ID code: '2LVY' 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' C A 1 alpha beta 4 24 10 7 41 C1' G A 2 alpha beta 36 59 42 39 75 C1' C A 3 alpha beta 70 90 76 73 107 C1' UPV A 4 alpha beta 113 126 96 108 154 C1' A A 5 alpha beta 149 171 155 152 187 C1' C A 6 alpha beta 182 202 188 185 218 C1' G A 7 alpha beta 213 236 219 216 252 C1' C A 8 alpha beta 247 267 253 250 282 C1' DT A 9 alpha beta 278 299 283 281 314 C1' G B 10 alpha beta 309 332 315 312 349 C1' C B 11 alpha beta 344 364 350 347 380 C1' G B 12 alpha beta 375 398 381 378 414 C1' U B 13 alpha beta 409 429 415 412 444 C1' A B 14 alpha beta 439 461 445 442 477 C1' G B 15 alpha beta 472 495 478 475 511 C1' C B 16 alpha beta 506 526 512 509 542 C1' G B 17 alpha beta 537 560 543 540 575 C1' DT B 18 alpha beta 571 592 576 574 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK OK 9 5 22 8 39 C2' G A 2 OK OK 41 37 57 40 73 C2' C A 3 OK OK 75 71 88 74 108 C2' UPV A 4 OK OK 107 110 130 109 152 C2' A A 5 OK OK 154 150 169 153 185 C2' C A 6 OK OK 187 183 200 186 216 C2' G A 7 OK OK 218 214 234 217 250 C2' C A 8 OK OK 252 248 265 251 281 C2' DT A 9 OK OK 282 279 297 298 312 C2' G B 10 OK OK 314 310 330 313 347 C2' C B 11 OK OK 349 345 362 348 378 C2' G B 12 OK OK 380 376 396 379 412 C2' U B 13 OK OK 414 410 427 413 442 C2' A B 14 OK OK 444 440 459 443 475 C2' G B 15 OK OK 477 473 493 476 509 C2' C B 16 OK OK 511 507 524 510 540 C2' G B 17 OK OK 542 538 558 541 574 C2' DT B 18 OK OK 575 572 590 591 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' G A 2 OK OK 35 56 38 39 71 C3' C A 3 OK OK 69 87 72 73 110 C3' UPV A 4 OK OK 112 134 111 108 150 C3' A A 5 OK OK 148 168 151 152 183 C3' C A 6 OK OK 181 199 184 185 214 C3' G A 7 OK OK 212 233 215 216 248 C3' C A 8 OK OK 246 264 249 250 279 C3' DT A 9 OK OK 277 295 280 281 310 C3' G B 10 OK OK 308 329 311 312 345 C3' C B 11 OK OK 343 361 346 347 376 C3' G B 12 OK OK 374 395 377 378 410 C3' U B 13 OK OK 408 426 411 412 440 C3' A B 14 OK OK 438 458 441 442 473 C3' G B 15 OK OK 471 492 474 475 507 C3' C B 16 OK OK 505 523 508 509 538 C3' G B 17 OK OK 536 557 539 540 572 C3' DT B 18 OK OK 570 588 573 574 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' G A 2 OK OK 37 55 34 36 69 C4' C A 3 OK OK 71 86 68 70 112 C4' UPV A 4 OK OK 110 138 114 113 148 C4' A A 5 OK OK 150 167 147 149 181 C4' C A 6 OK OK 183 198 180 182 212 C4' G A 7 OK OK 214 232 211 213 246 C4' C A 8 OK OK 248 263 245 247 277 C4' DT A 9 OK OK 279 294 276 278 308 C4' G B 10 OK OK 310 328 307 309 343 C4' C B 11 OK OK 345 360 342 344 374 C4' G B 12 OK OK 376 394 373 375 408 C4' U B 13 OK OK 410 425 407 409 438 C4' A B 14 OK OK 440 457 437 439 471 C4' G B 15 OK OK 473 491 470 472 505 C4' C B 16 OK OK 507 522 504 506 536 C4' G B 17 OK OK 538 556 535 537 570 C4' DT B 18 OK OK 572 587 569 571 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 34 C5' G A 2 OK OK 33 53 54 35 68 C5' C A 3 OK OK 67 84 85 69 114 C5' UPV A 4 115 112 147 C5' A A 5 OK OK 146 165 166 148 180 C5' C A 6 OK OK 179 196 197 181 211 C5' G A 7 OK OK 210 230 231 212 245 C5' C A 8 OK OK 244 261 262 246 276 C5' DT A 9 OK OK 275 292 293 277 307 C5' G B 10 OK OK 306 326 327 308 342 C5' C B 11 OK OK 341 358 359 343 373 C5' G B 12 OK OK 372 392 393 374 407 C5' U B 13 OK OK 406 423 424 408 437 C5' A B 14 OK OK 436 455 456 438 470 C5' G B 15 OK OK 469 489 490 471 504 C5' C B 16 OK OK 503 520 521 505 535 C5' G B 17 OK OK 534 554 555 536 569 C5' DT B 18 OK OK 568 585 586 570 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P G A 2 distorted distorted 6 31 32 33 64 P C A 3 distorted distorted 38 65 66 67 95 P UPV A 4 distorted distorted 72 142 121 115 143 P A A 5 distorted distorted 111 144 145 146 176 P C A 6 distorted distorted 151 177 178 179 207 P G A 7 distorted distorted 184 208 209 210 241 P C A 8 distorted distorted 215 242 243 244 272 P DT A 9 distorted distorted 249 273 274 275 338 P C B 11 distorted distorted 311 339 340 341 369 P G B 12 distorted distorted 346 370 371 372 403 P U B 13 distorted distorted 377 404 405 406 433 P A B 14 distorted distorted 411 434 435 436 466 P G B 15 distorted distorted 441 467 468 469 500 P C B 16 distorted distorted 474 501 502 503 531 P G B 17 distorted distorted 508 532 533 534 565 P DT B 18 distorted distorted 539 566 567 568 ---------------------------------------------------------------------------------