Contacts of the helix formed by residues 341 - 368 (chain F) 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 PHE 341 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F GLN 5.4 0.7 - - - -
269F ASP* 3.8 27.8 - - + -
270F MET* 4.3 9.6 - - + -
273F ILE* 3.7 31.2 - - + -
331F ALA* 3.8 9.4 - - - +
334F LEU* 3.8 20.0 - - + -
335F LYS* 3.5 37.2 - - + -
339F LYS 3.3 14.8 - - - -
340F PRO* 1.3 75.2 - - + +
342F ILE* 1.3 62.3 + - + +
343F LYS 3.4 2.2 - - - -
344F GLU* 3.4 10.8 - - + -
345F ALA* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 342 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F GLN* 6.6 0.2 - - + -
269F ASP* 3.6 39.6 - - + +
272F ARG* 5.5 0.5 + - - -
340F PRO* 3.9 4.1 - - + +
341F PHE* 1.3 77.0 - - + +
343F LYS* 1.3 65.7 + - - +
344F GLU* 3.8 0.4 + - - -
345F ALA* 4.0 1.8 - - - +
346F ALA* 3.2 22.3 + - - +
401F VAL* 3.7 13.7 - - + -
405F HIS* 3.3 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 343 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F ARG* 5.3 0.4 - - - +
341F PHE 3.4 0.2 - - - -
342F ILE* 1.3 81.3 - - - +
344F GLU* 1.3 78.8 + - - +
346F ALA* 3.3 6.8 + - - +
347F MET* 2.9 50.8 + - + +
401F VAL* 5.0 2.0 - - - -
402F ILE* 4.1 22.4 - - + +
405F HIS* 3.8 26.3 - - + -
406F LEU* 4.4 20.8 - - + +
409F SER* 5.9 3.6 + - - -
322H GLU* 2.7 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 344 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F LEU* 4.1 2.8 - - - +
330F ARG* 3.5 42.8 + - - +
331F ALA* 3.9 13.3 - - + +
334F LEU* 3.6 31.2 - - + +
340F PRO 3.9 5.0 - - - +
341F PHE* 3.4 17.5 - - - +
342F ILE 3.2 0.5 + - - -
343F LYS* 1.3 96.4 + - - +
345F ALA* 1.3 59.4 + - - +
347F MET* 3.4 3.0 + - - +
348F ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F ASP* 3.4 31.0 - - - +
272F ARG* 4.0 10.9 - - + +
273F ILE* 4.0 13.0 - - + -
331F ALA* 3.8 10.8 - - - +
341F PHE* 2.9 24.1 + - + +
342F ILE 4.0 3.4 - - - +
344F GLU* 1.3 72.4 - - - +
346F ALA* 1.3 60.4 + - - +
348F ALA* 3.4 2.9 + - - +
349F LYS* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F ARG* 4.6 5.8 - - - +
342F ILE 3.2 17.0 + - - +
343F LYS 3.5 4.5 - - - +
345F ALA* 1.3 79.1 - - - +
347F MET* 1.3 56.1 + - - +
349F LYS 3.4 0.3 + - - -
350F LEU* 3.0 31.0 + - - +
398F GLN* 3.3 29.5 - - - +
401F VAL* 3.9 17.3 - - + -
402F ILE* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 347 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F LEU* 4.3 7.6 - - + -
330F ARG* 3.6 11.0 - - - -
343F LYS* 2.9 31.9 + - + +
344F GLU* 3.7 5.2 - - - +
346F ALA* 1.3 72.7 - - - +
348F ALA* 1.3 61.4 + - - +
350F LEU* 3.8 1.1 - - - +
351F ALA* 2.8 33.6 + - - +
402F ILE* 3.8 31.9 - - + -
