Contacts of the helix formed by residues 419 - 447 (chain V) in PDB entry 1I84
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 419 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369V LYS* 3.5 13.9 - - - +
374V ASP* 3.3 25.4 - - + +
375V GLN* 4.3 6.3 - - - +
418V GLN* 1.3 72.1 - - - +
420V LYS* 1.3 70.4 + - - +
421V GLU* 2.4 13.4 + - - +
422V GLN* 2.5 42.9 + - - +
423V ALA* 3.0 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367V PHE* 2.8 25.4 + - + +
368V LYS* 4.6 6.9 - - - +
369V LYS* 2.9 35.4 - - + +
376V ALA* 3.1 32.3 + - + +
419V THR* 1.3 72.5 - - - +
421V GLU* 1.3 92.5 + - - +
423V ALA* 2.7 16.1 - - - +
424V ASP* 2.6 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 421 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369V LYS* 3.0 24.2 + - - +
419V THR* 2.4 13.4 + - - +
420V LYS* 1.3 99.0 + - + +
422V GLN* 1.3 57.6 - - + +
424V ASP* 2.5 31.7 + - - +
425V PHE* 2.8 14.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 422 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416V LYS* 3.7 12.5 + - - +
418V GLN* 2.9 45.5 + - + +
419V THR* 2.5 48.1 + - - +
421V GLU* 1.3 79.7 - - + +
423V ALA* 1.3 60.7 + - - +
424V ASP 3.0 1.4 + - - -
425V PHE* 3.8 10.6 - - - +
426V ALA* 3.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367V PHE* 2.9 47.3 - - + -
376V ALA* 5.2 2.5 - - + +
402V ILE* 4.1 19.1 - - - +
403V LEU* 5.2 6.3 - - + -
418V GLN* 4.3 5.8 - - + +
419V THR 3.0 7.2 + - - +
420V LYS* 2.7 23.3 - - - +
421V GLU 2.9 0.2 - - - -
422V GLN* 1.3 77.5 - - - +
424V ASP* 1.3 56.7 + - - +
426V ALA* 4.4 1.2 - - - +
427V ILE* 3.6 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 424 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279V ARG* 5.7 3.6 - - - +
365V ILE 4.4 9.5 - - - +
366V VAL* 5.1 0.9 - - - +
367V PHE* 3.0 32.6 + - - +
420V LYS* 2.6 30.0 - - - +
421V GLU* 2.5 16.6 + - - +
423V ALA* 1.3 71.6 - - - +
425V PHE* 1.3 52.6 + - - +
426V ALA 2.5 17.3 + - - -
427V ILE* 3.4 10.0 - - + +
428V GLU* 2.5 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 425 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279V ARG* 5.9 0.4 - - - +
421V GLU* 2.8 17.2 + - + +
422V GLN* 3.5 12.3 + - - +
424V ASP* 1.3 70.9 - - - +
426V ALA* 1.3 57.9 + - + +
428V GLU* 3.4 18.2 - - - +
429V ALA* 3.0 33.9 + - + +
599V THR* 3.2 36.6 - - + -
604V PRO* 4.2 26.0 - - + -
605V LEU* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402V ILE* 5.3 7.4 - - + +
418V GLN* 4.2 12.8 - - - +
422V GLN 3.3 16.3 + - - +
423V ALA 4.4 2.9 - - - +
424V ASP 2.5 5.3 + - - -
425V PHE* 1.3 77.2 - - + +
427V ILE* 1.3 53.3 + - - +
428V GLU 2.7 6.5 + - - -
429V ALA 3.1 0.5 + - - -
430V LEU* 2.7 39.3 + - - +
605V LEU* 3.3 9.1 - - + +
