Contacts of the helix formed by residues 358 - 390 (chain B) in PDB entry 6M04
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 MET 358 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B MET* 3.3 51.1 - - - +
46B GLN* 3.6 17.3 - - + +
49B LYS* 3.2 31.9 - - + +
50B ASP* 3.7 17.9 - - - +
356B HIS* 3.2 28.4 - - + +
357B ASN* 1.3 80.8 - - - +
359B ALA* 1.3 54.0 + - - +
360B TYR 3.3 1.9 + - - -
361B MET* 3.4 6.2 + - - +
362B LEU* 2.8 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A HIS* 5.2 0.4 - - - -
333B ILE* 4.2 12.9 - - + +
334B SER 3.4 26.9 - - - +
335B PHE* 3.9 25.5 - - + -
356B HIS* 3.7 12.2 + - + +
357B ASN 3.5 3.0 + - - -
358B MET* 1.3 77.0 - - - +
360B TYR* 1.3 60.9 + - + +
362B LEU* 4.1 2.1 - - - +
363B LYS* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A HIS* 3.7 44.9 + + + +
156A LEU* 5.0 6.2 - - - +
164A TYR* 3.5 19.1 - - - +
335B PHE* 3.5 47.9 - + + +
357B ASN 5.3 0.4 + - - -
358B MET 3.4 0.2 - - - -
359B ALA* 1.3 75.9 - - + +
361B MET* 1.3 64.6 + - - +
363B LYS* 3.3 22.8 + - - +
364B LYS* 3.0 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 6.2 0.4 - - - +
155A HIS* 6.1 0.8 - - - -
163A LYS* 4.7 2.0 - - + +
164A TYR* 3.6 34.9 + - + +
167A TYR* 3.6 37.9 - - + -
41B PHE* 5.0 7.6 - - - -
45B MET* 3.6 35.0 - - + -
49B LYS* 5.7 8.1 - - - +
357B ASN 5.6 2.2 + - - +
358B MET* 3.4 8.3 + - - +
360B TYR* 1.3 78.8 - - - +
362B LEU* 1.3 57.8 + - - +
364B LYS* 3.9 4.8 - - - -
365B LEU* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B MET* 4.9 7.1 - - + +
46B GLN* 5.6 4.3 - - + -
162B SER* 4.0 26.9 - - - +
163B LYS* 5.8 0.9 - - - -
165B PHE* 4.8 20.3 - - + -
166B PRO* 4.9 14.1 - - + -
329B PHE* 4.7 11.2 - - + -
333B ILE* 4.0 24.7 - - + -
356B HIS* 5.7 1.3 - - - +
358B MET* 2.8 41.2 + - + +
359B ALA* 4.1 2.2 - - - +
361B MET* 1.3 75.1 - - - +
363B LYS* 1.3 58.1 + - - +
365B LEU* 3.7 12.0 - - + +
366B LEU* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B VAL* 5.0 9.6 - - + +
333B ILE* 4.3 28.7 - - + +
359B ALA 2.9 19.2 + - - +
360B TYR* 3.9 23.3 - - - +
362B LEU* 1.3 78.9 - - - +
364B LYS* 1.3 78.2 + - + +
366B LEU* 3.3 7.8 + - + +
367B ILE* 3.0 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.6 40.8 - - + +
360B TYR* 3.0 23.5 + - - +
361B MET* 4.0 6.7 - - - +
363B LYS* 1.3 93.7 - - + +
365B LEU* 1.3 64.7 + - - +
367B ILE* 3.2 18.6 - - + +
368B SER* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.8 31.1 - - + +
41B PHE* 4.3 23.1 - - + -
42B ALA* 3.6 32.5 - - + +
45B MET* 4.1 19.7 - - + -
165B PHE* 5.5 8.3 - - + -
166B PRO* 6.0 0.9 - - + -
361B MET* 2.9 21.1 + - + +
362B LEU* 3.7 9.6 - - + +
364B LYS* 1.3 77.5 - - - +
366B LEU* 1.3 56.9 + - - +
368B SER* 3.4 7.9 + - - -
369B TYR* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 3.6 24.7 - - + -
326B THR* 4.5 3.4 - - + -
329B PHE* 3.6 42.8 - - + -
330B VAL* 3.7 29.4 - - + -
333B ILE* 3.8 19.1 - - + -
362B LEU* 2.9 20.8 + - + +
363B LYS* 3.4 7.6 - - + +
365B LEU* 1.3 77.1 - - - +
367B ILE* 1.3 58.4 + - - +
369B TYR* 3.3 4.6 + - - +
370B ILE* 2.9 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B VAL* 4.5 22.9 - - + -
363B LYS* 3.0 25.6 + - + +
364B LYS* 3.2 26.2 - - + +
366B LEU* 1.3 79.5 - - + +
