Contacts of the helix formed by residues 220 - 244 (chain A) in PDB entry 5J0Z
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 SER 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 3.2 11.5 + - - -
219A THR* 1.3 75.8 - - - +
221A TYR* 1.3 54.3 + - - +
222A GLU* 3.2 16.8 + - - +
223A ALA* 2.9 16.3 + - - +
224A ASN* 2.7 38.8 + - - +
221B TYR* 4.9 5.6 - - - -
222B GLU* 4.4 14.6 + - - +
277B HIS* 4.9 7.6 - - - -
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Residues in contact with TYR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR 3.9 3.2 + - - -
220A SER* 1.3 70.4 - - - +
222A GLU* 1.3 73.2 + - - +
224A ASN* 2.8 7.7 + - - +
225A VAL* 2.8 50.1 + - + +
273A VAL* 3.6 23.8 - - + -
274A THR* 3.4 29.5 + - + +
277A HIS* 3.4 49.8 - + + +
214E THR* 3.7 10.0 + - - -
218E SER* 3.4 29.2 - - - -
220E SER* 4.9 2.0 - - - -
223E ALA* 4.0 20.9 - - + -
224E ASN* 4.6 0.2 - - - -
227E LEU* 3.1 23.1 - - + +
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Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR 5.1 0.3 - - - +
220A SER* 3.5 16.9 + - - +
221A TYR* 1.3 96.4 + - - +
223A ALA* 1.3 54.1 + - - +
225A VAL* 4.5 3.1 + - - +
226A THR* 3.1 19.6 + - - -
277A HIS* 5.1 5.7 + - - -
222B GLU* 6.0 6.3 - - + +
220E SER* 4.0 23.2 + - - +
222E GLU* 5.5 6.3 - - + -
223E ALA* 4.2 20.6 - - + +
226E THR* 5.5 2.1 + - - +
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A SER* 2.9 21.3 + - - +
221A TYR 2.8 0.2 + - - -
222A GLU* 1.3 78.3 - - - +
224A ASN* 1.3 59.5 + - - +
225A VAL 3.3 1.8 - - - -
226A THR* 3.1 9.2 + - - -
227A LEU* 2.8 28.9 + - - +
221B TYR* 4.1 24.5 - - + -
222B GLU* 4.2 24.4 - - + +
225B VAL* 4.1 7.3 - - + +
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Residues in contact with ASN 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ALA* 3.1 34.3 + - + +
218A SER* 2.7 39.8 + - - -
220A SER 2.7 23.3 + - - +
221A TYR* 2.8 4.3 + - - +
223A ALA* 1.3 69.9 - - - +
225A VAL* 1.3 67.3 + - - +
227A LEU* 3.4 8.9 - - - +
228A VAL* 2.8 29.5 + - - +
273A VAL* 3.7 22.8 - - + +
276A GLN* 3.5 14.5 + - - -
221B TYR* 4.5 1.4 - - - -
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 2.8 54.5 + - + +
222A GLU 4.5 3.4 - - - +
224A ASN* 1.3 74.9 - - - +
226A THR* 1.3 55.8 + - - +
228A VAL* 3.8 2.0 - - - -
229A VAL* 2.8 49.0 + - + +
273A VAL* 4.7 4.0 - - + -
274A THR* 5.8 0.4 - - - +
223E ALA* 4.2 7.9 - - + +
226E THR* 4.0 12.8 - - + -
227E LEU* 3.8 41.7 - - + +
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Residues in contact with THR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU 3.1 15.9 + - - -
223A ALA* 3.1 11.0 + - - -
225A VAL* 1.3 77.5 - - - +
227A LEU* 1.3 65.7 + - - +
229A VAL* 5.1 0.7 - - - -
230A SER* 2.7 41.9 + - - +
222B GLU 5.5 1.5 + - - -
225B VAL* 4.0 12.6 - - + -
226B THR* 4.0 28.5 + - + +
229B VAL* 5.8 1.1 - - + -
226E THR* 4.1 18.9 - - + +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 3.4 33.4 - - + +
212A SER* 4.6 2.2 - - - +
214A THR* 3.1 22.0 - - - +
215A ALA* 4.0 21.1 - - + +
223A ALA 2.8 14.6 + - - +
224A ASN* 3.4 11.7 - - - +
226A THR* 1.3 74.7 - - - +
228A VAL* 1.3 53.1 + - + +
230A SER* 4.2 1.2 - - - -
231A THR* 2.7 37.4 + - - +
221B TYR* 3.2 35.4 - - + +
225B VAL* 3.8 23.9 - - + +
229B VAL* 4.6 4.9 - - + +
270B VAL* 5.0 2.7 - - + -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A SER* 3.8 24.2 - - - +
