ID code: '4XW0' 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' U A 4 beta 67 73 70 96 C1' LCG A 5 beta 99 87 93 116 C1' C A 6 beta 111 117 114 136 C1' C A 7 beta 131 137 134 156 C1' U A 8 beta 151 157 154 176 C1' G A 9 beta 171 177 174 199 C1' C A 10 beta 194 200 197 217 C1' G B 1 beta 212 218 215 240 C1' C B 2 beta 235 241 238 260 C1' C B 3 beta 255 261 258 280 C1' U B 4 beta 275 281 278 304 C1' LCG B 5 beta 307 295 301 324 C1' C B 6 beta 319 325 322 344 C1' C B 7 beta 339 345 342 364 C1' U B 8 beta 359 365 362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 4 OK 72 68 71 93 C2' LCG A 5 OK 96 85 103 114 C2' C A 6 OK 116 112 115 134 C2' C A 7 OK 136 132 135 154 C2' U A 8 OK 156 152 155 174 C2' G A 9 OK 176 172 175 197 C2' C A 10 OK 199 195 198 215 C2' G B 1 OK 217 213 216 238 C2' C B 2 OK 240 236 239 258 C2' C B 3 OK 260 256 259 278 C2' U B 4 OK 280 276 279 301 C2' LCG B 5 OK 304 293 311 322 C2' C B 6 OK 324 320 323 342 C2' C B 7 OK 344 340 343 362 C2' U B 8 OK 364 360 363 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK 66 69 70 85 C3' LCG A 5 OK 95 104 93 112 C3' C A 6 OK 110 113 114 132 C3' C A 7 OK 130 133 134 152 C3' U A 8 OK 150 153 154 172 C3' G A 9 OK 170 173 174 195 C3' C A 10 OK 193 196 197 213 C3' G B 1 OK 211 214 215 236 C3' C B 2 OK 234 237 238 256 C3' C B 3 OK 254 257 258 276 C3' U B 4 OK 274 277 278 293 C3' LCG B 5 OK 303 312 301 320 C3' C B 6 OK 318 321 322 340 C3' C B 7 OK 338 341 342 360 C3' U B 8 OK 358 361 362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK 68 65 67 95 C4' LCG A 5 OK 85 84 99 110 C4' C A 6 OK 112 109 111 130 C4' C A 7 OK 132 129 131 150 C4' U A 8 OK 152 149 151 170 C4' G A 9 OK 172 169 171 193 C4' C A 10 OK 195 192 194 211 C4' G B 1 OK 213 210 212 234 C4' C B 2 OK 236 233 235 254 C4' C B 3 OK 256 253 255 274 C4' U B 4 OK 276 273 275 303 C4' LCG B 5 OK 293 292 307 318 C4' C B 6 OK 320 317 319 338 C4' C B 7 OK 340 337 339 358 C4' U B 8 OK 360 357 359 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 64 66 84 C5' LCG A 5 83 95 109 C5' C A 6 108 110 129 C5' C A 7 128 130 149 C5' U A 8 148 150 169 C5' G A 9 168 170 192 C5' C A 10 191 193 210 C5' G B 1 209 211 233 C5' C B 2 232 234 253 C5' C B 3 252 254 273 C5' U B 4 272 274 292 C5' LCG B 5 291 303 317 C5' C B 6 316 318 337 C5' C B 7 336 338 357 C5' U B 8 356 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 4 distorted distorted 49 62 63 64 81 P LCG A 5 distorted distorted 69 82 100 83 105 P C A 6 distorted distorted 104 106 107 108 125 P C A 7 distorted distorted 113 126 127 128 145 P U A 8 distorted distorted 133 146 147 148 165 P G A 9 distorted distorted 153 166 167 168 188 P C A 10 distorted distorted 173 189 190 191 229 P C B 2 distorted distorted 214 230 231 232 249 P C B 3 distorted distorted 237 250 251 252 269 P U B 4 distorted distorted 257 270 271 272 289 P LCG B 5 distorted distorted 277 290 308 291 313 P C B 6 distorted distorted 312 314 315 316 333 P C B 7 distorted distorted 321 334 335 336 353 P U B 8 distorted distorted 341 354 355 356 373 P G B 9 361 374 P G B 9 361 419 P C B 10 420 P C B 10 ---------------------------------------------------------------------------------