Contacts of the helix formed by residues 604 - 629 (chain A) in PDB entry 5J3V
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 TYR 604 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A ILE* 3.8 32.2 + - + +
563A GLN* 5.7 2.4 + - - -
566A MET* 4.0 26.3 - - + +
567A PRO* 5.4 2.1 - - - +
570A ILE* 3.5 31.9 - - + -
600A GLY 4.3 5.2 - - - -
601A PHE* 3.1 29.1 + + + +
602A LEU 3.0 1.0 - - - -
603A PRO* 1.3 104.8 - - + +
605A CYS* 1.3 65.0 + - - +
606A GLU 3.5 1.8 - - - -
607A PRO* 3.3 16.4 - - + +
608A VAL* 3.2 22.4 - - + +
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Residues in contact with CYS 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A PHE* 3.2 15.0 + - - +
602A LEU* 3.2 30.3 - - - +
603A PRO 3.7 0.2 - - - -
604A TYR* 1.3 79.1 - - - +
606A GLU* 1.3 78.2 + - - +
608A VAL* 3.2 3.6 + - - +
609A TYR* 2.7 37.7 + - - +
651A LEU* 4.2 6.2 - - + +
655A LEU* 3.6 30.3 - - + -
658A ASN 5.7 2.0 - - - -
662A LEU* 3.9 13.0 - - + -
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Residues in contact with GLU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A PRO 5.6 0.2 - - - -
605A CYS* 1.3 95.0 - - - +
607A PRO* 1.3 69.1 - - + +
609A TYR* 3.9 1.0 - - - +
610A GLN* 3.0 32.9 + - + +
662A LEU* 3.9 28.9 - - + +
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Residues in contact with PRO 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A TRP* 3.4 22.3 + - - +
603A PRO 5.0 3.4 - - - +
604A TYR* 3.3 22.9 - - + +
606A GLU* 1.3 94.3 - - + +
608A VAL* 1.3 62.2 + - + +
610A GLN* 4.3 4.6 - - + +
611A ARG* 3.5 14.2 + - - +
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Residues in contact with VAL 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A MET* 6.4 0.2 - - + -
573A TRP* 3.6 26.6 - - + -
590A LEU* 5.2 4.3 - - + -
601A PHE* 4.2 20.2 - - + -
604A TYR* 3.2 18.2 - - + +
605A CYS 3.2 8.1 + - - +
607A PRO* 1.3 79.5 - - + +
609A TYR* 1.3 65.6 + - - +
611A ARG 3.5 0.7 + - - -
612A CYS* 3.2 23.4 + - - -
647A LEU* 3.7 36.3 - - + -
651A LEU* 4.0 14.1 - - + -
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Residues in contact with TYR 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A CYS 2.7 21.5 + - - +
606A GLU 3.9 2.5 - - - +
608A VAL* 1.3 74.5 - - - +
610A GLN* 1.3 73.3 + - + +
612A CYS* 3.3 3.5 + - - +
613A VAL* 3.2 42.6 + - + +
648A LEU* 3.6 25.6 - - + -
651A LEU* 4.0 10.5 - - + -
659A ILE* 4.1 28.0 - - + -
662A LEU* 2.9 52.2 + - + -
663A VAL* 3.3 10.4 - - + -
666A SER* 2.9 26.0 + - - -
668A ILE* 3.3 20.1 - - + +
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Residues in contact with GLN 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A GLU* 3.0 23.3 + - + +
607A PRO* 4.3 5.2 - - + +
609A TYR* 1.3 89.0 - - + +
611A ARG* 1.3 61.3 + - - +
613A VAL* 3.4 9.1 + - - +
614A ASN* 3.1 38.1 + - - +
662A LEU* 6.1 2.5 - - + -
666A SER* 5.9 2.4 - - - -
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Residues in contact with ARG 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A TRP* 2.8 61.9 + - + +
574A ASN* 4.9 1.4 - - - +
576A LEU 2.9 24.6 + - - -
577A LYS 3.9 0.2 - - - -
578A ASP* 3.5 31.2 + - - +
583A LEU* 3.5 35.4 - - - +
587A LEU* 6.3 1.0 - - + +
607A PRO 3.5 15.7 + - - +
608A VAL 3.5 1.4 + - - +
609A TYR 3.3 0.4 - - - -
610A GLN* 1.3 76.6 - - - +
612A CYS* 1.3 60.2 + - - +
614A ASN* 3.4 9.6 + - + +
615A LEU* 2.9 36.4 + - + +
