Contacts of the helix formed by residues 418 - 449 (chain G) in PDB entry 1MVW
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 THR 418 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368G GLN* 6.2 0.9 - - + -
373G GLU* 3.8 28.5 + - + +
375G ALA* 3.6 3.4 - - - -
417G GLU* 1.3 74.1 - - - +
419G VAL* 1.3 81.3 + - + +
420G SER* 3.8 14.4 - - - +
421G GLU* 2.9 37.4 + - - -
422G VAL* 3.0 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 419 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G PHE* 4.2 19.5 - - + +
367G MLY 4.2 3.6 - - - -
368G GLN* 3.8 42.8 - - + +
373G GLU 5.2 0.2 - - - +
374G GLN 4.5 1.1 - - - +
375G ALA* 3.7 14.5 - - + +
418G THR* 1.3 80.0 - - + +
420G SER* 1.3 66.7 + - - +
422G VAL* 2.9 15.2 + - - +
423G HIS* 3.2 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418G THR* 3.2 10.2 - - - +
419G VAL* 1.3 79.7 - - - +
421G GLU* 1.3 62.4 + - - +
423G HIS* 4.2 6.4 - - - +
424G ASN* 3.4 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 421 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416G GLY 3.9 3.8 - - - +
417G GLU* 3.2 34.8 - - - +
418G THR* 2.9 46.5 + - - +
420G SER* 1.3 78.4 - - - +
422G VAL* 1.3 60.7 + - - +
424G ASN* 3.6 4.5 + - - +
425G SER* 2.9 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 422 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G PHE* 3.6 39.0 - - + -
375G ALA* 3.6 21.8 - - + -
401G LEU* 4.0 29.2 - - + +
402G CYS* 4.7 4.5 - - - -
417G GLU* 4.2 9.0 - - + -
418G THR 3.1 15.9 - - - +
419G VAL 2.9 4.4 + - - +
421G GLU* 1.3 74.8 - - - +
423G HIS* 1.3 59.9 - - - +
424G ASN 2.9 1.1 - - - -
425G SER* 2.6 27.6 + - - +
426G VAL* 2.8 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 423 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G TYR* 4.6 2.9 + - - -
364G LEU 3.8 15.2 + - - -
365G LYS* 3.9 15.6 - - - +
366G PHE* 3.6 45.1 + + + -
419G VAL* 3.2 31.7 + - + +
420G SER* 4.4 7.0 - - - +
422G VAL* 1.3 77.3 - - - +
424G ASN* 1.3 67.0 + - - +
426G VAL* 3.7 7.5 + - - +
427G GLY* 3.3 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 424 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420G SER* 3.4 21.8 + - - +
421G GLU* 4.0 4.5 - - - +
422G VAL 2.9 0.8 - - - -
423G HIS* 1.3 85.3 - - - +
425G SER* 1.3 65.2 + - - +
427G GLY* 3.3 3.4 + - - -
428G ALA* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 425 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401G LEU* 4.5 10.4 + - - +
417G GLU* 4.1 13.3 + - - -
421G GLU 2.9 14.9 + - - -
422G VAL* 2.6 27.4 + - - +
424G ASN* 1.3 70.5 - - - +
426G VAL* 1.3 64.5 + - - +
428G ALA* 2.9 17.6 + - - +
429G LEU* 2.9 20.9 + - - +
604G ASN* 4.7 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 426 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G TYR* 3.8 6.1 - - - +
361G TYR* 3.7 46.6 - - + +
364G LEU* 4.8 5.8 - - + +
366G PHE* 4.3 10.3 - - + -
401G LEU* 4.1 19.7 - - + -
