ID code: '2KY0' 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' A A 2 alpha beta 39 61 45 42 77 C1' C A 3 alpha beta 72 92 78 75 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' C A 7 alpha beta 204 224 210 207 240 C1' G A 8 alpha beta 235 258 241 238 274 C1' U A 9 alpha beta 269 289 275 272 304 C1' C A 10 alpha beta 299 319 305 302 335 C1' A A 11 alpha beta 330 353 336 333 367 C1' G B 12 alpha beta 362 385 368 365 402 C1' A B 13 alpha beta 397 419 403 400 435 C1' C B 14 alpha beta 430 450 436 433 466 C1' G B 15 alpha beta 461 484 467 464 500 C1' A B 16 alpha beta 495 517 501 498 533 C1' G B 17 alpha beta 528 551 534 531 567 C1' C B 18 alpha beta 562 582 568 565 598 C1' G B 19 alpha beta 593 616 599 596 632 C1' U B 20 alpha beta 627 647 633 630 662 C1' C B 21 alpha beta 657 677 663 660 693 C1' A B 22 alpha beta 688 711 694 691 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' C A 3 OK OK 77 73 90 76 106 C2' G A 4 OK OK 108 104 124 107 140 C2' A A 5 OK OK 142 138 157 141 173 C2' G A 6 OK OK 175 171 191 174 207 C2' C A 7 OK OK 209 205 222 208 238 C2' G A 8 OK OK 240 236 256 239 272 C2' U A 9 OK OK 274 270 287 273 302 C2' C A 10 OK OK 304 300 317 303 333 C2' A A 11 OK OK 335 331 351 334 365 C2' G B 12 OK OK 367 363 383 366 400 C2' A B 13 OK OK 402 398 417 401 433 C2' C B 14 OK OK 435 431 448 434 464 C2' G B 15 OK OK 466 462 482 465 498 C2' A B 16 OK OK 500 496 515 499 531 C2' G B 17 OK OK 533 529 549 532 565 C2' C B 18 OK OK 567 563 580 566 596 C2' G B 19 OK OK 598 594 614 597 630 C2' U B 20 OK OK 632 628 645 631 660 C2' C B 21 OK OK 662 658 675 661 691 C2' A B 22 OK OK 693 689 709 692 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' C A 3 OK OK 71 89 74 75 104 C3' G A 4 OK OK 102 123 105 106 138 C3' A A 5 OK OK 136 156 139 140 171 C3' G A 6 OK OK 169 190 172 173 205 C3' C A 7 OK OK 203 221 206 207 236 C3' G A 8 OK OK 234 255 237 238 270 C3' U A 9 OK OK 268 286 271 272 300 C3' C A 10 OK OK 298 316 301 302 331 C3' A A 11 OK OK 329 349 332 333 363 C3' G B 12 OK OK 361 382 364 365 398 C3' A B 13 OK OK 396 416 399 400 431 C3' C B 14 OK OK 429 447 432 433 462 C3' G B 15 OK OK 460 481 463 464 496 C3' A B 16 OK OK 494 514 497 498 529 C3' G B 17 OK OK 527 548 530 531 563 C3' C B 18 OK OK 561 579 564 565 594 C3' G B 19 OK OK 592 613 595 596 628 C3' U B 20 OK OK 626 644 629 630 658 C3' C B 21 OK OK 656 674 659 660 689 C3' A B 22 OK OK 687 707 690 691 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' C A 3 OK OK 73 88 70 72 102 C4' G A 4 OK OK 104 122 101 103 136 C4' A A 5 OK OK 138 155 135 137 169 C4' G A 6 OK OK 171 189 168 170 203 C4' C A 7 OK OK 205 220 202 204 234 C4' G A 8 OK OK 236 254 233 235 268 C4' U A 9 OK OK 270 285 267 269 298 C4' C A 10 OK OK 300 315 297 299 329 C4' A A 11 OK OK 331 348 328 330 361 C4' G B 12 OK OK 363 381 360 362 396 C4' A B 13 OK OK 398 415 395 397 429 C4' C B 14 OK OK 431 446 428 430 460 C4' G B 15 OK OK 462 480 459 461 494 C4' A B 16 OK OK 496 513 493 495 527 C4' G B 17 OK OK 529 547 526 528 561 C4' C B 18 OK OK 563 578 560 562 592 C4' G B 19 OK OK 594 612 591 593 626 C4' U B 20 OK OK 628 643 625 627 656 C4' C B 21 OK OK 658 673 655 657 687 C4' A B 22 OK OK 689 706 686 688 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' C A 3 OK OK 69 86 87 71 101 C5' G A 4 OK OK 100 120 121 102 135 C5' A A 5 OK OK 134 153 154 136 168 C5' G A 6 OK OK 167 187 188 169 202 C5' C A 7 OK OK 201 218 219 203 233 C5' G A 8 OK OK 232 252 253 234 267 C5' U A 9 OK OK 266 283 284 268 297 C5' C A 10 OK OK 296 313 314 298 328 C5' A A 11 OK OK 327 346 347 329 360 C5' G B 12 OK OK 359 379 380 361 395 C5' A B 13 OK OK 394 413 414 396 428 C5' C B 14 OK OK 427 444 445 429 459 C5' G B 15 OK OK 458 478 479 460 493 C5' A B 16 OK OK 492 511 512 494 526 C5' G B 17 OK OK 525 545 546 527 560 C5' C B 18 OK OK 559 576 577 561 591 C5' G B 19 OK OK 590 610 611 592 625 C5' U B 20 OK OK 624 641 642 626 655 C5' C B 21 OK OK 654 671 672 656 686 C5' A B 22 OK OK 685 704 705 687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P C A 3 distorted distorted 41 67 68 69 97 P G A 4 distorted distorted 74 98 99 100 131 P A A 5 distorted distorted 105 132 133 134 164 P G A 6 distorted distorted 139 165 166 167 198 P C A 7 distorted distorted 172 199 200 201 229 P G A 8 distorted distorted 206 230 231 232 263 P U A 9 distorted distorted 237 264 265 266 293 P C A 10 distorted distorted 271 294 295 296 324 P A A 11 distorted distorted 301 325 326 327 391 P A B 13 distorted distorted 364 392 393 394 424 P C B 14 distorted distorted 399 425 426 427 455 P G B 15 distorted distorted 432 456 457 458 489 P A B 16 distorted distorted 463 490 491 492 522 P G B 17 distorted distorted 497 523 524 525 556 P C B 18 distorted distorted 530 557 558 559 587 P G B 19 distorted distorted 564 588 589 590 621 P U B 20 distorted distorted 595 622 623 624 651 P C B 21 distorted distorted 629 652 653 654 682 P A B 22 distorted distorted 659 683 684 685 ---------------------------------------------------------------------------------