ID code: '1KU7' 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' C B 2 beta 7 12 10 30 C1' T B 3 beta 26 31 29 50 C1' T B 4 beta 46 51 49 70 C1' G B 5 beta 66 71 69 92 C1' A B 6 beta 88 93 91 113 C1' C B 7 beta 109 114 112 132 C1' A B 8 beta 128 133 131 153 C1' A B 9 beta 149 154 152 174 C1' A B 10 beta 170 175 173 195 C1' G B 11 beta 191 196 194 218 C1' C C 14 beta 214 219 217 237 C1' T C 15 beta 233 238 236 257 C1' T C 16 beta 253 258 256 277 C1' T C 17 beta 273 278 276 297 C1' G C 18 beta 293 298 296 319 C1' T C 19 beta 315 320 318 339 C1' C C 20 beta 335 340 338 358 C1' A C 21 beta 354 359 357 379 C1' A C 22 beta 375 380 378 400 C1' G C 23 beta 396 401 399 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C B 2 11 8 29 C2' T B 3 30 27 49 C2' T B 4 50 47 69 C2' G B 5 70 67 91 C2' A B 6 92 89 112 C2' C B 7 113 110 131 C2' A B 8 132 129 152 C2' A B 9 153 150 173 C2' A B 10 174 171 194 C2' G B 11 195 192 217 C2' C C 14 218 215 236 C2' T C 15 237 234 256 C2' T C 16 257 254 276 C2' T C 17 277 274 296 C2' G C 18 297 294 318 C2' T C 19 319 316 338 C2' C C 20 339 336 357 C2' A C 21 358 355 378 C2' A C 22 379 376 399 C2' G C 23 400 397 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C B 2 OK 6 9 10 27 C3' T B 3 OK 25 28 29 47 C3' T B 4 OK 45 48 49 67 C3' G B 5 OK 65 68 69 89 C3' A B 6 OK 87 90 91 110 C3' C B 7 OK 108 111 112 129 C3' A B 8 OK 127 130 131 150 C3' A B 9 OK 148 151 152 171 C3' A B 10 OK 169 172 173 192 C3' G B 11 OK 190 193 194 215 C3' C C 14 OK 213 216 217 234 C3' T C 15 OK 232 235 236 254 C3' T C 16 OK 252 255 256 274 C3' T C 17 OK 272 275 276 294 C3' G C 18 OK 292 295 296 316 C3' T C 19 OK 314 317 318 336 C3' C C 20 OK 334 337 338 355 C3' A C 21 OK 353 356 357 376 C3' A C 22 OK 374 377 378 397 C3' G C 23 OK 395 398 399 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C B 2 OK 8 5 7 25 C4' T B 3 OK 27 24 26 45 C4' T B 4 OK 47 44 46 65 C4' G B 5 OK 67 64 66 87 C4' A B 6 OK 89 86 88 108 C4' C B 7 OK 110 107 109 127 C4' A B 8 OK 129 126 128 148 C4' A B 9 OK 150 147 149 169 C4' A B 10 OK 171 168 170 190 C4' G B 11 OK 192 189 191 213 C4' C C 14 OK 215 212 214 232 C4' T C 15 OK 234 231 233 252 C4' T C 16 OK 254 251 253 272 C4' T C 17 OK 274 271 273 292 C4' G C 18 OK 294 291 293 314 C4' T C 19 OK 316 313 315 334 C4' C C 20 OK 336 333 335 353 C4' A C 21 OK 355 352 354 374 C4' A C 22 OK 376 373 375 395 C4' G C 23 OK 397 394 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C B 2 4 6 24 C5' T B 3 23 25 44 C5' T B 4 43 45 64 C5' G B 5 63 65 86 C5' A B 6 85 87 107 C5' C B 7 106 108 126 C5' A B 8 125 127 147 C5' A B 9 146 148 168 C5' A B 10 167 169 189 C5' G B 11 188 190 212 C5' C C 14 211 213 231 C5' T C 15 230 232 251 C5' T C 16 250 252 271 C5' T C 17 270 272 291 C5' G C 18 290 292 313 C5' T C 19 312 314 333 C5' C C 20 332 334 352 C5' A C 21 351 353 373 C5' A C 22 372 374 394 C5' G C 23 393 395 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C B 2 distorted distorted 2 3 4 20 P T B 3 distorted distorted 9 21 22 23 40 P T B 4 distorted distorted 28 41 42 43 60 P G B 5 distorted distorted 48 61 62 63 82 P A B 6 distorted distorted 68 83 84 85 103 P C B 7 distorted distorted 90 104 105 106 122 P A B 8 distorted distorted 111 123 124 125 143 P A B 9 distorted distorted 130 144 145 146 164 P A B 10 distorted distorted 151 165 166 167 185 P G B 11 distorted distorted 172 186 187 188 208 P C C 14 distorted distorted 209 210 211 227 P T C 15 distorted distorted 216 228 229 230 247 P T C 16 distorted distorted 235 248 249 250 267 P T C 17 distorted distorted 255 268 269 270 287 P G C 18 distorted distorted 275 288 289 290 309 P T C 19 distorted distorted 295 310 311 312 329 P C C 20 distorted distorted 317 330 331 332 348 P A C 21 distorted distorted 337 349 350 351 369 P A C 22 distorted distorted 356 370 371 372 390 P G C 23 distorted distorted 377 391 392 393 ---------------------------------------------------------------------------------