ID code: '1M82' 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' A A 3 alpha beta 73 95 79 76 111 C1' A A 4 alpha beta 106 128 112 109 144 C1' G A 5 alpha beta 139 162 145 142 178 C1' C A 6 alpha beta 173 193 179 176 209 C1' A A 7 alpha beta 204 226 210 207 242 C1' G A 8 alpha beta 237 260 243 240 276 C1' G A 9 alpha beta 271 294 277 274 310 C1' C A 10 alpha beta 305 325 311 308 341 C1' U A 11 alpha beta 336 356 342 339 371 C1' U A 12 alpha beta 366 386 372 369 401 C1' C A 13 alpha beta 396 416 402 399 432 C1' G A 14 alpha beta 427 450 433 430 466 C1' G A 15 alpha beta 461 484 467 464 500 C1' C A 16 alpha beta 495 515 501 498 531 C1' C A 17 alpha beta 526 546 532 529 562 C1' U A 18 alpha beta 557 577 563 560 592 C1' U A 19 alpha beta 587 607 593 590 622 C1' G A 20 alpha beta 617 640 623 620 656 C1' U A 21 alpha beta 651 671 657 654 686 C1' U A 22 alpha beta 681 701 687 684 716 C1' U A 23 alpha beta 711 731 717 714 746 C1' C A 24 alpha beta 741 761 747 744 777 C1' C A 25 alpha beta 772 793 778 775 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' A A 4 OK OK 111 107 126 110 142 C2' G A 5 OK OK 144 140 160 143 176 C2' C A 6 OK OK 178 174 191 177 207 C2' A A 7 OK OK 209 205 224 208 240 C2' G A 8 OK OK 242 238 258 241 274 C2' G A 9 OK OK 276 272 292 275 308 C2' C A 10 OK OK 310 306 323 309 339 C2' U A 11 OK OK 341 337 354 340 369 C2' U A 12 OK OK 371 367 384 370 399 C2' C A 13 OK OK 401 397 414 400 430 C2' G A 14 OK OK 432 428 448 431 464 C2' G A 15 OK OK 466 462 482 465 498 C2' C A 16 OK OK 500 496 513 499 529 C2' C A 17 OK OK 531 527 544 530 560 C2' U A 18 OK OK 562 558 575 561 590 C2' U A 19 OK OK 592 588 605 591 620 C2' G A 20 OK OK 622 618 638 621 654 C2' U A 21 OK OK 656 652 669 655 684 C2' U A 22 OK OK 686 682 699 685 714 C2' U A 23 OK OK 716 712 729 715 744 C2' C A 24 OK OK 746 742 759 745 775 C2' C A 25 OK OK 777 773 791 776 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' A A 4 OK OK 105 125 108 109 140 C3' G A 5 OK OK 138 159 141 142 174 C3' C A 6 OK OK 172 190 175 176 205 C3' A A 7 OK OK 203 223 206 207 238 C3' G A 8 OK OK 236 257 239 240 272 C3' G A 9 OK OK 270 291 273 274 306 C3' C A 10 OK OK 304 322 307 308 337 C3' U A 11 OK OK 335 353 338 339 367 C3' U A 12 OK OK 365 383 368 369 397 C3' C A 13 OK OK 395 413 398 399 428 C3' G A 14 OK OK 426 447 429 430 462 C3' G A 15 OK OK 460 481 463 464 496 C3' C A 16 OK OK 494 512 497 498 527 C3' C A 17 OK OK 525 543 528 529 558 C3' U A 18 OK OK 556 574 559 560 588 C3' U A 19 OK OK 586 604 589 590 618 C3' G A 20 OK OK 616 637 619 620 652 C3' U A 21 OK OK 650 668 653 654 682 C3' U A 22 OK OK 680 698 683 684 712 C3' U A 23 OK OK 710 728 713 714 742 C3' C A 24 OK OK 740 758 743 744 773 C3' C A 25 OK OK 771 789 774 775 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' A A 4 OK OK 107 124 104 106 138 C4' G