Contacts of the helix formed by residues 597 - 621 (chain D) in PDB entry 5VOT
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 SER 597 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ALA* 4.5 7.0 - - - +
809A VAL* 3.6 29.8 - - - -
810A ALA* 4.5 7.4 - - - -
814A PHE* 4.3 8.8 - - - -
543D VAL* 3.2 20.9 - - - +
595D SER* 2.7 17.2 + - - -
596D LEU* 1.3 82.4 - - - +
598D GLY* 1.3 62.6 + - - -
599D ARG 3.0 1.3 - - - -
600D ILE* 2.7 39.6 + - - +
601D VAL 3.8 0.5 + - - -
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Residues in contact with GLY 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D LEU* 4.4 10.4 - - - +
543D VAL* 4.4 9.0 - - - -
593D PRO* 4.2 11.2 - - - +
595D SER* 2.4 26.4 + - - -
597D SER* 1.3 67.3 + - - +
599D ARG* 1.3 56.6 + - - -
600D ILE 3.0 0.2 - - - -
601D VAL* 2.8 36.9 + - - +
602D GLY* 2.9 12.1 + - - -
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Residues in contact with ARG 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A PHE* 4.0 25.6 - - + -
578A TRP* 3.1 46.7 - - + -
581A LEU* 5.2 0.2 - - - +
593D PRO* 4.2 14.1 - - + +
595D SER* 4.0 2.8 + - - -
596D LEU* 4.8 4.6 - - - +
597D SER 3.0 3.3 - - - +
598D GLY* 1.3 75.7 - - - +
600D ILE* 1.3 57.1 + - + +
603D GLY* 2.9 23.7 + - - -
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Residues in contact with ILE 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A GLY* 4.4 15.3 - - - +
805A LEU* 4.2 26.9 - - + -
806A ALA* 4.5 6.1 - - + -
809A VAL* 4.3 26.0 - - + -
596D LEU 5.1 4.3 - - - +
597D SER* 2.7 27.4 + - - +
599D ARG* 1.3 71.2 - - + +
601D VAL* 1.3 63.8 + - - +
603D GLY* 3.1 1.6 + - - -
604D VAL* 2.9 29.6 + - + +
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Residues in contact with VAL 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A GLY 5.6 0.7 - - - +
803A LEU* 5.3 9.9 - - + -
806A ALA* 3.8 25.4 - - + -
536D VAL* 3.8 27.4 - - + +
539D VAL* 5.1 7.4 - - + -
540D LEU* 3.8 36.6 - - + +
543D VAL* 5.3 3.6 - - + -
598D GLY* 2.8 23.8 + - - +
600D ILE* 1.3 71.2 - - - +
602D GLY* 1.3 65.4 + - - +
604D VAL* 3.1 11.3 - - + +
605D TRP* 2.9 24.1 + - - +
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Residues in contact with GLY 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A TRP* 4.7 5.8 - - - -
540D LEU* 5.2 1.4 - - - +
579D PHE* 5.0 17.0 - - - -
593D PRO* 5.3 5.4 - - - -
598D GLY 2.9 12.0 + - - -
599D ARG 3.9 2.0 - - - -
601D VAL* 1.3 77.9 - - - +
603D GLY* 1.3 61.1 + - - +
605D TRP* 3.4 6.1 + - - +
606D TRP* 2.9 40.4 + - - -
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Residues in contact with GLY 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A TRP* 4.3 0.6 - - - -
581A LEU* 4.1 23.1 - - - -
585A MET* 5.9 0.7 - - - +
599D ARG 2.9 17.3 + - - -
600D ILE* 3.1 3.5 + - - -
602D GLY* 1.3 74.9 - - - +
604D VAL* 1.3 65.8 + - - +
606D TRP* 2.9 11.9 + - - +
607D PHE* 2.9 21.3 + - - +