318H ALA* 3.8 27.4 - - + -
319H LEU* 3.7 26.3 - - + +
322H GLU* 3.5 41.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F ILE* 5.8 1.3 - - - -
276F ALA* 3.9 7.6 - - + -
324F ALA 5.0 0.6 - - - +
327F LEU* 3.6 15.3 - - - +
328F THR* 3.5 37.1 + - + +
331F ALA* 4.7 2.2 - - + -
344F GLU 3.0 17.6 + - - +
345F ALA* 3.7 7.4 - - - +
347F MET* 1.3 73.4 - - - +
349F LYS* 1.3 59.8 + - - +
351F ALA* 3.9 0.8 - - - +
352F ALA* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F ARG* 3.7 32.3 - - + +
275F ILE* 4.1 16.8 - - + -
276F ALA* 4.0 10.6 - - - +
345F ALA 3.0 17.8 + - - +
346F ALA 3.9 2.9 - - - +
348F ALA* 1.3 75.8 - - - +
350F LEU* 1.3 58.1 + - - +
352F ALA* 4.2 0.5 - - - +
353F SER* 3.0 35.9 + - - +
388F THR 2.8 27.1 + - - +
389F GLU* 3.9 9.7 + - - +
391F TYR 2.9 22.1 + - - -
392F GLU* 4.1 4.5 - - - -
393F GLY 2.7 25.8 + - - -
394F THR* 4.5 1.0 - - - +
395F SER* 4.7 0.6 + - - +
398F GLN* 3.7 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F ALA 3.0 18.0 + - - +
347F MET 3.8 3.1 - - - +
349F LYS* 1.3 76.0 - - - +
351F ALA* 1.3 62.8 + - - +
353F SER* 3.1 5.9 + - - -
354F GLU* 3.1 55.3 + - - +
395F SER* 3.7 23.1 - - - +
398F GLN* 4.0 9.9 - - + -
399F ARG* 3.7 36.3 - - + +
402F ILE* 3.6 25.4 - - + -
315H ALA* 6.0 0.7 - - + +
316H ASP* 4.9 1.3 - - - +
319H LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F ALA 5.1 0.2 - - - +
324F ALA* 4.1 13.3 - - + +
327F LEU* 3.4 24.7 - - + -
347F MET 2.8 22.6 + - - +
348F ALA 3.9 2.0 - - - +
350F LEU* 1.3 75.0 - - - +
352F ALA* 1.3 56.6 + - - +
354F GLU* 4.0 3.7 - - - +
355F ALA* 3.0 29.8 + - - +
319H LEU* 4.3 11.4 - - + +
323H SER* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F ALA* 3.3 33.7 - - + +
279F ALA* 3.5 13.9 - - + +
280F LEU* 4.0 15.5 - - + +
283F ALA* 5.4 0.3 - - - +
324F ALA* 3.8 11.0 - - + +
328F THR* 4.6 0.9 - - - +
348F ALA 2.8 22.1 + - - +
349F LYS 4.2 0.2 - - - +
351F ALA* 1.3 70.6 - - - +
353F SER* 1.3 61.2 + - - +
355F ALA* 3.4 2.8 + - - +
356F ALA* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 353 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F ILE* 5.9 0.4 - - - -
279F ALA* 3.8 3.3 - - - +
349F LYS* 3.0 24.2 + - - +
350F LEU* 3.1 8.8 + - - -
352F ALA* 1.3 76.2 - - - +
354F GLU* 1.3 66.2 + - - +
356F ALA* 3.4 3.5 + - - +
357F THR* 3.2 17.3 + - - -
388F THR* 3.2 49.2 + - - -
389F GLU* 3.7 22.0 - - - +
395F SER* 4.1 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 354 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F LEU* 3.1 27.4 + - - +
351F ALA* 4.2 3.2 - - - +
353F SER* 1.3 85.5 + - - +
355F ALA* 1.3 60.3 + - - +
357F THR* 3.5 2.8 + - - -
358F ALA* 3.1 23.9 + - - +
389F GLU* 3.6 21.6 - - + +
