ID code: '1L2B' 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' --------------------------------------------------------------------------------- 11 C1' G B 1 beta 7 12 10 33 C1' T B 2 beta 29 34 32 53 C1' A B 3 beta 49 54 52 74 C1' G B 4 beta 70 75 73 96 C1' A B 5 beta 92 97 95 117 C1' C B 6 beta 113 118 116 138 C1' G D 19 beta 134 139 137 160 C1' T D 20 beta 156 161 159 180 C1' C D 21 beta 176 181 179 199 C1' T D 22 beta 195 200 198 219 C1' A D 23 beta 215 220 218 240 C1' C D 24 beta 236 241 239 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G B 1 11 8 32 C2' T B 2 33 30 52 C2' A B 3 53 50 73 C2' G B 4 74 71 95 C2' A B 5 96 93 116 C2' C B 6 117 114 137 C2' G D 19 138 135 159 C2' T D 20 160 157 179 C2' C D 21 180 177 198 C2' T D 22 199 196 218 C2' A D 23 219 216 239 C2' C D 24 240 237 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G B 1 OK 6 9 10 30 C3' T B 2 OK 28 31 32 50 C3' A B 3 OK 48 51 52 71 C3' G B 4 OK 69 72 73 93 C3' A B 5 OK 91 94 95 114 C3' C B 6 OK 112 115 116 135 C3' G D 19 OK 133 136 137 157 C3' T D 20 OK 155 158 159 177 C3' C D 21 OK 175 178 179 196 C3' T D 22 OK 194 197 198 216 C3' A D 23 OK 214 217 218 237 C3' C D 24 OK 235 238 239 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G B 1 OK 8 5 7 28 C4' T B 2 OK 30 27 29 48 C4' A B 3 OK 50 47 49 69 C4' G B 4 OK 71 68 70 91 C4' A B 5 OK 93 90 92 112 C4' C B 6 OK 114 111 113 133 C4' G D 19 OK 135 132 134 155 C4' T D 20 OK 157 154 156 175 C4' C D 21 OK 177 174 176 194 C4' T D 22 OK 196 193 195 214 C4' A D 23 OK 216 213 215 235 C4' C D 24 OK 237 234 236 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G B 1 4 6 27 C5' T B 2 26 28 47 C5' A B 3 46 48 68 C5' G B 4 67 69 90 C5' A B 5 89 91 111 C5' C B 6 110 112 132 C5' G D 19 131 133 154 C5' T D 20 153 155 174 C5' C D 21 173 175 193 C5' T D 22 192 194 213 C5' A D 23 212 214 234 C5' C D 24 233 235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G B 1 OK OK 2 3 4 23 P T B 2 distorted distorted 9 24 25 26 43 P A B 3 distorted distorted 31 44 45 46 64 P G B 4 distorted distorted 51 65 66 67 86 P A B 5 distorted distorted 72 87 88 89 107 P C B 6 distorted distorted 94 108 109 110 128 P G D 19 distorted distorted 129 130 131 150 P T D 20 distorted distorted 136 151 152 153 170 P C D 21 distorted distorted 158 171 172 173 189 P T D 22 distorted distorted 178 190 191 192 209 P A D 23 distorted distorted 197 210 211 212 230 P C D 24 distorted distorted 217 231 232 233 ---------------------------------------------------------------------------------