ID code: '1D0T' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 111 C1' SRA A 4 alpha beta 107 128 112 110 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' C A 6 alpha beta 170 190 176 173 205 C1' SRA A 7 alpha beta 201 222 206 204 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' C A 9 alpha beta 265 285 271 268 300 C1' SRA A 10 alpha beta 296 317 301 299 334 C1' U A 11 alpha beta 329 349 335 332 364 C1' U A 12 alpha beta 359 379 365 362 393 C1' SRA A 13 alpha beta 389 410 394 392 427 C1' G A 14 alpha beta 422 445 428 425 461 C1' G A 15 alpha beta 456 479 462 459 495 C1' G A 16 alpha beta 490 513 496 493 528 C1' SRA A 17 alpha beta 524 545 529 527 562 C1' U A 18 alpha beta 557 577 563 560 592 C1' C A 19 alpha beta 587 607 593 590 623 C1' U A 20 alpha beta 618 638 624 621 653 C1' C A 21 alpha beta 648 669 654 651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' SRA A 4 OK OK 111 108 127 122 143 C2' U A 5 OK OK 145 141 158 144 173 C2' C A 6 OK OK 175 171 188 174 204 C2' SRA A 7 OK OK 205 202 221 216 237 C2' C A 8 OK OK 239 235 252 238 268 C2' C A 9 OK OK 270 266 283 269 299 C2' SRA A 10 OK OK 300 297 316 311 332 C2' U A 11 OK OK 334 330 347 333 362 C2' U A 12 OK OK 364 360 377 363 392 C2' SRA A 13 OK OK 393 390 409 404 425 C2' G A 14 OK OK 427 423 443 426 459 C2' G A 15 OK OK 461 457 477 460 493 C2' G A 16 OK OK 495 491 511 494 527 C2' SRA A 17 OK OK 528 525 544 539 560 C2' U A 18 OK OK 562 558 575 561 590 C2' C A 19 OK OK 592 588 605 591 621 C2' U A 20 OK OK 623 619 636 622 651 C2' C A 21 OK OK 653 649 667 652 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' SRA A 4 OK OK 106 126 109 110 141 C3' U A 5 OK OK 139 157 142 143 171 C3' C A 6 OK OK 169 187 172 173 202 C3' SRA A 7 OK OK 200 220 203 204 235 C3' C A 8 OK OK 233 251 236 237 266 C3' C A 9 OK OK 264 282 267 268 297 C3' SRA A 10 OK OK 295 315 298 299 330 C3' U A 11 OK OK 328 346 331 332 360 C3' U A 12 OK OK 358 376 361 362 390 C3' SRA A 13 OK OK 388 408 391 392 423 C3' G A 14 OK OK 421 442 424 425 457 C3' G A 15 OK OK 455 476 458 459 491 C3' G A 16 OK OK 489 510 492 493 525 C3' SRA A 17 OK OK 523 543 526 527 558 C3' U A 18 OK OK 556 574 559 560 588 C3' C A 19 OK OK 586 604 589 590 619 C3' U A 20 OK OK 617 635 620 621 649 C3' C A 21 OK OK 647 665 650 651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' SRA A 4 OK OK 108 125 105 107 139 C4' U A 5 OK OK 141 156 138 140 169 C4' C A 6 OK OK 171 186 168 170 200 C4' SRA A 7 OK OK 202 219 199 201 233 C4' C A 8 OK OK 235 250 232 234 264 C4' C A 9 OK OK 266 281 263 265 295 C4' SRA A 10 OK OK 297 314 294 296 328 C4' U A 11 OK OK 330 345 327 329 358 C4' U A 12 OK OK 360 375 357 359 388 C4' SRA A 13 OK OK 390 407 387 389 421 C4' G A 14 OK OK 423 441 420 422 455 C4' G A 15 OK OK 457 475 454 456 489 C4' G A 16 OK OK 491 509 488 490 523 C4' SRA A 17 OK OK 525 542 522 524 556 C4' U A 18 OK OK 558 573 555 557 586 C4' C A 19 OK OK 588 603 585 587 617 C4' U A 20 OK OK 619 634 616 618 647 C4' C A 21 OK OK 649 664 646 648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' SRA A 4 OK OK 104 123 124 106 138 C5' U A 5 OK OK 137 154 155 139 168 C5' C A 6 OK OK 167 184 185 169 199 C5' SRA A 7 OK OK 198 217 218 200 232 C5' C A 8 OK OK 231 248 249 233 263 C5' C A 9 OK OK 262 279 280 264 294 C5' SRA A 10 OK OK 293 312 313 295 327 C5' U A 11 OK OK 326 343 344 328 357 C5' U A 12 OK OK 356 373 374 358 387 C5' SRA A 13 OK OK 386 405 406 388 420 C5' G A 14 OK OK 419 439 440 421 454 C5' G A 15 OK OK 453 473 474 455 488 C5' G A 16 OK OK 487 507 508 489 522 C5' SRA A 17 OK OK 521 540 541 523 555 C5' U A 18 OK OK 554 571 572 556 585 C5' C A 19 OK OK 584 601 602 586 616 C5' U A 20 OK OK 615 632 633 617 646 C5' C A 21 OK OK 645 662 663 647 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P SRA A 4 75 102 104 134 P U A 5 distorted distorted 109 135 136 137 164 P C A 6 distorted distorted 142 165 166 167 195 P SRA A 7 172 196 198 228 P C A 8 distorted distorted 203 229 230 231 259 P C A 9 distorted distorted 236 260 261 262 290 P SRA A 10 267 291 293 323 P U A 11 distorted distorted 298 324 325 326 353 P U A 12 distorted distorted 331 354 355 356 383 P SRA A 13 361 384 386 416 P G A 14 distorted distorted 391 417 418 419 450 P G A 15 distorted distorted 424 451 452 453 484 P G A 16 distorted distorted 458 485 486 487 518 P SRA A 17 492 519 521 551 P U A 18 distorted distorted 526 552 553 554 581 P C A 19 distorted distorted 559 582 583 584 612 P U A 20 distorted distorted 589 613 614 615 642 P C A 21 distorted distorted 620 643 644 645 ---------------------------------------------------------------------------------