ID code: '1CEZ' 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' --------------------------------------------------------------------------------- 6733 C1' G T 5 beta 6729 6734 6732 6755 C1' T T 6 beta 6751 6756 6754 6775 C1' G T 7 beta 6771 6776 6774 6797 C1' A T 8 beta 6793 6798 6796 6818 C1' G T 9 beta 6814 6819 6817 6840 C1' T T 10 beta 6836 6841 6839 6860 C1' C T 11 beta 6856 6861 6859 6879 C1' G T 12 beta 6875 6880 6878 6901 C1' T T 13 beta 6897 6902 6900 6921 C1' A T 14 beta 6917 6922 6920 6942 C1' T T 15 beta 6938 6943 6941 6962 C1' T T 16 beta 6958 6963 6961 6982 C1' A T 17 beta 6978 6983 6981 7004 C1' T N 101 beta 7000 7005 7003 7024 C1' A N 102 beta 7020 7025 7023 7045 C1' A N 103 beta 7041 7046 7044 7066 C1' T N 104 beta 7062 7067 7065 7086 C1' A N 105 beta 7082 7087 7085 7107 C1' C N 106 beta 7103 7108 7106 7126 C1' G N 107 beta 7122 7127 7125 7148 C1' A N 108 beta 7144 7149 7147 7169 C1' C N 109 beta 7165 7170 7168 7188 C1' T N 110 beta 7184 7189 7187 7208 C1' C N 111 beta 7204 7209 7207 7227 C1' A N 112 beta 7223 7228 7226 7248 C1' C N 113 beta 7244 7249 7247 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6732 C2' G T 5 6733 6730 6754 C2' T T 6 6755 6752 6774 C2' G T 7 6775 6772 6796 C2' A T 8 6797 6794 6817 C2' G T 9 6818 6815 6839 C2' T T 10 6840 6837 6859 C2' C T 11 6860 6857 6878 C2' G T 12 6879 6876 6900 C2' T T 13 6901 6898 6920 C2' A T 14 6921 6918 6941 C2' T T 15 6942 6939 6961 C2' T T 16 6962 6959 6981 C2' A T 17 6982 6979 7003 C2' T N 101 7004 7001 7023 C2' A N 102 7024 7021 7044 C2' A N 103 7045 7042 7065 C2' T N 104 7066 7063 7085 C2' A N 105 7086 7083 7106 C2' C N 106 7107 7104 7125 C2' G N 107 7126 7123 7147 C2' A N 108 7148 7145 7168 C2' C N 109 7169 7166 7187 C2' T N 110 7188 7185 7207 C2' C N 111 7208 7205 7226 C2' A N 112 7227 7224 7247 C2' C N 113 7248 7245 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6730 C3' G T 5 OK 6728 6731 6732 6752 C3' T T 6 OK 6750 6753 6754 6772 C3' G T 7 OK 6770 6773 6774 6794 C3' A T 8 OK 6792 6795 6796 6815 C3' G T 9 OK 6813 6816 6817 6837 C3' T T 10 OK 6835 6838 6839 6857 C3' C T 11 OK 6855 6858 6859 6876 C3' G T 12 OK 6874 6877 6878 6898 C3' T T 13 OK 6896 6899 6900 6918 C3' A T 14 OK 6916 6919 6920 6939 C3' T T 15 OK 6937 6940 6941 6959 C3' T T 16 OK 6957 6960 6961 6979 C3' A T 17 OK 6977 6980 6981 7001 C3' T N 101 OK 6999 7002 7003 7021 C3' A N 102 OK 7019 7022 7023 7042 C3' A N 103 OK 7040 7043 7044 7063 C3' T N 104 OK 7061 7064 7065 7083 C3' A N 105 OK 7081 7084 7085 7104 C3' C N 106 OK 7102 7105 7106 7123 C3' G N 107 OK 7121 7124 7125 7145 C3' A N 108 OK 7143 7146 7147 7166 C3' C N 109 OK 7164 7167 7168 7185 C3' T N 110 OK 7183 7186 7187 7205 C3' C N 111 OK 7203 7206 7207 7224 C3' A N 112 OK 7222 7225 7226 7245 C3' C N 113 OK 7243 7246 7247 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6728 C4' G T 5 OK 6730 6727 6729 6750 C4' T T 6 OK 6752 6749 6751 6770 C4' G T 7 OK 6772 6769 6771 6792 C4' A T 8 OK 