Contacts of the helix formed by residues 310 - 342 (chain A) in PDB entry 4F5G
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 310 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 3.6 15.7 + - + +
307A ILE 3.1 4.2 + - - +
308A LEU 3.2 1.5 - - - -
309A SER* 1.3 81.7 + - - +
311A ASP* 1.3 60.5 + - - +
312A ALA* 3.1 12.6 + - - +
313A LEU* 3.0 37.9 + - + +
314A ARG* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU 5.5 1.7 - - - +
309A SER 4.2 1.4 - - - -
310A ASN* 1.3 74.2 + - - +
312A ALA* 1.3 62.7 + - - +
314A ARG* 3.4 7.2 + - - +
315A ALA* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN* 3.1 9.0 + - - +
311A ASP* 1.3 79.4 - - - +
313A LEU* 1.3 62.9 + - + +
315A ALA* 3.2 8.1 + - - +
316A ILE* 3.2 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 3.8 17.4 - - - +
61A LYS* 3.5 41.5 - - + -
62A ALA* 4.4 10.8 - - + +
65A TYR* 5.9 1.1 - - + -
306A THR* 4.0 34.1 - - + +
307A ILE* 3.8 19.9 - - + +
310A ASN* 3.0 19.8 + - + +
312A ALA* 1.3 76.3 - - + +
314A ARG* 1.3 65.8 + - - +
316A ILE* 3.1 10.3 + - + +
317A TRP* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 5.6 5.9 + - - +
91A LEU* 3.8 23.0 - - - +
95A LYS* 6.3 0.8 - - - +
231A LEU* 4.1 8.7 - - - +
232A GLU* 5.9 1.0 + - - -
307A ILE* 3.3 18.8 + - - +
308A LEU* 4.0 36.9 + - + +
310A ASN 2.8 19.1 + - - +
311A ASP* 3.8 7.4 - - - +
313A LEU* 1.3 78.0 - - - +
315A ALA* 1.3 58.0 + - - +
317A TRP* 3.2 8.3 + - + +
318A GLU* 2.7 57.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ASP 3.0 17.7 + - - +
312A ALA* 3.6 7.2 - - - +
313A LEU 3.2 0.2 - - - -
314A ARG* 1.3 78.2 - - - +
316A ILE* 1.3 62.0 + - + +
318A GLU* 3.5 7.9 + - - +
319A GLN* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 4.7 8.5 - - + -
58A SER* 4.0 13.5 - - - +
61A LYS* 3.9 31.9 - - + -
312A ALA* 3.2 17.0 + - + +
313A LEU* 3.1 13.2 + - + +
315A ALA* 1.3 77.8 - - + +
317A TRP* 1.3 64.0 + - - +
319A GLN* 3.2 8.3 + - - +
320A GLU* 3.0 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.8 15.9 - - + -
58A SER* 3.5 10.7 - - - +
91A LEU* 4.4 9.2 - - + -
231A LEU* 3.6 38.4 - - + -
257A ASN* 2.9 27.7 + - - -
258A PHE* 3.4 47.5 - + - -
307A ILE* 3.6 16.6 - - + -
308A LEU* 3.6 28.0 - - + -
313A LEU 2.9 4.8 + - - -
314A ARG* 3.6 9.4 - - + +
316A ILE* 1.3 78.5 - - - +
318A GLU* 1.3 76.2 + - + +
320A GLU* 3.0 10.8 + - - +
321A LEU* 2.8 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 4.0 14.9 - - + +
314A ARG* 2.7 55.2 + - + +
315A ALA* 3.9 6.5 - - - +
317A TRP* 1.3 92.5 - - + +
319A GLN* 1.3 59.2 + - - +
321A LEU* 3.3 7.3 + - - +
322A THR* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA 3.1 13.8 + - - +
316A ILE* 3.2 9.3 + - - +
318A GLU* 1.3 77.8 - - - +
320A GLU* 1.3 57.3 + - + +
322A THR* 3.3 6.7 + - - -
323A ASP* 2.8 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.5 25.7 - - + +
57A THR* 2.7 37.8 + - - -
58A SER* 2.7 38.2 + - - -
316A ILE* 3.0 20.2 + - + +
317A TRP* 3.0 8.9 + - - +
319A GLN* 1.3 76.7 - - + +
321A LEU* 1.3 62.6 + - - +
323A ASP* 3.2 11.4 + - - +
324A MET* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLN 3.8 6.7 - - - +
226A GLY* 3.9 23.8 - - - +
227A PHE* 4.0 10.3 - - + -
231A LEU* 3.7 26.9 - - + -
257A ASN* 3.9 20.0 - - + +
317A TRP* 2.8 47.4 + - + +
318A GLU* 3.6 5.8 - - - +
