Contacts of the helix formed by residues 595 - 625 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C VAL* 3.2 18.9 - - - +
593C PRO* 5.4 0.5 - - - +
594C ARG* 1.3 78.8 - - - +
596C LEU* 1.3 55.5 + - - +
597C SER* 3.9 7.6 - - - -
598C GLY* 2.9 20.3 + - - -
599C ARG* 2.7 32.4 + - - +
814D PHE* 5.5 6.5 - - - -
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Residues in contact with LEU 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C ARG 3.4 2.2 + - - -
595C SER* 1.3 71.8 - - - +
597C SER* 1.3 79.4 + - - +
599C ARG* 3.4 1.9 + - - +
600C ILE* 2.9 32.4 + - + +
574D PHE* 3.5 35.1 - - + -
810D ALA* 5.1 9.0 - - + -
813D GLU* 5.5 16.8 - - + +
814D PHE* 6.3 1.1 - - + -
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Residues in contact with SER 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C VAL* 3.0 28.0 - - - +
595C SER* 3.3 3.6 + - - -
596C LEU* 1.3 85.2 - - - +
598C GLY* 1.3 72.2 + - - +
600C ILE* 3.0 11.7 - - - +
601C VAL* 2.9 28.8 + - - +
806D ALA 4.5 6.5 - - - -
807D MET* 5.5 0.7 - - - -
810D ALA* 4.1 26.2 - - - -
814D PHE* 3.9 14.4 - - - -
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Residues in contact with GLY 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C LEU* 4.0 15.3 - - - +
543C VAL* 3.6 11.6 - - - +
593C PRO* 4.0 18.0 - - - +
595C SER* 2.9 20.3 + - - -
597C SER* 1.3 77.0 + - - +
599C ARG* 1.3 63.4 + - - +
601C VAL* 3.9 0.5 - - - +
602C GLY* 2.9 23.4 + - - -
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Residues in contact with ARG 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C PRO* 4.2 14.4 - - - +
595C SER 2.7 20.1 + - - +
596C LEU 3.7 4.0 - - - +
598C GLY* 1.3 72.5 - - - +
600C ILE* 1.3 58.0 + - - +
602C GLY* 3.9 0.6 - - - -
603C GLY* 2.9 24.6 + - - -
606C TRP* 6.2 0.2 - - - -
574D PHE* 4.2 18.2 - - + -
578D TRP* 3.4 40.3 + - + +
581D LEU* 5.6 1.4 - - - +
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Residues in contact with ILE 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C LEU* 2.9 18.4 + - + +
597C SER* 3.0 28.3 - - - +
599C ARG* 1.3 75.7 - - - +
601C VAL* 1.3 64.9 + - - +
603C GLY* 3.2 2.5 + - - -
604C VAL* 2.9 29.3 + - + +
806D ALA* 3.7 27.4 - - + +
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Residues in contact with VAL 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C VAL* 4.2 12.1 - - + +
539C VAL* 5.2 11.0 - - + -
540C LEU* 3.6 31.0 - - + -
543C VAL* 5.0 8.3 - - + -
597C SER* 2.9 23.5 + - - +
600C ILE* 1.3 75.3 - - - +
602C GLY* 1.3 62.9 + - - +
604C VAL* 3.0 12.4 + - - +
605C TRP* 2.9 18.7 + - - +
803D LEU* 4.0 26.4 - - + +
806D ALA* 3.8 25.4 - - + -
807D MET* 5.0 1.6 - - - +
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Residues in contact with GLY 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C LEU* 4.3 6.1 - - - +
579C PHE* 5.0 14.6 - - - -
593C PRO* 5.9 1.3 - - - -
598C GLY 2.9 16.1 + - - -
599C ARG 4.1 0.7 - - - -
601C VAL* 1.3 76.5 - - - +
603C GLY* 1.3 57.6 + - - +
605C TRP* 2.8 26.6 + - - +
606C TRP* 2.9 30.2 + - - -
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Residues in contact with GLY 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599C ARG 2.9 17.5 + - - -
600C ILE* 3.5 4.9 - - - -
601C VAL 3.1 0.4 - - - -
602C GLY* 1.3 74.2 - - - +
604C VAL* 1.3 62.6 + - - +
606C TRP* 2.9 32.2 + - - +
607C PHE* 2.9 20.0 + - - -