215A ALA* 4.3 9.4 - - + -
224A ASN 2.8 21.0 + - - +
225A VAL* 4.2 2.5 - - - +
227A LEU* 1.3 73.4 - - - +
229A VAL* 1.3 62.8 + - + +
231A THR* 2.8 17.8 + - - -
232A LEU* 3.1 12.7 + - + +
266A TYR* 3.9 20.6 - - + +
269A ALA* 4.3 17.0 - - + -
270A VAL* 3.3 35.9 - - + +
273A VAL* 4.6 10.3 - - + -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 2.8 41.3 + - + +
226A THR* 4.5 1.3 - - - +
228A VAL* 1.3 73.0 - - + +
230A SER* 1.3 56.1 + - - +
232A LEU* 3.2 14.1 + - + +
233A ILE* 3.0 28.0 + - + +
270A VAL* 4.8 8.3 - - + -
211E ILE* 4.5 20.4 - - + -
226E THR* 5.1 1.1 - - + +
227E LEU* 4.7 6.1 - - + -
230E SER* 3.2 37.7 - - - +
231E THR* 4.3 14.1 - - + +
234E ALA* 6.3 0.9 - - + -
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 2.7 37.4 + - - +
229A VAL* 1.3 74.7 - - - +
231A THR* 1.3 61.8 + - - +
233A ILE* 3.1 13.9 + - - +
234A ALA* 2.9 23.9 + - - +
229B VAL* 3.3 25.7 - - - +
230B SER* 6.4 0.2 - - - -
233B ILE* 3.5 15.4 - - - +
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Residues in contact with THR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 3.4 29.8 - - + +
211A ILE* 3.6 26.9 - - + -
212A SER* 3.6 6.3 - - - +
227A LEU 2.7 24.0 + - - +
228A VAL* 2.8 16.1 + - - -
230A SER* 1.3 79.1 - - - +
232A LEU* 1.3 55.2 + - - +
234A ALA* 3.4 8.6 + - + +
235A HIS* 2.9 28.1 + - - +
266A TYR* 3.4 14.6 + - - -
229B VAL* 4.3 9.6 - - + -
232B LEU* 5.6 2.9 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 3.1 16.9 + - + +
229A VAL* 3.3 18.6 - - + +
230A SER 3.1 0.4 - - - -
231A THR* 1.3 73.8 + - - +
233A ILE* 1.3 61.3 + - - +
235A HIS* 3.6 4.7 - - + +
236A ILE* 2.9 42.6 + - + +
263A TYR* 4.6 17.0 - - + +
266A TYR* 3.6 34.3 - - + -
208E ILE* 4.1 17.5 - - + -
211E ILE* 4.0 28.7 - - + -
231E THR* 5.6 2.9 - - + -
234E ALA* 5.3 4.3 - - + -
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Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 3.0 16.3 + - + +
230A SER* 3.1 11.4 + - - +
232A LEU* 1.3 77.4 - - + +
234A ALA* 1.3 64.2 + - - +
236A ILE* 2.9 19.5 + - - +
237A ALA* 3.0 11.1 + - - +
402A LMT 4.2 20.2 - - + -
403A LMT 4.7 9.7 - - + +
404A LMT 5.4 2.9 - - + -
233B ILE* 3.6 22.2 - - + -
230E SER* 3.6 23.6 - - - +
233E ILE* 3.6 28.9 - - + -
234E ALA* 4.1 20.6 - - + -
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 4.0 12.1 - - + -
230A SER 2.9 12.4 + - - +
231A THR* 3.5 13.0 - - - +
233A ILE* 1.3 76.3 - - - +
235A HIS* 1.3 61.4 + - - +
237A ALA* 3.1 22.4 - - - +
238A PHE* 3.4 12.2 - - - -
404A LMT 5.4 1.3 - - - -
229B VAL* 6.3 0.7 - - + -
232B LEU* 5.4 4.5 - - + -
233B ILE* 4.0 15.7 - - + -
236B ILE* 3.6 25.6 - - + -
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Residues in contact with HIS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A MET* 3.8 40.7 + - + +
208A ILE* 3.2 20.9 - - + +
231A THR 2.9 14.6 + - - +
232A LEU* 3.6 7.0 - - + +
233A ILE 3.2 0.2 - - - -
234A ALA* 1.3 74.1 - - - +
236A ILE* 1.3 67.0 + - - +
238A PHE* 3.1 8.8 + - - +
239A ASN* 3.0 18.2 + - + +
259A ILE* 3.9 8.1 + - + +
262A ILE* 3.2 35.0 - - + +
263A TYR* 3.4 40.5 - + - -
266A TYR* 3.8 16.3 - + + +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 2.9 29.9 + - + +
233A ILE* 2.9 12.2 + - - +
235A HIS* 1.3 77.1 - - - +
237A ALA* 1.3 60.6 + - - +
239A ASN* 3.1 11.1 + - - +
240A ILE* 3.2 16.9 + - + +
263A TYR* 3.5 25.4 - - + +
403A LMT 3.8 9.4 - - + +
208E ILE* 4.2 9.0 - - + -
