Contacts of the helix formed by residues 699 - 728 (chain B) in PDB entry 3KN5
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 699 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LYS* 5.3 7.6 - - - +
616B LEU 5.0 2.6 + - - -
617B SER 4.4 2.0 - - - +
651B GLU* 3.5 54.7 - - + +
652B ALA* 4.1 15.3 + - + +
697B PRO 5.6 0.4 - - - +
698B LEU* 1.3 75.0 - - - +
700B THR* 1.3 57.2 + - - +
701B PRO 3.6 1.1 - - - -
702B ASP* 2.7 43.0 - - + +
703B ILE* 3.1 40.6 + - + +
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Residues in contact with THR 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ILE* 3.5 6.6 - - - +
516B PHE* 3.7 12.8 - - + -
614B THR 4.2 1.2 + - - -
615B MET* 3.0 27.9 + - - +
616B LEU 4.2 4.9 - - - -
617B SER 4.1 6.2 + - - -
618B GLY* 3.7 22.0 - - - -
698B LEU* 3.7 12.8 - - + -
699B MET* 1.3 69.9 - - - +
701B PRO* 1.3 75.4 - - + +
702B ASP 2.8 6.0 + - - -
703B ILE 4.3 0.7 - - - +
704B LEU* 2.9 45.4 + - - +
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Residues in contact with PRO 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ILE* 3.3 22.2 - - + +
511B LYS* 3.8 13.9 - - - +
513B LYS 3.1 25.6 - - - +
514B LYS* 5.1 4.7 - - + +
516B PHE* 3.5 30.1 - - + +
698B LEU 3.7 12.8 - - - +
700B THR* 1.3 100.3 - - + +
702B ASP* 1.3 60.5 + - - +
705B GLY* 3.3 16.9 + - - -
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Residues in contact with ASP 702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LYS* 4.7 12.1 + - - -
514B LYS* 6.1 0.9 - - - +
698B LEU 5.0 1.7 - - - +
699B MET* 2.7 35.9 - - + +
700B THR 2.8 0.6 - - - -
701B PRO* 1.3 81.6 - - - +
703B ILE* 1.3 59.5 + - + +
705B GLY* 3.2 17.5 + - - -
706B SER* 3.5 10.0 + - - -
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Residues in contact with ILE 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B SER 3.0 26.7 - - - +
618B GLY* 3.7 21.3 - - - +
619B GLN* 4.7 9.9 - - + +
652B ALA* 4.2 9.9 - - + -
699B MET* 3.1 40.2 + - + +
700B THR 4.2 1.3 - - - +
702B ASP* 1.3 75.8 - - + +
704B LEU* 1.3 69.2 + - + +
705B GLY 3.0 1.1 - - - -
706B SER* 3.0 16.4 + - - +
707B SER* 3.0 30.0 + - - +
711B VAL* 5.4 2.5 - - + -
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Residues in contact with LEU 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B PHE* 3.6 40.2 - - + +
510B ILE* 3.9 11.4 - - + -
511B LYS* 3.6 24.3 + - + +
614B THR* 4.9 2.5 - - + -
618B GLY* 4.0 26.2 - - - +
700B THR* 2.9 34.0 + - - +
703B ILE* 1.3 76.7 - - - +
705B GLY* 1.3 58.4 + - - +
706B SER 3.1 1.9 + - - -
708B GLY* 2.9 31.3 + - - -
711B VAL* 4.3 24.2 - - + -
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Residues in contact with GLY 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B LYS* 3.9 17.7 - - - +
701B PRO 3.3 12.5 + - - -
702B ASP 3.2 11.0 + - - -
703B ILE 3.0 1.6 - - - -
704B LEU* 1.3 79.5 - - - +
706B SER* 1.3 56.6 + - - +
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Residues in contact with SER 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B ASP 3.5 8.2 + - - -
703B ILE* 3.0 11.9 + - - +
705B GLY* 1.3 78.5 - - - +
707B SER* 1.3 69.4 + - - +
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Residues in contact with SER 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B ILE* 3.0 23.9 + - - +
704B LEU 3.5 0.2 + - - -
706B SER* 1.3 88.8 + - - +
708B GLY* 1.3 56.5 + - - +
709B ALA* 3.2 7.1 + - - +
710B ALA* 3.3 14.3 + - - +
711B VAL* 3.2 26.9 + - - +
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Residues in contact with GLY 708 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B LYS* 5.5 7.4 - - - -
704B LEU* 2.9 32.6 + - - -
707B SER* 1.3 75.1 - - - +
709B ALA* 1.3 58.7 + - - +
711B VAL* 3.8 10.9 - - - +
712B HIS* 3.2 23.6 + - - +
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Residues in contact with ALA 709 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B SER* 3.2 1.3 - - - -
708B GLY* 1.3 77.3 - - - +
710B ALA* 1.3 64.5 + - - +
