ID code: '4TYW' 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' --------------------------------------------------------------------------------- 7924 C1' A B 1 alpha beta 7919 7941 7925 7922 7957 C1' A B 2 alpha beta 7952 7974 7958 7955 7990 C1' A B 3 alpha beta 7985 8007 7991 7988 8023 C1' A B 4 alpha beta 8018 8040 8024 8021 8056 C1' A B 5 alpha beta 8051 8073 8057 8054 8089 C1' A B 6 alpha beta 8084 8106 8090 8087 8122 C1' A B 7 alpha beta 8117 8140 8123 8120 8168 C1' ADP A 604 alpha beta 8163 8186 8169 8166 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7922 C2' A B 1 OK OK 7924 7920 7939 7923 7955 C2' A B 2 OK OK 7957 7953 7972 7956 7988 C2' A B 3 OK OK 7990 7986 8005 7989 8021 C2' A B 4 OK OK 8023 8019 8038 8022 8054 C2' A B 5 OK OK 8056 8052 8071 8055 8087 C2' A B 6 OK OK 8089 8085 8104 8088 8120 C2' A B 7 OK OK 8122 8118 8138 8121 8166 C2' ADP A 604 OK OK 8168 8164 8184 8167 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7920 C3' A B 1 OK OK 7918 7938 7921 7922 7953 C3' A B 2 OK OK 7951 7971 7954 7955 7986 C3' A B 3 OK OK 7984 8004 7987 7988 8019 C3' A B 4 OK OK 8017 8037 8020 8021 8052 C3' A B 5 OK OK 8050 8070 8053 8054 8085 C3' A B 6 OK OK 8083 8103 8086 8087 8118 C3' A B 7 OK OK 8116 8136 8119 8120 8164 C3' ADP A 604 OK OK 8162 8182 8165 8166 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7918 C4' A B 1 OK OK 7920 7937 7917 7919 7951 C4' A B 2 OK OK 7953 7970 7950 7952 7984 C4' A B 3 OK OK 7986 8003 7983 7985 8017 C4' A B 4 OK OK 8019 8036 8016 8018 8050 C4' A B 5 OK OK 8052 8069 8049 8051 8083 C4' A B 6 OK OK 8085 8102 8082 8084 8116 C4' A B 7 OK OK 8118 8135 8115 8117 8162 C4' ADP A 604 OK OK 8164 8181 8161 8163 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7917 C5' A B 1 OK OK 7916 7935 7936 7918 7950 C5' A B 2 OK OK 7949 7968 7969 7951 7983 C5' A B 3 OK OK 7982 8001 8002 7984 8016 C5' A B 4 OK OK 8015 8034 8035 8017 8049 C5' A B 5 OK OK 8048 8067 8068 8050 8082 C5' A B 6 OK OK 8081 8100 8101 8083 8115 C5' A B 7 OK OK 8114 8133 8134 8116 8161 C5' ADP A 604 OK OK 8160 8179 8180 8162 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7913 P A B 1 distorted distorted 7914 7915 7916 7946 P A B 2 distorted distorted 7921 7947 7948 7949 7979 P A B 3 distorted distorted 7954 7980 7981 7982 8012 P A B 4 distorted distorted 7987 8013 8014 8015 8045 P A B 5 distorted distorted 8020 8046 8047 8048 8078 P A B 6 distorted distorted 8053 8079 8080 8081 8111 P A B 7 distorted distorted 8086 8112 8113 8114 ---------------------------------------------------------------------------------