581D LEU* 4.2 16.3 - - - +
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Residues in contact with VAL 604 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C ILE* 2.9 22.4 + - + +
601C VAL* 3.4 8.5 - - - +
603C GLY* 1.3 73.7 - - - +
605C TRP* 1.3 57.9 + - - +
607C PHE* 3.0 19.3 + - + +
608C PHE* 2.9 28.8 + - + +
799D LEU* 4.0 29.6 - - + +
800D VAL* 5.5 0.2 - - - -
802D GLY 5.6 2.5 - - - -
803D LEU* 3.6 30.3 - - + +
806D ALA* 5.9 2.2 - - + -
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Residues in contact with TRP 605 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C ILE* 5.0 2.5 - - + -
532C ALA* 4.4 10.3 - - + -
533C TYR* 4.3 24.9 - + + -
536C VAL* 4.0 38.1 - - + -
540C LEU* 6.1 1.8 - - + -
579C PHE* 5.4 4.9 - + - -
580C SER* 3.6 38.1 + - - -
583C ALA* 4.0 22.1 - - + +
584C PHE* 4.1 27.1 - + + +
601C VAL 2.9 10.9 + - - +
602C GLY* 2.8 18.0 + - - +
604C VAL* 1.3 79.6 - - - +
606C TRP* 1.3 58.2 + + - +
608C PHE* 3.3 40.8 + + + +
609C THR* 2.9 25.9 + - - -
803D LEU* 5.6 2.9 - - + -
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Residues in contact with TRP 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579C PHE* 4.2 22.7 - + - -
583C ALA* 4.0 15.6 - - + +
589C CYS* 6.2 1.1 - - - -
593C PRO* 5.7 0.4 - - + -
602C GLY* 2.9 25.1 + - - -
603C GLY* 2.9 25.8 + - - +
605C TRP* 1.3 73.6 - + - +
607C PHE* 1.3 59.6 + - + +
608C PHE 2.8 10.8 + - - -
609C THR* 2.9 27.7 + - + +
610C LEU* 3.0 17.4 + - - +
578D TRP* 3.4 44.9 - + - -
581D LEU* 5.0 7.6 - - + -
582D GLY* 4.5 18.6 - - - -
585D MET* 3.9 20.6 - - + -
587D GLN* 3.1 52.6 + - + +
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Residues in contact with PHE 607 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603C GLY 2.9 15.2 + - - -
604C VAL* 3.0 21.7 + - + +
606C TRP* 1.3 77.1 - - + +
608C PHE* 1.3 56.1 + - - +
610C LEU* 4.6 7.6 - - + +
611C ILE* 3.9 6.8 - - - +
517D PHE* 3.2 42.3 - + + -
581D LEU* 3.6 38.6 - - + -
584D PHE* 5.6 9.2 - + - -
585D MET* 5.8 4.9 - - + -
799D LEU* 4.7 12.4 - - + +
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Residues in contact with PHE 608 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C ILE* 4.5 18.8 - - + -
532C ALA* 5.5 3.1 - - + -
584C PHE* 4.7 2.9 - + - -
604C VAL* 2.9 11.2 + - + +
605C TRP* 3.3 49.4 - + + +
606C TRP 2.8 2.0 + - - -
607C PHE* 1.3 76.6 - - - +
609C THR* 1.3 68.8 + - - +
610C LEU 3.2 2.5 + - - -
611C ILE* 3.2 4.4 + - + +
612C ILE* 3.0 60.1 + - + +
795D VAL* 4.7 15.5 - - + -
796D PHE* 3.2 41.1 - + - -
799D LEU* 6.2 0.2 - - - -
800D VAL* 5.8 2.5 - - + -
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Residues in contact with THR 609 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C ALA 3.8 10.5 + - - +
584C PHE* 3.1 32.1 + - - -
586C ARG* 5.7 1.9 + - - -
605C TRP* 2.9 13.9 + - + +
606C TRP* 2.9 37.2 + - + +
608C PHE* 1.3 78.9 - - - +
610C LEU* 1.3 68.3 + - + +
612C ILE* 3.5 9.2 - - - -
613C ILE* 3.0 31.7 + - - +
585D MET* 6.1 0.9 - - + -
586D ARG* 5.9 7.6 - - + +
587D GLN 6.1 0.2 - - - +
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Residues in contact with LEU 610 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C ARG* 5.7 3.1 - - - +
606C TRP 3.0 15.5 + - - +
607C PHE* 4.9 7.9 - - + +
609C THR* 1.3 78.6 - - + +
611C ILE* 1.3 77.4 + - + +
614C SER* 2.8 48.7 + - - +
584D PHE* 5.2 9.4 - - + -
