Contacts of the helix formed by residues 594 - 620 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A MET* 3.1 18.1 + - + +
591A SER* 2.7 29.2 + - - +
593A CYS* 1.3 67.8 - - - +
595A LYS* 1.3 53.6 + - - +
596A ASP* 3.0 3.8 - - - -
597A LEU* 2.6 46.2 + - + +
598A PHE* 4.0 5.0 + - + -
679A ILE* 5.4 4.7 - - - -
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Residues in contact with LYS 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A PHE* 5.5 15.1 - - + -
591A SER 3.4 5.9 + - - +
592A ARG 4.1 12.6 - - - +
593A CYS 3.1 2.5 - - - +
594A ALA* 1.3 75.8 - - - +
596A ASP* 1.3 63.2 + - - +
598A PHE* 3.0 47.8 + - + +
599A GLY* 3.7 1.9 + - - -
583D MET* 6.5 0.4 - - - -
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Residues in contact with ASP 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A CYS 3.9 6.3 + - - +
594A ALA 2.9 0.6 + - - -
595A LYS* 1.3 80.0 - - - +
597A LEU* 1.3 54.0 + - - +
599A GLY* 2.5 28.1 + - - +
600A PHE* 3.5 20.4 + - - +
679A ILE* 3.0 36.3 - - + +
683A THR* 6.4 0.2 - - + -
684D TYR* 2.5 29.5 + - - -
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Residues in contact with LEU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A ALA* 2.6 33.9 + - + +
596A ASP* 1.3 72.3 - - - +
598A PHE* 1.3 72.7 + - + +
600A PHE 4.2 0.2 + - - -
601A ALA* 3.0 31.4 + - + +
676A PHE* 5.4 15.3 - - + -
679A ILE* 4.6 8.3 - - + +
1009A PLM 6.2 1.1 - - + -
666B PHE* 4.4 30.7 - - + -
667B PHE* 6.2 2.7 - - + -
670B PHE* 5.9 3.6 - - + -
671B ILE* 6.0 7.0 - - + -
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Residues in contact with PHE 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A PHE* 5.9 7.2 - + - -
591A SER* 5.6 4.9 - - - -
594A ALA* 4.9 4.0 - - + -
595A LYS* 3.0 43.3 + - + +
597A LEU* 1.3 97.8 - - + +
599A GLY* 1.3 67.0 + - - +
601A ALA* 3.7 13.6 + - + +
602A ILE* 4.1 5.4 + - - +
1009A PLM 6.3 4.0 - - + -
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Residues in contact with GLY 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A LYS 3.7 1.8 + - - -
596A ASP* 2.5 24.4 + - - -
598A PHE* 1.3 71.8 - - - +
600A PHE* 1.3 61.6 + - - -
602A ILE* 3.0 25.1 - - - +
583D MET* 4.2 30.5 - - - +
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Residues in contact with PHE 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A ASP* 3.5 23.5 + - - +
599A GLY* 1.3 76.3 - - - +
601A ALA* 1.3 65.4 + - - +
602A ILE 3.1 1.1 - - - -
603A MET* 3.1 50.2 - - + +
604A PHE* 3.3 6.9 + - - +
675A MET* 5.1 17.7 - - + +
679A ILE* 4.7 11.9 - - + -
578D ASN* 5.6 4.0 - - - -
583D MET* 4.2 16.2 - - + -
586D LEU* 4.7 10.8 - - + -
587D SER* 3.6 42.2 - - - -
590D MET* 4.8 5.8 - - + -
684D TYR* 5.0 15.5 - + - -
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Residues in contact with ALA 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A LEU* 3.0 29.2 + - + +
598A PHE* 3.7 12.6 - - + +
599A GLY 3.3 0.4 - - - -
600A PHE* 1.3 77.3 - - - +
602A ILE* 1.3 56.6 + - - +
604A PHE* 3.2 6.0 + - - +
605A PHE* 2.8 61.7 + - + -
1009A PLM 5.2 3.6 - - + -
666B PHE* 5.7 1.1 - - + -
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Residues in contact with ILE 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A PHE 4.1 4.8 + - - +
599A GLY 3.0 23.3 - - - +
601A ALA* 1.3 77.7 - - - +
603A MET* 1.3 65.7 + - + +
605A PHE* 2.6 34.5 + - + +
606A ILE* 2.7 23.5 + - + +
577D ILE* 2.7 51.6 - - + -
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Residues in contact with MET 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.1 53.2 - - + +
602A ILE* 1.3 83.0 - - + +
604A PHE* 1.3 62.6 + - + +
606A ILE* 3.1 11.7 - - - +
607A ILE* 2.9 35.5 + - + +
671A ILE* 5.3 6.7 - - + -
675A MET* 6.0 2.2 - - - -
574D PHE* 3.8 32.3 - - + -
577D ILE* 6.4 1.1 - - - -
587D SER* 5.3 0.7 - - - +
590D MET* 4.0 28.9 - - + +
