Contacts of the helix formed by residues 281 - 307 (chain L) in PDB entry 4BOG
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 281 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L VAL* 6.3 0.7 - - + -
279L ILE 4.5 3.4 - - - +
280L ILE* 1.3 83.8 - - + +
282L SER* 1.3 53.9 + - - +
283L TYR 3.3 1.8 - - - -
284L LEU* 2.4 55.0 + - + +
285L MET* 2.5 58.0 + - + +
288L MET* 5.5 3.6 - - + -
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Residues in contact with SER 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L PRO* 6.4 0.7 - - - -
137L PHE* 5.4 0.4 - - - -
280L ILE* 3.3 17.4 - - - +
281L ILE* 1.3 77.7 - - - +
283L TYR* 1.3 86.0 + - - -
285L MET* 3.1 27.8 + - - +
286L PHE* 2.6 31.7 + - - -
460L HIS* 3.3 34.1 + - - +
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Residues in contact with TYR 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L PHE* 4.1 42.3 + + + -
136L PRO* 5.7 1.3 - - + -
137L PHE* 2.7 46.8 - + - -
221L ILE* 4.9 25.6 - - + -
280L ILE* 5.1 6.1 - - + -
281L ILE 2.7 2.4 + - - -
282L SER* 1.3 94.4 + - - +
284L LEU* 1.3 55.2 + - - +
286L PHE* 3.3 16.2 - + + -
287L ILE* 2.7 42.7 + - + +
457L ASP* 4.7 9.9 - - - +
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Residues in contact with LEU 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270L VAL* 3.7 34.8 - - + +
271L PRO* 6.3 0.2 - - + -
274L SER* 5.5 8.5 - - - +
281L ILE* 2.4 33.5 + - + +
283L TYR* 1.3 72.2 - - - +
285L MET* 1.3 51.2 + - - +
287L ILE* 3.2 28.7 - - + -
288L MET* 2.5 56.3 + - + +
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Residues in contact with MET 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L ILE* 2.5 43.4 + - + +
282L SER* 3.2 27.1 - - - +
284L LEU* 1.3 73.3 - - - +
286L PHE* 1.3 63.3 + - + +
288L MET* 2.9 12.2 - - - +
289L ILE* 2.9 23.3 - - + +
456L LEU* 6.0 4.0 - - + -
460L HIS* 5.2 7.9 - - + +
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Residues in contact with PHE 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282L SER* 2.6 37.7 - - - -
283L TYR* 3.3 13.5 - + - -
285L MET* 1.3 80.0 - - + +
287L ILE* 1.3 83.5 + - + +
288L MET 2.9 5.8 - - - -
289L ILE* 2.7 15.7 + - + +
290L LEU* 2.4 50.5 + - + +
453L SER* 3.3 15.5 - - - -
456L LEU* 4.4 12.8 - - + -
457L ASP* 2.7 41.1 - - - -
460L HIS* 3.7 21.8 - + - -
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Residues in contact with ILE 287 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224L THR* 6.0 6.7 - - + -
228L CYS* 5.1 14.4 - - - -
270L VAL* 6.0 3.6 - - + -
283L TYR* 2.7 36.2 + - + +
284L LEU* 3.2 34.3 - - + -
286L PHE* 1.3 96.7 - - + +
288L MET* 1.3 57.4 + - - +
290L LEU* 3.1 16.3 - - + +
291L VAL* 2.4 43.5 + - + +
457L ASP* 5.3 0.4 - - - +
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Residues in contact with MET 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216K VAL* 5.2 14.1 - - + -
217K ASN* 5.5 12.3 - - + +
220K ILE* 5.8 3.6 - - + -
281L ILE* 6.0 2.9 - - + -
284L LEU* 2.5 36.3 + - + +
285L MET* 2.9 12.6 - - - +
287L ILE* 1.3 79.7 - - + +
289L ILE* 1.3 60.7 + - + +
291L VAL* 2.6 38.1 - - + +
292L ALA* 2.9 8.9 + - + +
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Residues in contact with ILE 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285L MET* 2.9 21.3 - - + +
286L PHE* 2.7 17.9 + - + +
288L MET* 1.3 82.9 - - + +
290L LEU* 1.3 50.2 + - + +
291L VAL 3.0 1.6 - - - -
292L ALA* 3.1 5.6 + - + +
293L PHE* 2.6 86.1 + - + -
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Residues in contact with LEU 290 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228L CYS* 5.2 14.6 - - + -
286L PHE* 2.4 38.5 + - + +
287L ILE* 3.1 34.1 - - + +
289L ILE* 1.3 72.4 - - + +
291L VAL* 1.3 60.8 + - - +
293L PHE* 3.3 11.0 - - + +