422G VAL* 2.8 35.4 + - + +
423G HIS* 3.7 8.1 - - - +
425G SER* 1.3 76.1 + - - +
427G GLY* 1.3 58.6 + - - +
429G LEU* 2.7 28.9 + - - +
430G ALA* 2.9 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 427 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G THR* 4.6 7.4 - - - -
314G TYR* 3.3 19.3 + - - -
423G HIS 3.3 9.7 + - - -
424G ASN* 3.6 4.3 - - - -
425G SER 3.2 0.4 - - - -
426G VAL* 1.3 80.0 - - - +
428G ALA* 1.3 62.6 + - - +
430G ALA* 3.5 4.0 - - - +
431G MLY 3.0 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424G ASN 3.0 12.1 + - - +
425G SER* 2.9 13.8 + - - +
427G GLY* 1.3 79.9 - - - +
429G LEU* 1.3 58.1 + - + +
431G MLY 3.9 16.8 + - - +
432G ALA* 2.9 27.3 + - - +
601G ASP* 6.0 0.2 - - - +
602G PRO 4.1 20.2 - - - +
603G LEU* 4.1 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G TYR* 4.3 7.4 - - + -
401G LEU* 4.0 25.8 - - + -
425G SER* 2.9 19.5 + - - +
426G VAL* 2.7 14.7 + - - +
428G ALA* 1.3 72.9 - - + +
430G ALA* 1.4 56.3 - - - +
432G ALA* 2.7 5.6 + - + -
433G VAL* 2.6 39.5 + - + +
603G LEU* 4.2 15.9 - - + -
604G ASN* 4.6 11.9 - - + +
607G VAL* 4.2 15.7 - - + -
608G ILE* 4.2 25.1 - - + -
611G TYR* 3.6 26.5 - - + +
623G PHE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G VAL* 4.5 4.5 - - + -
276G THR* 4.8 3.8 - - - +
314G TYR* 3.8 28.7 - - + -
358G VAL* 4.0 23.9 - - + +
361G TYR* 4.3 14.4 - - + -
426G VAL 2.9 10.2 + - - +
427G GLY 3.5 9.2 - - - +
429G LEU* 1.4 74.3 - - - +
431G MLY 1.3 64.0 + - - +
433G VAL* 3.8 3.6 - - - +
434G TYR* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 431 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G MLY 3.4 50.0 - - + +
273G SER* 4.6 18.6 - - - -
275G VAL* 4.4 6.9 - - + +
276G THR* 3.6 29.1 + - + +
277G PHE* 6.6 0.2 - - - -
427G GLY 3.0 24.8 + - - +
428G ALA* 3.9 15.0 - - - +
430G ALA* 1.3 81.2 + - - +
432G ALA* 1.3 63.6 + - - +
434G TYR* 3.4 5.5 + - - +
435G GLU* 3.0 24.6 + - - +
598G MLY 6.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 432 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G MLY 5.4 2.5 - - - -
428G ALA 2.9 17.2 + - - +
429G LEU* 2.7 17.7 + - - +
431G MLY 1.3 74.1 + - - +
433G VAL* 1.3 62.1 + - - +
435G GLU* 3.5 3.0 - - - +
436G MLY 3.2 44.6 + - - +
601G ASP* 5.5 0.4 - - - +
603G LEU* 3.9 26.9 - - + -
623G PHE* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 433 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354G LEU* 4.8 10.1 - - + +
358G VAL* 4.7 10.1 - - + -
361G TYR* 5.6 0.4 - - + -
390G MET* 4.2 20.9 - - + -
429G LEU 2.6 26.5 + - - +
430G ALA* 3.8 4.7 - - - +
432G ALA* 1.3 70.8 - - - +
434G TYR* 1.3 66.8 + - - +
436G MLY 3.7 2.0 - - - +
437G MET* 3.1 24.7 + - + +
611G TYR* 3.7 34.3 - - + +
619G LEU* 4.5 14.8 - - + -
622G LEU* 4.3 5.6 - - + +
623G PHE* 3.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 434 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G PHE* 2.8 59.9 + + + -
