ID code: '1ICG' 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' U A 3 beta 47 53 50 72 C1' U A 4 beta 67 73 70 92 C1' C A 5 beta 87 93 90 112 C1' G A 6 beta 107 113 110 135 C1' G A 7 beta 130 136 133 158 C1' C A 8 beta 153 159 156 176 C1' G B 1 beta 171 177 174 199 C1' C B 2 beta 194 200 197 219 C1' U B 3 beta 214 220 217 239 C1' U B 4 beta 234 240 237 259 C1' C B 5 beta 254 260 257 279 C1' G B 6 beta 274 280 277 302 C1' G B 7 beta 297 303 300 325 C1' C B 8 beta 320 326 323 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK 52 48 51 70 C2' U A 4 OK 72 68 71 90 C2' C A 5 OK 92 88 91 110 C2' G A 6 OK 112 108 111 133 C2' G A 7 OK 135 131 134 156 C2' C A 8 OK 158 154 157 174 C2' G B 1 OK 176 172 175 197 C2' C B 2 OK 199 195 198 217 C2' U B 3 OK 219 215 218 237 C2' U B 4 OK 239 235 238 257 C2' C B 5 OK 259 255 258 277 C2' G B 6 OK 279 275 278 300 C2' G B 7 OK 302 298 301 323 C2' C B 8 OK 325 321 324 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK 46 49 50 68 C3' U A 4 OK 66 69 70 88 C3' C A 5 OK 86 89 90 108 C3' G A 6 OK 106 109 110 131 C3' G A 7 OK 129 132 133 154 C3' C A 8 OK 152 155 156 172 C3' G B 1 OK 170 173 174 195 C3' C B 2 OK 193 196 197 215 C3' U B 3 OK 213 216 217 235 C3' U B 4 OK 233 236 237 255 C3' C B 5 OK 253 256 257 275 C3' G B 6 OK 273 276 277 298 C3' G B 7 OK 296 299 300 321 C3' C B 8 OK 319 322 323 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK 48 45 47 66 C4' U A 4 OK 68 65 67 86 C4' C A 5 OK 88 85 87 106 C4' G A 6 OK 108 105 107 129 C4' G A 7 OK 131 128 130 152 C4' C A 8 OK 154 151 153 170 C4' G B 1 OK 172 169 171 193 C4' C B 2 OK 195 192 194 213 C4' U B 3 OK 215 212 214 233 C4' U B 4 OK 235 232 234 253 C4' C B 5 OK 255 252 254 273 C4' G B 6 OK 275 272 274 296 C4' G B 7 OK 298 295 297 319 C4' C B 8 OK 321 318 320 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 44 46 65 C5' U A 4 64 66 85 C5' C A 5 84 86 105 C5' G A 6 104 106 128 C5' G A 7 127 129 151 C5' C A 8 150 152 169 C5' G B 1 168 170 192 C5' C B 2 191 193 212 C5' U B 3 211 213 232 C5' U B 4 231 233 252 C5' C B 5 251 253 272 C5' G B 6 271 273 295 C5' G B 7 294 296 318 C5' C B 8 317 319 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P U A 3 distorted distorted 29 42 43 44 61 P U A 4 distorted distorted 49 62 63 64 81 P C A 5 distorted distorted 69 82 83 84 101 P G A 6 distorted distorted 89 102 103 104 124 P G A 7 distorted distorted 109 125 126 127 147 P C A 8 distorted distorted 132 148 149 150 188 P C B 2 distorted distorted 173 189 190 191 208 P U B 3 distorted distorted 196 209 210 211 228 P U B 4 distorted distorted 216 229 230 231 248 P C B 5 distorted distorted 236 249 250 251 268 P G B 6 distorted distorted 256 269 270 271 291 P G B 7 distorted distorted 276 292 293 294 314 P C B 8 distorted distorted 299 315 316 317 ---------------------------------------------------------------------------------