Contacts of the helix formed by residues 594 - 620 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B MET* 3.1 18.0 + - + +
591B SER* 2.7 23.9 + - - +
593B CYS* 1.3 74.0 - - - +
595B LYS* 1.3 54.1 + - - +
596B ASP* 3.0 4.0 - - - +
597B LEU* 2.6 47.1 + - + +
598B PHE* 4.0 4.7 + - + -
679B ILE* 5.4 4.5 - - - -
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Residues in contact with LYS 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A MET* 6.6 0.4 - - - -
506B PHE* 5.5 13.8 - - + -
591B SER 3.4 6.1 + - - +
592B ARG 4.1 12.1 - - - +
593B CYS* 3.1 3.3 - - - +
594B ALA* 1.3 74.3 - - - +
596B ASP* 1.3 62.6 + - - +
598B PHE* 3.0 48.2 + - + +
599B GLY* 3.7 1.9 + - - -
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Residues in contact with ASP 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A TYR* 2.5 30.1 + - - -
593B CYS 3.9 6.7 + - - +
594B ALA 3.0 0.4 - - - -
595B LYS* 1.3 79.8 - - - +
597B LEU* 1.3 54.1 + - - +
599B GLY* 2.5 28.5 + - - +
600B PHE* 3.5 20.8 + - - -
679B ILE* 3.0 33.7 - - + +
683B THR* 6.4 0.2 - - + -
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Residues in contact with LEU 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B ALA* 2.6 33.7 + - + +
596B ASP* 1.3 72.6 - - - +
598B PHE* 1.3 72.7 + - + +
601B ALA* 3.0 31.0 + - + +
676B PHE* 5.4 15.7 - - + -
679B ILE* 4.6 8.3 - - + +
1009B PLM 6.2 1.8 - - + -
666C PHE* 4.4 30.7 - - + -
667C PHE* 6.1 2.7 - - + -
670C PHE* 6.0 3.4 - - + -
671C ILE* 6.0 6.3 - - + -
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Residues in contact with PHE 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B PHE* 5.9 7.0 - + - -
591B SER* 5.6 5.2 - - - -
594B ALA* 4.8 3.6 - - + -
595B LYS* 3.0 42.9 + - + +
597B LEU* 1.3 99.2 - - + +
599B GLY* 1.3 65.8 + - - +
601B ALA* 3.7 13.2 + - + +
602B ILE* 4.1 5.4 + - - +
1009B PLM 6.4 3.1 - - + -
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Residues in contact with GLY 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A MET* 4.1 31.5 - - - +
595B LYS 3.7 2.0 + - - -
596B ASP* 2.5 24.7 + - - -
598B PHE* 1.3 73.3 - - - +
600B PHE* 1.3 60.8 + - - -
602B ILE* 3.0 25.8 - - - +
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Residues in contact with PHE 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASN* 5.5 4.0 - - - -
583A MET* 4.1 17.5 - - + -
586A LEU* 4.7 12.3 - - + -
587A SER* 3.6 41.7 - - - -
590A MET* 4.8 5.6 - - + -
684A TYR* 5.0 13.9 - + - -
596B ASP* 3.5 23.7 + - - +
597B LEU 4.2 0.2 + - - -
599B GLY* 1.3 76.1 - - - +
601B ALA* 1.3 65.5 + - - +
602B ILE 3.1 2.2 - - - -
603B MET* 3.1 49.8 - - + +
604B PHE* 3.3 6.9 + - - +
675B MET* 5.1 17.9 - - + +
679B ILE* 4.7 11.7 - - + -
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Residues in contact with ALA 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B LEU* 3.0 29.2 + - + +
598B PHE* 3.7 12.3 - - + +
599B GLY 3.3 0.2 - - - -
