ID code: '5A0T' 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' --------------------------------------------------------------------------------- 6965 C1' C E 0 beta 6960 6966 6963 6985 C1' G E 1 beta 6980 6986 6983 7008 C1' C E 2 beta 7003 7009 7006 7028 C1' C E 3 beta 7023 7029 7026 7048 C1' U E 4 beta 7043 7049 7046 7074 C1' C F 0 beta 7069 7075 7072 7094 C1' G F 1 beta 7089 7095 7092 7117 C1' C F 2 beta 7112 7118 7115 7137 C1' C F 3 beta 7132 7138 7135 7157 C1' U F 4 beta 7152 7158 7155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6963 C2' C E 0 OK 6965 6961 6964 6983 C2' G E 1 OK 6985 6981 6984 7006 C2' C E 2 OK 7008 7004 7007 7026 C2' C E 3 OK 7028 7024 7027 7046 C2' U E 4 OK 7048 7044 7047 7072 C2' C F 0 OK 7074 7070 7073 7092 C2' G F 1 OK 7094 7090 7093 7115 C2' C F 2 OK 7117 7113 7116 7135 C2' C F 3 OK 7137 7133 7136 7155 C2' U F 4 OK 7157 7153 7156 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6961 C3' C E 0 OK 6959 6962 6963 6981 C3' G E 1 OK 6979 6982 6983 7004 C3' C E 2 OK 7002 7005 7006 7024 C3' C E 3 OK 7022 7025 7026 7044 C3' U E 4 OK 7042 7045 7046 7070 C3' C F 0 OK 7068 7071 7072 7090 C3' G F 1 OK 7088 7091 7092 7113 C3' C F 2 OK 7111 7114 7115 7133 C3' C F 3 OK 7131 7134 7135 7153 C3' U F 4 OK 7151 7154 7155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6959 C4' C E 0 OK 6961 6958 6960 6979 C4' G E 1 OK 6981 6978 6980 7002 C4' C E 2 OK 7004 7001 7003 7022 C4' C E 3 OK 7024 7021 7023 7042 C4' U E 4 OK 7044 7041 7043 7068 C4' C F 0 OK 7070 7067 7069 7088 C4' G F 1 OK 7090 7087 7089 7111 C4' C F 2 OK 7113 7110 7112 7131 C4' C F 3 OK 7133 7130 7132 7151 C4' U F 4 OK 7153 7150 7152 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6958 C5' C E 0 6957 6959 6978 C5' G E 1 6977 6979 7001 C5' C E 2 7000 7002 7021 C5' C E 3 7020 7022 7041 C5' U E 4 7040 7042 7067 C5' C F 0 7066 7068 7087 C5' G F 1 7086 7088 7110 C5' C F 2 7109 7111 7130 C5' C F 3 7129 7131 7150 C5' U F 4 7149 7151 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6954 P C E 0 distorted distorted 6955 6956 6957 6974 P G E 1 distorted distorted 6962 6975 6976 6977 6997 P C E 2 distorted distorted 6982 6998 6999 7000 7017 P C E 3 distorted distorted 7005 7018 7019 7020 7037 P U E 4 distorted distorted 7025 7038 7039 7040 7057 P C E 5 OK OK 7045 7058 7059 7060 7063 P C F 0 distorted distorted 7064 7065 7066 7083 P G F 1 distorted distorted 7071 7084 7085 7086 7106 P C F 2 distorted distorted 7091 7107 7108 7109 7126 P C F 3 distorted distorted 7114 7127 7128 7129 7146 P U F 4 distorted distorted 7134 7147 7148 7149 7166 P C F 5 OK OK 7154 7167 7168 7169 ---------------------------------------------------------------------------------