ID code: '5US2' 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' --------------------------------------------------------------------------------- 9 C1' U B 1 beta 4 10 7 29 C1' C B 2 beta 24 30 27 49 C1' G B 3 beta 44 50 47 72 C1' A B 4 beta 67 73 70 94 C1' C B 5 beta 89 95 92 114 C1' A B 6 beta 109 115 112 133 C1' DA C 1 beta 129 134 132 153 C1' US3 C 2 beta 159 145 154 174 C1' DG C 3 beta 170 175 173 196 C1' DT C 4 beta 192 197 195 216 C1' DC C 5 beta 212 217 215 235 C1' DG C 6 beta 231 236 234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U B 1 OK 9 5 8 27 C2' C B 2 OK 29 25 28 47 C2' G B 3 OK 49 45 48 70 C2' A B 4 OK 72 68 71 92 C2' C B 5 OK 94 90 93 112 C2' A B 6 OK 114 110 113 132 C2' DA C 1 133 130 154 C2' US3 C 2 153 156 173 C2' DG C 3 174 171 195 C2' DT C 4 196 193 215 C2' DC C 5 216 213 234 C2' DG C 6 235 232 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U B 1 OK 3 6 7 25 C3' C B 2 OK 23 26 27 45 C3' G B 3 OK 43 46 47 68 C3' A B 4 OK 66 69 70 90 C3' C B 5 OK 88 91 92 110 C3' A B 6 OK 108 111 112 130 C3' DA C 1 OK 128 131 132 156 C3' US3 C 2 OK 158 157 154 171 C3' DG C 3 OK 169 172 173 193 C3' DT C 4 OK 191 194 195 213 C3' DC C 5 OK 211 214 215 232 C3' DG C 6 OK 230 233 234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U B 1 OK 5 2 4 23 C4' C B 2 OK 25 22 24 43 C4' G B 3 OK 45 42 44 66 C4' A B 4 OK 68 65 67 88 C4' C B 5 OK 90 87 89 108 C4' A B 6 OK 110 107 109 128 C4' DA C 1 OK 130 127 129 158 C4' US3 C 2 OK 156 160 159 169 C4' DG C 3 OK 171 168 170 191 C4' DT C 4 OK 193 190 192 211 C4' DC C 5 OK 213 210 212 230 C4' DG C 6 OK 232 229 231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U B 1 1 3 22 C5' C B 2 21 23 42 C5' G B 3 41 43 65 C5' A B 4 64 66 87 C5' C B 5 86 88 107 C5' A B 6 106 108 127 C5' DA C 1 126 128 160 C5' US3 C 2 161 158 168 C5' DG C 3 167 169 190 C5' DT C 4 189 191 210 C5' DC C 5 209 211 229 C5' DG C 6 228 230 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C B 2 distorted distorted 6 19 20 21 38 P G B 3 distorted distorted 26 39 40 41 61 P A B 4 distorted distorted 46 62 63 64 83 P C B 5 distorted distorted 69 84 85 86 103 P A B 6 distorted distorted 91 104 105 106 144 P US3 C 2 distorted distorted 131 163 155 161 164 P DG C 3 distorted distorted 157 165 166 167 186 P DT C 4 distorted distorted 172 187 188 189 206 P DC C 5 distorted distorted 194 207 208 209 225 P DG C 6 distorted distorted 214 226 227 228 ---------------------------------------------------------------------------------