606V ASN* 4.4 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 427 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315V PHE* 5.1 0.2 - - - -
362V LEU* 2.8 54.1 - - + +
365V ILE* 3.4 33.4 - - + +
367V PHE* 4.1 8.7 - - + -
398V PHE* 3.3 37.0 - - + -
402V ILE* 3.5 14.5 - - + +
423V ALA 3.6 8.8 + - - +
424V ASP* 2.8 32.6 + - + +
426V ALA* 1.3 75.4 - - - +
428V GLU* 1.3 65.8 + - + +
430V LEU* 3.9 7.2 - - - -
431V ALA* 3.6 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 428 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278V ILE* 3.6 27.0 - - + +
279V ARG* 3.0 46.1 + - - +
315V PHE* 4.9 9.6 - - + -
424V ASP* 2.5 23.7 + - + +
425V PHE* 3.4 19.0 - - - +
426V ALA 2.7 0.2 + - - -
427V ILE* 1.3 72.3 - - + +
429V ALA* 1.3 84.8 + - - +
430V LEU 2.6 14.6 + - - -
431V ALA* 3.1 4.2 + - - +
432V LYS* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 429 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425V PHE* 3.0 24.8 + - + +
426V ALA 3.1 1.6 + - - -
428V GLU* 1.3 93.5 + - - +
430V LEU* 1.3 58.5 + - - +
432V LYS* 3.9 17.8 - - + +
433V ALA* 3.6 12.6 + - - +
604V PRO* 4.4 11.6 - - + +
605V LEU* 3.2 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362V LEU* 3.6 21.3 - - + -
391V MET* 4.2 11.7 - - + -
398V PHE* 4.1 25.1 - - + -
402V ILE* 4.5 1.6 - - + -
426V ALA 2.7 16.4 + - - +
427V ILE* 3.8 7.2 - - - +
428V GLU 2.6 6.5 + - - -
429V ALA* 1.3 75.1 - - - +
431V ALA* 1.3 55.8 + - - +
433V ALA* 3.0 4.3 + - - +
434V LYS* 2.7 35.9 + - + +
605V LEU* 3.4 23.2 - - + +
609V VAL* 4.3 20.9 - - + -
610V THR* 5.6 1.1 - - - +
613V LEU* 4.7 9.4 - - + -
625V TRP* 4.2 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278V ILE* 5.5 0.2 - - + -
315V PHE* 4.3 9.9 - - + -
359V VAL* 4.0 26.7 - - + +
362V LEU* 3.6 33.0 - - + -
427V ILE 3.6 2.4 + - - +
428V GLU 3.1 5.5 + - - +
430V LEU* 1.3 80.9 - - - +
432V LYS* 1.3 58.0 + - - +
434V LYS* 2.7 30.1 + - - +
435V PHE* 2.8 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 432 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274V LYS* 4.1 45.3 - - + +
275V SER* 4.1 17.3 - - - +
277V ALA* 5.0 3.6 - - - -
278V ILE* 3.0 49.9 - - + +
359V VAL* 5.8 0.2 - - - -
428V GLU* 2.9 29.5 + - - +
429V ALA* 3.9 13.7 - - + +
431V ALA* 1.3 77.5 - - - +
433V ALA* 1.3 61.9 + - + +
435V PHE* 3.5 17.1 - - - +
436V GLU 3.7 3.5 + - - -
600V LYS* 5.4 8.3 - - - +
603V ASP* 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274V LYS* 4.6 8.1 - - - +
429V ALA 3.6 16.2 - - - +
430V LEU 3.0 5.2 + - - +
432V LYS* 1.3 79.3 - - + +
434V LYS* 1.3 66.6 + - - +
435V PHE 2.9 2.0 - - - -
436V GLU* 3.5 12.3 + - + +
437V ARG* 3.1 25.8 + - - +
603V ASP* 4.9 9.2 - - - +
605V LEU* 4.6 9.4 - - + -
625V TRP* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 434 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355V VAL* 4.3 18.0 - - + +