6794 6791 6793 6813 C4' G T 9 OK 6815 6812 6814 6835 C4' T T 10 OK 6837 6834 6836 6855 C4' C T 11 OK 6857 6854 6856 6874 C4' G T 12 OK 6876 6873 6875 6896 C4' T T 13 OK 6898 6895 6897 6916 C4' A T 14 OK 6918 6915 6917 6937 C4' T T 15 OK 6939 6936 6938 6957 C4' T T 16 OK 6959 6956 6958 6977 C4' A T 17 OK 6979 6976 6978 6999 C4' T N 101 OK 7001 6998 7000 7019 C4' A N 102 OK 7021 7018 7020 7040 C4' A N 103 OK 7042 7039 7041 7061 C4' T N 104 OK 7063 7060 7062 7081 C4' A N 105 OK 7083 7080 7082 7102 C4' C N 106 OK 7104 7101 7103 7121 C4' G N 107 OK 7123 7120 7122 7143 C4' A N 108 OK 7145 7142 7144 7164 C4' C N 109 OK 7166 7163 7165 7183 C4' T N 110 OK 7185 7182 7184 7203 C4' C N 111 OK 7205 7202 7204 7222 C4' A N 112 OK 7224 7221 7223 7243 C4' C N 113 OK 7245 7242 7244 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6727 C5' G T 5 6726 6728 6749 C5' T T 6 6748 6750 6769 C5' G T 7 6768 6770 6791 C5' A T 8 6790 6792 6812 C5' G T 9 6811 6813 6834 C5' T T 10 6833 6835 6854 C5' C T 11 6853 6855 6873 C5' G T 12 6872 6874 6895 C5' T T 13 6894 6896 6915 C5' A T 14 6914 6916 6936 C5' T T 15 6935 6937 6956 C5' T T 16 6955 6957 6976 C5' A T 17 6975 6977 6998 C5' T N 101 6997 6999 7018 C5' A N 102 7017 7019 7039 C5' A N 103 7038 7040 7060 C5' T N 104 7059 7061 7080 C5' A N 105 7079 7081 7101 C5' C N 106 7100 7102 7120 C5' G N 107 7119 7121 7142 C5' A N 108 7141 7143 7163 C5' C N 109 7162 7164 7182 C5' T N 110 7181 7183 7202 C5' C N 111 7201 7203 7221 C5' A N 112 7220 7222 7242 C5' C N 113 7241 7243 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6745 P T T 6 distorted distorted 6731 6746 6747 6748 6765 P G T 7 distorted distorted 6753 6766 6767 6768 6787 P A T 8 distorted distorted 6773 6788 6789 6790 6808 P G T 9 distorted distorted 6795 6809 6810 6811 6830 P T T 10 distorted distorted 6816 6831 6832 6833 6850 P C T 11 distorted distorted 6838 6851 6852 6853 6869 P G T 12 distorted distorted 6858 6870 6871 6872 6891 P T T 13 distorted distorted 6877 6892 6893 6894 6911 P A T 14 distorted distorted 6899 6912 6913 6914 6932 P T T 15 distorted distorted 6919 6933 6934 6935 6952 P T T 16 distorted distorted 6940 6953 6954 6955 6972 P A T 17 distorted distorted 6960 6973 6974 6975 7014 P A N 102 distorted distorted 7002 7015 7016 7017 7035 P A N 103 distorted distorted 7022 7036 7037 7038 7056 P T N 104 distorted distorted 7043 7057 7058 7059 7076 P A N 105 distorted distorted 7064 7077 7078 7079 7097 P C N 106 distorted distorted 7084 7098 7099 7100 7116 P G N 107 distorted distorted 7105 7117 7118 7119 7138 P A N 108 distorted distorted 7124 7139 7140 7141 7159 P C N 109 distorted distorted 7146 7160 7161 7162 7178 P T N 110 distorted distorted 7167 7179 7180 7181 7198 P C N 111 distorted distorted 7186 7199 7200 7201 7217 P A N 112 distorted distorted 7206 7218 7219 7220 7238 P C N 113 distorted distorted 7225 7239 7240 7241 ---------------------------------------------------------------------------------