Contacts of the helix formed by residues 594 - 620 (chain D) in PDB entry 5MKE
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 ALA 594 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590D MET 3.1 17.9 + - - +
591D SER* 2.7 29.9 + - - +
593D CYS* 1.3 68.9 - - - +
595D LYS* 1.3 52.9 + - - -
596D ASP* 3.0 3.8 - - - -
597D LEU* 2.6 46.6 + - + +
598D PHE* 4.0 4.9 + - + -
679D ILE* 5.4 4.5 - - - -
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Residues in contact with LYS 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C MET* 6.6 0.7 - - - -
506D PHE* 5.5 14.7 - - + -
591D SER 3.4 5.8 + - - +
592D ARG 4.1 11.9 - - - +
593D CYS 3.1 2.8 - - - +
594D ALA* 1.3 76.3 - - - +
596D ASP* 1.3 63.2 + - - +
598D PHE* 3.0 47.8 + - + +
599D GLY* 3.7 1.9 + - - -
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Residues in contact with ASP 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C TYR* 2.5 29.6 + - - -
593D CYS 3.9 7.0 + - - +
594D ALA 2.9 0.2 + - - -
595D LYS* 1.3 80.2 - - - +
597D LEU* 1.3 53.8 + - - +
599D GLY* 2.5 27.9 + - - +
600D PHE* 3.5 21.4 + - - +
679D ILE* 3.0 36.5 - - + +
683D THR* 6.4 0.7 - - + -
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Residues in contact with LEU 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A PHE* 4.4 30.3 - - + -
667A PHE* 6.1 3.1 - - + -
670A PHE* 6.0 3.1 - - + -
671A ILE* 6.0 6.7 - - + -
594D ALA* 2.6 33.5 + - + +
596D ASP* 1.3 71.5 - - - +
598D PHE* 1.3 73.1 + - + +
601D ALA* 3.0 31.8 + - + +
676D PHE* 5.4 15.7 - - + -
679D ILE* 4.6 8.2 - - + +
1009D PLM 6.2 1.8 - - + -
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Residues in contact with PHE 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D PHE* 5.9 7.6 - + - -
591D SER* 5.6 5.4 - - - -
594D ALA* 4.8 4.3 - - + -
595D LYS* 3.0 43.4 + - + +
597D LEU* 1.3 97.0 - - + +
599D GLY* 1.3 66.6 + - - +
601D ALA* 3.7 14.3 + - + +
602D ILE* 4.1 6.2 + - - +
1009D PLM 6.3 3.1 - - + -
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Residues in contact with GLY 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C MET* 4.2 31.6 - - - +
595D LYS 3.7 2.1 + - - -
596D ASP* 2.5 23.8 + - - -
598D PHE* 1.3 72.8 - - - +
600D PHE* 1.3 62.4 + - - -
602D ILE* 3.0 25.5 - - - +
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Residues in contact with PHE 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578C ASN* 5.5 4.3 - - - -
583C MET* 4.1 17.7 - - + -
586C LEU* 4.7 10.1 - - + -
587C SER* 3.6 41.1 - - - -
590C MET* 4.8 6.3 - - + -
684C TYR* 5.0 15.0 - + - -
596D ASP* 3.5 23.5 + - - +
599D GLY* 1.3 77.3 - - - +
601D ALA* 1.3 66.6 + - - +
602D ILE* 3.1 1.1 - - + -
603D MET* 3.1 49.5 - - + +
604D PHE* 3.3 6.6 + - - +
675D MET* 5.1 17.7 - - + +
679D ILE* 4.7 12.1 - - + -
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Residues in contact with ALA 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A PHE* 5.7 1.1 - - + -
