Contacts of the helix formed by residues 597 - 621 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B VAL* 3.2 20.3 - - - +
595B SER* 2.7 16.6 + - - -
596B LEU* 1.3 80.6 - - - +
598B GLY* 1.3 63.2 + - - -
599B ARG 3.0 1.6 - - - -
600B ILE* 2.7 39.0 + - - +
601B VAL 3.8 0.7 + - - -
806C ALA* 4.5 7.2 - - - +
809C VAL* 3.6 30.3 - - - -
810C ALA* 4.3 9.7 - - - +
814C PHE* 4.4 6.9 - - - -
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Residues in contact with GLY 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 4.4 10.3 - - - +
543B VAL* 4.3 8.7 - - - -
593B PRO* 4.2 11.1 - - - +
595B SER* 2.4 26.5 + - - -
597B SER* 1.3 67.5 + - - +
599B ARG* 1.3 55.1 + - - -
600B ILE 3.0 0.4 - - - -
601B VAL* 2.8 35.8 + - - +
602B GLY* 2.9 12.5 + - - -
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Residues in contact with ARG 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B PRO* 4.2 12.6 - - + +
594B ARG* 6.0 0.4 - - - -
595B SER* 4.0 3.0 + - - +
596B LEU* 4.8 4.5 - - - +
597B SER* 3.0 3.1 - - - +
598B GLY* 1.3 75.9 - - - +
600B ILE* 1.3 57.9 + - + +
603B GLY* 2.9 23.4 + - - -
574C PHE* 4.0 26.2 - - + -
578C TRP* 3.1 46.1 - - + -
581C LEU* 5.2 0.3 - - - +
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Residues in contact with ILE 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU 5.1 3.8 - - - +
597B SER* 2.7 28.6 + - - +
599B ARG* 1.3 71.6 - - + +
601B VAL* 1.3 65.1 + - - +
603B GLY* 3.1 1.4 + - - -
604B VAL* 2.9 28.7 + - + +
802C GLY* 4.4 15.7 - - - +
805C LEU* 4.2 27.1 - - + -
806C ALA* 4.5 6.1 - - + -
809C VAL* 4.3 25.4 - - + -
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Residues in contact with VAL 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B VAL* 3.8 27.8 - - + +
539B VAL* 5.1 8.1 - - + -
540B LEU* 3.8 35.9 - - + +
543B VAL* 5.3 3.4 - - + -
598B GLY* 2.8 24.8 + - - +
600B ILE* 1.3 72.1 - - - +
602B GLY* 1.3 64.3 + - - +
604B VAL* 3.1 9.8 - - - +
605B TRP* 2.9 24.3 + - - +
802C GLY 5.6 0.7 - - - +
803C LEU* 5.2 10.1 - - + -
806C ALA* 3.8 25.8 - - + -
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Residues in contact with GLY 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 5.2 1.4 - - - +
579B PHE* 5.0 17.7 - - - -
593B PRO* 5.3 4.7 - - - +
598B GLY 2.9 11.4 + - - -
599B ARG* 4.0 2.0 - - - -
601B VAL* 1.3 78.5 - - - +
603B GLY* 1.3 62.7 + - - +
605B TRP* 3.7 5.7 - - - +
606B TRP* 2.9 40.1 + - - -
578C TRP* 4.7 6.5 - - - -
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Residues in contact with GLY 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B ARG 2.9 16.3 + - - -
600B ILE* 3.1 4.0 + - - -
602B GLY* 1.3 74.8 - - - +
604B VAL* 1.3 64.6 + - - +
606B TRP* 2.9 11.8 + - - +
607B PHE* 2.9 22.5 + - - +
578C TRP* 4.3 1.0 - - - -
581C LEU* 4.1 23.6 - - - -
585C MET* 5.8 0.2 - - - +