368B SER* 1.3 57.1 + - - +
370B ILE* 3.8 6.5 - - - +
371B SER* 3.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 5.9 2.8 - - - +
38B VAL* 4.9 6.3 - - - +
364B LYS 3.1 16.6 + - - -
365B LEU* 3.7 11.4 - - - -
366B LEU 3.2 0.2 - - - -
367B ILE* 1.3 79.6 - - - +
369B TYR* 1.3 59.8 + - - +
371B SER* 2.6 23.6 + - - -
372B ILE* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B MET* 3.5 38.8 - - + -
38B VAL* 4.4 18.1 - - + +
39B ALA* 5.8 0.7 - - + -
165B PHE* 3.8 27.8 - + + -
168B LEU* 5.7 2.4 - - + +
169B ALA* 4.0 30.9 + - + -
172B HIS* 4.0 13.9 - - - +
322B ILE* 3.9 20.9 - - + +
326B THR* 5.2 2.9 - - + -
365B LEU* 2.9 18.1 + - + +
366B LEU* 3.5 4.9 - - - +
368B SER* 1.3 76.5 - - - +
370B ILE* 1.3 77.4 + - + +
372B ILE* 3.3 9.6 + - - +
373B ILE* 3.0 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ILE* 5.1 2.9 - - + +
323B LEU* 5.5 12.1 - - + -
326B THR* 3.3 37.7 - - + +
330B VAL* 4.9 8.1 - - + -
366B LEU* 2.9 34.0 + - + +
367B ILE* 4.0 6.5 - - - +
368B SER 3.2 0.4 - - - -
369B TYR* 1.3 95.2 - - + +
371B SER* 1.3 61.4 + - - +
373B ILE* 4.1 8.4 - - + +
374B CYS* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ILE 3.0 12.1 + - - -
368B SER* 2.6 27.9 + - - -
370B ILE* 1.3 77.1 - - - +
372B ILE* 1.3 63.1 + - - +
374B CYS* 3.8 5.2 - - - +
375B VAL* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.6 26.0 - - + +
34B VAL* 4.2 19.3 - - + -
35B MET* 3.9 26.7 - - + -
38B VAL* 4.1 25.6 - - + -
368B SER* 3.0 21.8 + - - +
369B TYR* 3.5 9.4 - - - +
371B SER* 1.3 84.2 + - - +
373B ILE* 1.3 58.1 + - + +
375B VAL* 3.3 7.7 + - - +
376B TYR* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.4 0.2 - - + -
35B MET* 3.8 35.4 - - + -
172B HIS* 5.7 0.4 - - + -
176B LEU* 4.7 8.7 - - + -
319B PHE* 3.3 21.5 - - + +
322B ILE* 3.6 27.6 - - + -
323B LEU* 5.6 4.0 - - + -
369B TYR* 3.0 37.5 + - + +
370B ILE* 4.1 9.2 - - + +
372B ILE* 1.3 77.1 - - + +
374B CYS* 1.3 60.1 + - - +
376B TYR* 3.4 13.4 - - + +
377B GLY 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PHE* 4.1 10.8 - - - -
323B LEU* 4.6 15.4 - - + +
370B ILE* 2.9 20.8 + - + +
371B SER* 3.8 6.5 - - - +
373B ILE* 1.3 76.6 - - - +
375B VAL* 1.3 57.2 + - - +
378B PHE* 3.0 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.9 20.2 - - + -
371B SER* 3.0 16.0 + - - +
372B ILE* 3.5 9.4 - - - +
374B CYS* 1.3 76.5 - - + +
376B TYR* 1.3 63.3 + - - +
378B PHE* 4.7 2.5 - - - -
379B ILE* 3.0 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B MET* 3.4 61.9 + - + +
31B LEU* 3.5 23.5 - - + +
32B ALA* 4.6 4.1 - - + +
176B LEU* 3.4 52.2 + - + +
180B SER* 4.9 7.4 - - - -
315B LYS* 3.8 22.9 - - + +
319B PHE* 5.5 5.4 - + + -
372B ILE 3.0 14.5 + - - +
373B ILE* 3.3 18.4 + - + +
375B VAL* 1.3 77.4 - - - +
377B GLY* 1.3 63.5 + - - +
380B CYS* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LYS* 4.2 3.8 + - - -
319B PHE* 3.5 38.3 - - - -
373B ILE 2.9 13.9 + - - -
376B TYR* 1.3 78.7 - - - +
378B PHE* 1.3 56.5 + - - +
380B CYS* 5.0 1.6 - - - -
381B LEU* 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PHE* 4.2 3.6 - - + -
374B CYS* 3.0 25.1 + - - +
375B VAL* 4.0 3.8 - - - +
377B GLY* 1.3 75.7 - - - +
379B ILE* 1.3 77.6 + - + +