A 5 OK OK 140 158 137 139 172 C4' C A 6 OK OK 174 189 171 173 203 C4' A A 7 OK OK 205 222 202 204 236 C4' G A 8 OK OK 238 256 235 237 270 C4' G A 9 OK OK 272 290 269 271 304 C4' C A 10 OK OK 306 321 303 305 335 C4' U A 11 OK OK 337 352 334 336 365 C4' U A 12 OK OK 367 382 364 366 395 C4' C A 13 OK OK 397 412 394 396 426 C4' G A 14 OK OK 428 446 425 427 460 C4' G A 15 OK OK 462 480 459 461 494 C4' C A 16 OK OK 496 511 493 495 525 C4' C A 17 OK OK 527 542 524 526 556 C4' U A 18 OK OK 558 573 555 557 586 C4' U A 19 OK OK 588 603 585 587 616 C4' G A 20 OK OK 618 636 615 617 650 C4' U A 21 OK OK 652 667 649 651 680 C4' U A 22 OK OK 682 697 679 681 710 C4' U A 23 OK OK 712 727 709 711 740 C4' C A 24 OK OK 742 757 739 741 771 C4' C A 25 OK OK 773 788 770 772 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' A A 4 OK OK 103 122 123 105 137 C5' G A 5 OK OK 136 156 157 138 171 C5' C A 6 OK OK 170 187 188 172 202 C5' A A 7 OK OK 201 220 221 203 235 C5' G A 8 OK OK 234 254 255 236 269 C5' G A 9 OK OK 268 288 289 270 303 C5' C A 10 OK OK 302 319 320 304 334 C5' U A 11 OK OK 333 350 351 335 364 C5' U A 12 OK OK 363 380 381 365 394 C5' C A 13 OK OK 393 410 411 395 425 C5' G A 14 OK OK 424 444 445 426 459 C5' G A 15 OK OK 458 478 479 460 493 C5' C A 16 OK OK 492 509 510 494 524 C5' C A 17 OK OK 523 540 541 525 555 C5' U A 18 OK OK 554 571 572 556 585 C5' U A 19 OK OK 584 601 602 586 615 C5' G A 20 OK OK 614 634 635 616 649 C5' U A 21 OK OK 648 665 666 650 679 C5' U A 22 OK OK 678 695 696 680 709 C5' U A 23 OK OK 708 725 726 710 739 C5' C A 24 OK OK 738 755 756 740 770 C5' C A 25 OK OK 769 786 787 771 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P A A 4 distorted distorted 75 101 102 103 133 P G A 5 distorted distorted 108 134 135 136 167 P C A 6 distorted distorted 141 168 169 170 198 P A A 7 distorted distorted 175 199 200 201 231 P G A 8 distorted distorted 206 232 233 234 265 P G A 9 distorted distorted 239 266 267 268 299 P C A 10 distorted distorted 273 300 301 302 330 P U A 11 distorted distorted 307 331 332 333 360 P U A 12 distorted distorted 338 361 362 363 390 P C A 13 distorted distorted 368 391 392 393 421 P G A 14 distorted distorted 398 422 423 424 455 P G A 15 distorted distorted 429 456 457 458 489 P C A 16 distorted distorted 463 490 491 492 520 P C A 17 distorted distorted 497 521 522 523 551 P U A 18 distorted distorted 528 552 553 554 581 P U A 19 distorted distorted 559 582 583 584 611 P G A 20 distorted distorted 589 612 613 614 645 P U A 21 distorted distorted 619 646 647 648 675 P U A 22 distorted distorted 653 676 677 678 705 P U A 23 distorted distorted 683 706 707 708 735 P C A 24 distorted distorted 713 736 737 738 766 P C A 25 distorted distorted 743 767 768 769 ---------------------------------------------------------------------------------