597D LEU* 3.0 30.7 + - + +
598D PHE* 3.7 11.7 - - + +
599D GLY 3.3 0.4 - - - -
600D PHE* 1.3 75.8 - - - +
602D ILE* 1.3 58.1 + - - +
604D PHE* 3.2 6.6 + - - +
605D PHE* 2.8 60.4 + - + -
1009D PLM 5.2 3.8 - - + -
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Residues in contact with ILE 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C ILE* 2.7 51.1 - - + -
598D PHE 4.1 4.6 + - - +
599D GLY 3.0 24.0 + - - +
600D PHE* 4.6 0.4 - - + -
601D ALA* 1.3 78.4 - - - +
603D MET* 1.3 64.5 + - + +
605D PHE* 2.6 34.2 + - + -
606D ILE* 2.7 22.7 + - + +
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Residues in contact with MET 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C PHE* 3.8 31.8 - - + -
577C ILE* 6.4 0.9 - - - -
587C SER* 5.2 0.4 - - - -
590C MET* 4.0 20.4 - - + +
1008C PLM 4.0 26.0 - - + +
600D PHE* 3.1 54.5 - - + +
602D ILE* 1.3 83.7 - - + +
604D PHE* 1.3 62.2 + - + +
606D ILE* 3.1 11.4 - - - +
607D ILE* 2.9 35.2 + - + +
671D ILE* 5.3 6.3 - - + -
675D MET* 6.0 2.5 - - - -
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Residues in contact with PHE 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A PHE* 5.8 1.1 - + - -
670A PHE* 5.0 17.0 - + - -
600D PHE 3.8 7.2 - - - +
601D ALA* 3.2 9.4 + - - +
602D ILE 3.0 0.2 - - - -
603D MET* 1.3 83.0 - - + +
605D PHE* 1.3 77.8 + + - +
607D ILE* 2.8 15.0 + - + -
608D PHE* 2.2 83.9 + + + -
637D PHE* 4.9 9.6 - + - -
640D ILE* 6.2 1.8 - - + -
664D PHE* 5.8 0.7 - + - -
668D MET* 5.1 7.6 - - + -
671D ILE* 6.2 1.8 - - + -
672D LEU* 4.4 33.7 - - + -
676D PHE* 5.0 12.6 - + + -
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Residues in contact with PHE 605 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A PHE* 4.3 15.0 - + - -
601D ALA* 2.8 48.7 + - + -
602D ILE* 2.6 16.1 + - + +
604D PHE* 1.3 91.4 - + - +
606D ILE* 1.3 52.2 + - - +
608D PHE* 3.1 8.5 - + + +
609D LEU* 2.3 49.4 + - + +
637D PHE* 6.4 1.3 - + - -
1009D PLM 3.5 34.1 - - + -
1010D PLM 5.7 12.8 - - + -
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Residues in contact with ILE 606 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C TRP* 3.0 28.3 - - + +
571C ILE* 5.9 2.7 - - + -
573C LEU* 1.9 49.1 - - + -
574C PHE* 4.4 20.2 - - + +
577C ILE* 4.9 5.6 - - + -
602D ILE* 2.7 22.7 + - + +
603D MET* 3.1 20.0 - - - +
605D PHE* 1.3 70.3 - - - +
607D ILE* 1.3 81.0 + - + +
609D LEU* 2.8 10.0 + - + +
610D ALA* 2.2 39.7 + - + +
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Residues in contact with ILE 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C PHE* 3.4 33.4 - - + -
571C ILE* 5.0 4.3 - - + -
574C PHE* 6.4 0.9 - - + -
1008C PLM 3.8 24.2 - - + -
603D MET* 3.1 19.3 - - + +
604D PHE* 2.8 32.5 + - + +
606D ILE* 1.3 85.5 - - + +
608D PHE* 1.3 64.9 + - - +
610D ALA* 3.5 3.6 - - + -
611D TYR* 3.0 49.4 + - + -
668D MET* 6.1 4.7 - - + -
671D ILE* 6.0 6.1 - - + -