711B VAL 3.2 0.4 - - - -
712B HIS* 3.3 8.4 + - - +
713B THR* 3.2 25.1 + - - -
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Residues in contact with ALA 710 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B CYS* 5.2 1.6 - - - +
707B SER* 3.3 17.8 + - - +
709B ALA* 1.3 78.6 - - - +
711B VAL* 1.3 57.6 + - + +
713B THR* 3.3 7.7 + - - +
714B CYS* 2.9 29.9 + - - +
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Residues in contact with VAL 711 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B PHE* 6.1 4.3 - - + -
614B THR* 4.2 15.9 - - + -
618B GLY 3.6 21.1 - - - +
619B GLN* 5.2 0.9 - - - -
620B VAL* 4.1 14.8 - - + -
703B ILE* 5.4 2.2 - - + -
704B LEU* 4.3 14.8 - - + -
707B SER* 3.2 17.8 + - - +
708B GLY* 3.9 7.9 - - - +
709B ALA 3.2 0.2 - - - -
710B ALA* 1.3 75.6 - - + +
712B HIS* 1.3 58.5 + - - +
713B THR 3.1 1.6 - - - -
714B CYS* 3.9 1.1 - - - +
715B VAL* 2.8 55.3 + - + +
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Residues in contact with HIS 712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ANP 5.8 2.2 - - - -
505B GLU* 4.8 14.6 + - - -
547B PRO* 6.3 0.4 - - - +
548B GLU* 3.9 25.5 + - + -
708B GLY 3.2 17.2 + - - +
709B ALA* 3.5 8.5 - - - +
711B VAL* 1.3 80.5 - - - +
713B THR* 1.3 65.1 + - - +
715B VAL* 4.1 4.8 - - - +
716B LYS* 3.3 49.2 + - + +
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Residues in contact with THR 713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B CYS* 5.4 6.3 - - + -
709B ALA 3.2 11.7 + - - -
710B ALA* 3.5 11.2 - - - -
711B VAL 3.1 0.6 - - - -
712B HIS* 1.3 82.9 - - - +
714B CYS* 1.3 61.4 + - - +
715B VAL 3.2 0.2 - - - -
716B LYS* 3.2 9.7 + - - +
717B ALA* 3.0 27.8 + - + +
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Residues in contact with CYS 714 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B VAL* 3.9 17.3 - - + -
623B GLN* 3.3 29.8 - - - -
631B CYS* 2.1 56.8 - - + -
710B ALA 2.9 16.7 + - - +
711B VAL* 4.5 0.7 - - - -
713B THR* 1.3 77.3 - - - +
715B VAL* 1.3 53.5 + - - +
717B ALA* 3.4 2.3 + - - +
718B THR* 2.7 35.6 + - - -
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Residues in contact with VAL 715 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B PHE* 5.9 1.3 - - + -
547B PRO* 3.6 33.2 - - + -
610B VAL* 5.2 4.7 - - + -
614B THR* 4.4 13.2 - - + +
620B VAL* 3.4 26.5 - - + -
711B VAL* 2.8 36.6 + - + +
712B HIS* 4.1 5.4 - - - +
714B CYS* 1.3 74.5 - - - +
716B LYS* 1.3 65.8 + - + +
718B THR* 3.2 3.3 + - - -
719B PHE* 3.1 40.4 + - + -
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Residues in contact with LYS 716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ANP 5.6 5.5 + - - -
546B LYS* 5.2 11.9 - - + +
548B GLU* 3.7 29.6 + - - +
712B HIS* 3.3 41.6 + - + +
713B THR* 3.2 10.3 + - - +
715B VAL* 1.3 76.4 - - + +
717B ALA* 1.3 65.5 + - - +
719B PHE* 3.5 6.2 + - - +
720B HIS* 3.0 24.7 + - - +
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Residues in contact with ALA 717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B CYS* 3.9 16.8 - - - -
632B THR 5.1 2.9 - - - +
634B ALA* 5.6 1.8 - - - +
637B ILE* 4.1 11.4 - - + +
713B THR* 3.0 14.9 + - + +
714B CYS 3.6 8.7 - - - +
716B LYS* 1.3 77.9 - - - +
718B THR* 1.3 57.5 + - - +
720B HIS* 3.3 11.4 + - + +
721B ALA* 2.9 29.6 + - - +
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Residues in contact with THR 718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B TRP* 4.1 18.8 - - + -
610B VAL* 5.1 8.5 - - + -
620B VAL* 3.2 18.6 - - + +
621B PRO* 4.2 4.5 - - + +
622B PHE* 4.1 16.8 - - + -
623B GLN* 3.4 10.9 + - - -
637B ILE* 4.1 20.4 - - + -
641B ILE* 4.1 1.1 - - + +
714B CYS 2.7 19.9 + - - -
715B VAL* 3.5 8.1 - - - -
716B LYS 3.2 0.2 - - - -
717B ALA* 1.3 73.6 - - - +
719B PHE* 1.3 67.2 + - - +
721B ALA* 3.2 3.3 + - - +
722B PHE* 3.0 21.8 + - - +
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Residues in contact with PHE 719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ASP* 6.0 1.1 - - - -
