Contacts of the helix formed by residues 309 - 336 (chain A) in PDB entry 6DWN
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 ASN 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 4.1 7.1 + - - -
119A GLN* 2.8 35.2 + - - +
120A SER* 5.4 0.4 - - - -
121A MET 5.1 0.6 + - - -
134A ARG* 3.0 20.3 + - - +
259A TYR* 3.4 31.1 + - + +
262A MET* 3.6 22.4 - - + +
305A GLU 2.9 17.9 + - - +
306A LYS* 3.2 7.3 - - - +
308A ILE* 1.3 74.3 - - - +
310A ILE* 1.3 66.1 + - - +
311A VAL 3.2 1.1 - - - -
312A LEU* 3.1 19.0 + - + +
313A ASP* 3.8 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 3.9 15.7 - - + -
134A ARG* 3.6 45.1 - - + +
137A LEU* 4.3 12.1 - - + -
138A ALA* 3.8 29.4 - - + -
281A ILE* 6.1 0.2 - - + -
285A LEU* 4.1 8.7 - - + -
306A LYS 3.4 18.2 - - - +
307A ILE* 3.5 20.4 - - - +
308A ILE 2.9 1.0 + - - -
309A ASN* 1.3 78.4 - - - +
311A VAL* 1.3 65.5 + - - +
312A LEU 3.0 1.4 + - - -
313A ASP* 3.0 16.5 + - - +
314A LEU* 3.2 16.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A CYS* 4.4 8.2 - - + +
203A PHE* 4.2 21.3 - - + -
262A MET* 4.8 14.1 - - + -
266A VAL* 5.5 1.3 - - + -
281A ILE* 3.7 21.8 - - + -
282A THR* 3.7 24.2 - - + +
285A LEU* 3.6 20.9 - - + -
308A ILE* 3.0 20.1 + - + +
309A ASN* 4.5 1.3 - - - -
310A ILE* 1.3 76.4 - - - +
312A LEU* 1.3 58.6 + - + +
314A LEU* 3.8 8.4 - - - +
315A PHE* 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 3.6 19.3 - - - +
203A PHE* 5.7 5.4 - - + -
255A ASN 5.7 0.2 - - - +
258A PHE* 3.6 44.4 - - + +
259A TYR* 3.5 42.8 - - + +
261A PHE* 5.9 3.1 - - + -
262A MET* 4.5 15.5 - - + +
309A ASN* 3.1 14.7 + - - +
310A ILE 3.0 1.4 + - - -
311A VAL* 1.3 82.0 - - + +
313A ASP* 1.3 58.7 + - - +
315A PHE* 3.9 6.8 - - + +
316A GLY* 2.9 26.5 + - - -
602A AQ4 3.9 10.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 3.4 11.8 + - - -
120A SER* 3.0 24.4 + - - -
121A MET* 3.2 20.7 + - + +
122A SER* 3.0 31.5 + - - +
309A ASN 3.8 6.1 + - - +
310A ILE* 3.0 7.9 + - - +
312A LEU* 1.3 73.9 - - - +
314A LEU* 1.3 61.7 + - - +
317A ALA* 2.9 34.3 + - - +
601A HEM 4.6 2.0 - - + -
602A AQ4 3.2 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 4.3 1.3 - - + -
138A ALA* 4.0 28.9 - - + +
142A LEU* 4.0 28.5 - - + -
198A ILE* 3.9 2.3 - - - +
202A CYS* 4.2 8.5 - - - -
281A ILE* 4.0 29.6 - - + -
310A ILE* 3.2 21.3 + - + +
311A VAL* 3.8 8.3 - - - +
313A ASP* 1.3 77.8 - - - +
315A PHE* 1.3 57.1 + - - +
318A GLY* 2.9 27.5 + - - -
458A ILE* 4.2 4.0 - - + -
601A HEM 3.6 43.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 3.6 32.3 - - + -
198A ILE* 4.0 23.1 - - + -
199A CYS* 4.1 19.1 - - + -
202A CYS* 4.2 3.7 - - - -
203A PHE* 3.7 31.9 - + + -
214A LEU* 5.3 2.2 - - + -
217A LEU* 5.5 7.6 - - + -
218A VAL* 4.7 6.3 - - + -
258A PHE* 3.9 30.5 - + - -
261A PHE* 5.4 9.2 - + - -
311A VAL 2.8 22.8 + - - +
312A LEU* 4.0 5.4 - - + +
314A LEU* 1.3 74.2 - - - +
316A GLY* 1.3 65.0 + - - +
319A PHE* 3.1 41.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 5.1 0.7 - - - -
312A LEU 2.9 14.8 + - - -
315A PHE* 1.3 80.7 - - - +
317A ALA* 1.3 60.7 + - - +
319A PHE* 3.8 9.6 - - - -
320A ASP* 3.3 24.8 + - - +
602A AQ4 3.5 38.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP 2.9 18.1 + - - +
316A GLY* 1.3 76.4 - - - +
318A GLY* 1.3 56.2 + - - +
320A ASP* 4.9 0.4 - - - -
321A THR* 2.6 38.6 + - + +
601A HEM 3.6 33.9 - - + +
