Contacts of the helix formed by residues 188 - 213 (chain A) in PDB entry 5M4G
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 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.8 2.1 + - - +
25A LEU* 3.7 30.4 - - + +
26A ASN* 3.8 6.1 + - - +
29A ARG* 3.5 36.3 - - - +
187A LYS* 1.3 76.7 - - - +
189A ASP* 1.3 65.4 + - - +
190A MET* 3.4 8.6 + - - +
191A GLU* 2.9 35.4 + - - +
192A LEU* 2.9 22.3 + - - +
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Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS 5.2 0.5 - - - +
188A THR* 1.3 75.6 - - - +
190A MET* 1.3 63.2 + - + +
192A LEU* 3.3 19.0 + - - +
193A GLU* 3.1 27.3 + - + +
196A ARG* 4.4 3.0 + - - +
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Residues in contact with MET 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 3.9 24.2 - - + +
21A ALA* 3.6 28.0 - - + +
22A LEU* 3.6 33.0 - - + +
25A LEU* 3.6 28.7 - - + -
188A THR* 3.1 5.8 + - - +
189A ASP* 1.3 78.5 - - + +
191A GLU* 1.3 62.0 + - - +
193A GLU* 3.3 17.9 + - - +
194A VAL* 3.4 15.8 + - - +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.9 24.0 - - + +
26A ASN* 3.5 11.3 + - - +
29A ARG* 4.3 1.2 + - - -
73A TRP* 3.2 30.3 + - - -
183A CYS 5.4 0.2 - - - +
184A ARG 5.5 1.8 - - - +
186A PHE 3.9 3.5 - - - +
187A LYS* 3.2 23.8 - - + +
188A THR* 2.9 46.1 + - - +
190A MET* 1.3 77.4 - - - +
192A LEU* 1.3 61.4 + - - +
194A VAL* 3.0 16.3 + - - +
195A LEU* 3.1 17.9 + - + +
284A PHE* 4.0 19.7 - - + -
374A ILE* 4.8 0.7 - - - +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS* 3.7 29.4 - - + +
188A THR 2.9 17.4 + - - +
189A ASP* 3.6 21.5 - - - +
191A GLU* 1.3 71.8 - - - +
193A GLU* 1.3 66.3 + - - +
195A LEU* 3.2 7.0 + - + +
196A ARG* 2.9 55.0 + - + +
406A GLY* 5.6 2.7 - - - -
408A VAL* 3.8 7.9 - - + -
456A VAL* 3.7 43.7 - - + -
463A GLU* 5.2 0.4 - - - +
465A LEU* 5.2 1.0 - - + +
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Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.9 13.0 - - + +
189A ASP* 3.1 18.9 + - + +
190A MET* 3.6 11.0 - - - +
191A GLU 3.2 0.6 - - - -
192A LEU* 1.3 76.9 - - - +
194A VAL* 1.3 63.5 + - + +
196A ARG* 3.0 34.7 + - - +
197A TYR* 3.2 20.3 + - - +
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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
----------------------------------------------------------
16A LEU* 3.7 15.7 - - + -
18A VAL* 4.0 31.9 - - + -
19A PRO* 6.2 0.4 - - + -
22A LEU* 4.0 7.9 - - + -
190A MET 3.5 14.8 - - - +
191A GLU* 3.0 7.4 + - - +
193A GLU* 1.3 77.5 - - + +
195A LEU* 1.3 57.7 + - - +
197A TYR* 3.1 4.5 + - - +
198A THR* 2.9 27.9 + - + +
281A TYR* 4.2 17.3 - - + +
284A PHE* 3.6 37.5 - - + -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS* 4.0 31.0 - - + -
191A GLU* 3.1 14.4 + - + +
192A LEU* 3.2 8.9 + - + +
194A VAL* 1.3 74.0 - - - +
196A ARG* 1.3 64.5 + - - +
198A THR* 3.1 5.6 + - - +
199A ASN* 3.1 29.9 + - - +
284A PHE* 4.1 22.7 - - + -
285A ALA 3.3 25.6 - - - +
372A LEU* 4.0 15.3 - - + +
373A GLY* 4.3 6.1 - - - +
408A VAL* 4.0 23.1 - - + -
465A LEU* 4.1 15.2 - - + +
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Residues in contact with ARG 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP* 4.4 2.8 + - - +
192A LEU* 2.9 48.0 + - - +
193A GLU* 3.0 40.8 + - - +
195A LEU* 1.3 75.7 - - - +
197A TYR* 1.3 58.0 + - - +