585D MET* 5.7 10.8 - - + -
586D ARG* 5.0 19.5 - - + +
613D ILE* 4.8 30.3 - - + -
616D TYR* 5.0 12.3 - - + -
617D THR* 4.6 5.8 - - - +
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Residues in contact with ILE 611 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607C PHE 3.9 4.9 - - - +
608C PHE* 3.2 6.3 + - + +
610C LEU* 1.3 84.2 - - + +
612C ILE* 1.3 60.0 + - - +
614C SER* 4.3 1.7 - - - -
615C SER* 2.9 34.3 + - - -
516D SER 5.6 1.8 - - - +
517D PHE* 3.4 48.5 - - + +
616D TYR* 3.4 37.5 - - + +
620D LEU* 4.4 9.2 - - + +
792D VAL* 4.8 19.1 - - + -
795D VAL* 4.8 11.4 - - + -
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Residues in contact with ILE 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LEU* 4.4 17.5 - - + +
525C ILE* 4.8 6.1 - - + -
529C ILE* 4.2 25.6 - - + -
584C PHE* 4.3 6.5 - - + -
608C PHE* 3.0 54.5 + - + +
609C THR* 3.4 14.1 - - - +
611C ILE* 1.3 79.9 - - - +
613C ILE* 1.3 79.5 + - + +
615C SER* 3.4 5.9 - - - -
616C TYR* 3.0 26.0 + - + +
792D VAL* 5.2 15.9 - - + -
796D PHE* 5.9 2.2 - - + -
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Residues in contact with ILE 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B LEU* 4.5 31.2 - - + -
526C TRP* 5.9 4.0 - - + -
584C PHE* 3.5 42.6 - - + +
585C MET* 5.7 0.2 - - - -
586C ARG* 3.8 29.2 - - + +
609C THR* 3.0 29.7 + - - +
612C ILE* 1.3 80.0 - - + +
614C SER* 1.3 67.9 + - - +
616C TYR* 2.8 22.4 + - + +
617C THR* 3.0 16.7 + - + +
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Residues in contact with SER 614 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C ARG* 4.0 13.8 + - - +
610C LEU* 2.8 37.3 + - - +
611C ILE* 4.3 2.2 - - - -
613C ILE* 1.3 76.7 - - - +
615C SER* 1.3 61.5 + - - +
617C THR* 2.7 24.5 + - - -
618C ALA* 2.9 11.5 + - - +
586D ARG* 6.0 0.5 + - - -
616D TYR* 5.6 2.5 - - - -
617D THR* 3.1 36.5 + - - +
620D LEU* 4.6 6.7 - - - -
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Residues in contact with SER 615 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LEU* 4.5 9.8 - - - +
611C ILE* 2.9 25.3 + - - -
612C ILE* 3.4 7.2 - - - -
614C SER* 1.3 76.7 - - - +
616C TYR* 1.3 62.8 + - - +
618C ALA* 3.1 1.6 + - - +
619C ASN* 3.0 38.6 + - - +
620D LEU* 3.5 27.5 - - - +
624D LEU* 5.7 1.9 - - - +
788D SER* 4.5 4.7 + - - -
792D VAL* 5.1 10.1 - - - +
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Residues in contact with TYR 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B LEU* 5.0 21.1 - - + -
611B ILE* 3.4 17.2 - - + +
614B SER* 4.8 7.4 - - - -
517C PHE* 3.3 26.5 + + - -
518C LEU* 5.4 0.4 - - - -
520C PRO* 3.4 32.3 - - + +
521C LEU* 4.7 16.3 - - + +
526C TRP* 4.5 28.0 - + + -
612C ILE 3.0 12.0 + - - +
613C ILE* 2.8 22.5 + - + +
615C SER* 1.3 72.0 + - - +
617C THR* 1.3 74.1 + - + +
619C ASN* 3.3 1.9 + - - +
620C LEU* 2.9 56.1 + - + +
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Residues in contact with THR 617 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B LEU* 5.0 4.0 - - + -
614B SER* 3.2 28.5 - - - +
618B ALA* 4.7 4.3 - - - +
586C ARG* 5.2 5.5 + - - +
613C ILE* 3.0 19.6 + - + +
614C SER* 2.7 24.5 + - - -
616C TYR* 1.3 83.4 - - + +
618C ALA* 1.3 57.4 + - - +
620C LEU* 4.1 3.3 - - - +
621C ALA* 2.9 31.4 + - - +
617D THR* 3.9 11.3 - - - +
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Residues in contact with ALA 618 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614C SER 2.9 14.7 + - - +