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Residues in contact with CYS 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A TRP* 5.0 3.1 - - - -
587A LEU* 5.1 3.8 - - - -
608A VAL* 3.2 27.0 + - - +
609A TYR 3.7 4.5 - - - +
611A ARG* 1.3 75.0 - - - +
613A VAL* 1.3 64.7 + - - +
615A LEU* 3.2 4.6 + - - +
616A VAL* 3.1 29.7 + - - +
644A ALA* 3.8 26.4 - - - +
647A LEU* 3.5 34.3 - - - -
648A LEU* 3.7 24.2 - - + -
651A LEU* 5.8 0.2 - - - -
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Residues in contact with VAL 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A TYR* 3.2 46.5 + - + +
610A GLN* 3.7 12.1 - - - +
611A ARG 3.3 0.2 - - - -
612A CYS* 1.3 76.4 - - - +
614A ASN* 1.3 56.6 + - - +
616A VAL* 3.3 6.7 + - - +
617A GLN* 2.8 38.6 + - - +
648A LEU* 4.7 9.0 - - + -
666A SER* 5.1 4.3 - - - -
667A ASN* 3.7 23.6 - - - +
668A ILE* 4.8 12.3 - - + +
671A LEU* 3.8 13.6 - - + +
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Residues in contact with ASN 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASP* 4.9 8.3 - - - +
610A GLN* 3.1 23.8 + - - +
611A ARG* 3.5 12.0 - - + +
612A CYS 3.3 0.2 - - - -
613A VAL* 1.3 82.3 - - - +
615A LEU* 1.3 55.5 + - - +
617A GLN* 3.9 10.0 - - - +
618A LYS* 2.9 43.6 + - + +
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Residues in contact with LEU 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASP* 3.5 47.3 - - + +
583A LEU* 4.6 11.2 - - + -
587A LEU* 4.1 21.8 - - + -
611A ARG* 2.9 27.8 + - + +
612A CYS* 3.5 10.1 - - - +
614A ASN* 1.3 77.2 - - - +
616A VAL* 1.3 53.4 + - - +
618A LYS* 4.1 6.2 - - - +
619A THR* 2.5 39.1 + - - +
640A PHE* 4.4 19.7 - - + +
644A ALA* 3.8 22.2 - - + -
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Residues in contact with VAL 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A CYS 3.1 15.3 + - - +
613A VAL* 3.7 6.1 - - - +
615A LEU* 1.3 72.6 - - - +
617A GLN* 1.3 61.3 + - - +
619A THR* 3.8 1.3 - - - -
620A LEU* 3.0 37.0 + - + +
641A MET* 4.0 14.1 - - + +
644A ALA* 3.9 16.2 - - + -
645A LEU* 3.7 28.3 - - + +
648A LEU* 4.7 4.0 - - + -
671A LEU* 4.2 14.6 - - + -
675A CYS* 3.8 29.2 - - - -
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Residues in contact with GLN 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A VAL* 2.8 26.9 + - - +
614A ASN* 3.9 9.9 - - - +
616A VAL* 1.3 75.3 - - - +
618A LYS* 1.3 59.9 + - + +
620A LEU* 3.5 2.3 + - - +
621A ALA* 3.0 28.9 + - + +
667A ASN* 3.2 31.5 + - - +
671A LEU* 3.9 19.3 - - + +
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Residues in contact with LYS 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A LYS* 5.7 2.2 - - - +
578A ASP* 3.2 43.7 + - - +
579A GLU* 4.2 10.1 + - - -
614A ASN* 2.9 28.7 + - + +
615A LEU* 4.1 5.8 - - - +
617A GLN* 1.3 75.5 - - + +
619A THR* 1.3 61.4 + - - +
621A ALA* 3.2 7.4 + - - +
622A GLN* 2.8 35.0 + - + +
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Residues in contact with THR 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LEU* 2.5 25.0 + - - +
616A VAL 3.8 3.8 - - - -
618A LYS* 1.3 76.3 - - - +
620A LEU* 1.3 57.9 + - - +
622A GLN* 4.7 0.4 - - - -
623A ALA* 3.1 26.6 + - + +
636A PRO* 3.5 21.3 - - + +
637A ASP 3.9 17.0 - - - +
638A LYS* 4.2 4.9 - - + -
640A PHE* 4.0 15.8 - - - +
641A MET* 3.7 34.1 + - + -
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A VAL* 3.0 19.7 + - + +
617A GLN* 3.8 4.0 - - - +
619A THR* 1.3 75.6 - - - +