1008D PLM 4.0 16.2 - - + +
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Residues in contact with PHE 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE 3.8 7.2 - - - +
601A ALA* 3.2 10.0 + - - +
602A ILE 2.9 0.6 + - - -
603A MET* 1.3 82.5 - - + +
605A PHE* 1.3 79.0 + + - +
607A ILE* 2.8 14.7 + - + -
608A PHE* 2.2 84.0 + + + +
637A PHE* 4.9 9.4 - + - -
640A ILE* 6.2 1.8 - - + -
664A PHE* 5.8 0.2 - + - -
668A MET* 5.1 8.7 - - + -
671A ILE* 6.2 2.2 - - + -
672A LEU* 4.4 32.8 - - + -
676A PHE* 5.0 12.1 - + + -
666B PHE* 5.9 0.7 - + - -
670B PHE* 5.0 17.7 - + - -
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Residues in contact with PHE 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ALA* 2.8 47.2 + - + -
602A ILE* 2.6 17.2 + - + +
604A PHE* 1.3 90.8 - + - +
606A ILE* 1.3 52.6 + - - +
608A PHE* 3.1 9.0 - + + +
609A LEU* 2.3 49.6 + - + +
637A PHE* 6.4 1.6 - + - -
1009A PLM 3.5 35.2 - - + -
1010A PLM 5.7 13.0 - - + -
666B PHE* 4.3 14.6 - + - -
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Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A ILE* 2.7 22.3 + - + +
603A MET* 3.1 19.7 - - - +
605A PHE* 1.3 70.1 - - - +
607A ILE* 1.3 79.9 + - + +
609A LEU* 2.8 9.8 + - - +
610A ALA* 2.2 39.7 + - + +
570D TRP* 3.0 28.9 - - + +
571D ILE* 5.9 3.1 - - + -
573D LEU* 1.9 48.9 - - + -
574D PHE* 4.4 19.7 - - + +
577D ILE* 4.9 5.4 - - + -
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Residues in contact with ILE 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A MET* 3.1 19.1 - - + +
604A PHE* 2.8 33.0 + - + +
606A ILE* 1.3 86.0 - - + +
608A PHE* 1.3 65.6 + - - +
610A ALA* 3.5 3.6 - - + -
611A TYR* 3.0 48.7 + - + +
668A MET* 6.1 4.9 - - + -
671A ILE* 6.0 5.8 - - + -
567D PHE* 3.4 33.0 - - + -
571D ILE* 5.0 4.3 - - + -
574D PHE* 6.4 0.7 - - + -
1008D PLM 3.8 23.8 - - + -
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Residues in contact with PHE 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A PHE* 2.2 67.7 + + + +
605A PHE* 3.1 13.0 - + - +
607A ILE* 1.3 69.6 - - - +
609A LEU* 1.3 64.0 + - + +
610A ALA 3.0 0.2 + - - -
611A TYR* 5.1 0.2 - - - -
612A ALA 3.0 3.8 + - - -
633A ILE* 3.3 31.6 - - + -
636A GLN* 2.2 96.5 + - + +
637A PHE* 3.4 34.3 - + - -
640A ILE* 5.6 2.0 - - + -
664A PHE* 4.8 7.2 - + - -
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Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A PHE* 2.3 40.1 + - + +
606A ILE* 2.8 7.4 + - + +
608A PHE* 1.3 68.4 - - + +
610A ALA* 1.3 52.1 + - - +
612A ALA* 3.8 3.6 - - - -
613A GLN* 2.4 42.9 + - - +
629A PHE* 3.5 33.2 - - + -
633A ILE* 3.5 23.3 - - + -
1010A PLM 4.4 27.6 - - + -
570D TRP* 5.3 9.6 - - + -
1005D CHS 4.2 24.7 - - + -
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Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ILE* 2.2 31.8 + - + +
607A ILE* 3.2 16.4 - - + +
608A PHE 3.0 0.6 + - - -
609A LEU* 1.3 67.0 - - - +
611A TYR* 1.3 54.1 + - - +
613A GLN* 2.9 9.8 + - - +
614A LEU* 2.6 37.5 + - - +
567D PHE* 3.8 30.6 - - + +
570D TRP* 4.7 15.0 - - + +
571D ILE* 5.0 1.6 - - + -
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Residues in contact with TYR 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ILE* 3.0 48.3 + - + +
610A ALA* 1.3 77.4 - - + +
612A ALA* 1.3 52.3 + - - +
614A LEU* 2.9 13.4 + - + +
615A ALA* 2.1 42.4 + - - +
636A GLN* 3.6 10.1 - - - +
660A TYR* 3.3 35.1 + + + +
663A THR* 3.7 19.1 - - - -
664A PHE* 4.1 26.5 - + + -
667A PHE* 3.8 19.4 - - + +
668A MET* 5.6 2.9 - - + -
567D PHE* 4.9 3.5 - + - -
1008D PLM 3.6 43.9 - - + +
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Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A PHE 3.0 5.6 + - - +
609A LEU* 3.3 12.1 - - - +
611A TYR* 1.3 75.7 - - - +
613A GLN* 1.3 51.9 + - - +
615A ALA* 2.9 10.1 + - - +
616A TYR* 2.5 37.1 + - - +