615C SER 3.3 9.0 - - - +
617C THR* 1.3 77.1 + - - +
619C ASN* 1.3 64.0 + - - +
621C ALA* 2.9 8.3 + - - +
622C ALA 2.9 20.4 + - - -
617D THR* 4.3 7.6 - - - +
620D LEU* 3.7 14.4 - - + -
621D ALA* 3.6 39.8 - - + +
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Residues in contact with ASN 619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C PRO* 4.2 19.5 - - + +
521C LEU* 4.2 3.9 - - + +
615C SER* 3.0 34.0 + - - +
616C TYR 4.3 0.4 - - - +
618C ALA* 1.3 74.6 - - - +
620C LEU* 1.3 56.9 + - - +
622C ALA* 3.7 5.0 - - - +
623C PHE* 2.7 32.2 + - - +
620D LEU* 4.7 3.7 - - - +
621D ALA* 4.2 18.2 + - - +
624D LEU* 6.0 3.0 - - - +
786D ALA* 4.5 21.3 + - - +
788D SER* 3.3 27.8 + - - -
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Residues in contact with LEU 620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B ILE* 4.0 13.7 - - + -
614B SER* 5.2 3.1 - - - +
615B SER* 4.3 25.6 - - - +
618B ALA* 4.5 8.1 - - + -
516C SER 5.8 2.0 - - - +
517C PHE 4.8 3.8 - - - +
520C PRO* 4.5 11.5 - - + +
616C TYR* 2.9 56.5 + - + +
617C THR* 4.1 3.8 - - - +
619C ASN* 1.3 74.4 - - - +
621C ALA* 1.3 67.6 + - - +
623C PHE* 3.9 5.4 - - + -
624C LEU* 2.9 55.6 + - + +
791C ASN* 6.1 2.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ALA* 3.6 33.2 - - + +
617C THR 2.9 21.0 + - - +
618C ALA* 3.2 7.2 - - - +
620C LEU* 1.3 77.3 - - - +
622C ALA* 1.3 61.7 + - - +
623C PHE 3.0 1.6 + - - -
624C LEU* 3.3 2.5 + - - +
625C THR* 3.3 22.8 + - - -
621D ALA* 5.6 1.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C ALA 2.9 16.8 + - - +
619C ASN* 3.7 5.4 - - - +
621C ALA* 1.3 71.9 - - - +
623C PHE* 1.3 58.3 + - - +
625C THR* 3.3 23.5 - - + +
626C VAL* 4.3 7.3 + - - +
621D ALA* 4.3 18.1 - - + +
622D ALA* 5.5 0.7 - - - +
785D SER* 5.2 6.3 - - - -
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Residues in contact with PHE 623 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C SER 5.7 1.1 - - - -
519C ASP* 2.8 38.8 - - + -
520C PRO* 5.7 4.0 - - + -
619C ASN 2.7 21.0 + - - +
620C LEU* 3.5 6.3 - - + +
621C ALA 3.0 0.6 - - - -
622C ALA* 1.3 79.5 - - - +
624C LEU* 1.3 76.4 + - + +
625C THR 3.3 2.4 + - - -
626C VAL* 3.9 14.6 - - - +
785D SER* 3.7 33.8 - - - -
786D ALA 5.3 0.4 - - - -
787D LEU* 4.5 14.6 - - + -
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Residues in contact with LEU 624 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B SER* 4.1 19.7 - - - +
618B ALA* 6.3 0.9 - - + -
619B ASN* 5.6 2.8 - - - +
516C SER 6.1 0.9 - - - +
620C LEU* 2.9 42.8 + - + +
621C ALA* 4.0 2.5 - - - +
623C PHE* 1.3 97.3 - - + +
625C THR* 1.3 58.9 + - - +
626C VAL 3.5 2.7 - - - -
627C GLU* 5.2 5.5 + - - +
787C LEU* 5.8 8.3 - - + -
788C SER 6.2 1.1 - - - +
791C ASN* 4.6 17.7 - - - +
----------------------------------------------------------
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Residues in contact with THR 625 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ALA 6.0 1.6 - - - -
622B ALA* 4.3 18.5 - - - +
621C ALA 3.3 14.6 + - - +
622C ALA* 3.3 27.4 - - + +
624C LEU* 1.3 79.6 - - - +
626C VAL* 1.3 61.0 + - + +
627C GLU 3.9 2.2 + - - -
----------------------------------------------------------
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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