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Residues in contact with VAL 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A VAL* 6.4 1.1 - - + -
798A ILE* 3.8 18.6 - - + +
799A LEU* 3.6 45.1 - - + +
802A GLY* 4.8 14.1 - - - -
803A LEU* 5.3 3.6 - - + +
536D VAL* 6.3 0.4 - - + -
600D ILE* 2.9 20.7 + - + +
601D VAL* 3.1 22.4 - - + +
603D GLY* 1.3 71.8 - - - -
605D TRP* 1.3 56.5 + - + +
607D PHE* 3.3 11.3 + - + +
608D PHE* 2.9 27.3 + - + +
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Residues in contact with TRP 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A LEU* 4.5 9.0 - - + -
529D ILE* 5.1 3.6 - - + -
532D ALA* 4.6 4.9 - - + -
533D TYR* 4.1 32.8 - + + -
536D VAL* 4.1 38.6 - - + -
579D PHE* 5.4 6.3 - + - -
580D SER* 3.8 10.7 + - - +
583D ALA* 3.7 30.8 - - + +
584D PHE* 4.0 31.3 - + + +
601D VAL 2.9 19.3 + - - +
602D GLY* 3.7 5.4 - - - +
604D VAL* 1.3 76.0 - - + +
606D TRP* 1.3 73.7 + + - +
608D PHE* 3.1 40.6 + + + +
609D THR* 2.9 25.5 + - - -
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Residues in contact with TRP 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A TRP* 3.7 37.2 - + - -
581A LEU* 4.6 5.8 - - + -
582A GLY* 3.7 29.2 - - - -
585A MET* 4.3 23.8 - - + -
587A GLN* 3.4 30.8 - - + +
588A GLY 5.0 6.1 - - - -
590A ASP* 5.3 3.8 - - - -
579D PHE* 4.5 19.3 - + - -
583D ALA* 4.5 22.9 + - + +
592D SER* 6.1 2.5 - - - -
593D PRO* 6.0 0.9 - - + -
602D GLY* 2.9 23.6 + - - -
603D GLY* 3.3 12.1 - - - +
605D TRP* 1.3 85.3 - + - +
607D PHE* 1.3 56.9 + - - +
609D THR* 2.6 30.8 + - - -
610D LEU* 2.9 13.2 + - - +
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Residues in contact with PHE 607 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 3.3 40.8 - + - -
518A LEU* 5.3 2.5 - - + -
526A TRP* 5.1 15.7 - + - -
584A PHE* 5.8 1.1 - + - -
585A MET* 3.5 31.3 - - + +
795A VAL* 4.1 17.2 - - + +
798A ILE* 4.8 20.0 - - + -
603D GLY 2.9 12.1 + - - +
604D VAL* 3.6 14.8 - - + +
606D TRP* 1.3 75.7 - - - +
608D PHE* 1.3 60.0 + - - +
610D LEU* 4.1 12.1 + - + +
611D ILE* 3.8 17.2 + - - +
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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
----------------------------------------------------------
792A VAL* 4.8 6.7 - - + -
795A VAL* 3.9 26.7 - - + +
796A PHE* 4.3 23.8 - + - -
799A LEU* 4.6 15.3 - - + -
529D ILE* 4.9 23.3 - - + -
532D ALA* 5.1 5.4 - - + -
584D PHE* 5.0 4.3 - + - -
604D VAL* 2.9 13.0 + - + +
605D TRP* 3.3 47.8 - + + +
606D TRP 3.0 0.2 - - - -
607D PHE* 1.3 76.9 - - - +
609D THR* 1.3 68.8 + - - +
611D ILE* 3.1 8.7 - - - +
612D ILE* 3.0 55.3 + - + +
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Residues in contact with THR 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583D ALA 4.2 6.2 + - - +
584D PHE* 3.2 48.1 - - + +
585D MET 5.5 0.2 - - - -
586D ARG* 5.8 4.5 - - - +
605D TRP* 2.9 18.4 + - - -
606D TRP* 2.6 20.4 + - - -
608D PHE* 1.3 74.4 - - - +