381B LEU* 3.9 7.4 - - + +
382B TYR* 3.0 51.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 5.5 5.4 - - + +
24B TRP* 5.0 8.7 - - + -
27B PHE* 5.1 9.9 - - + -
28B MET* 3.9 20.0 - - + -
31B LEU* 6.1 0.7 - - + -
375B VAL* 3.0 32.3 + - + +
376B TYR 4.0 1.8 - - - +
378B PHE* 1.3 88.9 - - + +
380B CYS* 1.3 65.4 + - - +
382B TYR* 4.1 1.1 - - - -
383B THR* 3.0 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 4.8 4.0 - - - -
28B MET* 3.6 35.2 - - + -
315B LYS* 3.2 34.8 - - + +
376B TYR* 3.0 17.3 + - + +
379B ILE* 1.3 77.8 - - - +
381B LEU* 1.3 58.1 + - - +
383B THR* 5.2 0.4 - - - -
384B LEU* 2.9 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B THR* 6.2 0.2 - - - -
315B LYS* 3.1 12.2 - - - +
316B THR* 3.7 28.9 - - + +
319B PHE* 4.5 14.6 - - + -
320B ILE* 5.0 5.8 - - + -
377B GLY 2.8 21.4 + - - +
378B PHE* 3.9 7.9 - - + +
380B CYS* 1.3 76.9 - - - +
382B TYR* 1.3 68.2 + - + +
384B LEU* 4.2 1.4 - - - +
385B PHE* 2.9 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B PHE* 3.0 42.3 + + + +
379B ILE* 4.1 2.2 - - - +
381B LEU* 1.3 87.0 - - + +
383B THR* 1.3 63.0 + - - +
385B PHE* 3.4 9.7 + + + +
386B TRP* 3.0 81.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.6 35.8 + - + -
24B TRP* 3.6 25.4 - - + -
379B ILE* 3.0 22.9 + - - +
380B CYS* 4.7 1.1 - - - -
382B TYR* 1.3 83.4 - - - +
384B LEU* 1.3 63.0 + - - +
386B TRP* 3.3 10.1 + - + +
387B LEU* 2.9 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.4 43.7 - - + +
308B TYR* 3.7 25.4 - - + +
312B THR* 3.3 43.4 - - + +
380B CYS* 2.9 39.4 + - - +
381B LEU* 4.2 1.6 - - - +
383B THR* 1.3 75.3 - - - +
385B PHE* 1.3 60.1 + - - +
387B LEU* 3.6 8.0 - - + +
388B PHE* 2.8 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 2.9 24.8 + - + +
382B TYR* 3.4 10.8 - + - +
384B LEU* 1.3 76.8 - - - +
386B TRP* 1.3 80.2 + + - +
388B PHE* 3.1 12.4 + + - +
389B ARG* 3.0 75.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B TYR* 3.0 62.8 + + - +
383B THR* 3.3 11.2 + - + +
385B PHE* 1.3 102.8 - + - +
387B LEU* 1.3 60.3 + - - +
388B PHE 3.2 0.2 - - - -
389B ARG* 6.1 0.4 - - + -
390B ILE* 3.4 42.2 + - + +
391B PRO* 4.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.6 36.8 - - + -
305B TYR* 6.0 2.1 - - - -
308B TYR* 5.9 5.4 - - + -
383B THR* 2.9 15.7 + - + +
384B LEU* 3.6 9.5 - - + +
386B TRP* 1.3 76.4 - - - +
388B PHE* 1.3 59.6 + - - +
391B PRO* 3.8 30.4 - - + +
421B HIS* 6.2 5.2 - - + -
422B MET* 5.8 9.6 - - + -
425B GLN* 4.6 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TYR* 4.3 24.2 + + - -
309B VAL* 3.6 44.9 - - + -
312B THR* 6.1 4.0 - - + -
384B LEU 2.8 18.9 + - - +
385B PHE* 3.1 16.1 + + - +
387B LEU* 1.3 81.1 - - - +
389B ARG* 1.3 79.2 + - + +
390B ILE 3.6 0.4 + - - -
391B PRO* 4.7 0.6 - - - +
392B LEU* 4.7 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PHE* 3.0 56.9 + - + +
386B TRP* 6.1 0.4 - - + -
388B PHE* 1.3 93.8 - - + +
390B ILE* 1.3 82.1 + - + +
392B LEU* 4.0 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B TRP* 3.4 33.3 + - + +
389B ARG* 1.3 100.5 - - + +
391B PRO* 1.3 70.7 - - + +
392B LEU* 3.4 8.7 + - - +
----------------------------------------------------------
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