545B LEU 4.0 21.3 - - - -
546B LYS* 4.2 26.5 - - + -
547B PRO* 3.9 9.0 - - + -
606B TRP* 4.1 11.7 - + - -
607B SER* 3.8 34.1 - - - -
610B VAL* 3.8 30.1 - - + -
611B ILE* 4.6 2.9 - - + -
715B VAL* 3.1 49.1 + - + +
716B LYS* 4.0 4.3 - - - +
718B THR* 1.3 75.5 - - - +
720B HIS* 1.3 63.2 + - - +
722B PHE* 3.2 10.8 + + - +
723B ASN* 3.0 32.9 + - - +
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Residues in contact with HIS 720 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ALA* 4.4 19.3 - - + +
716B LYS 3.0 19.3 + - - +
717B ALA* 3.3 10.3 - - + +
719B PHE* 1.3 76.2 - - - +
721B ALA* 1.3 66.5 + - - +
723B ASN* 3.2 11.2 + - - +
724B LYS* 3.0 33.5 + - + +
727B ARG* 4.9 12.3 + - - -
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Residues in contact with ALA 721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ALA* 3.8 26.9 - - - +
637B ILE* 3.8 20.4 - - + -
638B MET* 3.9 10.0 - - + +
641B ILE* 4.4 2.7 - - + -
717B ALA 2.9 16.9 + - - +
718B THR 3.2 5.1 + - - +
720B HIS* 1.3 81.0 - - - +
722B PHE* 1.3 57.6 + - - +
724B LYS* 3.3 6.9 + - - +
725B TYR* 2.8 31.5 + - - +
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Residues in contact with PHE 722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B SER 5.1 0.4 - - - -
603B CYS* 4.0 30.5 - - + -
606B TRP* 3.5 78.1 - + + -
607B SER* 5.4 0.9 - - - -
641B ILE* 3.9 17.4 - - + +
718B THR 3.0 6.4 + - - +
719B PHE* 3.5 11.0 - + - +
721B ALA* 1.3 75.9 - - - +
723B ASN* 1.3 69.5 + - - +
725B TYR* 3.4 12.3 + + - +
726B LYS* 2.8 65.6 + - + +
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Residues in contact with ASN 723 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ARG* 4.7 13.8 + - - +
544B ASP* 5.7 0.5 - - - +
603B CYS* 6.1 1.2 - - - -
719B PHE* 3.0 20.7 + - - +
720B HIS* 3.2 10.3 + - - +
722B PHE* 1.3 88.1 - - - +
724B LYS* 1.3 67.0 - - - +
726B LYS* 2.8 9.8 + - - +
727B ARG* 2.8 44.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ALA* 5.0 6.3 - - + -
635B VAL* 6.0 4.2 - - - +
638B MET* 3.2 30.2 - - + +
720B HIS* 3.0 26.1 + - - +
721B ALA* 3.6 9.0 - - - +
723B ASN* 1.3 74.1 - - - +
725B TYR* 1.3 59.5 + - - +
727B ARG* 3.0 27.2 + - - +
728B GLU* 2.8 54.9 + - + +
----------------------------------------------------------
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Residues in contact with TYR 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B MET* 3.6 22.8 - - + +
641B ILE* 4.0 25.1 - - + -
642B LYS* 3.6 46.0 + - + +
670B VAL* 5.1 11.2 - - + +
721B ALA 2.8 21.7 + - - +
722B PHE* 3.5 14.1 - + - +
724B LYS* 1.3 72.6 - - - +
726B LYS* 1.3 84.1 + - + +
728B GLU* 2.6 34.9 - - - +
729B GLY 3.6 1.3 + - - -
----------------------------------------------------------
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Residues in contact with LYS 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP* 2.8 29.7 + - - +
602B SER* 4.2 5.7 + - - -
603B CYS* 3.9 14.1 - - - -
722B PHE* 2.8 50.7 + - + +
723B ASN* 2.8 10.1 + - - +
725B TYR* 1.3 98.6 - - + +
727B ARG* 1.3 64.0 + - + +
728B GLU 4.6 0.2 - - - -
729B GLY 3.7 12.5 - - - +
----------------------------------------------------------
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Residues in contact with ARG 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B HIS* 4.9 11.3 + - - -
723B ASN* 2.8 24.2 + - - +
724B LYS* 3.5 38.8 - - - +
726B LYS* 1.3 78.1 - - + +
728B GLU* 1.3 56.3 + - + +
729B GLY* 2.7 24.3 - - - +
----------------------------------------------------------
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Residues in contact with GLU 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B MET* 4.2 16.7 - - - +
642B LYS* 5.5 3.6 + - - -
724B LYS* 2.8 40.5 + - + +
725B TYR* 2.6 30.2 - - - +
727B ARG* 1.3 78.2 - - + +
729B GLY* 1.3 48.8 + - - +
----------------------------------------------------------
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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