Contacts of the helix formed by residues 516 - 548 (chain C) in PDB entry 2XER
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 PRO 516 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C ASP* 1.3 96.4 - - + +
517C ASP* 1.3 64.0 + - - +
519C ARG* 3.2 8.9 + - + +
520C ARG* 3.2 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C ASP 3.3 16.7 + - - -
516C PRO* 1.3 72.8 - - - +
518C LYS* 1.3 64.2 + - - +
519C ARG 3.0 4.7 - - - -
520C ARG* 3.3 30.3 - - - +
521C LYS* 3.0 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 518 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C ASP* 2.9 40.8 + - + +
517C ASP* 1.3 84.0 + - - +
519C ARG* 1.3 56.6 + - - +
521C LYS* 4.3 12.8 - - - +
522C THR* 3.4 21.5 + - - -
582C ASP* 4.8 2.9 - - - +
586C GLN* 3.1 36.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 519 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C ASP* 2.9 12.7 + - - +
516C PRO* 3.4 12.3 - - + +
517C ASP 3.0 0.2 - - - -
518C LYS* 1.3 78.9 - - - +
520C ARG* 1.3 65.7 + - - +
521C LYS 3.3 0.2 - - - -
522C THR* 3.3 13.2 + - - -
523C LEU* 3.4 42.3 + - + +
590C ILE* 4.4 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 520 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C PRO* 3.2 13.2 + - - +
517C ASP* 3.3 44.8 + - - +
519C ARG* 1.3 82.0 - - - +
521C LYS* 1.3 63.1 + - - +
523C LEU* 3.0 17.5 + - + +
524C VAL* 2.9 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 521 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C ASP* 3.0 35.5 + - + +
518C LYS* 4.6 9.4 - - - +
520C ARG* 1.3 83.3 - - + +
522C THR* 1.3 57.7 + - - +
524C VAL* 3.6 10.6 - - + +
525C ILE* 3.0 36.1 + - + +
573C LEU* 5.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 522 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LYS 3.4 8.3 + - - -
519C ARG* 3.3 13.3 + - - -
520C ARG 3.1 0.6 - - - -
521C LYS* 1.3 78.1 - - - +
523C LEU* 1.3 58.6 + - - +
525C ILE* 3.5 7.2 + - - +
526C ILE* 3.0 33.6 + - + +
583C HIS* 5.1 4.3 + - - -
586C GLN* 3.1 57.8 + - + +
587C ILE* 4.2 11.3 - - + +
590C ILE* 3.6 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 523 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C ARG* 3.4 39.5 + - + +
520C ARG* 3.0 17.1 + - + +
522C THR* 1.3 75.1 - - - +
524C VAL* 1.3 66.1 + - + +
526C ILE* 3.1 10.2 + - + +
527C GLU* 2.9 29.8 + - + +
590C ILE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 524 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C ARG* 2.9 32.8 + - + +
521C LYS* 3.6 12.3 - - + +
523C LEU* 1.3 76.1 - - + +
525C ILE* 1.3 67.3 + - + +
527C GLU* 3.1 8.7 + - - +
528C LYS* 3.0 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 525 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LYS* 3.0 23.7 + - + +
522C THR* 3.7 5.6 - - - +
523C LEU 3.3 0.2 - - - -
524C VAL* 1.3 80.0 - - + +
526C ILE* 1.3 56.1 + - - +
528C LYS* 4.0 10.8 - - + +
529C THR* 2.7 45.7 + - - +
568C ASN* 3.7 34.1 - - + +
583C HIS* 4.0 22.9 - - + +
587C ILE* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 526 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C THR* 3.0 22.5 + - + +
523C LEU* 3.1 12.8 + - + +
525C ILE* 1.3 76.4 - - - +
527C GLU* 1.3 60.9 + - - +
529C THR* 4.5 3.4 - - - -
530C TYR* 2.8 30.7 + - + +
587C ILE* 4.2 22.7 - - + +
590C ILE* 3.6 44.6 - - + -
592C LYS* 4.0 31.6 - - + -
593C GLY* 3.9 15.7 - - - +
596C MET* 3.6 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ASP* 4.8 9.7 - - - +
558A ARG* 5.2 3.9 + - - -
561A LYS* 5.7 3.3 + - - -
523C LEU* 2.9 19.7 + - + +
524C VAL* 3.1 10.3 + - - +
526C ILE* 1.3 78.2 - - - +
528C LYS* 1.3 65.3 + - + +
530C TYR* 3.1 7.4 + - - +
531C SER* 3.0 26.9 + - - -
592C LYS* 3.8 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 528 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C VAL* 3.0 33.8 + - + +