602A AQ4 3.3 34.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 4.1 2.4 - - - +
198A ILE* 4.0 15.9 - - - -
314A LEU 2.9 19.6 + - - -
315A PHE 3.2 1.3 + - - -
317A ALA* 1.3 80.2 - - - +
319A PHE* 1.3 62.0 + - - +
322A VAL* 3.7 26.0 + - - +
466A GLU* 5.6 0.5 - - - +
601A HEM 3.8 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 5.6 1.7 + - - -
191A VAL* 4.4 6.7 - - + -
194A VAL* 4.1 8.7 - - - -
195A THR* 3.4 24.5 - - + +
198A ILE* 3.9 13.4 - - + +
217A LEU 4.3 5.2 - - - -
218A VAL* 3.5 43.7 - - + -
258A PHE* 4.1 6.7 - + - -
315A PHE* 3.1 50.6 + + - +
316A GLY* 3.8 18.4 - - - -
318A GLY* 1.3 76.0 - - - +
320A ASP* 1.3 60.4 + - - +
323A THR* 2.4 31.5 + - - -
602A AQ4 3.2 37.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 4.9 3.0 + - - -
224A PHE* 5.0 5.5 - - - -
225A GLY* 5.0 2.9 + - - -
316A GLY 3.3 18.0 + - - +
317A ALA* 4.4 0.7 - - - +
318A GLY 3.3 0.4 - - - -
319A PHE* 1.3 84.9 - - - +
321A THR* 1.3 68.5 + - + +
323A THR* 3.9 1.8 - - - -
324A THR* 3.0 20.6 + - - -
496A LEU* 5.6 2.3 - - - +
497A THR* 3.1 22.8 + - - +
499A LYS* 3.0 22.3 + - - -
602A AQ4 2.5 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 2.6 29.7 + - - +
318A GLY 4.0 1.0 + - - -
320A ASP* 1.3 77.6 - - + +
322A VAL* 1.3 63.7 + - - +
324A THR* 3.3 4.7 + - - -
325A ALA* 3.0 27.2 + - - +
381A PHE* 3.7 10.7 - - - -
382A VAL* 5.1 0.4 - - + -
497A THR* 3.9 22.9 - - + -
601A HEM 3.0 51.9 - - + +
602A AQ4 4.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 3.8 16.4 - - + -
318A GLY 3.7 18.0 + - - +
320A ASP 3.5 0.4 - - - -
321A THR* 1.3 84.6 + - - +
323A THR* 1.3 67.1 + - - +
325A ALA* 3.2 6.8 + - - +
326A ILE* 2.9 38.6 + - + +
463A ALA* 4.1 20.0 - - + -
466A GLU* 3.9 26.2 - - + +
467A VAL* 4.1 12.8 - - + -
601A HEM 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 3.5 30.3 - - + -
190A VAL* 4.3 5.9 - - + +
191A VAL* 3.5 35.9 + - + +
194A VAL* 3.3 25.1 - - - +
319A PHE 2.4 27.9 + - - -
320A ASP 3.9 2.5 - - - -
321A THR 3.3 0.6 - - - -
322A VAL* 1.3 78.0 - - - +
324A THR* 1.3 57.2 + - - +
326A ILE* 3.4 2.9 + - - +
327A SER* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 4.7 3.5 - - - -
320A ASP* 3.0 18.6 + - - -
321A THR* 3.6 4.5 - - - -
323A THR* 1.3 77.1 - - - +
325A ALA* 1.3 63.4 + - - +
327A SER* 3.6 6.0 - - - -
328A TRP* 3.0 42.9 + - + +
381A PHE* 3.7 17.9 - - + -
497A THR* 4.2 3.8 + - - -
498A MET 3.2 28.9 - - - +
499A LYS* 3.5 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A THR 3.0 14.2 + - - +
322A VAL* 3.2 8.9 + - - +
324A THR* 1.3 78.2 - - - +
326A ILE* 1.3 63.0 + - - +
328A TRP* 3.4 3.8 + - - +
329A SER* 3.0 25.7 + - - -
375A THR* 4.1 3.1 - - - +
376A PHE* 4.0 17.0 - - + -
381A PHE* 3.8 26.0 - - + -
467A VAL* 4.1 17.3 - - + -
601A HEM 4.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 6.4 0.4 - - + -
190A VAL* 3.7 20.2 - - + -
194A VAL* 3.8 20.6 - - + -
322A VAL* 2.9 25.9 + - + +
323A THR 3.9 3.1 - - - +
325A ALA* 1.3 74.3 - - - +
327A SER* 1.3 64.9 + - - +
329A SER* 3.1 8.6 + - - -
330A LEU* 2.9 37.2 + - + +
467A VAL* 4.5 18.6 - - + +
470A PHE* 3.7 41.7 - - + -
471A LEU* 4.6 13.0 - - + -
474A LEU* 6.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 5.5 4.5 - - - +
187A TYR* 3.8 27.1 + - - +
190A VAL* 5.1 3.1 - - - +
323A THR 2.9 19.4 + - - -
324A THR* 3.6 6.5 - - - -
326A ILE* 1.3 76.7 - - - +