395F SER* 3.7 7.5 + - - +
399F ARG* 3.0 40.6 + - - -
319H LEU* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F ALA* 5.2 2.0 - - + -
320F ALA* 4.0 35.7 - - + +
321F LEU* 4.6 1.3 - - - +
324F ALA* 4.7 1.6 - - + -
351F ALA 3.0 20.5 + - - +
352F ALA* 3.7 6.1 - - - +
354F GLU* 1.3 75.2 - - - +
356F ALA* 1.3 56.8 + - - +
358F ALA* 4.5 4.5 - - - +
359F ILE* 2.7 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F ALA* 3.7 26.2 - - + +
282F ILE* 4.6 1.9 - - + +
283F ALA* 4.0 16.8 - - + +
352F ALA 2.9 20.7 + - - +
353F SER 3.4 6.2 + - - +
355F ALA* 1.3 71.6 - - - +
357F THR* 1.3 51.9 + - - +
359F ILE* 4.3 0.2 - - - +
360F SER* 2.7 39.7 + - - -
385F ALA* 3.4 19.1 - - + +
388F THR* 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 357 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361E HIS* 3.7 11.4 - - + +
382E TYR* 3.6 21.7 + - - +
353F SER 3.2 5.6 + - - -
354F GLU 4.0 3.6 - - - +
355F ALA 3.2 0.2 - - - -
356F ALA* 1.3 78.3 - - - +
358F ALA* 1.3 58.1 + - - +
360F SER* 3.1 6.8 + - - -
361F HIS* 2.9 32.1 + - + +
382F TYR* 4.2 3.9 + - + -
385F ALA* 3.6 19.9 + - - +
386F ARG* 3.9 3.6 + - - -
389F GLU* 2.6 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F MET* 5.2 0.6 - - - +
354F GLU 3.1 18.1 + - - +
355F ALA* 4.0 4.9 - - - +
357F THR* 1.3 78.9 - - - +
359F ILE* 1.3 62.1 + - + +
361F HIS* 3.6 5.8 + - - +
362F GLN* 3.2 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 359 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F ALA* 3.5 42.8 - - + +
286F ALA* 4.1 3.1 - - + -
287F LEU* 4.0 11.7 - - + +
317F MET* 3.4 61.0 - - + +
320F ALA* 4.4 3.6 - - + -
321F LEU* 3.8 14.4 - - + +
355F ALA* 2.7 36.0 + - + +
356F ALA 4.3 1.6 - - - +
358F ALA* 1.3 74.1 - - + +
360F SER* 1.3 57.7 + - - +
362F GLN 3.2 1.2 + - - -
363F ALA* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 360 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F ILE* 5.2 1.3 - - - -
286F ALA* 4.0 12.3 - - - +
356F ALA 2.7 24.5 + - - -
357F THR* 3.1 8.0 + - - -
359F ILE* 1.3 75.7 - - - +
361F HIS* 1.3 62.5 + - - +
363F ALA* 3.3 3.2 + - - +
364F ILE* 3.1 26.3 + - - +
378F ALA 4.7 1.3 - - - +
381F HIS* 3.8 14.4 - - - -
382F TYR* 3.3 39.7 - - - +
385F ALA* 3.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 361 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E THR* 3.8 10.9 - - + +
386E ARG* 2.8 54.2 + - - +
389E GLU* 2.8 40.1 + - - -
357F THR* 2.9 20.3 + - + +
358F ALA* 3.7 8.5 - - - +
360F SER* 1.3 75.6 + - - +
362F GLN* 1.3 78.4 + - + +
364F ILE* 3.2 3.7 + - - +
365F GLN* 3.0 11.7 + - - -
382F TYR* 3.5 28.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 362 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E GLU* 5.4 0.4 + - - -
