ID code: '4QVD' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 2892 C1' U H 4 beta 2887 2893 2890 2912 C1' A H 5 beta 2907 2913 2910 2934 C1' A H 6 beta 2929 2935 2932 2956 C1' A H 7 beta 2951 2957 2954 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2890 C2' U H 4 OK 2892 2888 2891 2910 C2' A H 5 OK 2912 2908 2911 2932 C2' A H 6 OK 2934 2930 2933 2954 C2' A H 7 OK 2956 2952 2955 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2888 C3' U H 4 OK 2886 2889 2890 2908 C3' A H 5 OK 2906 2909 2910 2930 C3' A H 6 OK 2928 2931 2932 2952 C3' A H 7 OK 2950 2953 2954 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2886 C4' U H 4 OK 2888 2885 2887 2906 C4' A H 5 OK 2908 2905 2907 2928 C4' A H 6 OK 2930 2927 2929 2950 C4' A H 7 OK 2952 2949 2951 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2885 C5' U H 4 2884 2886 2905 C5' A H 5 2904 2906 2927 C5' A H 6 2926 2928 2949 C5' A H 7 2948 2950 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2882 P U H 4 2883 2884 2901 P A H 5 distorted distorted 2889 2902 2903 2904 2923 P A H 6 distorted distorted 2909 2924 2925 2926 2945 P A H 7 distorted distorted 2931 2946 2947 2948 ---------------------------------------------------------------------------------