629A PHE* 4.0 10.9 - - + -
632A CYS* 3.8 21.3 - - + +
633A ILE* 4.1 6.5 - - + -
636A GLN* 3.1 27.4 - - - +
660A TYR* 4.9 0.4 + - - -
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Residues in contact with GLN 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A LEU* 2.4 32.4 + - - +
610A ALA* 3.2 4.5 - - - +
612A ALA* 1.3 66.4 - - - +
614A LEU* 1.3 64.7 + - - +
616A TYR* 2.7 15.7 + - + +
617A LEU* 2.8 29.8 + - + +
629A PHE* 3.7 20.2 - - + -
235D CYS* 4.4 11.1 - - - -
566D VAL* 3.5 23.5 - - + +
570D TRP* 2.9 57.4 - - - +
1005D CHS 5.5 9.3 + - - +
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Residues in contact with LEU 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ALA 2.6 17.4 + - - +
611A TYR* 3.2 14.1 - - + +
613A GLN* 1.3 72.8 - - - +
615A ALA* 1.3 52.2 + - - +
617A LEU* 4.6 4.7 - - - -
618A VAL* 2.6 65.4 + - + +
619A PHE* 5.8 0.2 - - + -
660A TYR* 4.6 21.5 - - + -
563D ALA* 3.6 31.6 - - + +
564D VAL* 4.2 9.9 - - + +
566D VAL* 5.8 1.3 - - - +
567D PHE* 4.9 17.7 - - + +
1008D PLM 4.4 24.2 - - + -
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Residues in contact with ALA 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A TYR 2.1 30.9 + - - +
612A ALA* 3.0 14.6 - - - +
614A LEU* 1.3 67.0 - - - +
616A TYR* 1.3 53.9 + - - +
619A PHE* 2.4 57.7 + - + +
626A PHE* 3.6 31.2 - - + -
627A SER* 4.6 0.2 - - - -
632A CYS* 4.9 0.2 - - - -
660A TYR* 3.9 11.2 - - - +
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Residues in contact with TYR 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ALA 2.5 15.3 + - - +
613A GLN* 2.7 10.5 + - + +
615A ALA* 1.3 69.4 - - - +
617A LEU* 1.3 73.1 + - + +
620A GLY* 2.4 39.8 + - - -
627A SER* 3.5 44.4 - - - -
629A PHE* 3.8 39.3 - + + -
632A CYS* 4.5 4.6 - - - -
238D THR* 5.7 4.3 - - - -
239D TYR* 6.4 0.7 - - - -
242D MET* 4.0 15.2 + - + +
243D SER 3.5 7.1 + - - -
244D SER* 3.0 34.1 + - - -
1005D CHS 4.6 17.8 + - - -
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Residues in contact with LEU 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A GLN* 2.8 39.0 + - + +
614A LEU* 3.7 7.0 - - - +
616A TYR* 1.3 93.6 - - + +
618A VAL* 1.3 65.6 + - - +
620A GLY* 3.6 4.9 + - - -
621A THR* 4.8 1.0 + - - +
238D THR* 4.7 22.9 - - + +
559D ASN* 4.2 15.9 + - - +
563D ALA* 3.6 25.1 - - + +
566D VAL* 3.5 37.5 - - + -
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Residues in contact with VAL 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A LEU* 2.6 50.9 + - + +
617A LEU* 1.3 75.4 - - - +
619A PHE* 1.3 87.4 + - + +
621A THR* 3.1 24.9 + - - +
656A LEU* 3.5 43.1 - - + +
657A GLY* 4.9 0.2 - - - -
660A TYR* 6.2 0.9 - - + -
559D ASN* 5.5 2.5 + - - -
560D ASN* 5.4 4.3 - - - +
563D ALA* 4.2 10.3 - - + -
564D VAL* 5.7 2.5 - - + -
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Residues in contact with PHE 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A LEU* 5.8 0.4 - - + -
615A ALA* 2.4 48.7 + - + +
618A VAL* 1.3 86.8 - - + +
620A GLY* 1.3 50.3 + - - +
621A THR* 2.5 40.9 - - - +
623A VAL* 3.0 25.3 - - + +
626A PHE* 4.4 14.4 - + + -
627A SER* 3.0 7.7 + - - +
649A ILE* 4.0 29.4 - - + -
652A ALA* 4.8 7.6 - - + -
656A LEU* 4.7 1.6 - - + -
657A GLY* 3.8 25.8 - - - -
660A TYR* 3.3 43.7 - + + -
----------------------------------------------------------
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Residues in contact with GLY 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A TYR* 2.4 25.7 + - - -
617A LEU 3.6 3.8 + - - -
618A VAL 3.3 1.8 - - - -
619A PHE* 1.3 69.1 - - - +
621A THR* 1.3 60.7 + - - +
627A SER* 3.0 18.6 - - - -
246D VAL* 4.2 3.6 - - - +
247D TYR* 3.3 16.6 + - - -
250D THR* 3.2 16.0 - - - +
459D PRO* 5.8 2.9 - - - -
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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