525C ILE* 4.0 14.1 - - + +
527C GLU* 1.3 77.9 - - + +
529C THR* 1.3 61.5 + - - +
531C SER* 3.4 14.4 + - - -
532C LEU* 3.4 19.6 + - + +
568C ASN* 4.7 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 529 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C ILE* 2.7 25.8 + - - +
528C LYS* 1.3 74.9 - - - +
530C TYR* 1.3 65.2 + - - +
532C LEU* 3.2 8.2 + - - +
533C LEU* 3.1 19.9 + - - +
565C MET* 4.3 18.7 - - + +
568C ASN* 3.2 27.8 + - - +
569C LEU* 4.2 8.1 - - + +
596C MET* 3.5 30.2 - - + +
600C ILE* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 530 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ASP* 4.7 7.0 - - - -
538A ASP* 2.6 30.5 + - - -
542A ARG* 3.7 2.3 + - - -
526C ILE 2.8 19.5 + - - +
527C GLU* 3.1 11.6 + - - +
529C THR* 1.3 74.0 - - - +
531C SER* 1.3 60.4 + - - +
533C LEU* 3.4 6.4 + - + +
534C LEU* 2.9 50.7 + - + +
592C LYS* 3.7 43.2 - - + -
595C ARG* 3.6 12.8 + - - -
596C MET* 3.6 32.1 - - + -
599C ARG* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 531 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A SER* 4.1 20.8 + - - -
534A LEU* 5.5 0.7 - - - +
535A ASP* 6.0 1.9 - - - +
527C GLU 3.0 15.2 + - - -
528C LYS* 3.5 13.2 - - - -
529C THR 3.2 0.4 - - - -
530C TYR* 1.3 77.2 - - - +
532C LEU* 1.3 52.6 - - - +
534C LEU* 3.4 10.2 + - - +
535C ASP* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 532 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C LYS 3.5 15.7 - - - +
529C THR* 3.2 8.0 + - - +
531C SER* 1.3 76.0 - - - +
533C LEU* 1.3 54.9 + - - +
535C ASP* 3.1 7.7 + - - +
536C VAL* 2.8 37.8 + - - +
560C HIS* 5.9 2.0 - - + +
561C LYS* 3.6 36.9 - - + +
564C SER* 3.7 24.2 - - - -
565C MET* 3.5 29.8 - - + +
568C ASN* 4.1 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 533 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C THR 3.1 10.4 + - - +
530C TYR* 3.6 14.6 - - + +
531C SER 3.3 0.2 - - - -
532C LEU* 1.3 75.0 - - - +
534C LEU* 1.3 53.0 + - - +
536C VAL* 3.0 3.2 + - - -
537C GLU* 2.8 60.8 + - + +
565C MET* 3.5 25.0 - - + +
596C MET* 3.8 27.8 - - + +
599C ARG* 3.7 55.4 - - + +
600C ILE* 4.3 0.7 - - + -
603C PHE* 3.9 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 534 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A SER 5.7 0.2 - - - +
534A LEU* 3.9 18.3 - - + +
535A ASP* 3.8 33.0 - - + +
538A ASP* 3.8 16.2 - - + +
541A ARG* 6.4 0.2 - - - +
530C TYR* 2.9 55.1 + - + +
531C SER* 3.5 9.0 - - - +
533C LEU* 1.3 77.1 - - + +
535C ASP* 1.3 57.8 + - - +
537C GLU* 3.7 19.5 - - - +
538C ASP* 2.8 32.2 + - - +
541C ARG* 5.2 0.3 + - - -
599C ARG* 3.7 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 535 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU* 5.7 1.8 - - - +
530A TYR* 5.5 3.2 - - - -
531A SER* 5.6 2.5 + - - -
534A LEU* 4.2 15.5 - - - +
531C SER 2.7 21.1 + - - +
532C LEU* 3.1 11.9 + - - +
534C LEU* 1.3 75.5 - - - +
536C VAL* 1.3 61.5 + - - +
538C ASP* 3.5 4.7 + - - +
539C TYR* 3.3 20.3 + - - +
542C ARG* 5.4 3.5 + - - -
561C LYS* 3.1 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C LEU 2.8 18.6 + - - +
533C LEU* 3.6 8.3 - - - +
535C ASP* 1.3 72.0 - - - +
537C GLU* 1.3 63.7 + - - +
539C TYR* 3.2 9.1 + - - +
540C GLU* 3.1 21.3 + - + +
558C ARG* 4.1 23.3 - - + -
561C LYS* 3.6 30.1 - - + -
562C ILE* 4.6 4.7 - - + -
565C MET* 4.3 10.1 - - - -
603C PHE* 3.4 44.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C LEU* 2.8 40.1 + - + +
534C LEU* 3.7 13.8 - - - +
536C VAL* 1.3 69.8 - - - +
538C ASP* 1.3 61.0 + - - +
540C GLU* 3.3 10.6 + - - +
541C ARG* 2.9 48.7 + - - +
599C ARG* 2.6 52.5 + - - +
603C PHE* 4.3 11.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A TYR* 2.7 36.8 + - - -
534A LEU* 3.4 19.9 - - + +
599A ARG* 3.4 16.8 + - - -
534C LEU 2.8 19.3 + - - +