610D LEU* 1.3 65.1 + - - +
612D ILE* 3.1 3.8 + - - -
613D ILE* 2.9 39.6 + - + +
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Residues in contact with LEU 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 6.2 4.0 - - + -
526A TRP* 6.2 3.4 - - + -
584A PHE* 5.7 1.1 - - + -
585A MET* 4.3 27.1 - - + -
586A ARG* 5.3 6.5 - - + +
613A ILE* 4.5 33.9 - - + -
616A TYR* 4.9 15.7 - - + -
617A THR* 5.0 5.4 - - + -
586D ARG* 4.9 14.8 - - - +
606D TRP 2.9 11.6 + - - +
607D PHE* 4.2 12.8 - - + +
608D PHE 3.3 0.4 - - - -
609D THR* 1.3 77.6 - - - +
611D ILE* 1.3 57.0 + - - +
613D ILE* 4.9 2.0 - - - -
614D SER* 2.6 49.8 + - - +
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Residues in contact with ILE 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 3.5 32.7 - - + +
616A TYR* 3.4 27.1 - - + +
620A LEU* 4.0 15.5 - - + -
791A ASN* 5.1 18.4 - - + +
795A VAL* 3.7 29.2 - - + -
607D PHE 3.8 10.4 + - - +
608D PHE 3.1 15.7 - - - +
610D LEU* 1.3 80.6 - - - +
612D ILE* 1.3 71.8 + - + +
614D SER* 4.5 2.0 - - - -
615D SER* 2.9 30.0 + - - +
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Residues in contact with ILE 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A ASN* 5.8 2.7 - - + +
792A VAL* 5.4 13.9 - - + +
795A VAL* 5.0 3.4 - - + -
521D LEU* 4.2 15.9 - - + +
529D ILE* 4.7 19.1 - - + -
584D PHE* 4.3 14.4 - - + -
608D PHE* 3.0 57.5 + - + +
609D THR 3.9 2.0 - - - +
611D ILE* 1.3 89.1 - - + +
613D ILE* 1.3 70.4 + - + +
615D SER* 3.5 3.5 - - - -
616D TYR* 3.0 23.6 + - + +
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Residues in contact with ILE 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610C LEU* 4.8 25.6 - - + -
584D PHE* 3.5 44.9 - - + +
585D MET* 5.9 1.3 - - - -
586D ARG* 2.5 48.9 - - + +
609D THR* 2.9 34.0 + - + +
610D LEU* 4.5 1.6 - - - +
612D ILE* 1.3 74.8 - - + +
614D SER* 1.3 59.5 + - - +
616D TYR* 3.6 8.8 - - + +
617D THR* 2.9 38.2 + - - +
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Residues in contact with SER 614 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A TYR* 4.8 7.4 - - - -
617A THR* 3.2 33.2 - - - +
620A LEU* 5.3 4.4 - - - +
586D ARG* 5.0 3.6 - - - +
610D LEU* 2.6 36.5 + - - -
611D ILE* 4.1 2.5 - - - -
613D ILE* 1.3 82.3 - - - +
615D SER* 1.3 65.4 + - - +
617D THR* 3.3 4.8 + - - -
618D ALA* 2.9 25.7 + - - +
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Residues in contact with SER 615 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LEU* 4.3 19.4 - - - +
624A LEU* 4.1 18.7 - - - +
787A LEU* 5.0 7.8 - - - +
791A ASN* 5.2 5.9 + - - -
521D LEU* 4.6 9.5 - - - +
611D ILE* 2.9 27.6 + - - +
612D ILE* 3.5 4.3 - - - -
614D SER* 1.3 75.6 - - - +
616D TYR* 1.3 63.7 + - - +
618D ALA* 3.3 2.1 + - - +
619D ASN* 2.9 23.0 + - - +
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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
----------------------------------------------------------