320A GLU* 1.3 74.2 - - - +
322A THR* 1.3 66.3 + - - +
324A MET* 3.2 21.0 + - + +
325A ARG* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 2.8 21.1 + - - +
319A GLN* 3.5 8.0 - - - -
321A LEU* 1.3 77.1 - - - +
323A ASP* 1.3 59.5 + - - +
325A ARG* 3.1 34.7 + - - +
326A GLN* 2.8 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 4.9 0.7 - - - -
319A GLN* 2.8 36.7 + - - +
320A GLU* 3.2 11.6 + - - +
322A THR* 1.3 80.6 - - - +
324A MET* 1.3 58.2 + - + +
326A GLN* 3.9 8.6 + - - +
327A ARG* 2.9 30.7 + - - +
330A ARG* 4.6 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 3.6 49.1 - - + +
56A LEU* 4.3 26.7 - - + -
227A PHE* 3.7 29.6 - - + -
256A LLP 4.0 5.8 - - - +
257A ASN 4.0 12.8 - - - +
259A GLY 5.4 0.4 - - - +
320A GLU* 3.0 14.8 + - + +
321A LEU* 3.2 27.8 + - + +
323A ASP* 1.3 73.7 - - + +
325A ARG* 1.3 66.0 + - - +
327A ARG* 3.3 2.8 + - - +
328A ILE* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLY* 2.8 41.5 + - - +
227A PHE* 3.7 21.8 - - - +
228A GLY 3.5 17.5 - - - -
229A ARG 3.4 24.3 + - - -
230A GLY* 3.7 11.0 - - - -
231A LEU* 4.8 0.8 - - - +
321A LEU* 2.9 10.4 + - - +
322A THR* 3.1 45.9 + - - +
324A MET* 1.3 77.8 - - - +
326A GLN* 1.3 71.0 + - - +
328A ILE* 3.3 5.0 + - - +
329A GLN* 3.1 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A THR* 2.8 43.6 + - + +
323A ASP* 4.2 7.8 + - - +
325A ARG* 1.3 79.0 + - - +
327A ARG* 1.3 60.5 + - - +
329A GLN* 3.3 18.1 + - - +
330A ARG* 2.9 52.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 3.1 28.6 + - - +
47A LYS 3.0 12.4 + - - -
48A ASP 3.6 11.6 + - - -
49A GLU* 3.6 40.8 - - + +
323A ASP 2.9 18.9 + - - +
324A MET 3.3 0.6 + - - +
326A GLN* 1.3 75.7 - - - +
328A ILE* 1.3 62.9 - - - +
330A ARG* 3.2 24.7 + - - +
331A MET* 3.0 49.2 + - + +
388A ALA* 2.8 37.4 + - - +
390A MET 3.0 24.0 + - - -
391A THR* 4.1 3.2 - - - +
392A PRO* 4.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 3.9 20.6 - - + -
227A PHE* 3.7 29.6 - - + +
324A MET 3.1 16.5 + - - +
325A ARG* 3.6 7.9 - - - +
326A GLN 3.2 0.2 - - - -
327A ARG* 1.3 76.5 - - - +
329A GLN* 1.3 64.6 + - + +
331A MET* 3.2 6.6 + - - +
332A ARG* 3.0 27.7 + - - +
356A GLY* 3.1 33.9 - - - +
357A MET* 3.9 20.9 - - + +
387A VAL* 3.4 17.0 - - + +
388A ALA* 4.4 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE 5.6 1.8 - - - +
228A GLY 3.0 26.7 + - - -
229A ARG* 4.8 3.0 - - - +
325A ARG* 3.1 25.9 + - + +
326A GLN* 3.7 26.2 - - - +
328A ILE* 1.3 77.9 - - + +
330A ARG* 1.3 62.7 + - + +
332A ARG* 3.3 14.5 + - - +
333A GLN* 3.1 22.5 + - - +
352A ILE* 5.7 2.8 - - - +
354A GLN 5.9 1.1 - - - +
355A ASN* 5.3 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 6.1 0.6 - - - +
323A ASP* 4.6 3.2 + - - +
326A GLN* 2.9 45.4 + - + +
327A ARG* 3.2 31.9 + - - +
329A GLN* 1.3 76.8 - - + +
331A MET* 1.3 69.6 + - + +
333A GLN* 3.3 7.2 + - - +
334A LEU* 2.9 30.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
327A ARG* 3.0 33.7 + - + +
328A ILE* 3.2 8.7 + - - +
330A ARG* 1.3 91.6 - - + +
332A ARG* 1.3 59.1 + - - +
334A LEU* 3.9 17.7 - - + -
335A PHE* 2.8 32.6 + - - +
387A VAL* 3.7 20.2 - - + +
390A MET* 3.5 34.5 - - + +
391A THR* 3.7 18.4 - - - -
392A PRO* 4.0 15.3 - - + -
395A MET* 3.7 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 3.0 23.4 + - - +
