3.3 7.9 + - - +
221B GLN* 3.1 23.9 + - - +
79L GLU* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 4.1 10.3 - - + +
31B PHE* 3.9 21.3 - - + -
120B PRO* 4.3 15.7 - - + -
122B SER* 4.0 20.4 - - - +
149B TYR* 5.0 4.7 - - + +
150B TYR* 4.5 6.3 - - - +
214B TYR* 3.1 43.5 + - + +
215B GLN 3.7 4.5 - - - +
217B LYS* 1.3 72.9 - - + +
219B LYS* 1.3 65.8 + - - +
220B ARG 3.2 0.2 + - - -
221B GLN* 3.2 4.0 + - - -
222B ILE* 2.9 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.5 44.4 + - + +
215B GLN* 2.9 21.2 + - - +
216B SER* 3.8 5.4 - - - +
218B VAL* 1.3 75.5 - - - +
220B ARG* 1.3 58.8 + - - +
223B PHE* 2.8 67.4 + - + +
103J ASN* 3.8 20.2 + - - +
77K LEU 4.2 6.1 - - - +
78K THR* 4.1 8.4 - - - +
79K GLU* 3.1 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B SER 3.1 15.2 + - - +
217B LYS* 3.7 8.1 - - - +
218B VAL 3.1 0.4 - - - -
219B LYS* 1.3 77.8 - - - +
221B GLN* 1.3 58.8 + - - +
224B SER* 2.6 36.7 + - - +
78K THR* 3.3 25.4 - - - +
79K GLU 5.4 0.4 - - - +
80K ALA* 5.1 11.8 - - - +
81K LYS 5.6 2.6 - - - +
102K ALA 5.4 0.4 + - - -
103K ASN* 2.8 35.4 + - - +
76L TYR* 3.1 42.4 + - - -
77L LEU* 2.9 27.2 + - + +
79L GLU* 3.8 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG* 4.6 13.3 + - + +
149B TYR* 3.5 58.8 - - + +
217B LYS 3.1 16.5 + - - +
218B VAL* 3.9 2.7 - - - +
220B ARG* 1.3 83.0 - - - +
222B ILE* 1.3 76.2 + - + +
224B SER* 4.0 1.8 - - - -
225B GLY* 3.4 14.6 + - - -
77L LEU 4.8 1.1 + - - -
78L THR* 2.8 38.9 + - - +
79L GLU* 4.5 4.9 + - - +
77M LEU 4.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 6.2 0.7 - - + -
122B SER* 3.4 37.0 - - - +
144B GLY 4.6 1.3 - - - +
146B ARG* 3.8 32.1 + - + +
150B TYR* 5.4 1.6 - - + +
218B VAL* 2.9 26.9 + - + +
219B LYS* 5.1 0.2 - - - -
221B GLN* 1.3 88.2 - - + +
223B PHE* 1.3 73.3 + - + +
225B GLY* 3.3 4.9 + - - -
226B TYR* 3.2 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 4.0 24.5 - + - -
219B LYS* 2.8 46.6 + - + +
222B ILE* 1.3 79.6 - - + +
224B SER* 1.3 62.9 + - - +
226B TYR* 3.4 23.7 + + - +
227B GLN* 2.9 36.0 + - - +
77J LEU 5.1 0.4 - - - -
78J THR* 3.4 55.0 - - + -
77K LEU 3.5 20.6 - - - +
78K THR* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 2.6 25.1 + - - -
221B GLN 4.0 0.2 - - - -
222B ILE 3.2 0.8 - - - -
223B PHE* 1.3 74.9 - - - +
225B GLY* 1.3 67.1 + - - +
227B GLN* 2.9 11.5 + - - -
228B SER 3.3 2.4 + - - -
78K THR* 3.1 20.6 - - - +
74L ILE* 3.3 22.3 - - - +
77L LEU* 3.2 27.1 - - - +
78L THR* 3.6 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG* 6.1 1.1 - - - -
221B GLN 3.4 7.8 + - - -
222B ILE 3.3 7.4 + - - -
224B SER* 1.3 77.5 - - - +
226B TYR* 1.3 60.8 + - - +
228B SER* 2.6 26.9 + - - -
78L THR* 3.6 11.4 - - - +
74M ILE* 3.4 9.5 - - - +
77M LEU* 5.0 6.5 - - - -
78M THR* 3.9 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TYR* 6.1 0.7 - - - -
146B ARG* 4.1 19.1 + - - -
222B ILE* 3.2 34.9 + - + +
223B PHE* 3.6 38.6 - + - +
224B SER 3.2 0.8 - - - -
225B GLY* 1.3 76.2 - - - +
227B GLN* 1.3 59.0 + - - +
228B SER 3.5 0.7 - - - -
229B ASP* 3.6 9.2 - - - +
74J ILE* 4.3 15.7 - - + +
77J LEU* 4.5 13.2 - - + -
78J THR* 4.5 8.5 - - + -
74M ILE* 4.3 0.9 - - - -
78M THR* 5.0 3.8 - - + -
74N ILE* 3.4 28.2 - - + +
77N LEU* 4.9 2.5 - - + -
78N THR* 3.7 44.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 2.9 25.3 + - - +
224B SER 2.9 8.4 + - - +
226B TYR* 1.3 81.4 - - - +
228B SER* 1.3 54.4 + - - +
229B ASP* 3.2 13.8 + - - -
230B ILE* 3.5 30.8 + - + +
74J ILE* 3.8 26.5 - - + +
78J THR* 5.4 0.2 - - - +
73K ARG* 4.5 6.5 - - - +
74K ILE* 3.4 41.4 - - + +
77K LEU* 3.7 23.5 - - - +
78K THR* 3.7 15.4 - - - +
74L ILE* 4.1 11.4 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il