199A ASN* 3.5 3.6 + - - +
200A LYS* 2.9 28.5 + - - +
463A GLU* 2.8 39.6 + - - +
465A LEU* 3.6 24.7 - - + +
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Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU 4.2 10.0 + - - -
15A THR* 3.3 14.7 - - - -
16A LEU* 3.6 44.6 - - + -
193A GLU 3.2 9.9 + - - +
194A VAL 3.1 9.0 + - - +
196A ARG* 1.3 76.7 - - - +
198A THR* 1.3 66.7 + - - +
200A LYS* 3.1 19.5 + - + +
201A ILE* 2.9 51.0 + - + +
233A ARG 4.3 0.3 + - - -
234A GLY* 2.7 30.0 + - - -
236A MET* 4.8 1.6 - - + -
281A TYR* 3.6 40.2 - + + -
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 2.9 21.3 + - + +
195A LEU* 3.1 12.8 + - - -
197A TYR* 1.3 71.9 - - + +
199A ASN* 1.3 60.8 + - - +
202A SER* 3.0 34.5 + - - -
236A MET* 3.5 14.0 - - + +
279A GLY 4.3 0.2 - - - -
281A TYR* 3.7 25.8 - - + +
284A PHE* 3.5 29.6 - - + +
285A ALA 2.8 22.9 + - - +
286A SER* 3.6 10.4 - - - -
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Residues in contact with ASN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.1 23.5 + - - +
196A ARG 3.7 2.2 - - - +
198A THR* 1.3 85.0 + - - +
200A LYS* 1.3 56.6 + - - +
203A SER* 2.7 37.9 + - - -
285A ALA 4.8 1.0 + - - -
286A SER* 4.0 6.0 - - - +
288A ILE* 3.6 9.1 - - - +
372A LEU* 5.6 1.6 - - - +
454A ASP* 3.1 31.3 + - - +
465A LEU* 3.5 33.1 - - + +
466A THR* 2.7 29.7 + - - +
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 5.2 6.9 + - - +
196A ARG 2.9 18.8 + - - +
197A TYR* 3.1 21.6 + - + +
199A ASN* 1.3 77.0 - - - +
201A ILE* 1.3 77.2 + - + +
203A SER* 3.6 4.7 - - - -
204A GLU* 3.0 50.1 + - + +
465A LEU 4.8 0.6 + - - -
467A CYS* 4.5 12.7 - - - -
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Residues in contact with ILE 201 (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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14A GLU 5.9 0.9 - - - +
197A TYR* 2.9 56.2 + - + +
200A LYS* 1.3 88.0 - - - +
202A SER* 1.3 57.4 + - - +
204A GLU* 3.2 20.5 + - - +
205A ALA* 2.9 26.9 + - - +
229A TYR* 3.9 9.5 - - + -
230A CYS* 3.9 14.8 - - - -
233A ARG* 4.3 7.0 - - + +
234A GLY* 3.9 19.1 - - - -
236A MET* 3.7 25.8 - - + -
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A THR 3.0 15.7 + - - -
201A ILE* 1.3 76.6 - - - +
203A SER* 1.3 57.5 + - - +
205A ALA* 3.3 2.7 + - - +
206A HIS* 2.9 37.2 + - - -
226A PHE* 3.9 14.2 - - - -
230A CYS* 4.2 2.3 - - - -
236A MET* 4.2 0.7 - - - +
277A MET 4.7 0.4 - - - -
278A GLY* 4.3 2.0 - - - -
279A GLY* 2.8 21.5 + - - -
286A SER* 2.7 24.8 + - - -
288A ILE* 3.7 15.0 - - - -
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN 2.7 24.9 + - - -
200A LYS 3.6 1.3 - - - -
202A SER* 1.3 74.9 - - - +
204A GLU* 1.3 65.3 + - - +
206A HIS* 3.3 3.3 + - - +
207A ARG* 3.0 29.8 + - - +
288A ILE* 3.6 11.5 - - - +
466A THR* 3.7 2.6 - - - +
467A CYS* 3.0 51.2 + - - -
468A VAL* 3.7 11.0 - - - +
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS* 3.0 47.5 + - + +
201A ILE* 3.5 17.4 - - - +
203A SER* 1.3 76.3 - - - +
205A ALA* 1.3 58.3 + - - +
207A ARG* 3.2 34.7 + - - +
208A GLU* 3.0 30.8 + - - +
229A TYR* 2.6 39.2 + - + +
233A ARG* 5.0 1.0 + - - +
467A CYS* 6.1 0.2 - - - -
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE 2.9 15.7 + - - +
202A SER 3.6 0.2 - - - +
204A GLU* 1.3 73.6 - - - +
206A HIS* 1.3 65.8 + - - +
208A GLU* 3.3 4.2 + - - +