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Residues in contact with PHE 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D PHE* 2.2 67.5 + + + +
605D PHE* 3.1 13.2 - + - +
607D ILE* 1.3 70.6 - - - +
609D LEU* 1.3 64.3 + - + +
612D ALA 3.0 3.5 + - - -
633D ILE* 3.3 32.8 - - + -
636D GLN* 2.2 96.7 + - + +
637D PHE* 3.4 33.4 - + - -
640D ILE* 5.6 2.0 - - + -
664D PHE* 4.8 7.0 - + - -
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Residues in contact with LEU 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C TRP* 5.3 9.9 - - + -
1005C CHS 4.1 25.1 - - + -
605D PHE* 2.3 39.0 + - + +
606D ILE* 2.8 6.9 + - + +
608D PHE* 1.3 69.1 - - + +
610D ALA* 1.3 53.1 + - - +
612D ALA* 3.8 3.8 - - - -
613D GLN* 2.4 42.2 + - + +
629D PHE* 3.5 33.2 - - + -
633D ILE* 3.5 24.5 - - + -
1010D PLM 4.4 27.4 - - + -
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Residues in contact with ALA 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C PHE* 3.8 30.4 - - + +
570C TRP* 4.7 15.2 - - + +
571C ILE* 5.0 1.6 - - + -
606D ILE 2.2 31.4 + - - +
607D ILE* 3.2 16.4 - - + +
608D PHE 3.0 1.2 + - - -
609D LEU* 1.3 67.5 - - - +
611D TYR* 1.3 53.5 + - - +
613D GLN* 3.2 9.5 - - - +
614D LEU* 2.6 37.6 + - - +
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Residues in contact with TYR 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C PHE* 4.8 3.6 - + - -
1008C PLM 3.5 44.4 - - + +
607D ILE* 3.0 49.3 + - + +
610D ALA* 1.3 77.6 - - + +
612D ALA* 1.3 52.5 + - - +
614D LEU* 2.9 13.4 + - + +
615D ALA* 2.1 42.1 + - - +
636D GLN* 3.6 10.3 - - - +
660D TYR* 3.3 35.7 + + + +
663D THR* 3.7 18.6 - - - -
664D PHE* 4.1 26.9 - + + -
667D PHE* 3.8 19.3 - - + +
668D MET* 5.6 3.1 - - + -
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Residues in contact with ALA 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D PHE 3.0 5.8 + - - +
609D LEU* 3.3 12.1 - - - +
611D TYR* 1.3 75.7 - - - +
613D GLN* 1.3 52.2 + - - +
615D ALA* 2.9 9.5 + - - +
616D TYR* 2.5 36.9 + - - +
629D PHE* 4.0 10.7 - - + -
632D CYS* 3.8 21.3 - - - +
633D ILE* 4.1 7.0 - - + -
636D GLN* 3.1 27.9 - - - +
660D TYR* 5.2 0.4 - - - -
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Residues in contact with GLN 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C CYS* 4.3 11.1 - - - -
566C VAL* 3.5 21.8 - - + +
570C TRP* 2.8 58.2 - - - -
1005C CHS 5.6 8.4 + - - +
609D LEU* 2.4 31.7 + - + +
610D ALA* 3.2 4.7 - - - +
612D ALA* 1.3 66.1 - - - +
614D LEU* 1.3 64.9 + - - +
616D TYR* 2.7 15.1 + - + +
617D LEU* 2.8 31.0 + - + +
629D PHE* 3.7 20.2 - - + -
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Residues in contact with LEU 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C ALA* 3.6 31.6 - - + +
564C VAL* 4.2 10.1 - - + +
566C VAL* 5.7 2.4 - - - +
567C PHE* 4.9 18.4 - - + +
1008C PLM 4.4 24.0 - - + -
610D ALA 2.6 16.5 + - - +
611D TYR* 3.2 13.2 - - + +
613D GLN* 1.3 72.9 - - - +
615D ALA* 1.3 53.8 + - - +
617D LEU* 4.6 4.9 - - + -
618D VAL* 2.6 65.9 + - + +