600B PHE* 1.3 76.3 - - - +
602B ILE* 1.3 58.7 + - - +
604B PHE* 3.2 6.9 + - - +
605B PHE* 2.8 60.6 + - + -
1009B PLM 5.2 3.4 - - + -
666C PHE* 5.7 1.1 - - + -
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Residues in contact with ILE 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A ILE* 2.7 54.1 - - + -
598B PHE 4.1 5.5 + - - +
599B GLY 3.0 23.3 + - - +
601B ALA* 1.3 77.8 - - - +
603B MET* 1.3 64.6 + - + +
605B PHE* 2.6 34.2 + - + +
606B ILE* 2.7 23.2 + - + +
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Residues in contact with MET 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A PHE* 3.8 31.8 - - + -
577A ILE* 6.4 1.6 - - - -
578A ASN* 6.3 0.2 - - - +
587A SER* 5.2 0.4 - - - -
590A MET* 4.0 20.6 - - + +
1008A PLM 4.0 25.6 - - + +
600B PHE* 3.1 52.5 - - + +
602B ILE* 1.3 84.8 - - + +
604B PHE* 1.3 63.5 + - + +
606B ILE* 3.1 11.3 - - - +
607B ILE* 2.9 35.6 + - + +
671B ILE* 5.3 6.7 - - + -
675B MET* 6.0 2.5 - - - -
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Residues in contact with PHE 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B PHE 3.8 6.5 - - - +
601B ALA* 3.2 10.7 + - - +
602B ILE 2.9 0.6 + - - -
603B MET* 1.3 82.2 - - + +
605B PHE* 1.3 78.3 + + - +
607B ILE* 2.8 16.1 + - + +
608B PHE* 2.2 84.8 + + + +
637B PHE* 4.9 9.4 - + - -
640B ILE* 6.2 1.8 - - + -
664B PHE* 5.8 0.9 - + - -
668B MET* 5.1 8.3 - - + -
671B ILE* 6.3 2.0 - - + -
672B LEU* 4.4 31.9 - - + -
676B PHE* 5.0 12.8 - + + -
666C PHE* 5.8 0.9 - + - -
670C PHE* 5.1 17.9 - + - -
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Residues in contact with PHE 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B ALA* 2.8 48.2 + - + -
602B ILE* 2.6 18.0 + - + +
604B PHE* 1.3 90.2 - + - +
606B ILE* 1.3 51.9 + - - +
608B PHE* 3.1 9.2 - + + +
609B LEU* 2.3 49.5 + - + +
637B PHE* 6.4 1.8 - + - -
1009B PLM 3.5 34.5 - - + -
1010B PLM 5.6 13.2 - - + -
666C PHE* 4.4 14.6 - + - -
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Residues in contact with ILE 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A TRP* 3.0 28.3 - - + +
571A ILE* 5.9 2.7 - - + -
573A LEU* 1.8 49.4 - - + -
574A PHE* 4.3 19.5 - - + +
577A ILE* 4.9 6.5 - - + -
602B ILE* 2.7 23.1 + - + +
603B MET* 3.1 20.6 - - - +
605B PHE* 1.3 69.9 - - - +
607B ILE* 1.3 80.0 + - + +
609B LEU* 2.8 10.0 + - - +
610B ALA* 2.2 40.8 + - + +
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Residues in contact with ILE 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A PHE* 3.4 38.1 - - + -
571A ILE* 4.9 4.3 - - + -
574A PHE* 6.3 1.3 - - + -
1008A PLM 3.8 20.0 - - + -
603B MET* 2.9 20.2 + - + +
604B PHE* 2.8 33.0 + - + +
606B ILE* 1.3 86.0 - - + +
608B PHE* 1.3 64.5 + - - +
610B ALA* 3.5 3.8 - - + -
611B TYR* 3.0 48.0 + - + -
668B MET* 6.1 4.7 - - + -
671B ILE* 6.0 6.3 - - + -
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Residues in contact with PHE 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B PHE* 2.2 68.0 + + + +