234E ALA* 3.7 28.9 - - + -
237E ALA* 3.7 21.5 - - + -
238E PHE* 3.5 32.1 - - + -
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Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE 3.0 5.7 + - - -
234A ALA* 3.1 16.8 - - - +
235A HIS 3.1 0.2 - - - -
236A ILE* 1.3 76.2 - - - +
238A PHE* 1.3 55.9 + - - +
241A LEU 3.5 8.7 + - - -
403A LMT 3.3 27.9 - - - +
404A LMT 3.2 39.0 - - + -
236B ILE* 3.7 14.4 - - + -
240B ILE* 3.3 15.8 - - + +
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASN 3.9 15.3 - - - -
201A ILE* 4.4 17.8 - - + +
204A PRO* 3.8 22.0 - - + -
205A MET* 3.3 34.8 - - + +
208A ILE* 5.5 4.3 - - + -
234A ALA 3.4 13.7 - - - -
235A HIS* 3.1 8.5 + - - +
237A ALA* 1.3 79.0 - - + +
239A ASN* 1.3 62.8 + - - +
241A LEU* 4.0 16.3 - - + +
242A VAL* 3.5 20.8 + - - +
236B ILE* 3.4 36.1 - - + -
239B ASN* 4.4 4.0 - - - -
240B ILE* 4.3 11.0 - - + -
243B GLU* 6.0 0.2 - - - -
263B TYR* 3.5 30.1 - + - -
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Residues in contact with ASN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A MET* 4.5 0.2 - - - +
235A HIS* 3.0 10.5 + - + +
236A ILE 3.1 3.7 + - - +
238A PHE* 1.3 75.8 - - - +
240A ILE* 1.3 63.2 + - + +
242A VAL* 3.4 1.9 + - - +
243A GLU* 3.1 42.2 + - - +
259A ILE* 3.7 27.0 - - + +
263A TYR* 2.8 45.6 + - + +
199E PRO 5.3 1.4 + - - -
200E ASN* 4.4 18.6 + - - +
204E PRO* 4.9 3.2 - - - +
238E PHE* 4.4 5.9 - - - -
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.2 13.5 + - + +
239A ASN* 1.3 78.4 - - + +
241A LEU* 1.4 53.7 + - - +
243A GLU* 4.6 6.5 - - - +
244A THR* 2.5 35.0 + - + +
403A LMT 3.8 25.8 - - + +
403D LMT 3.8 22.9 - - + -
237E ALA* 3.3 32.8 - - + +
238E PHE* 4.4 15.9 - - + -
241E LEU* 3.4 45.3 - - + -
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 4.8 18.4 - - + -
237A ALA 3.5 19.7 + - - +
238A PHE* 4.3 13.7 - - + +
239A ASN 3.3 0.8 - - - -
240A ILE* 1.4 77.2 - - - +
242A VAL* 1.4 54.6 + - + +
244A THR* 4.2 2.1 + - - -
245A ASN* 2.7 41.2 + - - +
403A LMT 3.6 16.9 - - + +
240B ILE* 3.4 36.1 - - + -
243B GLU* 3.5 31.4 - - - +
244B THR* 4.7 14.1 - - + -
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 5.1 5.8 - - + -
197A TYR* 6.0 0.4 - - + -
201A ILE* 3.7 42.4 - - + -
238A PHE 3.5 15.5 + - - +
239A ASN* 3.4 3.1 + - - +
241A LEU* 1.4 74.0 - - + +
243A GLU* 1.3 69.5 + - + +
244A THR 3.2 2.9 + - - -
245A ASN* 3.5 25.2 + - - +
246A LEU* 3.9 18.9 + - + +
255A THR* 4.1 18.2 - - + -
256A GLY* 5.7 2.5 - - - +
259A ILE* 3.6 24.9 - - + -
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASN* 3.1 30.4 + - - +
240A ILE* 4.6 6.0 - - - +
241A LEU 3.6 0.2 - - - -
242A VAL* 1.3 80.0 - - + +
244A THR* 1.3 62.5 + - - +
245A ASN 3.8 0.2 - - - -
246A LEU* 3.5 19.2 - - - +
247A PRO 5.5 0.5 - - - +
248A LYS* 5.0 16.1 - - - +
200E ASN* 3.4 47.1 + - - +
201E ILE* 5.0 7.3 - - - +
238E PHE* 6.0 0.3 - - - -
241E LEU* 3.6 33.8 - - - +
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Residues in contact with THR 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 3.3 33.9 - - - +
240A ILE* 2.5 29.2 + - + +
241A LEU* 4.2 3.7 + - - -
242A VAL 3.2 0.2 - - - -
243A GLU* 1.3 82.8 - - - +
245A ASN* 1.3 62.1 + - - +
246A LEU 3.2 3.1 - - - -
403A LMT 6.0 0.3 - - - +
241E LEU* 4.8 18.4 - - + -
245E ASN* 6.0 1.1 - - - +
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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