328A TRP* 1.3 62.9 + - - +
330A LEU* 3.3 11.6 + - - +
331A MET* 3.1 24.9 + - - +
500A HIS* 2.5 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR* 3.0 39.7 + - + +
325A ALA* 3.8 4.3 - - - +
327A SER* 1.3 76.3 - - - +
329A SER* 1.3 57.4 + - - +
331A MET* 3.1 9.3 + - + +
332A TYR* 2.8 72.0 + + + -
375A THR* 4.2 7.2 - - + -
379A SER* 4.1 12.8 - - - +
381A PHE* 3.9 12.9 - + + +
490A MET* 3.5 37.5 - - + -
492A PRO* 3.8 25.1 - - + -
498A MET* 3.0 20.4 + - + -
499A LYS 3.5 21.0 - - - -
500A HIS* 3.9 30.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ALA 3.0 17.0 + - - -
326A ILE* 3.4 10.2 - - - -
328A TRP* 1.3 77.0 - - - +
330A LEU* 1.3 57.9 + - - +
332A TYR* 3.1 3.2 + - - +
333A LEU* 2.8 35.1 + - - +
371A PHE* 3.7 21.1 - - - -
372A ILE* 5.5 1.2 - - - +
375A THR* 3.6 20.6 + - - +
467A VAL* 4.9 4.2 - - - +
471A LEU* 4.0 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 3.8 28.5 - - + -
190A VAL* 4.2 17.7 - - + -
326A ILE* 2.9 26.9 + - + +
327A SER* 3.7 9.0 - - - +
329A SER* 1.3 75.2 - - - +
331A MET* 1.3 58.9 + - - +
333A LEU* 3.3 15.8 + - + +
334A VAL* 2.9 31.5 + - - +
471A LEU* 4.6 12.8 - - + -
474A LEU* 5.3 6.5 - - + -
475A LEU* 5.6 0.2 - - + -
480A PHE* 4.1 38.7 - - + +
506A PHE* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 5.9 0.4 - - + -
327A SER 3.1 16.2 + - - +
328A TRP* 3.1 10.3 + - + +
330A LEU* 1.3 76.4 - - - +
332A TYR* 1.3 56.6 + - - +
334A VAL* 3.4 2.2 + - - +
335A MET* 3.0 33.8 + - - +
488A VAL* 3.9 16.6 - - + -
489A ASP 3.8 15.5 - - - +
490A MET* 3.7 30.5 - - + -
500A HIS* 3.5 46.9 - - + +
501A ALA 4.5 3.8 - - - +
503A CYS* 4.6 4.3 - - + -
506A PHE* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TRP* 2.8 60.5 + + + +
329A SER 3.7 3.8 - - - +
331A MET* 1.3 73.6 - - - +
333A LEU* 1.3 61.6 + - - +
336A ASN* 2.8 42.0 + - - +
371A PHE* 4.3 4.0 - - + -
375A THR* 3.9 13.9 - - + -
378A HIS* 2.9 37.9 + + - -
379A SER* 3.3 27.6 + - - -
427A PHE* 3.5 45.1 - + + -
490A MET* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER 2.8 24.8 + - - +
330A LEU* 3.7 16.8 - - + +
332A TYR* 1.3 78.3 - - - +
334A VAL* 1.3 60.0 + - - +
336A ASN 3.2 21.0 - - - +
337A PRO 3.4 2.4 - - - -
339A VAL* 4.0 3.8 - - + -
340A GLN* 3.5 40.9 + - + -
343A ILE* 3.7 18.6 - - + -
371A PHE* 3.4 30.5 - - + -
471A LEU* 4.7 4.7 - - + -
475A LEU* 3.8 33.2 - - + -
480A PHE* 5.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU 2.9 14.3 + - - +
331A MET* 3.9 4.7 - - - +
333A LEU* 1.3 77.4 - - - +
335A MET* 1.3 74.1 + - + +
336A ASN 3.5 0.3 + - - -
337A PRO* 3.7 14.6 - - - +
340A GLN* 4.8 2.5 - - - +
480A PHE* 4.0 5.8 - - + -
481A SER* 3.4 42.2 - - - +
482A VAL* 3.5 30.8 + - + +
488A VAL* 5.2 2.2 - - + -
506A PHE* 3.5 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A MET 3.0 19.3 + - - +
334A VAL* 1.3 93.0 - - + +
336A ASN* 1.3 72.6 + - - +
337A PRO* 3.6 6.3 - - - +
482A VAL* 3.9 8.7 - - + -
488A VAL* 3.4 45.3 - - + +
490A MET* 3.9 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A TYR* 2.8 32.1 + - - +
333A LEU 3.2 8.6 - - - +
335A MET* 1.3 89.9 + - - +
337A PRO* 1.3 66.6 - - - +
338A ARG* 3.1 8.1 + - + +
339A VAL* 3.2 36.9 + - + +
340A GLN 3.4 1.2 + - - -
427A PHE* 3.9 31.8 - - - +
490A MET* 5.7 0.2 - - - +
----------------------------------------------------------
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