358V SER* 3.3 26.2 + - - +
359V VAL* 4.0 11.3 - - + +
362V LEU* 5.2 2.2 - - + -
390V LEU 5.0 1.2 + - - -
391V MET* 3.2 42.7 - - + +
430V LEU* 2.7 14.3 + - + +
431V ALA* 2.7 16.0 + - - +
433V ALA* 1.3 78.8 - - - +
435V PHE* 1.3 63.1 + - - +
437V ARG* 3.3 12.9 - - - +
438V LEU* 3.5 5.0 + - - +
621V VAL* 3.7 17.5 - - - +
624V LEU* 4.2 5.4 - - + +
625V TRP* 3.4 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 435 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234V PHE* 4.3 21.5 - + + -
272V LEU* 4.6 10.1 - - + -
274V LYS* 3.9 16.8 - - + -
277V ALA* 4.5 7.6 - - + -
287V PHE* 3.6 49.6 - + + -
289V ILE* 4.9 4.3 - - + -
290V PHE* 3.8 32.8 - + - -
356V VAL* 5.5 3.1 - - + -
359V VAL* 4.1 17.7 - - + +
431V ALA 2.8 8.9 + - - +
432V LYS* 3.5 13.0 - - - +
434V LYS* 1.3 73.9 - - - +
436V GLU* 1.3 60.4 + - - +
437V ARG 2.9 1.3 - - - -
438V LEU* 2.3 51.2 + - + +
439V PHE* 3.2 5.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 436 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272V LEU* 4.9 15.5 - - + +
274V LYS* 4.0 37.4 + - + +
432V LYS 3.7 3.7 + - - +
433V ALA* 3.5 12.8 + - - +
435V PHE* 1.3 85.3 - - - +
437V ARG* 1.3 65.1 + - - +
438V LEU 3.0 0.9 + - - -
439V PHE* 3.9 5.8 - - - +
440V ARG* 3.1 39.8 + - + +
603V ASP* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433V ALA 3.1 15.7 + - - +
434V LYS* 3.3 13.9 - - - +
435V PHE 2.8 0.6 + - - -
436V GLU* 1.3 79.2 + - - +
438V LEU* 1.3 59.8 + - - +
440V ARG* 4.6 3.8 - - - +
441V TRP* 3.3 19.7 + - - +
624V LEU* 2.9 47.6 + - + +
625V TRP* 2.8 52.4 + - + +
627V ASP* 3.0 34.0 + - - -
628V VAL* 3.3 15.8 - - - +
631V ILE* 4.4 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234V PHE* 5.6 9.6 - - + -
352V ILE* 3.6 44.2 - - + +
355V VAL* 4.1 17.7 - - + +
356V VAL* 4.7 7.9 - - + -
359V VAL* 6.5 0.2 - - + -
434V LYS 3.5 5.1 + - - +
435V PHE* 2.3 46.1 + - + +
437V ARG* 1.3 66.5 - - - +
439V PHE* 1.3 67.6 + - - +
441V TRP* 2.7 20.8 + - + +
442V ILE* 2.9 18.5 + - + +
620V PHE* 3.7 23.1 - - + -
624V LEU* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 439 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231V LEU* 4.2 14.1 - - + -
234V PHE* 2.9 40.1 - + + +
235V GLY* 4.4 0.4 - - - -
248V PHE* 3.8 38.4 - + - -
269V THR* 3.0 27.1 - - + -
272V LEU* 3.3 32.5 - - + -
435V PHE* 3.2 7.9 + - + +
436V GLU* 3.9 7.0 - - - +
438V LEU* 1.3 79.4 - - - +
440V ARG* 1.3 63.8 + - + +
441V TRP 2.8 11.6 + - - -
442V ILE* 3.0 7.7 + - + +
443V LEU* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 440 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268V GLU* 5.3 5.5 + - - -
269V THR* 2.8 54.6 + - - +
270V TYR* 3.2 21.4 + - - +
272V LEU* 5.9 1.2 - - - +
436V GLU* 3.1 31.9 + - + +
437V ARG* 4.6 3.8 - - - +
439V PHE* 1.3 84.9 - - + +
441V TRP* 1.3 49.9 + - - +
