Contacts of the helix formed by residues 307 - 337 (chain A) in PDB entry 2VIG
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 LEU 307 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA* 5.4 7.9 - - + +
300A PHE* 5.5 6.1 - - + -
303A PRO 4.8 2.7 - - - +
304A LEU* 2.9 28.1 + - + +
306A LYS* 1.3 78.9 - - - +
308A GLN* 1.3 65.1 + - - +
310A ILE* 3.2 15.9 + - + +
311A GLN* 3.2 22.7 + - - +
501B FAD 3.4 61.0 - - + +
308D GLN* 3.8 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LYS 3.7 3.7 + - - +
307A LEU* 1.3 72.3 - - - +
309A VAL* 1.3 58.5 + - - +
311A GLN* 3.2 14.9 + - - +
312A PHE* 2.8 36.5 + - + -
400C LEU* 4.1 18.3 - - + +
501C FAD 2.9 35.6 + - - -
307D LEU* 3.8 11.9 - - - +
308D GLN* 3.1 38.7 + - + +
309D VAL* 3.1 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU 3.3 0.8 - - - -
308A GLN* 1.3 77.6 - - - +
310A ILE* 1.3 57.2 + - + +
312A PHE* 3.4 8.8 + - + +
313A LYS* 2.8 48.8 + - + +
396B GLU* 4.3 4.0 - - + -
501B FAD 4.7 5.8 - - + +
308D GLN* 3.2 37.9 + - + +
309D VAL* 4.5 4.5 - - + +
312D PHE* 3.3 48.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
294A ALA* 4.1 20.9 - - + -
304A LEU* 3.4 38.6 - - + +
305A THR* 4.2 2.0 - - - +
307A LEU* 3.2 20.9 + - + +
309A VAL* 1.3 76.3 - - + +
311A GLN* 1.3 58.2 + - - +
313A LYS* 3.3 18.7 + - + +
314A LEU* 2.9 39.6 + - + +
366A ILE* 4.0 25.4 - - + -
501B FAD 4.0 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 3.3 29.3 + - - +
306A LYS* 3.7 13.5 + - - +
307A LEU 3.2 13.5 + - - +
308A GLN* 3.2 16.5 + - - +
310A ILE* 1.3 76.4 - - - +
312A PHE* 1.3 51.6 + - - +
314A LEU* 3.4 7.7 + - - +
315A ALA* 2.8 29.6 + - - +
400C LEU* 3.6 25.9 - - + +
403C ALA* 3.4 31.4 - - + +
404C GLY* 5.2 1.9 + - - -
407C LEU* 4.7 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN 2.8 21.0 + - - +
309A VAL* 3.4 12.1 - - + +
310A ILE 3.3 0.2 - - - -
311A GLN* 1.3 73.4 - - - +
313A LYS* 1.3 65.3 + - - +
315A ALA* 3.1 6.1 + - - +
316A ASP* 3.0 32.3 + - - +
396C GLU* 3.7 36.6 - - + -
399C ARG* 3.6 32.7 - - + +
400C LEU* 3.7 27.6 - - + -
501C FAD 5.1 0.9 - + - -
309D VAL* 3.2 41.3 - - + -
313D LYS* 5.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 2.8 26.7 + - + +
310A ILE* 3.3 22.6 + - + +
312A PHE* 1.3 71.1 - - - +
314A LEU* 1.3 58.6 + - - +
316A ASP* 3.4 7.4 + - - +
317A MET* 3.0 35.1 + - - +
362A GLN* 2.8 36.7 + - + +
365A GLN* 4.4 5.7 - - + +
366A ILE* 3.8 30.1 - - + -
396B GLU* 2.6 44.5 + - - +
399B ARG* 6.0 0.2 - - - +
501B FAD 4.8 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
287A LEU* 4.2 3.7 - - + +
290A ALA* 4.1 11.2 - - + +
291A VAL* 3.9 23.6 - - + +
294A ALA* 4.4 4.7 - - + -
305A THR* 4.1 26.7 - - + -