621A ALA* 1.3 64.9 + - - +
623A ALA* 3.2 10.1 + - + +
624A MET* 3.0 29.2 + - - +
641A MET* 3.6 25.4 - - + -
671A LEU* 3.7 42.2 - - + +
674A GLN* 3.6 37.5 - - + +
675A CYS* 3.9 11.2 - - - -
678A ASP* 4.8 7.0 - - - +
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Residues in contact with ALA 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A GLN* 3.0 21.4 + - + +
618A LYS* 3.2 8.3 + - - +
620A LEU* 1.3 78.4 - - - +
622A GLN* 1.3 60.3 + - - +
624A MET* 3.2 16.0 + - - +
625A LEU* 3.1 29.5 + - + +
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Residues in contact with GLN 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A LYS* 2.8 18.7 + - + +
619A THR* 4.7 0.2 - - - -
621A ALA* 1.3 73.9 - - + +
623A ALA* 1.3 60.5 + - - +
625A LEU* 3.4 20.4 + - + +
626A ASN* 3.0 27.2 + - - +
633A TYR* 4.4 14.3 - - - +
634A GLU* 3.1 28.9 + - - +
636A PRO* 3.6 22.4 - - + +
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Residues in contact with ALA 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A THR* 3.1 19.8 + - + +
620A LEU* 3.4 14.4 - - + +
621A ALA 3.2 0.2 - - - -
622A GLN* 1.3 76.2 - - - +
624A MET* 1.3 59.3 + - + +
626A ASN* 3.5 3.5 + - - +
627A ASN* 3.0 28.4 + - - +
636A PRO* 3.4 16.4 - - + +
638A LYS* 5.7 10.3 - - + -
641A MET* 6.5 1.1 - - + -
678A ASP* 5.9 2.0 - - - +
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Residues in contact with MET 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A LEU* 3.0 20.2 + - + +
621A ALA* 3.2 14.8 + - - +
623A ALA* 1.3 75.2 - - + +
625A LEU* 1.3 66.4 + - + +
627A ASN* 3.2 8.4 + - - +
628A ALA* 3.1 22.7 + - - +
674A GLN* 4.7 14.8 - - - +
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Residues in contact with LEU 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A ALA* 3.1 21.5 + - + +
622A GLN* 3.7 25.1 - - + +
624A MET* 1.3 78.3 - - + +
626A ASN* 1.3 57.6 + - - +
628A ALA* 3.2 5.8 + - + +
629A GLN 2.9 30.0 + - - +
633A TYR* 3.7 49.2 - - + +
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Residues in contact with ASN 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A GLN 3.0 17.9 + - - +
623A ALA* 3.9 5.7 - - - +
625A LEU* 1.3 76.2 - - - +
627A ASN* 1.3 64.3 + - - +
629A GLN 4.3 0.2 - - - -
630A PRO* 3.2 35.2 + - - +
633A TYR* 2.8 28.7 + - - +
634A GLU* 3.3 11.6 - - - +
635A ALA* 3.0 36.5 - - - +
636A PRO* 4.6 0.4 - - + +
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Residues in contact with ASN 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ALA 3.0 18.6 + - - +
624A MET* 3.5 9.3 + - - +
625A LEU 3.2 0.2 - - - -
626A ASN* 1.3 79.5 + - - +
628A ALA* 1.3 63.4 + - - +
630A PRO* 4.5 4.9 - - - +
679A LYS* 5.8 1.2 + - - -
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Residues in contact with ALA 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A MET 3.1 16.0 + - - +
625A LEU* 3.2 6.7 + - + +
627A ASN* 1.3 81.7 - - - +
629A GLN* 1.3 68.5 + - + +
630A PRO* 3.4 7.9 - - - +
633A TYR* 6.1 0.2 - - + -
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Residues in contact with GLN 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU 2.9 6.4 + - - -
626A ASN 3.7 2.9 - - - -
628A ALA* 1.3 87.7 - - + +
630A PRO* 1.3 61.7 - - - +
631A ASP* 3.1 18.0 + - - +
632A GLN* 3.2 29.2 + - + +
633A TYR* 2.8 52.4 + - + +
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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