619D PHE* 5.8 0.2 - - + -
660D TYR* 4.6 21.3 - - + -
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Residues in contact with ALA 615 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611D TYR 2.1 30.7 + - - +
612D ALA* 3.0 14.1 - - - +
614D LEU* 1.3 68.2 - - - +
616D TYR* 1.3 53.4 + - - +
619D PHE* 2.4 56.9 + - + +
626D PHE* 3.6 32.1 - - + -
627D SER* 4.6 0.4 - - - -
632D CYS* 4.9 0.2 - - - -
660D TYR* 3.9 11.0 - - - +
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Residues in contact with TYR 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C THR* 5.6 5.2 - - - -
239C TYR* 6.4 0.9 - - - -
242C MET* 4.0 16.1 + - + +
243C SER 3.5 6.8 + - - -
244C SER* 3.0 33.1 + - - -
1005C CHS 4.6 18.8 + - - -
612D ALA 2.5 15.5 + - - +
613D GLN* 2.7 10.3 + - + +
615D ALA* 1.3 68.6 - - - +
617D LEU* 1.3 72.6 + - + +
620D GLY* 2.4 39.0 + - - -
627D SER* 3.5 44.2 - - - -
629D PHE* 3.8 39.5 - + + -
632D CYS* 4.5 5.5 - - - -
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Residues in contact with LEU 617 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C THR* 4.6 23.1 - - + +
559C ASN* 4.2 16.9 + - - +
562C ALA 5.1 0.2 - - - -
563C ALA* 3.6 25.8 - - + +
566C VAL* 3.5 37.9 - - + -
613D GLN* 2.8 39.7 + - + +
614D LEU* 3.7 6.3 - - - +
616D TYR* 1.3 92.8 - - + +
618D VAL* 1.3 65.7 + - - +
620D GLY* 3.6 5.2 + - - -
621D THR* 4.8 0.7 + - - +
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Residues in contact with VAL 618 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C ASN* 5.4 2.3 + - - -
560C ASN* 5.3 4.7 - - - +
563C ALA* 4.1 9.9 - - + -
564C VAL* 5.6 3.1 - - + +
614D LEU* 2.6 51.0 + - + +
617D LEU* 1.3 75.0 - - - +
619D PHE* 1.3 88.1 + - + +
621D THR* 3.1 25.1 + - - +
656D LEU* 3.5 40.9 - - + +
657D GLY* 4.9 0.2 - - - -
660D TYR* 6.2 0.9 - - + -
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Residues in contact with PHE 619 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614D LEU* 5.8 0.4 - - + -
615D ALA* 2.4 47.9 + - + +
618D VAL* 1.3 87.1 - - + +
620D GLY* 1.3 51.0 + - - +
621D THR* 2.5 39.2 - - - +
623D VAL* 3.0 25.3 - - + +
626D PHE* 4.4 14.4 - + + -
627D SER* 3.0 6.5 + - - -
649D ILE* 4.0 29.4 - - + -
652D ALA* 4.8 7.9 - - + -
656D LEU* 4.7 2.0 - - + -
657D GLY* 3.8 25.6 - - - -
660D TYR* 3.3 43.3 - + - -
----------------------------------------------------------
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Residues in contact with GLY 620 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C VAL* 4.2 5.1 - - - +
247C TYR* 3.3 16.7 + - - -
250C THR* 3.2 15.1 - - - +
459C PRO* 5.8 3.4 - - - -
616D TYR* 2.4 25.4 + - - -
617D LEU 3.6 4.2 + - - -
618D VAL 3.3 2.0 - - - -
619D PHE* 1.3 69.8 - - - +
621D THR* 1.3 61.7 + - - +
627D SER* 3.0 18.8 - - - -
----------------------------------------------------------
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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