310A ILE* 2.9 28.2 + - + +
311A GLN* 3.7 7.4 - - - +
313A LYS* 1.3 77.0 - - - +
315A ALA* 1.3 57.6 + - - +
317A MET* 3.5 12.4 + - - +
318A ALA* 3.0 27.4 + - - +
366A ILE* 3.7 24.2 - - + -
403C ALA* 5.4 1.8 - - + -
406C LEU* 3.6 16.0 - - + +
407C LEU* 4.2 17.3 - - + -
----------------------------------------------------------
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 GLN 2.8 19.3 + - - +
312A PHE 3.1 4.2 + - - +
314A LEU* 1.3 69.4 - - - +
316A ASP* 1.3 60.8 + - - +
318A ALA* 3.3 2.9 + - - +
319A LEU* 2.9 31.1 + - - +
399C ARG* 3.4 40.2 - - + +
402C ILE* 4.0 25.3 - - + +
403C ALA* 4.0 4.7 - - - +
406C LEU* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 3.0 23.8 + - - +
313A LYS* 3.7 6.9 + - - +
315A ALA* 1.3 70.7 - - - +
317A MET* 1.3 61.6 + - + +
319A LEU* 3.4 7.6 + - - +
320A ALA* 2.9 32.4 + - - +
350C LEU* 5.0 2.6 - - - +
399C ARG* 3.0 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.9 21.1 - - + -
290A ALA* 3.9 26.2 - - + -
313A LYS 3.0 25.4 + - - +
314A LEU* 3.6 12.6 - - - +
316A ASP* 1.3 78.5 - - + +
318A ALA* 1.3 63.1 + - - +
320A ALA* 3.3 0.6 + - - -
321A LEU* 3.0 20.4 + - - +
359A ILE* 3.5 59.9 - - + +
362A GLN* 3.9 22.0 - - + -
363A ALA* 4.0 5.4 - - + +
366A ILE* 3.9 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.1 11.9 - - + +
314A LEU 3.0 17.0 + - - +
315A ALA* 3.7 5.4 - - - +
317A MET* 1.3 75.9 - - - +
319A LEU* 1.3 56.3 + - - +
321A LEU* 3.4 2.4 + - - +
322A GLU* 3.0 39.7 + - - +
347C MET* 3.7 16.2 - - + -
402C ILE* 4.6 2.0 - - + -
406C LEU* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA 2.9 16.8 + - - +
316A ASP* 3.8 7.4 - - - +
318A ALA* 1.3 74.3 - - - +
320A ALA* 1.3 65.0 + - - +
322A GLU* 4.1 0.2 - - - -
323A SER* 3.1 29.0 + - - -
327C LEU* 3.5 33.2 - - + -
347C MET* 3.5 40.3 - - + +
350C LEU* 3.8 34.3 - - + -
351C ALA* 4.3 11.2 - - + +
354C GLU* 5.9 1.1 - - - +
399C ARG* 5.9 0.9 - - - +
402C ILE* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP 2.9 21.6 + - - +
317A MET* 3.8 4.5 - - - +
319A LEU* 1.3 72.8 - - - +
321A LEU* 1.3 62.3 + - - +
323A SER* 3.9 4.5 - - - -
324A ALA* 3.2 23.4 + - - +
355A ALA* 3.9 22.8 - - + +
358A ALA* 6.2 2.0 - - + -
359A ILE* 4.4 5.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
280A LEU* 3.7 35.9 - - + +
283A ALA* 3.9 11.7 - - + +
284A GLN* 3.5 47.8 - - - +
287A LEU* 4.0 13.2 - - + -
317A MET 3.0 16.5 + - - +
318A ALA* 3.9 3.8 - - - +
320A ALA* 1.3 77.2 - - - +
322A GLU* 1.3 60.4 + - + +
324A ALA* 3.3 4.0 + - + +
325A ARG* 2.9 43.8 + - - +
355A ALA* 4.9 1.3 - - + -
359A ILE* 3.9 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 3.0 24.1 + - - +