294L SER* 3.0 25.5 + - - -
449L ILE* 3.9 24.2 - - + +
450L GLY* 4.8 5.2 - - - -
453L SER* 2.8 32.3 - - - +
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Residues in contact with VAL 291 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263L LEU* 3.3 36.5 - - + +
287L ILE* 2.4 31.3 + - + +
288L MET* 2.6 28.9 - - + +
290L LEU* 1.3 72.4 - - - +
292L ALA* 1.3 80.1 + - + +
293L PHE 2.9 1.1 + - - -
294L SER* 3.1 2.6 + - - -
295L VAL* 2.7 46.4 + - + +
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Residues in contact with ALA 292 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288L MET* 2.9 10.7 + - + +
289L ILE* 3.4 12.6 - - + +
291L VAL* 1.3 85.0 - - + +
293L PHE* 1.3 63.6 + - + +
295L VAL* 3.4 9.3 - - - +
296L ILE* 2.8 39.1 + - + +
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Residues in contact with PHE 293 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289L ILE* 2.6 55.5 + - + +
290L LEU* 3.3 13.2 - - + +
291L VAL 2.9 1.2 - - - -
292L ALA* 1.3 79.0 - - + +
294L SER* 1.3 52.4 + - - +
296L ILE* 4.2 1.7 - - + +
297L LEU* 2.7 40.5 + - - +
445L THR* 5.8 1.1 - - + -
449L ILE* 3.5 56.1 - - + -
452L PHE* 6.1 0.4 - + - -
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Residues in contact with SER 294 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228L CYS 5.3 1.4 + - - -
231L ILE* 5.4 4.4 - - - +
232L SER* 4.8 9.5 + - - -
235L ALA* 4.8 11.7 - - - +
239L PHE* 5.5 4.6 - - - -
259L LEU* 5.2 8.3 - - - +
263L LEU* 5.0 15.3 - - - -
290L LEU 3.0 17.4 + - - -
291L VAL* 3.9 2.9 - - - -
293L PHE* 1.3 72.4 - - - +
295L VAL* 1.3 58.4 + - - +
297L LEU* 4.3 6.1 - - - -
298L SER* 2.8 32.7 + - - -
449L ILE* 5.3 0.6 - - - +
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Residues in contact with VAL 295 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224K LEU* 5.9 7.4 - - + -
259L LEU* 6.4 0.9 - - - -
260L THR* 6.0 8.1 - - + +
263L LEU* 5.4 12.8 - - + -
291L VAL* 2.7 42.3 + - + +
292L ALA* 3.4 11.0 - - - +
294L SER* 1.3 72.8 - - - +
296L ILE* 1.3 68.6 + - + +
298L SER* 2.6 22.3 + - - -
299L VAL* 2.9 22.9 + - + +
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Residues in contact with ILE 296 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227K PHE* 5.8 5.8 - - + -
292L ALA* 2.8 23.0 + - + +
293L PHE* 4.2 2.0 - - + +
295L VAL* 1.3 77.0 - - + +
297L LEU* 1.3 59.9 + - - +
298L SER 3.2 1.8 - - - -
299L VAL* 3.5 13.9 - - + +
300L VAL* 2.6 42.4 + - + +
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Residues in contact with LEU 297 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239L PHE* 4.9 12.1 - - + -
293L PHE 2.7 25.0 + - - +
294L SER* 4.1 4.3 - - - +
296L ILE* 1.3 75.5 - - - +
298L SER* 1.3 59.2 + - - +
300L VAL* 3.7 9.9 - - + +
301L VAL* 2.8 55.1 + - + +
441L TYR* 4.7 9.0 - - + +
442L ILE* 3.9 22.0 - - + -
445L THR* 3.1 43.7 - - + +
446L MET* 5.0 5.4 - - + +
449L ILE* 5.3 2.7 - - + -
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Residues in contact with SER 298 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239L PHE* 4.4 13.0 - - - -
256L LEU* 2.8 48.7 - - - +
259L LEU* 4.9 6.2 - - - +
260L THR* 5.2 3.8 + - - -
294L SER 2.8 15.6 + - - -
295L VAL* 2.6 23.7 + - - -
297L LEU* 1.3 74.1 - - - +
299L VAL* 1.3 57.3 + - - +
301L VAL* 2.6 29.7 - - - +
302L LEU 3.1 3.5 + - - -
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Residues in contact with VAL 299 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224K LEU* 5.5 10.5 - - + +
227K PHE* 4.2 26.5 - - + -
228K LEU* 4.9 10.8 - - + -
231K LEU* 4.5 13.1 - - + +
256L LEU* 5.0 2.0 - - + -
260L THR* 5.6 5.6 - - - +
295L VAL* 2.9 30.0 + - + +
296L ILE* 3.1 16.7 + - + +
298L SER* 1.3 80.7 - - - +
300L VAL* 1.3 61.2 + - - +
302L LEU* 2.8 17.4 - - + +