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Residues in contact with VAL 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B VAL* 6.3 0.2 - - + -
600B ILE* 2.9 21.1 + - + +
601B VAL* 3.1 22.2 - - + +
603B GLY* 1.3 69.9 - - - -
605B TRP* 1.3 56.9 + - + +
607B PHE* 3.3 10.9 + - + -
608B PHE* 2.9 27.8 + - + +
795C VAL* 6.6 0.2 - - + -
798C ILE* 3.8 18.6 - - + +
799C LEU* 3.7 46.0 - - + +
802C GLY* 4.8 13.5 - - - -
803C LEU* 5.3 3.8 - - + +
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Residues in contact with TRP 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ILE* 5.1 4.0 - - + -
532B ALA* 4.6 4.7 - - + -
533B TYR* 4.1 33.4 - + + -
536B VAL* 4.1 39.5 - - + -
579B PHE* 5.4 5.8 - + - -
580B SER* 3.8 10.2 + - - +
583B ALA* 3.7 30.5 - - + +
584B PHE* 4.0 31.3 - + + +
601B VAL* 2.9 20.1 + - + +
602B GLY* 3.7 5.6 - - - +
604B VAL* 1.3 74.9 - - + +
606B TRP* 1.3 71.6 + + - +
608B PHE* 3.1 40.4 + + + +
609B THR* 2.9 25.5 + - - -
799C LEU* 4.5 9.9 - - + -
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Residues in contact with TRP 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B PHE* 4.5 21.6 - + - -
583B ALA* 4.5 22.7 + - + +
592B SER* 6.1 2.7 - - - -
593B PRO* 6.0 0.7 - - + -
602B GLY* 2.9 21.7 + - - -
603B GLY* 2.9 12.3 + - - +
605B TRP* 1.3 84.7 - + - +
607B PHE* 1.3 54.4 + - - +
609B THR* 2.6 30.0 + - - -
610B LEU* 2.9 13.3 + - - +
578C TRP* 3.7 34.8 - + - -
581C LEU* 4.6 6.5 - - + -
582C GLY* 3.8 29.4 - - - -
585C MET* 4.3 24.5 - - + -
587C GLN* 3.4 31.9 - - + +
588C GLY 5.3 3.1 - - - -
590C ASP* 5.3 5.4 - - - -
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Residues in contact with PHE 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B GLY 2.9 12.3 + - - +
604B VAL* 3.6 14.4 - - + +
606B TRP* 1.3 76.0 - - - +
608B PHE* 1.3 58.8 + - - +
610B LEU* 4.2 12.6 - - + +
611B ILE* 3.8 17.3 + - - +
517C PHE* 3.3 42.7 - + - -
518C LEU* 5.3 2.9 - - + -
526C TRP* 5.1 15.0 - + - -
584C PHE* 5.9 1.3 - + - -
585C MET* 3.5 30.9 - - + +
795C VAL* 4.1 16.4 - - + +
798C ILE* 4.8 21.1 - - + -
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Residues in contact with PHE 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ILE* 4.8 24.0 - - + -
532B ALA* 5.2 4.5 - - + -
584B PHE* 4.9 4.0 - + - -
604B VAL* 2.9 13.2 + - + +
605B TRP* 3.3 47.1 - + + +
606B TRP 3.0 0.2 - - - -
607B PHE* 1.3 75.0 - - - +
609B THR* 1.3 68.5 + - - +
610B LEU 3.3 0.4 - - - -
611B ILE* 3.1 8.0 - - - +
612B ILE* 3.0 54.6 + - + +
792C VAL* 4.9 5.2 - - + -
795C VAL* 3.9 27.3 - - + +
796C PHE* 4.2 22.2 - + - -
799C LEU* 4.6 17.3 - - + -
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Residues in contact with THR 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B ALA 4.2 6.6 + - - +
584B PHE* 3.2 48.3 - - + +
585B MET 5.3 0.7 - - - +
586B ARG* 5.8 4.9 - - - +
