Contacts of the helix formed by residues 191 - 217 (chain U) in PDB entry 5LN3
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 ILE 191 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364O GLU* 5.9 0.2 - - + -
367O VAL* 3.8 44.6 - - + +
368O GLU* 5.1 11.7 - - + +
370O GLN 4.6 2.0 - - - +
371O ALA 4.1 4.5 - - - +
372O HIS* 4.1 11.9 - - - +
373O ASP* 3.6 34.3 - - + +
190U ARG* 1.4 75.9 - - + +
192U THR* 1.4 61.6 + - - +
194U GLN* 3.2 22.9 + - + +
195U VAL* 3.3 18.0 + - + +
223V LYS* 4.1 1.1 - - - +
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Residues in contact with THR 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190U ARG 3.4 0.4 - - - -
191U ILE* 1.4 75.3 - - - +
193U ASN* 1.4 67.1 + - - +
195U VAL* 3.5 11.5 - - + +
196U HIS* 3.5 30.7 + - + +
222V LYS* 4.5 15.0 - - - +
223V LYS* 4.0 37.5 + - - +
240V HIS* 4.1 17.3 - - - +
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Residues in contact with ASN 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190U ARG* 2.8 31.4 + - - +
192U THR* 1.4 78.2 - - - +
194U GLN* 1.4 63.4 + - - +
196U HIS* 3.1 7.6 + - - +
197U GLY* 3.0 24.6 + - - -
223V LYS* 4.8 5.7 + - - +
240V HIS* 3.6 43.0 + - + +
241V ASN* 5.0 13.7 + - - +
244V VAL* 3.5 29.9 - - - +
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Residues in contact with GLN 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360O VAL* 4.2 17.3 - - - +
363O MET* 3.4 43.6 - - - +
364O GLU* 3.1 25.8 + - + +
367O VAL* 4.4 6.5 - - + -
190U ARG* 3.6 34.7 + - + +
191U ILE* 3.3 13.5 - - - +
193U ASN* 1.4 78.5 - - - +
195U VAL* 1.4 62.9 + - - +
197U GLY* 3.1 12.0 + - - +
198U LEU* 3.2 8.1 + - - +
240U VAL* 6.3 0.6 - - - +
241V ASN* 6.1 1.0 - - - +
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Residues in contact with VAL 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364O GLU* 3.4 28.3 - - + +
368O GLU* 5.7 4.9 - - + -
131U LEU* 5.9 6.1 - - + -
191U ILE* 3.3 19.9 + - + +
192U THR* 3.5 17.0 - - + +
194U GLN* 1.4 75.4 - - - +
196U HIS* 1.3 78.7 + - + +
198U LEU* 3.5 5.5 + - - +
199U LYS* 3.2 20.0 + - - +
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Residues in contact with HIS 196 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130U ASP* 5.8 1.3 - - - -
131U LEU* 3.4 28.5 + - + +
132U GLY* 3.8 23.8 - - - -
192U THR* 3.6 11.3 + - + +
193U ASN 3.1 9.5 + - - +
195U VAL* 1.3 91.5 - - + +
197U GLY* 1.3 59.4 - - - +
199U LYS* 3.0 34.1 + - + +
200U GLY 3.2 5.5 + - - -
222V LYS* 4.3 11.3 + - - -
236V GLU* 4.8 1.1 - - + -
237V HIS* 3.3 33.0 + - + +
240V HIS* 3.4 31.4 + - + -
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Residues in contact with GLY 197 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360O VAL* 4.9 3.8 - - - -
193U ASN 3.0 12.8 + - - -
194U GLN* 3.1 5.7 + - - -
196U HIS* 1.3 76.0 - - - +
198U LEU* 1.4 64.0 + - - +
199U LYS 3.4 0.2 + - - -
200U GLY* 3.5 2.3 + - - -
201U LEU* 3.4 26.3 + - - +
237V HIS* 3.9 13.4 - - - -
241V ASN* 5.1 11.0 - - - -
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Residues in contact with LEU 198 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357O CYS 3.2 29.2 - - - +
360O VAL* 4.3 5.2 - - + +
361O LYS* 4.0 40.4 - - + +
364O GLU* 3.6 33.2 - - - +
365O MET* 6.1 0.9 - - + -
194U GLN 3.2 4.6 + - - +
195U VAL 3.6 6.1 - - - +
197U GLY* 1.4 73.1 - - - +
199U LYS* 1.3 62.4 + - - +
201U LEU* 3.2 16.8 + - + +
202U ASN* 3.0 41.6 + - - +
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Residues in contact with LYS 199 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129U LYS 3.6 19.6 + - - -
130U ASP* 3.4 28.2 + - - +
131U LEU* 4.0 26.0 - - + +
