Contacts of the helix formed by residues 595 - 625 (chain A) 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 595 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A VAL* 3.2 18.6 - - - +
593A PRO* 5.4 0.5 - - - +
594A ARG* 1.3 80.9 + - - +
596A LEU* 1.3 55.6 + - - +
597A SER* 4.0 7.4 - - - -
598A GLY* 2.9 20.8 + - - -
599A ARG* 2.8 33.3 + - - +
814B PHE* 5.5 6.5 - - - -
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Residues in contact with LEU 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A ARG 3.4 2.4 + - - -
595A SER* 1.3 71.6 - - - +
597A SER* 1.3 77.6 + - - +
599A ARG* 3.4 1.9 + - - +
600A ILE* 2.9 30.9 + - + +
574B PHE* 3.5 34.9 - - + -
810B ALA* 5.1 9.4 - - + -
813B GLU* 5.5 16.6 - - + +
814B PHE* 6.3 1.3 - - + -
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Residues in contact with SER 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A VAL* 3.0 28.5 - - - +
595A SER* 3.4 3.8 + - - -
596A LEU* 1.3 85.1 - - - +
598A GLY* 1.3 67.9 + - - +
600A ILE* 3.0 12.0 - - - +
601A VAL* 2.9 28.6 + - - +
806B ALA 4.5 6.3 - - - -
807B MET* 5.4 0.4 - - - -
810B ALA* 4.1 25.1 - - - -
814B PHE* 3.9 15.1 - - - -
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Residues in contact with GLY 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LEU* 4.0 16.4 - - - +
543A VAL* 3.6 10.5 - - - +
593A PRO* 4.0 18.2 - - - +
595A SER* 2.9 20.7 + - - -
597A SER* 1.3 77.6 + - - +
599A ARG* 1.3 62.8 + - - +
601A VAL* 3.4 0.9 + - - +
602A GLY* 2.9 22.9 + - - -
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Residues in contact with ARG 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PRO* 4.2 14.8 - - - +
594A ARG 5.0 0.2 - - - +
595A SER 2.8 19.7 + - - +
596A LEU 3.7 4.3 - - - +
598A GLY* 1.3 72.2 - - - +
600A ILE* 1.3 58.5 + - - +
602A GLY* 4.1 0.6 - - - -
603A GLY* 2.9 24.6 + - - -
606A TRP* 4.6 0.6 - - - -
574B PHE* 4.2 17.9 - - + -
578B TRP* 3.4 39.2 + - + +
581B LEU* 5.6 1.2 - - - +
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Residues in contact with ILE 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LEU* 2.9 17.0 + - + +
597A SER* 3.0 28.0 - - - +
599A ARG* 1.3 76.5 - - - +
601A VAL* 1.3 65.1 + - - +
603A GLY* 3.2 2.3 + - - -
604A VAL* 2.9 29.7 + - + +
806B ALA* 3.7 27.4 - - + +
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Residues in contact with VAL 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A VAL* 4.2 11.9 - - + +
539A VAL* 5.2 11.9 - - + -
540A LEU* 3.6 30.1 - - + -
543A VAL* 5.0 8.3 - - + -
597A SER* 2.9 22.8 + - - +
600A ILE* 1.3 75.7 - - - +
602A GLY* 1.3 64.8 + - - +
604A VAL* 3.0 11.6 + - - +
605A TRP* 2.9 19.1 + - - +
803B LEU* 4.0 25.7 - - + +
806B ALA* 3.8 26.2 - - + -
807B MET 5.0 1.1 - - - +
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Residues in contact with GLY 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LEU* 4.3 5.7 - - - +
579A PHE* 5.0 14.6 - - - -
593A PRO* 5.9 1.3 - - - -
598A GLY 2.9 16.9 + - - -
599A ARG* 4.1 0.7 - - - -
601A VAL* 1.3 77.0 - - - +
603A GLY* 1.3 57.7 + - - +
605A TRP* 2.8 25.6 + - - +
606A TRP* 2.9 30.4 + - - -
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Residues in contact with GLY 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A ARG 2.9 17.7 + - - -
600A ILE* 3.5 4.7 - - - -
601A VAL 3.1 0.6 - - - -
602A GLY* 1.3 75.6 - - - +
604A VAL* 1.3 62.2 + - - +
606A TRP* 2.9 30.5 + - - +