319A LEU 4.2 1.8 - - - +
321A LEU* 1.3 77.7 - - + +
323A SER* 1.3 57.0 + - - +
325A ARG* 3.3 9.2 + - - +
326A LEU* 3.0 31.7 + - - +
502A EDO 3.3 24.1 + - - +
327C LEU* 4.6 1.8 - - + -
330C ARG* 2.7 43.5 + - - +
343C LYS* 2.7 32.1 + - - +
347C MET* 3.3 21.4 - - - +
406C LEU* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.1 20.2 + - - -
320A ALA* 3.9 5.2 - - - -
322A GLU* 1.3 73.5 - - - +
324A ALA* 1.3 65.6 + - - +
326A LEU* 3.2 6.9 + - - +
327A LEU* 3.0 25.3 + - - +
351A ALA* 6.1 0.2 - - - +
323C SER* 2.1 39.5 + - - +
326C LEU* 5.3 0.3 - - - +
327C LEU* 4.2 23.5 - - - +
351C ALA* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 3.7 10.3 - - + -
320A ALA 3.2 17.1 + - - +
321A LEU* 3.7 3.6 - - - +
323A SER* 1.3 74.2 - - - +
325A ARG* 1.3 67.8 + - - +
327A LEU* 3.2 5.7 + - - +
328A THR* 2.9 25.3 + - - -
348A ALA* 5.0 1.3 - - - +
351A ALA* 3.9 17.2 - - + +
352A ALA* 3.7 34.5 - - - +
355A ALA* 4.6 3.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
103A GLU* 2.7 36.3 + - - -
280A LEU* 3.4 17.2 - - + +
284A GLN* 2.9 24.8 + - - +
321A LEU* 2.9 32.1 + - - +
322A GLU* 3.6 18.9 - - - +
323A SER 3.3 0.2 - - - -
324A ALA* 1.3 76.4 - - - +
326A LEU* 1.3 62.8 + - - +
328A THR* 3.1 3.1 + - - -
329A TRP* 3.0 61.9 + - + +
502A EDO 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU 3.0 16.3 + - - +
323A SER* 3.2 4.7 + - - +
325A ARG* 1.3 74.6 - - - +
327A LEU* 1.3 62.2 + - - +
329A TRP* 3.4 12.2 + - + +
330A ARG* 3.0 24.1 + - - +
502A EDO 3.6 29.8 - - - +
326C LEU* 3.7 38.0 - - + +
327C LEU* 3.6 36.3 - - + +
330C ARG* 4.1 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A SER 3.0 18.9 + - - +
324A ALA* 3.5 6.5 - - - +
326A LEU* 1.3 74.8 - - - +
328A THR* 1.3 62.2 + - - +
330A ARG* 3.6 30.8 + - - +
331A ALA* 3.3 17.5 + - - +
344A GLU 4.4 2.4 - - - +
347A MET* 4.0 6.1 - - + +
348A ALA* 3.6 19.2 - - - +
351A ALA* 3.4 32.3 - - + -
319C LEU* 3.5 22.9 - - + -
323C SER* 4.1 28.5 - - - +
326C LEU* 3.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA* 4.2 12.3 - - + -
273A ILE* 4.2 14.0 - - + +
276A ALA* 3.6 19.2 - - + +
277A SER* 3.5 24.2 - - - +
280A LEU* 3.6 19.1 - - + +
324A ALA 2.9 13.4 + - - -
325A ARG 3.3 8.3 - - - -
327A LEU* 1.3 76.6 - - - +
329A TRP* 1.3 62.3 + - + +
331A ALA* 3.2 4.9 + - - +
332A ALA* 3.1 24.8 + - - +
348A ALA* 3.6 11.0 + - - +
352A ALA* 4.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.3 28.5 - - + -
42A LEU* 5.9 3.6 - - + -
96A LEU* 3.8 25.1 - - + +
99A ALA* 4.4 9.9 - - + +
100A ILE* 4.1 27.4 - - + +
103A GLU* 4.8 7.0 + - - -
280A LEU* 5.3 1.4 - - - +
325A ARG* 3.0 47.1 + - + +
326A LEU* 3.9 12.3 - - + +
328A THR* 1.3 87.7 - - + +