605B TRP* 2.9 18.6 + - - -
606B TRP* 2.6 20.1 + - - -
608B PHE* 1.3 74.5 - - - +
610B LEU* 1.3 65.0 + - - +
612B ILE* 3.1 3.9 + - - -
613B ILE* 2.9 39.1 + - + +
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Residues in contact with LEU 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ARG* 4.9 15.7 - - - +
606B TRP 2.9 11.7 + - - +
607B PHE* 4.2 14.6 - - + +
608B PHE 3.3 0.2 - - - -
609B THR* 1.3 77.0 - - - +
611B ILE* 1.3 57.6 + - - +
613B ILE* 4.9 2.2 - - - -
614B SER* 2.6 49.7 + - - +
517C PHE* 6.2 3.6 - - + -
526C TRP* 6.2 3.6 - - + -
584C PHE* 5.6 0.9 - - + -
585C MET* 4.3 27.4 - - + -
586C ARG* 5.3 6.3 - - + +
613C ILE* 4.5 34.3 - - + -
616C TYR* 5.0 16.2 - - + -
617C THR* 5.0 4.7 - - + -
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Residues in contact with ILE 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B PHE 3.8 10.4 + - - +
608B PHE 3.1 15.9 - - - +
610B LEU* 1.3 81.2 - - - +
612B ILE* 1.3 72.5 + - + +
614B SER* 4.5 1.3 - - - -
615B SER* 2.9 30.1 + - - +
517C PHE* 3.5 32.5 - - + +
616C TYR* 3.4 27.4 - - + +
620C LEU* 4.0 16.2 - - + -
791C ASN* 5.0 17.9 - - + +
795C VAL* 3.7 28.9 - - + -
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Residues in contact with ILE 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 4.2 16.4 - - + +
526B TRP* 6.5 0.2 - - + -
529B ILE* 4.7 18.6 - - + -
584B PHE* 4.3 15.5 - - + -
608B PHE* 3.0 56.9 + - + +
609B THR 3.1 2.4 + - - +
611B ILE* 1.3 88.4 - - + +
613B ILE* 1.3 71.2 + - + +
615B SER* 3.5 4.5 - - - -
616B TYR* 3.0 22.8 + - + +
791C ASN* 5.9 2.2 - - + +
792C VAL* 5.4 13.5 - - + -
795C VAL* 5.0 3.8 - - + -
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Residues in contact with ILE 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LEU* 4.8 25.1 - - + -
614A SER* 5.9 0.2 - - - +
584B PHE* 3.5 43.7 - - + +
585B MET* 5.9 1.1 - - - -
586B ARG* 2.5 49.4 - - + +
609B THR* 2.9 34.0 + - + +
610B LEU* 4.5 2.0 - - - +
612B ILE* 1.3 74.4 - - + +
614B SER* 1.3 59.1 + - - +
616B TYR* 3.6 9.4 - - + +
617B THR* 2.9 38.3 + - - +
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Residues in contact with SER 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ARG* 5.0 3.4 - - - +
610B LEU* 2.6 36.5 + - - -
611B ILE* 4.1 2.7 - - - -
613B ILE* 1.3 82.4 - - - +
615B SER* 1.3 65.2 + - - +
617B THR* 3.3 4.4 + - - -
618B ALA* 2.9 25.5 + - - +
616C TYR* 4.8 7.6 - - - -
617C THR* 3.2 33.0 - - - +
620C LEU* 5.3 3.8 - - - +
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Residues in contact with SER 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 4.7 8.2 - - - +
611B ILE* 2.9 28.1 + - - +
612B ILE* 3.5 3.8 - - - -
614B SER* 1.3 75.4 + - - +
616B TYR* 1.3 64.2 + - - +
618B ALA* 3.3 3.0 + - - +
619B ASN* 2.9 24.0 + - - +
620C LEU* 4.3 18.1 - - - +
624C LEU* 4.1 19.3 - - - +
787C LEU* 5.2 7.3 - - - +