610C LEU* 5.0 15.0 - - + -
611C ILE* 3.4 25.6 - - + +
614C SER* 5.6 2.0 - - - -
516D SER 3.9 9.0 + - - -
517D PHE 3.1 23.0 + - - -
520D PRO* 3.5 30.7 - - + +
521D LEU* 3.6 30.4 - - + +
526D TRP* 4.5 22.4 - + - -
612D ILE* 3.0 11.7 + - + +
613D ILE* 3.6 11.4 - - - +
615D SER* 1.3 75.2 - - - +
617D THR* 1.3 72.9 + - - +
619D ASN* 2.9 16.9 + - + +
620D LEU* 3.0 33.1 + - + +
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Residues in contact with THR 617 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C ARG* 5.8 2.0 - - - +
610C LEU* 4.6 4.9 - - - +
614C SER* 3.1 40.7 + - - +
617C THR* 3.9 16.8 - - - +
618C ALA* 4.3 9.7 - - - +
586D ARG* 5.2 2.2 + - - -
613D ILE* 2.9 24.9 + - - +
614D SER* 3.9 4.3 - - - -
616D TYR* 1.3 79.7 - - - +
618D ALA* 1.3 63.4 + - - +
620D LEU* 3.3 17.2 + - - +
621D ALA* 5.3 0.2 - - - +
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Residues in contact with ALA 618 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A THR* 4.6 4.0 - - - +
620A LEU* 4.6 6.1 - - + -
621A ALA* 3.6 43.2 - - + +
624A LEU* 6.3 1.3 - - + -
625A THR* 6.0 1.6 - - - -
614D SER* 2.9 17.9 + - - +
615D SER* 3.6 7.4 - - - +
617D THR* 1.3 79.1 - - - +
619D ASN* 1.3 62.4 + - - +
620D LEU 3.5 0.2 + - - -
621D ALA* 4.0 10.7 + - - +
622D ALA 5.2 0.2 + - - -
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Residues in contact with ASN 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU 5.6 3.1 - - - +
785A SER* 3.7 25.2 + - - +
786A ALA 4.7 0.6 - - - -
787A LEU* 4.5 11.8 - - + +
520D PRO* 3.9 24.9 - - + +
521D LEU* 4.3 12.0 - - + +
615D SER* 2.9 14.0 + - - +
616D TYR* 2.9 12.0 + - + +
618D ALA* 1.3 78.0 - - - +
620D LEU* 1.3 66.3 + - - +
621D ALA 3.0 1.7 + - - -
622D ALA* 3.6 6.9 + - - +
623D PHE* 3.5 16.5 + - - +
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Residues in contact with LEU 620 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611C ILE* 4.4 12.1 - - + +
614C SER* 4.6 5.4 - - - +
615C SER* 3.5 49.4 - - - +
618C ALA* 3.7 9.9 - - + -
619C ASN* 4.7 4.7 - - - +
516D SER 6.1 0.2 - - - +
520D PRO* 5.8 3.1 - - - -
616D TYR* 3.0 39.2 + - + +
617D THR* 3.3 12.9 + - - +
619D ASN* 1.3 76.8 - - - +
621D ALA* 1.3 64.6 + - - +
623D PHE* 3.0 28.1 + - + +
624D LEU* 4.3 14.5 - - + +
----------------------------------------------------------
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Residues in contact with ALA 621 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C ALA* 3.6 41.7 - - + +
619C ASN* 4.2 15.4 + - - +
621C ALA* 5.6 1.6 - - + -
622C ALA* 4.3 16.4 - - + +
618D ALA 4.0 9.8 + - - +
619D ASN 3.0 2.6 + - - -
620D LEU* 1.3 78.1 - - - +
622D ALA* 1.3 58.6 + - - +
623D PHE 3.0 15.6 - - - +
624D LEU* 5.2 0.2 - - - +
----------------------------------------------------------
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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