330A ARG* 1.3 58.7 + - - +
332A ALA* 3.8 1.8 - - - +
333A MET* 2.9 46.9 + - + +
502A EDO 4.0 24.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
326A LEU 3.0 17.2 + - - +
327A LEU* 3.7 21.9 + - - +
328A THR 3.3 0.2 - - - -
329A TRP* 1.3 76.3 - - - +
331A ALA* 1.3 57.2 + - - +
333A MET* 3.2 16.0 + - + +
334A LEU* 2.9 42.4 + - + +
343A LYS* 5.0 0.8 - - - +
344A GLU* 3.7 30.4 + - - +
347A MET* 3.5 21.2 - - - +
322C GLU* 2.9 36.6 + - - +
326C LEU* 4.1 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 4.0 14.5 - - + +
327A LEU 3.3 8.0 + - - +
328A THR 3.2 9.2 + - - +
330A ARG* 1.3 77.8 - - - +
332A ALA* 1.3 58.4 + - - +
334A LEU* 3.2 5.6 + - - +
335A LYS* 2.9 29.3 + - - +
341A PHE* 3.8 6.0 - - - +
344A GLU* 3.8 15.7 - - + +
345A ALA* 3.7 33.4 - - + +
348A ALA* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.6 35.6 - - + +
96A LEU* 3.7 8.5 - - + +
99A ALA* 4.5 3.6 - - + -
273A ILE* 4.1 16.7 - - + +
328A THR 3.1 16.0 + - - +
329A TRP* 3.9 7.2 - - - +
331A ALA* 1.3 75.1 - - - +
333A MET* 1.3 57.1 + - - +
335A LYS* 3.3 2.1 + - - +
336A ASP* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.1 32.8 - - + -
329A TRP* 2.9 40.1 + - + +
330A ARG* 3.6 10.8 - - + +
332A ALA* 1.3 78.5 - - - +
334A LEU* 1.3 55.9 + - + +
336A ASP* 3.3 6.1 + - - -
337A ASN* 2.9 42.0 + - - +
----------------------------------------------------------
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 28.3 + - + +
331A ALA 3.5 5.8 - - - +
333A MET* 1.3 72.4 - - - +
335A LYS* 1.3 65.9 + - - +
337A ASN* 3.1 9.3 + - + -
339A LYS* 2.9 49.1 + - + +
340A PRO 3.7 9.0 - - - +
341A PHE* 3.8 8.5 - - + -
344A GLU* 3.4 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 3.8 13.5 + - - -
95A TYR* 3.5 45.5 - - + -
270A MET* 3.6 25.4 - - + -
273A ILE* 4.5 3.6 - - + -
331A ALA 2.9 13.3 + - - +
332A ALA* 3.6 8.1 - - - +
334A LEU* 1.3 76.5 - - - +
336A ASP* 1.3 65.8 + - - +
338A LYS* 3.1 21.0 + - - +
339A LYS 4.3 0.4 - - - -
341A PHE* 3.6 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 4.7 2.3 - - - +
94A ASP* 3.3 23.3 - - + +
95A TYR* 2.7 31.2 + - - +
96A LEU* 3.0 28.4 + - - +
332A ALA 2.9 21.8 + - - +
333A MET* 3.8 6.9 - - - +
335A LYS* 1.3 74.1 + - - +
337A ASN* 1.3 63.6 + - - +
338A LYS* 3.4 8.2 + - - +
----------------------------------------------------------
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 MET* 2.9 31.8 + - - +
334A LEU* 3.1 4.7 + - + +
335A LYS 3.1 0.8 - - - -
336A ASP* 1.3 83.8 - - - +
338A LYS* 1.3 71.3 - - - +
339A LYS* 3.3 24.8 + - + +
----------------------------------------------------------
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