270G LEU* 4.4 16.8 - - + -
272G MLY 6.3 0.2 - - - -
275G VAL* 3.9 30.7 - - + -
285G TYR* 3.7 19.1 - + - +
287G ILE* 4.0 2.8 - - + +
288G PHE* 3.9 24.5 - + - -
355G THR* 5.0 4.0 - - + -
358G VAL* 4.8 11.4 - - + +
430G ALA 3.1 15.4 + - - +
431G MLY 3.5 4.9 - - - +
433G VAL* 1.3 78.4 - - - +
435G GLU* 1.4 72.7 + - - +
437G MET* 3.1 20.1 - - + +
438G PHE* 2.9 19.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G LEU* 4.5 17.8 + - + +
272G MLY 2.8 57.0 - - + +
431G MLY 3.0 9.8 + - - +
432G ALA 3.5 6.7 - - - +
434G TYR* 1.4 80.8 - - - +
436G MLY 1.3 69.4 + - - +
438G PHE* 2.5 38.9 + - - +
439G LEU* 2.8 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 436 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G MLY 4.2 2.9 - - - -
432G ALA* 3.2 38.4 + - - +
433G VAL* 3.7 5.2 - - - +
435G GLU* 1.3 101.5 + - - +
437G MET* 1.3 52.3 + - - +
439G LEU* 2.8 20.2 + - + +
440G TRP* 2.7 34.5 + - - +
601G ASP* 3.6 22.9 - - - -
603G LEU* 4.3 5.1 - - - +
622G LEU* 3.5 36.5 - - + +
623G PHE* 4.0 15.0 - - + -
626G TYR* 0.8 136.2 + - + -
646G PHE* 5.3 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 437 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G PHE* 4.0 21.5 - - + -
351G ILE* 3.9 14.4 - - + +
354G LEU* 3.8 30.5 - - + -
355G THR* 2.9 33.7 - - - +
433G VAL* 3.1 12.6 + - - +
434G TYR* 3.1 25.6 - - + +
436G MLY 1.3 79.8 + - - +
438G PHE* 1.3 64.6 + - - +
440G TRP* 2.9 20.4 + - + +
441G MET* 2.8 32.8 + - + +
622G LEU* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 438 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G LEU* 3.9 23.1 - - + -
232G PHE* 3.8 21.3 - - + -
233G GLY* 3.8 22.0 - - - -
246G PHE* 4.1 27.6 - + - -
267G THR* 3.4 34.8 - - + -
270G LEU* 4.1 20.6 - - + -
434G TYR* 2.9 12.2 + + + +
435G GLU* 2.5 19.1 + - - +
437G MET* 1.3 77.3 - - - +
439G LEU* 1.3 73.9 + - + -
441G MET* 3.4 15.1 + - + +
442G VAL* 3.2 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G THR* 4.7 13.5 - - + -
270G LEU* 5.6 1.8 - - + -
435G GLU* 2.8 42.6 + - + +
436G MLY 2.8 20.0 + - + +
438G PHE* 1.3 95.6 - - + +
440G TRP* 1.3 62.4 + - - +
442G VAL* 3.1 9.7 + - - +
443G ILE* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 440 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G PHE* 4.2 7.2 - + - -
347G GLU* 3.5 45.5 - - + -
351G ILE* 4.1 26.5 - - + -
436G MLY 2.7 13.8 + - - +
437G MET* 3.1 25.4 - - + +
439G LEU* 1.3 73.4 - - - +
441G MET* 1.3 64.5 - - + +
443G ILE* 2.8 21.0 + - + +
444G ARG* 2.7 54.0 + - + +
618G THR* 3.6 32.3 - - + -
621G LEU* 5.2 14.6 - - + +
622G LEU* 4.2 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 441 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU* 4.3 15.0 - - + -
229G LEU* 5.1 4.3 - - + -
232G PHE* 3.8 44.0 - - + -
343G PHE* 3.7 21.0 - - + -
351G ILE* 3.6 31.2 - - + -
437G MET* 2.8 24.2 + - + +
438G PHE* 3.5 33.2 - - + +
440G TRP* 1.3 75.0 - - + +