313F LYS* 2.8 46.3 + - + +
317F MET* 3.7 29.4 - - + -
358F ALA* 3.2 18.7 + - + +
359F ILE 3.9 0.7 - - - +
361F HIS* 1.3 102.4 + - - +
363F ALA* 1.3 60.7 + - - +
365F GLN* 3.7 10.8 - - - +
366F ILE* 3.0 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F ALA* 3.5 34.1 - - + +
289F CYS* 5.4 1.1 - - + -
290F ALA* 4.0 14.8 - - + +
317F MET* 4.3 0.7 - - + -
359F ILE 2.9 16.4 + - - +
360F SER 3.5 7.0 - - - +
361F HIS 3.3 0.2 - - - -
362F GLN* 1.3 74.9 - - - +
364F ILE* 1.3 65.3 + - - +
366F ILE* 3.4 1.2 + - - +
367F LEU* 3.2 29.9 + - + +
378F ALA* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E LEU* 4.3 7.9 - - + -
386E ARG* 3.6 25.1 - - + +
390E ILE* 3.9 15.0 - - + +
360F SER 3.1 10.6 + - - +
361F HIS 3.2 7.4 + - - +
363F ALA* 1.3 76.8 - - - +
365F GLN* 1.3 63.3 + - - +
367F LEU* 3.2 4.0 + - - +
368F GLY 3.0 21.3 + - - +
371F GLY* 3.6 31.6 - - - +
372F TYR* 4.4 1.1 - - - +
378F ALA* 3.8 16.6 - - + +
379F GLU* 4.0 7.2 - - - -
382F TYR* 3.6 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386E ARG* 2.9 31.1 + - - +
389E GLU* 3.1 26.9 + - - +
390E ILE* 4.0 7.1 - - - +
394E THR* 3.9 6.3 - - - +
395E SER* 3.7 12.0 + - - +
396E GLU* 2.9 41.0 + - - +
501E FAD 2.7 23.4 + - - +
313F LYS* 4.2 6.3 - - - +
361F HIS* 3.0 11.5 + - - +
362F GLN* 3.8 22.2 - - - +
363F ALA 3.3 0.2 - - - -
364F ILE* 1.3 74.7 - - - +
366F ILE* 1.3 58.6 + - - +
368F GLY* 3.1 12.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501E FAD 3.1 27.5 - - - +
290F ALA* 3.9 30.3 - - + +
293F TYR* 4.0 1.6 - - + -
294F ALA* 4.1 14.8 - - + -
304F LEU* 3.6 13.7 - - + +
310F ILE* 4.1 12.6 - - + -
313F LYS* 3.8 28.9 - - + -
314F LEU* 3.8 29.8 - - + -
317F MET* 4.0 11.4 - - - -
362F GLN 3.0 20.9 + - - +
363F ALA 3.9 3.4 - - - +
364F ILE 3.2 0.2 - - - -
365F GLN* 1.3 78.3 - - - +
367F LEU* 1.3 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501E FAD 4.4 5.2 + - - +
289F CYS* 3.9 9.2 - - - +
290F ALA* 4.1 15.3 - - - -
293F TYR* 3.7 49.8 + - + -
363F ALA 3.2 18.3 + - - +
364F ILE 3.2 1.6 + - - +
366F ILE* 1.3 77.0 - - - +
368F GLY* 1.3 61.2 + - - +
369F GLY 3.5 0.5 + - - -
370F MET* 3.4 16.0 + - + +
371F GLY* 3.4 19.3 - - - +
376F MET* 3.5 42.4 - - + -
378F ALA* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E ILE* 3.8 22.9 - - - +
394E THR* 5.3 0.9 - - - -
501E FAD 4.0 19.3 - - - -
364F ILE 3.0 11.7 + - - +
365F GLN* 3.1 14.7 + - - -
366F ILE 3.1 0.4 - - - -
367F LEU* 1.3 74.6 - - - +
369F GLY* 1.3 65.0 + - - -
371F GLY* 3.0 11.6 + - - -
372F TYR 3.9 2.4 + - - -
----------------------------------------------------------
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