ID code: '1BC7' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 beta 4 9 7 30 C1' A A 2 beta 26 31 29 51 C1' C A 3 beta 47 52 50 70 C1' A A 4 beta 66 71 69 91 C1' G A 5 beta 87 92 90 113 C1' G A 6 beta 109 114 112 135 C1' A A 7 beta 131 136 134 156 C1' T A 8 beta 152 157 155 176 C1' G A 9 beta 172 177 175 198 C1' T A 10 beta 194 199 197 218 C1' G A 11 beta 214 219 217 238 C1' C B 12 beta 234 239 237 257 C1' A B 13 beta 253 258 256 278 C1' C B 14 beta 274 279 277 297 C1' A B 15 beta 293 298 296 318 C1' T B 16 beta 314 319 317 338 C1' C B 17 beta 334 339 337 357 C1' C B 18 beta 353 358 356 376 C1' T B 19 beta 372 377 375 396 C1' G B 20 beta 392 397 395 418 C1' T B 21 beta 414 419 417 438 C1' C B 22 beta 434 439 437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 29 C2' A A 2 30 27 50 C2' C A 3 51 48 69 C2' A A 4 70 67 90 C2' G A 5 91 88 112 C2' G A 6 113 110 134 C2' A A 7 135 132 155 C2' T A 8 156 153 175 C2' G A 9 176 173 197 C2' T A 10 198 195 217 C2' G A 11 218 215 237 C2' C B 12 238 235 256 C2' A B 13 257 254 277 C2' C B 14 278 275 296 C2' A B 15 297 294 317 C2' T B 16 318 315 337 C2' C B 17 338 335 356 C2' C B 18 357 354 375 C2' T B 19 376 373 395 C2' G B 20 396 393 417 C2' T B 21 418 415 437 C2' C B 22 438 435 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 27 C3' A A 2 OK 25 28 29 48 C3' C A 3 OK 46 49 50 67 C3' A A 4 OK 65 68 69 88 C3' G A 5 OK 86 89 90 110 C3' G A 6 OK 108 111 112 132 C3' A A 7 OK 130 133 134 153 C3' T A 8 OK 151 154 155 173 C3' G A 9 OK 171 174 175 195 C3' T A 10 OK 193 196 197 215 C3' G A 11 OK 213 216 217 235 C3' C B 12 OK 233 236 237 254 C3' A B 13 OK 252 255 256 275 C3' C B 14 OK 273 276 277 294 C3' A B 15 OK 292 295 296 315 C3' T B 16 OK 313 316 317 335 C3' C B 17 OK 333 336 337 354 C3' C B 18 OK 352 355 356 373 C3' T B 19 OK 371 374 375 393 C3' G B 20 OK 391 394 395 415 C3' T B 21 OK 413 416 417 435 C3' C B 22 OK 433 436 437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 25 C4' A A 2 OK 27 24 26 46 C4' C A 3 OK 48 45 47 65 C4' A A 4 OK 67 64 66 86 C4' G A 5 OK 88 85 87 108 C4' G A 6 OK 110 107 109 130 C4' A A 7 OK 132 129 131 151 C4' T A 8 OK 153 150 152 171 C4' G A 9 OK 173 170 172 193 C4' T A 10 OK 195 192 194 213 C4' G A 11 OK 215 212 214 233 C4' C B 12 OK 235 232 234 252 C4' A B 13 OK 254 251 253 273 C4' C B 14 OK 275 272 274 292 C4' A B 15 OK 294 291 293 313 C4' T B 16 OK 315 312 314 333 C4' C B 17 OK 335 332 334 352 C4' C B 18 OK 354 351 353 371 C4' T B 19 OK 373 370 372 391 C4' G B 20 OK 393 390 392 413 C4' T B 21 OK 415 412 414 433 C4' C B 22 OK 435 432 434 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 24 C5' A A 2 23 25 45 C5' C A 3 44 46 64 C5' A A 4 63 65 85 C5' G A 5 84 86 107 C5' G A 6 106 108 129 C5' A A 7 128 130 150 C5' T A 8 149 151 170 C5' G A 9 169 171 192 C5' T A 10 191 193 212 C5' G A 11 211 213 232 C5' C B 12 231 233 251 C5' A B 13 250 252 272 C5' C B 14 271 273 291 C5' A B 15 290 292 312 C5' T B 16 311 313 332 C5' C B 17 331 333 351 C5' C B 18 350 352 370 C5' T B 19 369 371 390 C5' G B 20 389 391 412 C5' T B 21 411 413 432 C5' C B 22 431 433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A A 2 OK OK 6 21 22 23 41 P C A 3 OK OK 28 42 43 44 60 P A A 4 OK OK 49 61 62 63 81 P G A 5 OK OK 68 82 83 84 103 P G A 6 OK OK 89 104 105 106 125 P A A 7 OK OK 111 126 127 128 146 P T A 8 OK OK 133 147 148 149 166 P G A 9 OK OK 154 167 168 169 188 P T A 10 OK OK 174 189 190 191 208 P G A 11 OK OK 196 209 210 211 247 P A B 13 OK OK 236 248 249 250 268 P C B 14 OK OK 255 269 270 271 287 P A B 15 OK OK 276 288 289 290 308 P T B 16 OK OK 295 309 310 311 328 P C B 17 OK OK 316 329 330 331 347 P C B 18 OK OK 336 348 349 350 366 P T B 19 OK OK 355 367 368 369 386 P G B 20 OK OK 374 387 388 389 408 P T B 21 OK OK 394 409 410 411 428 P C B 22 OK OK 416 429 430 431 ---------------------------------------------------------------------------------