303L ASN* 2.8 21.8 + - - +
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Residues in contact with VAL 300 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227K PHE* 5.6 5.8 - - + -
296L ILE* 2.6 31.5 + - + +
297L LEU* 3.7 13.9 - - + +
299L VAL* 1.3 69.6 - - - +
301L VAL* 1.3 61.2 + - + +
302L LEU 2.9 1.1 - - - -
303L ASN* 2.7 17.8 + - + +
304L LEU* 2.4 32.6 + - - +
441L TYR* 5.5 9.4 - - + +
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Residues in contact with VAL 301 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238L VAL* 5.2 0.9 - - + -
239L PHE* 4.3 19.1 - - + -
256L LEU* 4.8 1.1 - - + -
297L LEU* 2.8 44.1 + - + +
298L SER* 2.6 37.7 - - - +
300L VAL* 1.3 79.1 - - + +
302L LEU* 1.3 52.5 + - - +
304L LEU* 2.8 20.1 + - + +
305L HIS* 2.5 51.5 + - + +
442L ILE* 3.8 17.9 - - + -
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Residues in contact with LEU 302 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228K LEU* 4.2 21.8 - - + -
231K LEU* 4.9 7.9 - - + -
235K LEU* 5.8 1.9 - - + +
242K LYS* 4.3 4.2 + - - +
252L SER* 4.9 0.9 - - - +
253L ILE* 3.2 51.8 - - + +
256L LEU* 3.3 29.8 - - + -
298L SER 3.2 6.3 - - - +
299L VAL* 2.8 20.2 - - + +
301L VAL* 1.3 82.9 - - - +
303L ASN* 1.3 55.6 + - - +
305L HIS* 3.1 23.0 + - + +
306L HIS* 2.8 25.3 + - - +
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Residues in contact with ASN 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227K PHE* 2.8 37.2 - - + -
231K LEU* 3.6 15.9 - - + +
299L VAL 2.8 10.9 + - - +
300L VAL* 2.7 22.3 + - + +
302L LEU* 1.3 74.5 - - - +
304L LEU* 1.3 63.5 + - - +
305L HIS 3.1 0.2 - - - -
306L HIS* 3.5 14.5 - - - +
307L ARG* 3.0 25.5 + - - +
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Residues in contact with LEU 304 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L PRO* 6.1 3.1 - - + -
300L VAL* 2.4 18.5 + - + +
301L VAL* 2.9 33.7 - - + +
303L ASN* 1.3 71.0 - - - +
305L HIS* 1.3 77.5 + - + +
307L ARG* 3.8 29.3 + - - +
434L VAL* 3.8 33.2 - - + -
435L ALA* 4.4 19.1 - - + +
438L LEU* 4.2 21.1 - - + -
442L ILE* 5.1 3.1 - - + -
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Residues in contact with HIS 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K LYS* 4.3 2.5 - - - +
238L VAL* 4.1 23.2 + - + +
239L PHE* 6.0 0.2 - - - -
242L PRO* 4.3 16.0 - - + +
248L LYS* 3.9 22.8 - - + +
249L MET* 5.5 1.2 + - - -
252L SER* 4.3 11.0 - - - -
301L VAL* 2.5 43.2 + - + +
302L LEU* 3.1 26.5 - - + +
304L LEU* 1.3 89.7 - - + +
306L HIS* 1.3 51.0 + - - +
308L SER* 4.3 4.5 + - - -
311L THR* 4.6 1.9 - - - +
312L HIS* 2.6 49.8 + + + +
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Residues in contact with HIS 306 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K LEU* 5.5 6.7 - - + -
234K TYR* 3.1 3.4 + - + -
235K LEU* 2.6 63.7 + - + -
238K ASP* 3.0 44.0 + - + -
239K SER* 3.5 4.9 - - - -
242K LYS* 4.1 4.9 - - - +
302L LEU 2.8 15.2 + - - +
303L ASN* 3.3 16.1 + - - +
305L HIS* 1.3 72.0 - - - +
307L ARG* 1.3 55.6 + - - +
308L SER 2.4 21.6 + - - +
312L HIS 2.4 23.4 - - - -
----------------------------------------------------------
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Residues in contact with ARG 307 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238K ASP* 5.9 3.6 - - - -
303L ASN* 3.0 17.0 + - - +
304L LEU* 3.8 23.6 + - - +
305L HIS 3.5 2.0 - - - -
306L HIS* 1.3 77.7 - - - +
308L SER* 1.3 75.6 + - - +
309L PRO* 3.7 7.7 - - - +
429L GLN 3.4 21.0 + - - -
430L TYR* 4.1 8.9 - - - +
431L VAL* 4.9 2.6 - - - +
432L ALA 5.7 1.8 - - - +
434L VAL* 2.9 39.8 - - - +
----------------------------------------------------------
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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