791C ASN* 5.3 4.7 + - - -
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Residues in contact with TYR 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LEU* 5.1 14.6 - - + -
611A ILE* 3.4 25.6 - - + +
614A SER* 5.6 1.6 - - - -
516B SER 3.9 8.8 + - - -
517B PHE 3.1 23.2 + - - -
520B PRO* 3.6 27.6 - - + +
521B LEU* 3.6 32.9 - - + +
526B TRP* 4.5 21.8 - + + -
612B ILE* 3.0 10.8 + - + +
613B ILE* 3.6 13.0 - - + +
615B SER* 1.3 75.6 - - - +
617B THR* 1.3 71.5 + - - +
619B ASN* 2.9 17.3 + - + +
620B LEU* 3.0 33.1 + - + +
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Residues in contact with THR 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ARG* 5.8 1.8 - - - +
610A LEU* 4.7 4.7 - - - +
614A SER* 3.1 39.8 + - - +
617A THR* 3.9 17.5 - - - +
618A ALA* 4.3 8.0 - - + +
586B ARG* 5.2 2.8 + - - -
613B ILE* 2.9 24.5 + - - +
614B SER* 3.9 4.7 - - - -
616B TYR* 1.3 78.5 - - - +
618B ALA* 1.3 64.5 + - - +
620B LEU* 3.3 17.2 + - - +
621B ALA 4.3 1.9 + - - -
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Residues in contact with ALA 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B SER* 2.9 18.3 + - - +
615B SER* 3.6 7.4 - - - +
617B THR* 1.3 78.7 - - - +
619B ASN* 1.3 62.3 + - - +
620B LEU 3.5 0.2 + - - -
621B ALA* 4.0 10.9 + - - +
622B ALA 5.2 0.5 + - - -
617C THR* 4.7 4.0 - - - +
620C LEU* 4.5 6.3 - - + -
621C ALA* 3.6 42.8 - - + +
624C LEU* 6.3 1.1 - - + -
625C THR* 6.0 1.6 - - - -
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Residues in contact with ASN 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B PRO* 3.9 25.6 - - + +
521B LEU* 4.3 2.9 - - + +
615B SER* 2.9 13.6 + - - +
616B TYR* 2.9 13.9 + - + +
618B ALA* 1.3 78.0 - - - +
620B LEU* 1.3 65.3 + - - +
621B ALA 3.0 1.9 + - - -
622B ALA* 3.6 7.3 + - - +
623B PHE* 3.4 16.6 + - - +
624C LEU 5.6 2.3 - - - +
785C SER* 3.7 24.9 + - - +
787C LEU* 4.0 24.0 - - + +
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ILE* 4.4 11.9 - - + +
614A SER* 4.6 5.4 - - - +
615A SER* 3.5 49.1 - - - +
618A ALA* 3.7 9.0 - - + -
619A ASN* 4.7 5.2 - - - +
516B SER 6.1 0.2 - - - +
520B PRO* 5.8 3.4 - - - -
616B TYR* 3.0 37.6 + - + +
617B THR* 3.3 13.3 + - - +
619B ASN* 1.3 76.8 - - - +
621B ALA* 1.3 65.1 + - - +
623B PHE* 3.0 28.2 + - + +
624B LEU* 4.3 13.6 - - + +
----------------------------------------------------------
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Residues in contact with ALA 621 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA* 3.6 41.9 - - + +
619A ASN* 4.2 13.5 + - - +
621A ALA* 5.6 1.3 - - + -
622A ALA* 4.3 16.8 - - + +
618B ALA 4.0 9.1 + - - +
619B ASN 3.0 3.2 + - - -
620B LEU* 1.3 76.8 - - - +
622B ALA* 1.3 58.4 + - - +
623B PHE 3.0 15.8 - - - +
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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