209A VAL* 2.9 27.4 + - - +
226A PHE* 3.5 30.5 - - + +
229A TYR* 3.7 30.2 - - + -
230A CYS* 3.9 10.5 - - - -
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Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER 2.9 27.1 + - - +
203A SER* 3.3 5.8 + - - +
205A ALA* 1.3 76.8 - - - +
207A ARG* 1.3 56.7 + - - +
209A VAL* 3.3 8.2 + - - +
210A MET* 2.9 33.4 + - - +
226A PHE* 3.6 8.5 - + - -
275A PHE* 3.3 27.5 + - - +
277A MET* 2.9 48.2 + - + +
288A ILE* 3.3 29.1 + - + +
290A CYS* 3.6 29.8 - - - +
292A PHE* 6.2 0.4 - - - -
468A VAL* 4.0 5.6 - - + -
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Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER 3.0 14.3 + - - +
204A GLU* 3.5 42.6 + - - +
205A ALA 3.2 0.2 - - - -
206A HIS* 1.3 73.1 - - - +
208A GLU* 1.3 65.4 + - + +
210A MET* 3.2 9.1 + - + +
211A LYS* 3.0 34.1 + - - +
467A CYS* 3.3 28.9 + - - -
468A VAL* 4.3 0.9 - - + +
469A PRO* 3.5 23.3 - - + -
478A CYS* 4.1 6.5 - - - -
485A ALA* 5.8 4.5 - - - +
486A PHE* 3.4 33.8 - - + -
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLU 3.0 18.2 + - - +
205A ALA* 3.3 8.9 + - - +
207A ARG* 1.3 76.3 - - - +
209A VAL* 1.3 62.1 + - - +
211A LYS* 2.9 35.3 + - - +
212A ALA* 3.0 24.6 + - - +
225A LEU* 4.0 13.8 - - + +
229A TYR* 3.8 31.2 - - + -
233A ARG* 5.4 3.6 + - - -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ALA 2.9 17.4 + - - +
206A HIS* 3.5 11.4 - - - +
207A ARG 3.2 0.2 - - - -
208A GLU* 1.3 76.8 - - - +
210A MET* 1.3 64.1 + - - +
212A ALA* 3.0 1.8 + - - +
213A VAL* 3.0 24.2 + - + +
222A LEU* 3.8 30.5 - - + +
225A LEU* 4.2 13.7 - - + -
226A PHE* 4.0 20.0 - - + +
275A PHE* 3.5 37.7 - - + -
277A MET* 4.1 7.0 - - + -
292A PHE* 4.8 1.8 - - + -
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Residues in contact with MET 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A HIS* 2.9 25.7 + - + +
207A ARG* 3.2 6.0 + - - +
209A VAL* 1.3 77.8 - - - +
211A LYS* 1.3 60.9 + - - +
212A ALA 3.5 0.2 + - - -
213A VAL* 3.8 5.1 + - - +
290A CYS* 3.8 28.3 - - + -
292A PHE* 3.4 46.7 - - + -
469A PRO* 3.7 37.5 - - + +
475A ILE* 4.5 20.4 - - - -
478A CYS* 4.0 11.7 - - - -
479A MET* 3.7 31.2 - - + +
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Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 3.0 23.4 + - - +
208A GLU* 2.9 44.3 + - - +
209A VAL 3.2 0.2 - - - -
210A MET* 1.3 77.0 - - - +
212A ALA* 1.3 59.8 + - - +
213A VAL 4.6 2.1 - - - +
214A LYS* 5.8 0.5 - - - +
478A CYS* 3.7 31.2 - - - +
479A MET* 4.8 7.7 - - - +
481A GLY* 5.4 8.3 - - - -
482A CYS 5.9 2.7 - - - +
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU 3.0 16.3 + - - +
209A VAL 3.0 2.4 + - - +
211A LYS* 1.3 78.9 - - + +
213A VAL* 1.3 66.3 + - - +
214A LYS* 3.2 13.5 + - - +
217A MET* 3.5 16.2 - - + +
222A LEU* 4.4 5.4 - - + -
225A LEU* 3.5 24.0 - - + -
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL 3.0 19.9 + - - +
210A MET 3.8 8.4 + - - +
211A LYS 3.6 4.0 - - - +
212A ALA* 1.3 76.4 - - - +
214A LYS* 1.3 71.7 + - - +
217A MET* 4.1 4.7 - - - -
222A LEU* 3.6 24.5 - - + -
267A ILE* 4.5 13.7 - - + -
273A CYS* 4.7 1.1 - - - -
275A PHE* 3.9 16.6 - - + -
292A PHE* 4.0 16.6 - - + -
294A ALA* 3.7 33.6 - - + +
479A MET* 4.5 5.1 - - + +
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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