605B PHE* 3.1 13.5 - + - +
607B ILE* 1.3 71.2 - - - +
609B LEU* 1.3 64.0 + - + +
611B TYR* 5.1 0.2 - - - -
612B ALA 3.0 3.6 + - - -
633B ILE* 3.3 31.9 - - + -
636B GLN* 2.2 97.1 + - + +
637B PHE* 3.4 33.7 - + - -
640B ILE* 5.6 2.0 - - + -
664B PHE* 4.8 7.6 - + - -
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Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A TRP* 5.2 9.6 - - + -
1005A CHS 4.1 25.1 - - + -
605B PHE* 2.3 39.2 + - + +
606B ILE* 2.8 6.7 + - - +
608B PHE* 1.3 68.7 - - + +
610B ALA* 1.3 51.5 + - - +
612B ALA* 3.8 2.9 - - - -
613B GLN* 2.4 42.8 + - - +
629B PHE* 3.5 33.7 - - + -
633B ILE* 3.5 22.7 - - + -
636B GLN* 4.3 0.2 - - - -
1010B PLM 4.4 26.9 - - + -
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Residues in contact with ALA 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A PHE* 3.8 30.3 - - + +
570A TRP* 4.6 16.5 - - + +
571A ILE* 4.9 1.6 - - + -
606B ILE* 2.2 30.5 + - + +
607B ILE* 3.2 16.6 - - + +
608B PHE 3.0 1.0 + - - -
609B LEU* 1.3 67.0 - - - +
611B TYR* 1.3 54.3 + - - +
613B GLN* 2.9 9.5 + - - +
614B LEU* 2.6 36.7 + - - +
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Residues in contact with TYR 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A PHE* 4.7 3.8 - + - -
1008A PLM 3.5 45.3 - - + +
607B ILE* 3.0 50.6 + - + +
610B ALA* 1.3 77.8 - - + +
612B ALA* 1.3 52.7 + - - +
614B LEU* 2.9 12.9 + - + -
615B ALA* 2.1 43.4 + - - +
636B GLN* 3.6 10.1 - - - +
660B TYR* 3.3 35.7 + + + +
663B THR* 3.7 18.8 - - - -
664B PHE* 4.1 27.4 - + + -
667B PHE* 3.8 18.4 - - + +
668B MET* 5.6 3.1 - - + -
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Residues in contact with ALA 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B PHE 3.0 5.8 + - - +
609B LEU* 3.3 12.3 - - - +
611B TYR* 1.3 75.6 - - - +
613B GLN* 1.3 51.7 + - - +
615B ALA* 2.9 9.9 + - - +
616B TYR* 2.5 36.4 + - - +
629B PHE* 4.0 10.0 - - + -
632B CYS* 3.8 21.1 - - - +
633B ILE* 4.1 7.2 - - + -
636B GLN* 3.1 26.8 - - - +
660B TYR* 5.2 0.4 - - - -
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Residues in contact with GLN 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A CYS* 4.3 12.3 - - - -
566A VAL* 3.5 22.5 - - + +
570A TRP* 2.7 58.1 - - - +
1005A CHS 5.4 9.1 + - - +
609B LEU* 2.4 31.8 + - + +
610B ALA* 3.2 3.8 - - - +
612B ALA* 1.3 65.5 - - - +
614B LEU* 1.3 65.1 + - - +
616B TYR* 2.7 15.1 + - + +
617B LEU* 2.8 30.0 + - + +
629B PHE* 3.7 20.4 - - + -
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Residues in contact with LEU 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ALA* 3.5 32.8 - - + +
564A VAL* 4.1 10.3 - - + +
566A VAL* 5.6 2.2 - - - +
567A PHE* 4.8 17.9 - - + +
1008A PLM 4.5 22.9 - - + -
610B ALA 2.6 18.0 + - - +
611B TYR* 3.2 12.6 - - + +
613B GLN* 1.3 72.6 - - - +
615B ALA* 1.3 53.0 + - - +
617B LEU* 4.6 4.9 - - - -