535C ASP* 3.6 7.5 - - - +
536C VAL 3.2 0.2 - - - -
537C GLU* 1.3 74.1 - - - +
539C TYR* 1.3 58.4 + - - +
541C ARG* 3.3 16.9 + - - +
542C ARG* 2.8 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 5.3 2.3 - - - +
638B SER* 5.9 0.7 - - - -
738B SER* 3.0 28.6 + - - -
535C ASP 3.3 10.1 + - - +
536C VAL* 3.2 10.4 + - - +
538C ASP* 1.3 79.7 + - - +
540C GLU* 1.3 55.5 + - - +
542C ARG* 3.9 16.9 - - - +
543C TYR* 2.7 53.7 + + + +
554C LEU* 3.2 28.9 - - + +
555C MET 3.5 26.0 - - - -
556C ASP* 3.7 14.0 + - - -
557C ASP 5.2 0.4 - - - -
558C ARG* 3.3 52.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B SER* 2.8 26.3 + - - -
642B LEU* 4.4 8.1 - - - +
536C VAL 3.1 14.8 + - - +
537C GLU* 3.5 9.4 - - - +
538C ASP 3.3 0.2 - - - -
539C TYR* 1.3 77.8 - - - +
541C ARG* 1.3 62.8 + - - +
543C TYR* 3.3 5.4 + - - +
544C LEU* 3.2 33.3 + - + +
558C ARG* 2.6 29.8 + - - +
603C PHE* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 6.0 1.6 - - - +
541A ARG* 3.9 46.5 - - - +
599A ARG* 5.9 3.1 - - - +
534C LEU 5.2 0.4 + - - -
537C GLU* 2.9 38.9 + - - +
538C ASP* 3.3 22.9 + - - +
540C GLU* 1.3 79.2 - - - +
542C ARG* 1.3 63.9 + - + +
543C TYR 3.4 0.3 + - - -
544C LEU* 3.6 8.6 + - - +
545C LEU* 3.5 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 542 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A TYR* 3.2 15.7 + - - -
592A LYS* 4.4 8.2 - - - +
599A ARG* 4.4 4.5 - - - +
535C ASP* 5.4 3.8 + - - -
538C ASP* 2.8 44.1 + - - +
539C TYR* 3.9 23.8 - - - +
541C ARG* 1.3 77.0 - - + +
543C TYR* 1.3 57.7 + - - +
545C LEU* 3.3 12.7 + - + +
546C SER* 2.9 25.2 + - - -
551C ARG* 3.5 5.1 - - - +
554C LEU* 2.9 31.3 - - + +
555C MET 5.0 1.0 + - - -
1765C SO4 2.7 31.6 + - - -
1767C SO4 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 543 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B PRO 2.6 28.2 + - - -
635B CYS* 5.3 1.1 - - - -
637B LEU* 2.9 28.6 - - + +
638B SER* 3.8 31.2 - - - -
737B ILE* 3.3 34.6 - - + +
738B SER* 5.1 1.6 - - - -
539C TYR* 2.7 39.9 + + + +
540C GLU* 3.7 6.5 - - - +
541C ARG 3.2 0.4 - - - -
542C ARG* 1.3 70.5 - - - +
544C LEU* 1.3 71.8 + - + +
546C SER* 2.8 23.6 + - - -
547C LEU* 3.3 23.5 + - + +
554C LEU* 3.8 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B CYS 6.2 0.2 - - - +
638B SER* 5.5 5.4 - - - -
540C GLU* 3.2 19.4 + - + +
541C ARG* 4.0 7.4 - - - +
543C TYR* 1.3 89.1 - - + +
545C LEU* 1.3 61.5 + - - +
547C LEU* 3.2 26.0 + - + +
548C GLU* 3.3 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A ARG* 4.4 24.0 - - - +
541C ARG* 3.5 11.2 + - + +
542C ARG* 3.3 14.6 + - + +
543C TYR 3.1 0.2 - - - -
544C LEU* 1.3 75.2 - - - +
546C SER* 1.3 58.0 + - - +
547C LEU 3.0 5.2 - - - -
548C GLU* 3.9 13.7 + - + +
549C GLU* 2.9 49.3 + - + +
551C ARG* 6.5 1.6 - - + -
1767C SO4 4.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B LYS* 5.7 2.9 + - - -
737B ILE* 3.6 24.1 + - - +
542C ARG 2.9 13.7 + - - -
543C TYR* 2.8 22.3 + - - -
545C LEU* 1.3 76.6 - - - +
547C LEU* 1.3 59.9 + - - +
549C GLU 3.3 15.7 - - - +
550C GLU* 4.4 5.5 - - - -
551C ARG* 3.9 29.0 + - - +
554C LEU* 4.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 547 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B PRO* 3.3 39.0 - - + +
635B CYS* 3.7 30.5 - - + -
737B ILE* 4.7 4.7 - - + -
543C TYR* 3.7 31.6 - - + +
544C LEU* 3.2 20.6 + - + +
545C LEU 3.0 0.6 - - - -
546C SER* 1.3 82.7 - - - +
548C GLU* 1.3 66.2 + - + +
549C GLU* 3.2 3.4 + - - -
550C GLU 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 548 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C LEU* 3.3 25.8 + - - +
545C LEU* 3.3 16.5 + - + +
547C LEU* 1.3 77.5 - - + +
549C GLU* 1.3 72.8 + - + +
----------------------------------------------------------
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