607A PHE* 2.9 21.7 + - - -
581B LEU* 4.2 14.5 - - - +
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Residues in contact with VAL 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A ILE* 2.9 23.3 + - + +
601A VAL* 3.4 7.4 - - - +
603A GLY* 1.3 73.9 - - - +
605A TRP* 1.3 57.0 + - - +
607A PHE* 3.0 20.3 + - + +
608A PHE* 2.9 27.9 + - + +
799B LEU* 4.0 29.8 - - + +
802B GLY* 5.6 2.5 - - - -
803B LEU* 3.6 31.2 - - + +
806B ALA* 5.9 2.5 - - + -
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Residues in contact with TRP 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ILE* 5.0 2.7 - - + -
532A ALA* 4.4 10.3 - - + -
533A TYR* 4.3 23.6 - + + -
536A VAL* 4.0 37.9 - - + -
540A LEU* 6.1 1.6 - - + -
579A PHE* 5.4 5.4 - + - -
580A SER* 3.6 37.9 + - - -
583A ALA* 3.9 21.8 - - + +
584A PHE* 4.1 26.4 - + + +
601A VAL 2.9 11.4 + - - +
602A GLY* 2.8 18.4 + - - +
604A VAL* 1.3 78.3 - - - +
606A TRP* 1.3 57.6 + + - +
608A PHE* 3.3 40.2 + + + +
609A THR* 2.9 25.2 + - - -
803B LEU* 5.0 3.1 - - + +
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Residues in contact with TRP 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A PHE* 4.2 22.4 - + - -
583A ALA* 4.0 14.4 - - + +
589A CYS* 6.2 0.9 - - + -
593A PRO* 5.6 0.9 - - + -
599A ARG* 6.2 0.2 - - - -
602A GLY* 2.9 16.4 + - - -
603A GLY* 2.9 33.6 + - - +
605A TRP* 1.3 75.7 - + - +
607A PHE* 1.3 60.9 + - + +
608A PHE 2.8 11.1 + - - -
609A THR* 3.0 27.5 + - + +
610A LEU* 3.0 18.3 + - - +
578B TRP* 3.4 43.5 - + - -
581B LEU* 5.0 7.6 - - + -
582B GLY* 4.5 18.4 - - - -
585B MET* 3.9 20.1 - - + +
587B GLN* 3.1 55.0 + - + +
588B GLY 5.3 0.2 - - - -
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Residues in contact with PHE 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A GLY 2.9 15.8 + - - -
604A VAL* 3.3 21.8 - - + +
606A TRP* 1.3 77.3 - - + +
608A PHE* 1.3 56.2 + - - +
610A LEU* 4.6 7.6 - - + +
611A ILE* 3.9 6.1 - - - +
517B PHE* 3.2 41.4 - + + -
581B LEU* 3.6 40.2 - - + -
584B PHE* 5.6 8.5 - + - -
585B MET* 5.8 4.7 - - + -
795B VAL* 5.1 0.2 - - - +
799B LEU* 4.7 11.8 - - + +
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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
----------------------------------------------------------
529A ILE* 4.5 18.4 - - + -
532A ALA* 5.5 3.1 - - + -
584A PHE* 4.6 2.9 - + - -
604A VAL* 2.9 11.7 + - + +
605A TRP* 3.3 50.0 - + + +
606A TRP 2.8 1.6 + - - -
607A PHE* 1.3 76.8 - - - +
609A THR* 1.3 68.0 + - - +
610A LEU 3.1 2.7 + - - -
611A ILE* 3.2 4.6 + - + +
612A ILE* 3.0 61.3 + - + +
795B VAL* 4.7 15.3 - - + -
796B PHE* 3.2 41.3 - + - -
799B LEU* 6.2 0.4 - - + -
800B VAL* 5.8 2.9 - - + -
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Residues in contact with THR 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA 3.8 10.9 + - - +
584A PHE* 3.2 31.6 + - - -
586A ARG* 5.7 2.3 + - - -
605A TRP* 2.9 13.7 + - - +
606A TRP* 3.0 37.4 + - + +
608A PHE* 1.3 79.2 - - - +
610A LEU* 1.3 67.9 + - + +
612A ILE* 3.5 8.5 - - - -
613A ILE* 3.0 30.5 + - - +
585B MET* 6.1 1.1 - - + -
586B ARG* 6.0 6.7 - - + +
587B GLN 6.2 0.9 - - - +
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Residues in contact with LEU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ARG* 5.7 1.8 - - - +
606A TRP 3.0 15.5 + - - +
607A PHE* 4.9 7.0 - - + +
609A THR* 1.3 79.4 - - + +
611A ILE* 1.3 76.2 + - + +
613A ILE* 5.5 0.2 - - - -