195U VAL 3.2 10.8 + - - +
196U HIS* 3.0 26.4 + - + +
198U LEU* 1.3 80.0 - - - +
200U GLY* 1.3 56.1 + - - +
202U ASN* 3.2 13.7 + - - +
203U SER* 3.1 33.9 + - - +
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Residues in contact with GLY 200 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439P VAL* 5.5 7.5 - - - +
196U HIS 3.2 7.8 + - - -
197U GLY 3.5 4.2 + - - -
198U LEU 3.2 0.4 - - - -
199U LYS* 1.3 76.6 - - - +
201U LEU* 1.4 62.6 + - - +
203U SER* 3.0 19.5 + - - -
204U LYS* 3.2 20.8 + - - +
237V HIS* 4.1 16.6 - - - -
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Residues in contact with LEU 201 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353O LEU* 4.6 6.0 - - + +
356O TRP* 4.0 40.4 - - + +
357O CYS* 3.7 41.1 - - + +
360O VAL* 4.0 25.1 - - + -
435P LEU* 5.8 5.4 - - + -
197U GLY 3.4 13.9 + - - +
198U LEU* 3.2 14.5 + - - +
200U GLY* 1.4 74.4 - - - +
202U ASN* 1.4 57.7 + - - +
204U LYS* 3.5 17.5 + - + +
205U LEU* 3.2 25.8 + - - +
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Residues in contact with ASN 202 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357O CYS* 3.9 22.8 - - - +
361O LYS* 5.1 5.9 - - - +
198U LEU* 3.0 37.1 + - - +
199U LYS* 3.2 10.1 + - - +
201U LEU* 1.4 73.7 - - - +
203U SER* 1.4 65.0 + - - +
205U LEU* 3.2 13.5 + - + +
206U LEU* 3.0 35.3 + - + +
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Residues in contact with SER 203 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442P THR* 5.9 0.2 - - - -
446P ILE* 5.7 6.5 - - - -
199U LYS* 3.1 22.9 + - - +
200U GLY* 3.0 11.9 + - - -
202U ASN* 1.4 76.0 - - - +
204U LYS* 1.3 57.3 + - - +
206U LEU* 3.4 15.3 + - - +
207U ASP* 2.7 31.3 + - - +
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Residues in contact with LYS 204 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349O MET* 6.5 0.2 - - - -
353O LEU* 4.0 28.5 - - + -
356O TRP* 5.6 5.2 - - - -
435P LEU* 5.5 8.4 - - + +
438P LEU* 3.9 27.1 - - - +
439P VAL* 5.4 17.4 - - + +
442P THR* 4.1 25.9 + - + +
200U GLY 3.2 15.6 + - - +
201U LEU* 3.6 18.8 - - + +
203U SER* 1.3 76.4 - - - +
205U LEU* 1.3 57.4 + - - +
207U ASP* 3.0 26.5 + - - +
208U ILE* 3.1 19.4 + - + +
230U LEU* 4.4 15.7 - - - +
233U VAL* 5.1 4.8 - - - +
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Residues in contact with LEU 205 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350O LYS* 4.0 4.9 - - - +
353O LEU* 3.7 20.2 - - + -
354O GLU* 3.3 50.0 - - - +
357O CYS* 4.1 11.7 - - + -
201U LEU 3.2 12.0 + - - +
202U ASN* 3.2 17.9 + - + +
204U LYS* 1.3 74.7 - - - +
206U LEU* 1.4 68.7 + - + +
208U ILE* 3.4 5.9 + - + +
209U ARG* 3.3 51.3 + - + +
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Residues in contact with LEU 206 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202U ASN* 3.0 21.4 + - + +
203U SER* 3.4 16.2 - - - +
205U LEU* 1.4 79.7 - - + +
207U ASP* 1.4 58.1 - - - +
209U ARG* 3.3 14.4 + - - +
210U SER* 3.0 33.0 + - - +
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Residues in contact with ASP 207 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442P THR* 4.0 9.2 - - + +
446P ILE* 3.6 36.2 - - - +
449P GLU* 4.2 17.1 - - - +
203U SER 2.7 21.2 - - - +
204U LYS* 3.0 18.9 + - - +
206U LEU* 1.4 77.3 - - - +
208U ILE* 1.4 51.8 + - + +
210U SER* 3.2 9.1 + - - -
211U TYR* 2.6 34.9 + - - +
214U LYS* 5.1 1.6 + - - -
226U ILE* 5.6 6.3 - - + -
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Residues in contact with ILE 208 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346O ILE* 4.4 19.0 - - + +
349O MET* 4.9 5.6 - - + -
350O LYS* 3.9 36.1 - - + +
353O LEU* 3.8 20.4 - - + -
204U LYS* 3.1 16.3 + - + +
