ID code: '1ZAA' 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' --------------------------------------------------------------------------------- 29 C1' G A 2 beta 25 30 28 51 C1' C A 3 beta 47 52 50 70 C1' G A 4 beta 66 71 69 92 C1' T A 5 beta 88 93 91 112 C1' G A 6 beta 108 113 111 134 C1' G A 7 beta 130 135 133 156 C1' G A 8 beta 152 157 155 178 C1' C A 9 beta 174 179 177 197 C1' G A 10 beta 193 198 196 219 C1' T A 11 beta 215 220 218 257 C1' A B 2 beta 253 258 256 278 C1' C B 3 beta 274 279 277 297 C1' G B 4 beta 293 298 296 319 C1' C B 5 beta 315 320 318 338 C1' C B 6 beta 334 339 337 357 C1' C B 7 beta 353 358 356 376 C1' A B 8 beta 372 377 375 397 C1' C B 9 beta 393 398 396 416 C1' G B 10 beta 412 417 415 438 C1' C B 11 beta 434 439 437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 28 C2' G A 2 29 26 50 C2' C A 3 51 48 69 C2' G A 4 70 67 91 C2' T A 5 92 89 111 C2' G A 6 112 109 133 C2' G A 7 134 131 155 C2' G A 8 156 153 177 C2' C A 9 178 175 196 C2' G A 10 197 194 218 C2' T A 11 219 216 256 C2' A B 2 257 254 277 C2' C B 3 278 275 296 C2' G B 4 297 294 318 C2' C B 5 319 316 337 C2' C B 6 338 335 356 C2' C B 7 357 354 375 C2' A B 8 376 373 396 C2' C B 9 397 394 415 C2' G B 10 416 413 437 C2' C B 11 438 435 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 26 C3' G A 2 OK 24 27 28 48 C3' C A 3 OK 46 49 50 67 C3' G A 4 OK 65 68 69 89 C3' T A 5 OK 87 90 91 109 C3' G A 6 OK 107 110 111 131 C3' G A 7 OK 129 132 133 153 C3' G A 8 OK 151 154 155 175 C3' C A 9 OK 173 176 177 194 C3' G A 10 OK 192 195 196 216 C3' T A 11 OK 214 217 218 254 C3' A B 2 OK 252 255 256 275 C3' C B 3 OK 273 276 277 294 C3' G B 4 OK 292 295 296 316 C3' C B 5 OK 314 317 318 335 C3' C B 6 OK 333 336 337 354 C3' C B 7 OK 352 355 356 373 C3' A B 8 OK 371 374 375 394 C3' C B 9 OK 392 395 396 413 C3' G B 10 OK 411 414 415 435 C3' C B 11 OK 433 436 437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 24 C4' G A 2 OK 26 23 25 46 C4' C A 3 OK 48 45 47 65 C4' G A 4 OK 67 64 66 87 C4' T A 5 OK 89 86 88 107 C4' G A 6 OK 109 106 108 129 C4' G A 7 OK 131 128 130 151 C4' G A 8 OK 153 150 152 173 C4' C A 9 OK 175 172 174 192 C4' G A 10 OK 194 191 193 214 C4' T A 11 OK 216 213 215 252 C4' A B 2 OK 254 251 253 273 C4' C B 3 OK 275 272 274 292 C4' G B 4 OK 294 291 293 314 C4' C B 5 OK 316 313 315 333 C4' C B 6 OK 335 332 334 352 C4' C B 7 OK 354 351 353 371 C4' A B 8 OK 373 370 372 392 C4' C B 9 OK 394 391 393 411 C4' G B 10 OK 413 410 412 433 C4' C B 11 OK 435 432 434 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 23 C5' G A 2 22 24 45 C5' C A 3 44 46 64 C5' G A 4 63 65 86 C5' T A 5 85 87 106 C5' G A 6 105 107 128 C5' G A 7 127 129 150 C5' G A 8 149 151 172 C5' C A 9 171 173 191 C5' G A 10 190 192 213 C5' T A 11 212 214 251 C5' A B 2 250 252 272 C5' C B 3 271 273 291 C5' G B 4 290 292 313 C5' C B 5 312 314 332 C5' C B 6 331 333 351 C5' C B 7 350 352 370 C5' A B 8 369 371 391 C5' C B 9 390 392 410 C5' G B 10 409 411 432 C5' C B 11 431 433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 41 P C A 3 OK OK 27 42 43 44 60 P G A 4 OK OK 49 61 62 63 82 P T A 5 OK OK 68 83 84 85 102 P G A 6 distorted distorted 90 103 104 105 124 P G A 7 OK OK 110 125 126 127 146 P G A 8 OK OK 132 147 148 149 168 P C A 9 OK OK 154 169 170 171 187 P G A 10 OK OK 176 188 189 190 209 P T A 11 OK OK 195 210 211 212 268 P C B 3 OK OK 255 269 270 271 287 P G B 4 OK OK 276 288 289 290 309 P C B 5 OK OK 295 310 311 312 328 P C B 6 OK OK 317 329 330 331 347 P C B 7 OK OK 336 348 349 350 366 P A B 8 OK OK 355 367 368 369 387 P C B 9 OK OK 374 388 389 390 406 P G B 10 OK OK 395 407 408 409 428 P C B 11 OK OK 414 429 430 431 ---------------------------------------------------------------------------------