443V LEU* 3.8 6.8 - - - +
444V THR* 2.5 31.5 + - - +
666V GLN* 4.9 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 441 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344V PHE* 4.6 1.1 - + - -
348V GLU* 4.1 19.3 - - + -
352V ILE* 3.4 31.6 - - + -
437V ARG 3.3 15.3 + - - +
438V LEU* 2.7 21.7 + - + +
440V ARG* 1.3 71.8 - - - +
442V ILE* 1.3 100.1 + - + +
444V THR* 2.9 18.1 + - - -
445V ARG* 3.1 37.8 + - + +
620V PHE* 3.6 36.1 - + - -
623V ASP* 5.5 9.6 + - - +
624V LEU* 5.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 442 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230V ILE* 4.0 22.0 - - + -
231V LEU* 4.7 3.1 - - + -
234V PHE* 3.7 26.9 - - + -
344V PHE* 3.5 21.3 - - + -
352V ILE* 3.2 43.7 - - + -
438V LEU* 2.9 25.3 + - + +
439V PHE* 3.6 5.8 - - + +
441V TRP* 1.3 88.3 - - + +
443V LEU* 1.3 52.6 + - - +
444V THR 2.8 0.2 + - - -
445V ARG* 2.4 28.7 + - - +
446V VAL* 2.6 17.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231V LEU* 3.9 23.3 - - + +
267V ILE* 3.2 29.8 - - + +
269V THR* 2.9 35.9 - - + -
439V PHE* 2.9 39.0 + - + +
440V ARG* 3.8 10.8 - - - +
442V ILE* 1.3 79.1 - - - +
444V THR* 1.3 59.3 + - + +
446V VAL* 3.9 8.5 - - + +
447V ASN* 3.0 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 444 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440V ARG 2.5 27.8 + - - +
441V TRP* 2.9 8.4 + - - -
442V ILE 2.8 1.0 + - - -
443V LEU* 1.3 77.0 - - + +
445V ARG* 1.3 60.5 + - - +
447V ASN* 4.0 9.5 - - + -
448V LYS* 3.2 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 445 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342V MET* 4.3 7.2 + - - +
343V GLY* 3.5 30.1 + - - -
344V PHE* 3.2 21.0 - - + -
348V GLU* 2.9 32.9 + - - -
441V TRP* 3.1 43.0 + - + +
442V ILE* 2.4 22.3 + - - +
444V THR* 1.3 73.3 - - - +
446V VAL* 1.3 63.4 + - - +
448V LYS* 3.2 34.0 + - - +
449V ALA* 3.7 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227V ALA* 4.1 10.5 - - + -
230V ILE* 4.1 15.7 - - + -
231V LEU* 4.1 24.2 - - + -
267V ILE* 3.9 12.1 - - + -
342V MET* 3.7 25.3 - - + +
344V PHE* 4.2 8.3 - - + -
442V ILE* 2.6 13.9 + - + +
443V LEU* 4.0 6.5 - - + +
445V ARG* 1.3 74.2 - - - +
447V ASN* 1.3 55.6 + - - +
448V LYS 2.7 15.1 + - - -
449V ALA* 2.9 14.6 + - - -
450V LEU* 3.2 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 447 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265V ALA 3.3 4.2 - - - +
266V ASN* 2.9 39.2 + - - +
267V ILE* 2.9 50.4 + - - +
443V LEU* 3.0 21.7 + - - +
444V THR* 4.0 11.7 - - + -
445V ARG 3.4 0.2 - - - -
446V VAL* 1.3 79.8 - - - +
448V LYS* 1.3 58.5 + - - +
449V ALA 3.3 0.7 - - - -
450V LEU* 4.2 6.1 - - - -
451V ASP* 3.4 23.4 - - - +
----------------------------------------------------------
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