614A SER* 2.9 50.0 + - - +
584B PHE* 5.3 8.3 - - + -
585B MET* 5.7 10.8 - - + -
586B ARG* 5.0 20.6 - - + +
613B ILE* 4.8 31.4 - - + -
616B TYR* 5.1 12.8 - - + -
617B THR* 4.7 6.1 - - - +
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Residues in contact with ILE 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PHE 3.9 4.5 - - - +
608A PHE* 3.2 7.2 + - + +
610A LEU* 1.3 84.4 - - + +
612A ILE* 1.3 60.8 + - - +
614A SER* 4.8 1.3 - - - -
615A SER* 2.9 34.5 + - - -
516B SER 5.6 1.6 - - - +
517B PHE* 3.4 48.2 - - + +
616B TYR* 3.4 37.9 - - + +
620B LEU* 4.4 8.4 - - + +
792B VAL* 4.8 19.3 - - + -
795B VAL* 4.8 11.2 - - + -
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Residues in contact with ILE 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 4.4 18.1 - - + +
525A ILE* 4.8 6.1 - - + -
529A ILE* 4.2 25.8 - - + -
584A PHE* 4.3 6.5 - - + -
608A PHE* 3.0 54.9 + - + +
609A THR* 3.4 13.5 - - - +
611A ILE* 1.3 80.3 - - - +
613A ILE* 1.3 82.9 + - + +
615A SER* 3.4 5.7 - - - -
616A TYR* 3.0 25.7 + - + +
792B VAL* 5.2 16.4 - - + -
796B PHE* 5.9 1.8 - - + -
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Residues in contact with ILE 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A TRP* 5.9 4.0 - - + -
584A PHE* 3.5 44.6 - - + +
585A MET* 5.7 0.2 - - - -
586A ARG* 3.9 27.8 - - + +
609A THR* 3.0 30.1 + - - +
610A LEU* 5.5 0.2 - - - -
612A ILE* 1.3 78.5 - - + +
614A SER* 1.3 68.8 + - - +
616A TYR* 2.8 21.3 + - + +
617A THR* 3.0 18.0 + - + +
610D LEU* 4.5 31.2 - - + -
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Residues in contact with SER 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ARG* 4.0 12.8 + - - +
610A LEU* 2.9 36.7 + - - +
611A ILE* 4.3 1.8 - - - -
613A ILE* 1.3 76.4 - - - +
615A SER* 1.3 61.7 + - - +
617A THR* 2.7 24.7 + - - -
618A ALA* 2.9 12.6 + - - +
586B ARG* 6.0 0.3 + - - -
616B TYR* 5.6 2.5 - - - -
617B THR* 3.1 36.0 + - - +
620B LEU* 4.6 6.3 - - - -
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Residues in contact with SER 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 4.5 8.4 - - - +
611A ILE* 2.9 25.3 + - - -
612A ILE* 3.4 7.4 - - - -
614A SER* 1.3 77.6 - - - +
616A TYR* 1.3 62.6 + - - +
618A ALA* 3.0 1.7 + - - +
619A ASN* 3.0 38.6 + - - +
620B LEU* 3.5 26.7 - - - +
624B LEU* 5.7 1.6 - - - +
788B SER* 4.5 5.9 + - - -
792B VAL* 5.1 10.4 - - - +
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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
----------------------------------------------------------
517A PHE* 3.3 27.5 + + - -
518A LEU* 5.4 0.2 - - - -
520A PRO* 3.4 32.8 - - + +
521A LEU* 4.7 16.5 - - + +
526A TRP* 4.4 26.9 - + + -
612A ILE 3.0 12.3 + - - +
613A ILE* 2.8 22.3 + - + +
615A SER* 1.3 71.3 - - - +
617A THR* 1.3 73.2 + - + +
618A ALA 3.1 0.3 + - - -
619A ASN* 4.0 2.3 - - - +
620A LEU* 2.9 56.8 + - + +
610D LEU* 4.9 21.1 - - + -
611D ILE* 3.4 17.1 - - + +
614D SER* 4.8 7.4 - - - -
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Residues in contact with THR 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ARG* 5.2 6.1 + - - +
613A ILE* 3.0 20.0 + - + +
614A SER* 2.7 24.5 + - - -
616A TYR* 1.3 83.8 - - + +
618A ALA* 1.3 56.2 + - - +
620A LEU* 4.1 3.3 - - - +
621A ALA* 2.9 30.8 + - - +
617B THR* 3.9 10.9 - - - +
610D LEU* 5.0 4.5 - - + -
614D SER* 3.2 28.5 - - - +
618D ALA* 4.6 4.3 - - - +