205U LEU* 3.4 6.2 + - + +
207U ASP* 1.4 73.7 - - + +
209U ARG* 1.3 58.3 + - - +
211U TYR* 2.9 11.0 + - + +
212U LEU* 2.9 29.7 + - + +
226U ILE* 5.2 9.9 - - + -
230U LEU* 4.2 31.9 - - + -
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Residues in contact with ARG 209 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350O LYS* 3.6 50.5 + - + +
351O ASP* 5.0 0.8 - - - +
354O GLU* 3.1 33.8 + - - +
205U LEU* 3.3 34.7 + - - +
206U LEU* 3.3 13.9 + - - +
208U ILE* 1.3 73.5 - - - +
210U SER* 1.3 61.8 - - - +
212U LEU* 3.3 4.5 + - - +
213U GLU* 3.2 37.3 + - - +
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Residues in contact with SER 210 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449P GLU* 5.5 0.9 - - - -
206U LEU* 3.0 17.5 + - - +
207U ASP* 3.3 13.0 - - - -
209U ARG* 1.3 74.9 - - - +
211U TYR* 1.4 65.1 + - - +
213U GLU* 3.4 17.2 + - - +
214U LYS* 3.1 43.2 + - - +
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Residues in contact with TYR 211 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341O LEU* 6.0 2.1 - - - +
343O LEU* 5.5 4.1 - - + +
346O ILE* 3.7 36.8 - - + -
207U ASP 2.6 17.3 + - - +
208U ILE* 2.9 16.5 + - + +
210U SER* 1.4 73.4 - - - +
212U LEU* 1.4 55.9 + - - +
214U LYS* 3.1 14.6 + - + +
215U VAL* 3.0 51.3 + - + +
221U PRO* 3.7 41.0 + - + -
222U ILE* 4.7 10.4 - - - +
223U ASN 5.0 2.3 + - - -
226U ILE* 4.7 28.7 - - + -
227U ILE* 4.6 15.8 - - + +
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Residues in contact with LEU 212 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346O ILE* 5.9 5.8 - - + -
347O LYS* 4.2 31.9 - - + -
350O LYS* 3.9 34.1 - - + +
208U ILE* 2.9 11.4 + - + +
209U ARG 3.4 11.0 - - - +
211U TYR* 1.4 73.5 - - - +
213U GLU* 1.3 66.5 + - + +
215U VAL* 3.4 15.6 - - + +
216U ALA* 3.1 35.5 + - + +
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Residues in contact with GLU 213 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209U ARG* 3.2 31.3 + - - +
210U SER* 3.5 16.7 + - - +
212U LEU* 1.3 82.2 - - + +
214U LYS* 1.3 62.6 - - + +
216U ALA* 3.3 8.6 - - - +
217U THR* 2.8 34.2 + - + +
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Residues in contact with LYS 214 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449P GLU* 3.0 30.1 + - - -
453P HIS* 3.4 36.0 + - + +
207U ASP 5.1 0.8 + - - -
210U SER* 3.1 36.2 + - - +
211U TYR* 3.1 16.8 + - - +
213U GLU* 1.3 83.2 - - + +
215U VAL* 1.4 55.0 + - - +
217U THR* 3.2 8.2 + - - -
218U GLY 3.0 23.9 + - - -
219U LYS* 3.1 39.0 + - + +
221U PRO* 3.7 23.2 - - + +
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Residues in contact with VAL 215 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341O LEU* 6.4 0.7 - - + -
343O LEU* 3.9 33.4 - - + -
346O ILE* 6.3 0.9 - - + -
211U TYR* 3.0 39.1 + - + +
212U LEU* 3.4 26.9 - - + +
214U LYS* 1.4 71.9 - - - +
216U ALA* 1.4 62.2 + - - +
217U THR 3.5 0.3 + - - -
218U GLY* 3.5 11.4 + - - +
219U LYS 5.2 2.5 - - - +
221U PRO 4.9 9.0 - - - +
222U ILE* 5.8 6.3 - - + -
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Residues in contact with ALA 216 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212U LEU* 3.1 21.4 + - + +
213U GLU* 3.3 13.7 - - - +
215U VAL* 1.4 78.4 - - - +
217U THR* 1.4 63.2 + - + +
218U GLY 3.9 0.7 + - - -
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Residues in contact with THR 217 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213U GLU* 2.8 22.9 + - + +
214U LYS* 3.2 8.2 + - - -
216U ALA* 1.4 78.3 - - + +
218U GLY* 1.4 62.3 + - - +
219U LYS* 3.5 18.9 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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