329A GLN* 3.5 15.0 - - - +
330A ARG 3.3 0.2 - - - -
331A MET* 1.3 78.2 - - - +
333A GLN* 1.3 61.4 + - - +
335A PHE* 3.5 2.7 - - - +
336A VAL* 3.2 28.6 + - - +
351A VAL* 2.8 48.1 + - + +
352A ILE* 4.3 11.9 - - + +
354A GLN* 3.1 32.1 + - - +
355A ASN 4.2 0.4 - - - -
356A GLY 2.8 30.7 + - - +
357A MET 4.1 1.0 - - - -
358A PHE 2.9 30.9 + - - +
359A SER* 2.8 21.2 + - - -
387A VAL* 4.0 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN 3.1 12.8 + - - +
330A ARG* 3.6 9.6 - - - +
332A ARG* 1.3 76.4 - - - +
334A LEU* 1.3 63.5 + - - +
336A VAL* 3.4 2.9 + - - +
337A ASN* 3.0 63.2 + - - +
352A ILE* 3.6 40.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG 2.9 17.5 + - - +
331A MET* 3.9 20.4 - - + +
333A GLN* 1.3 74.9 - - - +
335A PHE* 1.3 58.5 - - - +
337A ASN* 3.8 8.5 - - + +
338A THR* 2.7 49.1 + - - +
392A PRO* 4.0 23.3 - - + +
395A MET* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A MET 2.8 18.7 + - - +
332A ARG* 3.5 5.2 - - - +
334A LEU* 1.3 76.0 - - - +
336A VAL* 1.3 67.0 + - + +
339A LEU* 3.0 54.3 + - + +
348A PHE* 4.4 9.4 - + - -
351A VAL* 4.1 32.3 - - + -
361A SER* 5.7 7.2 - - - -
385A VAL* 5.4 10.1 - - + -
387A VAL* 5.7 0.7 - - + -
390A MET* 3.5 39.7 - - + -
395A MET* 3.7 11.2 - - - +
398A LEU* 4.1 3.1 - - + -
399A CYS* 3.7 16.6 - - - -
402A ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ARG 3.2 14.1 + - - +
333A GLN 3.8 6.3 - - - +
335A PHE* 1.3 78.1 - - + +
337A ASN* 1.3 66.7 + - - +
339A LEU* 3.3 8.4 + - - +
340A GLN* 3.1 24.0 + - + +
347A ASP* 4.9 3.1 - - - +
348A PHE* 3.1 28.9 - - + +
349A SER* 3.9 22.7 - - - +
351A VAL* 3.7 15.0 - - + -
352A ILE* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN* 3.0 51.7 + - - +
334A LEU* 4.0 9.2 - - + +
336A VAL* 1.3 81.1 - - - +
338A THR* 1.3 58.4 + - - +
340A GLN* 3.5 16.4 + - - +
341A GLU* 3.0 40.9 + - + +
352A ILE* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 2.7 34.3 + - - +
337A ASN* 1.3 74.9 - - - +
339A LEU* 1.3 61.8 + - - +
341A GLU* 3.3 13.5 + - + +
342A LYS* 2.9 49.0 + - + +
395A MET* 3.6 17.6 - - + +
396A ALA* 4.1 12.1 - - + -
399A CYS* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 3.0 52.5 + - + +
336A VAL* 3.3 4.2 + - - +
338A THR* 1.3 75.6 - - - +
340A GLN* 1.3 61.4 + - - +
342A LYS* 3.3 3.4 + - - +
343A GLY 3.2 4.5 + - - -
344A ALA* 2.9 38.1 + - + +
348A PHE* 3.6 33.2 - - + -
399A CYS* 3.7 31.9 - - + +
402A ILE* 3.8 26.2 - - + -
403A VAL* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A VAL* 3.1 14.9 + - + +
337A ASN* 3.6 20.6 - - - +
339A LEU* 1.3 77.6 - - - +
341A GLU* 1.3 61.8 + - + +
343A GLY* 2.9 20.6 + - - -
344A ALA* 4.7 4.5 - - - +
346A ARG 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASN* 3.0 27.5 + - + +
338A THR* 3.8 16.9 + - + +
340A GLN* 1.3 82.1 - - + +
342A LYS* 1.3 63.0 + - + +
343A GLY 3.1 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A THR* 2.9 32.5 + - + +
339A LEU* 3.8 0.9 - - - +
340A GLN 3.2 0.4 - - - -
341A GLU* 1.3 79.3 - - - +
343A GLY* 1.3 61.0 + - - +
344A ALA 3.4 0.2 - - - -
396A ALA* 4.2 17.0 - - - +
399A CYS* 4.3 6.7 - - + +
400A GLU* 3.1 44.6 + - + +
403A VAL* 3.5 33.8 - - + +
----------------------------------------------------------
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