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Residues in contact with ALA 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A SER 2.9 14.3 + - - +
615A SER 3.0 8.7 + - - +
617A THR* 1.3 77.5 + - - +
619A ASN* 1.3 64.4 + - - +
621A ALA* 2.9 6.9 + - - +
622A ALA 2.9 20.3 + - - -
617B THR* 4.3 11.0 - - - +
620B LEU* 3.7 10.8 - - + -
621B ALA* 3.6 40.4 - - + +
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Residues in contact with ASN 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A PRO* 4.2 19.1 - - + +
521A LEU* 4.2 4.2 - - + +
615A SER* 3.0 33.6 + - - +
616A TYR 4.3 0.4 - - - +
618A ALA* 1.3 75.0 - - - +
620A LEU* 1.3 58.3 + - - +
622A ALA* 3.7 6.0 + - - +
623A PHE* 2.8 31.6 + - - +
620B LEU* 4.7 2.9 - - - +
621B ALA* 4.2 18.6 + - - +
623B PHE 5.7 0.2 + - - -
624B LEU* 6.0 2.6 - - - +
786B ALA* 4.5 20.2 + - - +
787B LEU* 6.3 0.2 - - + -
788B SER* 3.3 28.7 + - - +
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A SER 5.8 1.6 - - - +
517A PHE 4.8 4.5 - - - +
520A PRO* 4.5 11.3 - - + +
616A TYR* 2.9 57.2 + - + +
617A THR* 4.1 4.0 - - - +
619A ASN* 1.3 73.8 - - - +
621A ALA* 1.3 66.8 + - - +
623A PHE* 3.9 5.8 - - + -
624A LEU* 2.9 55.6 + - + +
791A ASN* 6.4 0.2 - - - +
611D ILE* 4.0 13.7 - - + -
614D SER* 5.2 4.0 - - - +
615D SER* 4.3 25.4 - - - +
618D ALA* 4.6 7.6 - - + -
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Residues in contact with ALA 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A THR 2.9 22.1 + - - +
618A ALA* 3.2 7.0 - - - +
620A LEU* 1.3 78.2 - - - +
622A ALA* 1.3 61.9 + - - +
623A PHE 3.0 1.0 + - - -
624A LEU* 3.3 2.0 + - - +
625A THR* 3.3 22.2 + - - -
621B ALA* 5.6 1.8 - - + -
618D ALA* 3.6 34.5 - - + +
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Residues in contact with ALA 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA 2.9 16.6 + - - +
619A ASN* 3.8 5.4 - - - +
621A ALA* 1.3 72.7 - - - +
623A PHE* 1.3 58.2 + - - +
624A LEU 3.6 0.2 - - - -
625A THR* 3.3 22.7 - - + +
626A VAL* 4.3 7.4 + - - +
621B ALA* 4.3 17.7 - - + -
622B ALA* 5.5 1.1 - - - +
785B SER* 5.2 6.0 - - - -
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Residues in contact with PHE 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A SER 5.7 1.1 - - - -
519A ASP* 2.8 40.2 - - + -
520A PRO* 5.7 3.8 - - + -
619A ASN 2.8 21.5 + - - +
620A LEU* 3.5 6.7 - - - +
621A ALA 3.0 0.2 - - - -
622A ALA* 1.3 79.7 - - - +
624A LEU* 1.3 78.2 + - + +
625A THR 3.3 1.2 + - - -
626A VAL* 3.9 14.4 - - - +
785B SER* 3.7 33.7 - - - -
786B ALA 5.3 0.4 - - - -
787B LEU* 4.5 14.1 - - + -
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A SER 6.0 1.6 - - - +
620A LEU* 2.9 44.5 + - + +
621A ALA* 4.0 2.7 - - - +
623A PHE* 1.3 97.1 - - + +
625A THR* 1.3 57.7 + - - +
626A VAL 3.5 2.7 - - - -
627A GLU* 5.2 5.9 + - - +
787A LEU* 5.7 8.1 - - + -
791A ASN* 4.5 17.9 - - - +
615D SER* 4.1 19.7 - - - +
618D ALA* 6.3 1.1 - - + -
619D ASN* 5.6 2.6 - - - +
----------------------------------------------------------
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Residues in contact with THR 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A ALA 3.3 12.9 + - - +
622A ALA* 3.3 26.9 - - + +
624A LEU* 1.3 80.0 - - - +
626A VAL* 1.3 60.9 + - + +
627A GLU* 3.9 2.2 + - - -
618D ALA 6.0 1.6 - - - -
622D ALA* 4.3 18.2 - - - +
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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