ID code: '4E59' 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' G A 1 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' C A 3 beta 47 53 50 72 C1' G A 4 beta 67 73 70 95 C1' C A 5 beta 90 96 93 115 C1' C A 6 beta 110 116 113 135 C1' G A 7 beta 130 136 133 160 C1' G B 1 beta 155 161 158 183 C1' C B 2 beta 178 184 181 203 C1' C B 3 beta 198 204 201 223 C1' G B 4 beta 218 224 221 246 C1' C B 5 beta 241 247 244 266 C1' C B 6 beta 261 267 264 286 C1' G B 7 beta 281 287 284 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' C A 3 OK 52 48 51 70 C2' G A 4 OK 72 68 71 93 C2' C A 5 OK 95 91 94 113 C2' C A 6 OK 115 111 114 133 C2' G A 7 OK 135 131 134 158 C2' G B 1 OK 160 156 159 181 C2' C B 2 OK 183 179 182 201 C2' C B 3 OK 203 199 202 221 C2' G B 4 OK 223 219 222 244 C2' C B 5 OK 246 242 245 264 C2' C B 6 OK 266 262 265 284 C2' G B 7 OK 286 282 285 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' C A 3 OK 46 49 50 68 C3' G A 4 OK 66 69 70 91 C3' C A 5 OK 89 92 93 111 C3' C A 6 OK 109 112 113 131 C3' G A 7 OK 129 132 133 156 C3' G B 1 OK 154 157 158 179 C3' C B 2 OK 177 180 181 199 C3' C B 3 OK 197 200 201 219 C3' G B 4 OK 217 220 221 242 C3' C B 5 OK 240 243 244 262 C3' C B 6 OK 260 263 264 282 C3' G B 7 OK 280 283 284 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' C A 3 OK 48 45 47 66 C4' G A 4 OK 68 65 67 89 C4' C A 5 OK 91 88 90 109 C4' C A 6 OK 111 108 110 129 C4' G A 7 OK 131 128 130 154 C4' G B 1 OK 156 153 155 177 C4' C B 2 OK 179 176 178 197 C4' C B 3 OK 199 196 198 217 C4' G B 4 OK 219 216 218 240 C4' C B 5 OK 242 239 241 260 C4' C B 6 OK 262 259 261 280 C4' G B 7 OK 282 279 281 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' C A 3 44 46 65 C5' G A 4 64 66 88 C5' C A 5 87 89 108 C5' C A 6 107 109 128 C5' G A 7 127 129 153 C5' G B 1 152 154 176 C5' C B 2 175 177 196 C5' C B 3 195 197 216 C5' G B 4 215 217 239 C5' C B 5 238 240 259 C5' C B 6 258 260 279 C5' G B 7 278 280 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P C A 3 distorted distorted 29 42 43 44 61 P G A 4 distorted distorted 49 62 63 64 84 P C A 5 distorted distorted 69 85 86 87 104 P C A 6 distorted distorted 92 105 106 107 124 P G A 7 distorted distorted 112 125 126 127 147 P C A 8 distorted distorted 132 148 149 150 172 P C B 2 distorted distorted 157 173 174 175 192 P C B 3 distorted distorted 180 193 194 195 212 P G B 4 distorted distorted 200 213 214 215 235 P C B 5 distorted distorted 220 236 237 238 255 P C B 6 distorted distorted 243 256 257 258 275 P G B 7 distorted distorted 263 276 277 278 298 P C B 8 distorted distorted 283 299 300 301 ---------------------------------------------------------------------------------