442G VAL* 1.3 65.9 + - + +
444G ARG* 3.2 1.2 + - - -
445G ILE* 2.8 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 442 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G LEU* 4.1 24.2 - - + -
265G ILE* 3.9 39.5 - - + +
266G GLU* 4.9 2.2 - - - -
267G THR* 3.7 23.3 - - - +
438G PHE* 3.2 19.0 + - + +
439G LEU* 3.1 9.6 + - - +
440G TRP 3.0 0.2 - - - -
441G MET* 1.3 77.4 - - - +
443G ILE* 1.3 63.8 + - + +
445G ILE* 2.9 19.1 + - - +
446G ASN* 2.9 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 443 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G LEU* 3.0 22.7 + - + +
440G TRP* 2.8 21.2 + - + +
442G VAL* 1.3 78.7 - - + +
444G ARG* 1.3 69.0 + - + +
446G ASN* 3.1 16.9 + - + +
447G GLN* 2.8 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G GLY 3.3 24.7 + - - -
343G PHE* 3.5 27.8 - - + +
344G SER* 4.5 0.6 - - - +
347G GLU* 3.4 32.9 + - - -
440G TRP* 2.7 45.9 + - + +
441G MET 3.7 0.2 - - - +
443G ILE* 1.3 75.8 - - + +
445G ILE* 1.3 65.8 + - - +
447G GLN* 3.0 49.4 + - - +
448G GLN* 3.2 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G ALA* 4.4 11.7 - - + +
228G LEU* 3.9 15.9 - - + -
229G LEU* 3.9 35.7 - - + -
265G ILE* 4.2 13.7 - - + -
341G LEU* 3.9 21.1 - - + -
343G PHE* 4.3 14.8 - - + -
441G MET 2.8 26.4 + - - +
442G VAL* 3.0 9.2 - - - +
444G ARG* 1.3 74.6 - - - +
446G ASN* 1.3 65.6 + - - +
448G GLN* 2.7 20.5 + - - +
449G LEU* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 446 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G ALA 4.8 2.2 - - - +
264G ASP* 3.4 10.4 + - - -
265G ILE* 2.6 50.7 + - - +
442G VAL* 2.9 17.9 + - - +
443G ILE* 3.2 19.4 - - + +
445G ILE* 1.3 75.4 - - - +
447G GLN* 1.3 62.2 + - + +
449G LEU* 3.1 20.1 + - - +
450G ASP* 3.2 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 447 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443G ILE* 2.8 37.3 + - - +
444G ARG* 3.2 46.9 + - - +
445G ILE 2.8 1.2 + - - -
446G ASN* 1.3 75.3 - - + +
448G GLN* 1.3 65.1 + - - +
450G ASP* 3.4 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 448 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G LEU* 5.8 1.0 - - - +
221G GLN* 4.0 15.8 - - - +
340G ILE 5.1 0.4 - - - +
341G LEU* 2.6 34.2 + - + +
342G GLY* 3.5 12.8 - - - +
444G ARG* 3.2 41.9 + - - +
445G ILE* 2.7 12.6 + - - +
447G GLN* 1.3 71.6 - - - +
449G LEU* 1.3 64.0 + - + +
450G ASP 2.8 22.1 + - - +
451G THR* 4.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G LEU* 4.5 14.7 - - + +
221G GLN* 3.6 33.0 - - + +
222G ILE* 4.7 11.0 - - + +
225G ALA* 5.2 1.1 - - + -
262G SER* 3.7 8.7 - - - -
263G ALA* 3.5 53.6 + - + +
265G ILE* 4.7 12.8 - - + -
341G LEU* 4.5 4.5 - - + -
445G ILE* 3.0 33.3 + - + +
446G ASN* 3.1 14.1 + - - +
448G GLN* 1.3 83.4 - - + +
450G ASP* 1.3 56.0 + - - +
451G THR* 3.9 3.9 + - - +
----------------------------------------------------------
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