ID code: '1QPS' 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' --------------------------------------------------------------------------------- 28 C1' C M 2 beta 24 29 27 47 C1' G M 3 beta 43 48 46 69 C1' C M 4 beta 65 70 68 88 C1' G M 5 beta 84 89 87 111 C1' A M 6 beta 107 112 110 132 C1' A M 7 beta 128 133 131 153 C1' T M 8 beta 149 154 152 173 C1' T M 9 beta 169 174 172 193 C1' C M 10 beta 189 194 192 212 C1' G M 11 beta 208 213 211 234 C1' C M 12 beta 230 235 233 253 C1' G M 13 beta 249 254 252 293 C1' C O 2 beta 289 294 292 312 C1' G O 3 beta 308 313 311 334 C1' C O 4 beta 330 335 333 353 C1' G O 5 beta 349 354 352 375 C1' A O 6 beta 371 376 374 396 C1' A O 7 beta 392 397 395 417 C1' T O 8 beta 413 418 416 437 C1' T O 9 beta 433 438 436 457 C1' C O 10 beta 453 458 456 476 C1' G O 11 beta 472 477 475 498 C1' C O 12 beta 494 499 497 517 C1' G O 13 beta 513 518 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 27 C2' C M 2 28 25 46 C2' G M 3 47 44 68 C2' C M 4 69 66 87 C2' G M 5 88 85 110 C2' A M 6 111 108 131 C2' A M 7 132 129 152 C2' T M 8 153 150 172 C2' T M 9 173 170 192 C2' C M 10 193 190 211 C2' G M 11 212 209 233 C2' C M 12 234 231 252 C2' G M 13 253 250 292 C2' C O 2 293 290 311 C2' G O 3 312 309 333 C2' C O 4 334 331 352 C2' G O 5 353 350 374 C2' A O 6 375 372 395 C2' A O 7 396 393 416 C2' T O 8 417 414 436 C2' T O 9 437 434 456 C2' C O 10 457 454 475 C2' G O 11 476 473 497 C2' C O 12 498 495 516 C2' G O 13 517 514 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 25 C3' C M 2 OK 23 26 27 44 C3' G M 3 OK 42 45 46 66 C3' C M 4 OK 64 67 68 85 C3' G M 5 OK 83 86 87 108 C3' A M 6 OK 106 109 110 129 C3' A M 7 OK 127 130 131 150 C3' T M 8 OK 148 151 152 170 C3' T M 9 OK 168 171 172 190 C3' C M 10 OK 188 191 192 209 C3' G M 11 OK 207 210 211 231 C3' C M 12 OK 229 232 233 250 C3' G M 13 OK 248 251 252 290 C3' C O 2 OK 288 291 292 309 C3' G O 3 OK 307 310 311 331 C3' C O 4 OK 329 332 333 350 C3' G O 5 OK 348 351 352 372 C3' A O 6 OK 370 373 374 393 C3' A O 7 OK 391 394 395 414 C3' T O 8 OK 412 415 416 434 C3' T O 9 OK 432 435 436 454 C3' C O 10 OK 452 455 456 473 C3' G O 11 OK 471 474 475 495 C3' C O 12 OK 493 496 497 514 C3' G O 13 OK 512 515 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 23 C4' C M 2 OK 25 22 24 42 C4' G M 3 OK 44 41 43 64 C4' C M 4 OK 66 63 65 83 C4' G M 5 OK 85 82 84 106 C4' A M 6 OK 108 105 107 127 C4' A M 7 OK 129 126 128 148 C4' T M 8 OK 150 147 149 168 C4' T M 9 OK 170 167 169 188 C4' C M 10 OK 190 187 189 207 C4' G M 11 OK 209 206 208 229 C4' C M 12 OK 231 228 230 248 C4' G M 13 OK 250 247 249 288 C4' C O 2 OK 290 287 289 307 C4' G O 3 OK 309 306 308 329 C4' C O 4 OK 331 328 330 348 C4' G O 5 OK 350 347 349 370 C4' A O 6 OK 372 369 371 391 C4' A O 7 OK 393 390 392 412 C4' T O 8 OK 414 411 413 432 C4' T O 9 OK 434 431 433 452 C4' C O 10 OK 454 451 453 471 C4' G O 11 OK 473 470 472 493 C4' C O 12 OK 495 492 494 512 C4' G O 13 OK 514 511 513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 22 C5' C M 2 21 23 41 C5' G M 3 40 42 63 C5' C M 4 62 64 82 C5' G M 5 81 83 105 C5' A M 6 104 106 126 C5' A M 7 125 127 147 C5' T M 8 146 148 167 C5' T M 9 166 168 187 C5' C M 10 186 188 206 C5' G M 11 205 207 228 C5' C M 12 227 229 247 C5' G M 13 246 248 287 C5' C O 2 286 288 306 C5' G O 3 305 307 328 C5' C O 4 327 329 347 C5' G O 5 346 348 369 C5' A O 6 368 370 390 C5' A O 7 389 391 411 C5' T O 8 410 412 431 C5' T O 9 430 432 451 C5' C O 10 450 452 470 C5' G O 11 469 471 492 C5' C O 12 491 493 511 C5' G O 13 510 512 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 37 P G M 3 distorted distorted 26 38 39 40 59 P C M 4 distorted distorted 45 60 61 62 78 P G M 5 distorted distorted 67 79 80 81 101 P A M 6 OK OK 102 103 104 122 P A M 7 distorted distorted 109 123 124 125 143 P T M 8 distorted distorted 130 144 145 146 163 P T M 9 distorted distorted 151 164 165 166 183 P C M 10 distorted distorted 171 184 185 186 202 P G M 11 distorted distorted 191 203 204 205 224 P C M 12 distorted distorted 210 225 226 227 243 P G M 13 distorted distorted 232 244 245 246 302 P G O 3 distorted distorted 291 303 304 305 324 P C O 4 distorted distorted 310 325 326 327 343 P G O 5 distorted distorted 332 344 345 346 365 P A O 6 OK OK 366 367 368 386 P A O 7 distorted distorted 373 387 388 389 407 P T O 8 distorted distorted 394 408 409 410 427 P T O 9 distorted distorted 415 428 429 430 447 P C O 10 distorted distorted 435 448 449 450 466 P G O 11 distorted distorted 455 467 468 469 488 P C O 12 distorted distorted 474 489 490 491 507 P G O 13 distorted distorted 496 508 509 510 ---------------------------------------------------------------------------------