618B VAL* 2.6 65.6 + - + +
619B PHE* 5.8 0.2 - - + -
660B TYR* 4.6 21.3 - - + -
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Residues in contact with ALA 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B TYR 2.1 30.3 + - - +
612B ALA* 3.0 14.1 - - - +
614B LEU* 1.3 68.1 - - - +
616B TYR* 1.3 54.2 + - - +
619B PHE* 2.4 56.6 + - + +
626B PHE* 3.6 31.6 - - + -
627B SER* 4.6 0.4 - - - -
632B CYS* 4.9 0.7 - - - -
660B TYR* 3.9 11.4 - - - +
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Residues in contact with TYR 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A THR* 5.6 5.4 - - - -
239A TYR* 6.3 0.9 - - - -
242A MET* 3.9 15.7 + - + +
243A SER 3.5 7.1 + - - -
244A SER* 3.1 33.5 + - - -
1005A CHS 4.5 18.6 + - - -
612B ALA 2.5 15.3 + - - +
613B GLN* 2.7 11.0 + - - +
615B ALA* 1.3 68.1 - - - +
617B LEU* 1.3 73.3 + - + +
620B GLY* 2.4 38.4 + - - -
627B SER* 3.5 43.3 - - - -
629B PHE* 3.8 37.5 - + + -
632B CYS* 4.5 5.0 - - - -
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Residues in contact with LEU 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A THR* 4.5 24.2 - - + +
559A ASN* 4.1 16.1 + - - +
562A ALA 5.1 0.2 - - - -
563A ALA* 3.6 25.4 - - + +
566A VAL* 3.4 39.0 - - + -
613B GLN* 2.8 38.5 + - + +
614B LEU* 3.7 5.6 - - - +
616B TYR* 1.3 93.7 - - + +
618B VAL* 1.3 65.3 + - - +
620B GLY* 3.6 4.7 + - - -
621B THR* 4.8 1.0 + - - +
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Residues in contact with VAL 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A ASN* 5.3 3.1 + - - -
560A ASN* 5.3 4.9 - - - +
563A ALA* 4.0 11.0 - - + -
564A VAL* 5.5 2.9 - - + +
614B LEU* 2.6 49.7 + - + +
617B LEU* 1.3 76.1 - - - +
619B PHE* 1.3 87.5 + - + +
621B THR* 3.1 24.6 + - - +
656B LEU* 3.5 42.3 - - + +
657B GLY* 4.9 0.2 - - - -
660B TYR* 6.2 1.3 - - + -
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Residues in contact with PHE 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B LEU* 5.2 0.4 - - + -
615B ALA* 2.4 47.7 + - + +
618B VAL* 1.3 90.1 - - + +
620B GLY* 1.3 50.7 + - - +
621B THR* 2.5 39.9 - - - +
623B VAL* 3.0 25.1 - - + +
626B PHE* 4.4 14.4 - + + -
627B SER* 3.0 7.3 + - - -
649B ILE* 4.0 30.1 - - + -
652B ALA* 4.8 7.6 - - + -
656B LEU 4.7 2.0 - - - -
657B GLY* 3.8 26.0 - - - -
660B TYR* 3.3 41.7 - + - -
----------------------------------------------------------
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Residues in contact with GLY 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 4.1 6.5 - - - +
247A TYR* 3.3 16.2 + - - -
250A THR* 3.2 15.1 - - - +
459A PRO* 5.7 3.1 - - - -
616B TYR* 2.4 25.2 + - - -
617B LEU 3.6 3.5 + - - -
618B VAL 3.3 1.8 - - - -
619B PHE* 1.3 68.6 - - - +
621B THR* 1.3 60.5 + - - +
627B SER* 3.0 18.6 - - - -
----------------------------------------------------------
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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