ID code: '1YSV' 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' U A 3 alpha beta 73 93 79 76 108 C1' A A 4 alpha beta 103 125 109 106 141 C1' A A 5 alpha beta 136 158 142 139 174 C1' C A 6 alpha beta 169 189 175 172 205 C1' A A 7 alpha beta 200 222 206 203 238 C1' A A 8 alpha beta 233 255 239 236 271 C1' U A 9 alpha beta 266 286 272 269 301 C1' A A 10 alpha beta 296 318 302 299 334 C1' U A 11 alpha beta 329 349 335 332 364 C1' G A 12 alpha beta 359 382 365 362 398 C1' C A 13 alpha beta 393 413 399 396 429 C1' U A 14 alpha beta 424 444 430 427 459 C1' A A 15 alpha beta 454 476 460 457 492 C1' A A 16 alpha beta 487 509 493 490 525 C1' A A 17 alpha beta 520 542 526 523 558 C1' U A 18 alpha beta 553 573 559 556 588 C1' G A 19 alpha beta 583 606 589 586 622 C1' U A 20 alpha beta 617 637 623 620 652 C1' U A 21 alpha beta 647 667 653 650 682 C1' G A 22 alpha beta 677 700 683 680 716 C1' U A 23 alpha beta 711 731 717 714 746 C1' U A 24 alpha beta 741 761 747 744 776 C1' A A 25 alpha beta 771 793 777 774 809 C1' C A 26 alpha beta 804 824 810 807 840 C1' C A 27 alpha beta 835 856 841 838 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 78 74 91 77 106 C2' A A 4 OK OK 108 104 123 107 139 C2' A A 5 OK OK 141 137 156 140 172 C2' C A 6 OK OK 174 170 187 173 203 C2' A A 7 OK OK 205 201 220 204 236 C2' A A 8 OK OK 238 234 253 237 269 C2' U A 9 OK OK 271 267 284 270 299 C2' A A 10 OK OK 301 297 316 300 332 C2' U A 11 OK OK 334 330 347 333 362 C2' G A 12 OK OK 364 360 380 363 396 C2' C A 13 OK OK 398 394 411 397 427 C2' U A 14 OK OK 429 425 442 428 457 C2' A A 15 OK OK 459 455 474 458 490 C2' A A 16 OK OK 492 488 507 491 523 C2' A A 17 OK OK 525 521 540 524 556 C2' U A 18 OK OK 558 554 571 557 586 C2' G A 19 OK OK 588 584 604 587 620 C2' U A 20 OK OK 622 618 635 621 650 C2' U A 21 OK OK 652 648 665 651 680 C2' G A 22 OK OK 682 678 698 681 714 C2' U A 23 OK OK 716 712 729 715 744 C2' U A 24 OK OK 746 742 759 745 774 C2' A A 25 OK OK 776 772 791 775 807 C2' C A 26 OK OK 809 805 822 808 838 C2' C A 27 OK OK 840 836 854 839 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 72 90 75 76 104 C3' A A 4 OK OK 102 122 105 106 137 C3' A A 5 OK OK 135 155 138 139 170 C3' C A 6 OK OK 168 186 171 172 201 C3' A A 7 OK OK 199 219 202 203 234 C3' A A 8 OK OK 232 252 235 236 267 C3' U A 9 OK OK 265 283 268 269 297 C3' A A 10 OK OK 295 315 298 299 330 C3' U A 11 OK OK 328 346 331 332 360 C3' G A 12 OK OK 358 379 361 362 394 C3' C A 13 OK OK 392 410 395 396 425 C3' U A 14 OK OK 423 441 426 427 455 C3' A A 15 OK OK 453 473 456 457 488 C3' A A 16 OK OK 486 506 489 490 521 C3' A A 17 OK OK 519 539 522 523 554 C3' U A 18 OK OK 552 570 555 556 584 C3' G A 19 OK OK 582 603 585 586 618 C3' U A 20 OK OK 616 634 619 620 648 C3' U A 21 OK OK 646 664 649 650 678 C3' G A 22 OK OK 676 697 679 680 712 C3' U A 23 OK OK 710 728 713 714 742 C3' U A 24 OK OK 740 758 743 744 772 C3' A A 25 OK OK 770 790 773 774 805 C3' C A 26 OK OK 803 821 806 807 836 C3' C A 27 OK OK 834 852 837 838 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 74 89 71 73 102 C4' A A 4 OK OK 104 121 101 103 135 C4' A A 5 OK OK 137 154 134 136 168 C4' C A 6 OK OK 170 185 167 169 199 C4' A A 7 OK OK 201 218 198 200 232 C4' A A 8 OK OK 234 251 231 233 265 C4' U A 9 OK OK 267 282 264 266 295 C4' A A 10 OK OK 297 314 294 296 328 C4' U A 11 OK OK 330 345 327 329 358 C4' G A 12 OK OK 360 378 357 359 392 C4' C A 13 OK OK 394 409 391 393 423 C4' U A 14 OK OK 425 440 422 424 453 C4' A A 15 OK OK 455 472 452 454 486 C4' A A 16 OK OK 488 505 485 487 519 C4' A A 17 OK OK 521 538 518 520 552 C4' U A 18 OK OK 554 569 551 553 582 C4' G A 19 OK OK 584 602 581 583 616 C4' U A 20 OK OK 618 633 615 617 646 C4' U A 21 OK OK 648 663 645 647 676 C4' G A 22 OK OK 678 696 675 677 710 C4' U A 23 OK OK 712 727 709 711 740 C4' U A 24 OK OK 742 757 739 741 770 C4' A A 25 OK OK 772 789 769 771 803 C4' C A 26 OK OK 805 820 802 804 834 C4' C A 27 OK OK 836 851 833 835 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 70 87 88 72 101 C5' A A 4 OK OK 100 119 120 102 134 C5' A A 5 OK OK 133 152 153 135 167 C5' C A 6 OK OK 166 183 184 168 198 C5' A A 7 OK OK 197 216 217 199 231 C5' A A 8 OK OK 230 249 250 232 264 C5' U A 9 OK OK 263 280 281 265 294 C5' A A 10 OK OK 293 312 313 295 327 C5' U A 11 OK OK 326 343 344 328 357 C5' G A 12 OK OK 356 376 377 358 391 C5' C A 13 OK OK 390 407 408 392 422 C5' U A 14 OK OK 421 438 439 423 452 C5' A A 15 OK OK 451 470 471 453 485 C5' A A 16 OK OK 484 503 504 486 518 C5' A A 17 OK OK 517 536 537 519 551 C5' U A 18 OK OK 550 567 568 552 581 C5' G A 19 OK OK 580 600 601 582 615 C5' U A 20 OK OK 614 631 632 616 645 C5' U A 21 OK OK 644 661 662 646 675 C5' G A 22 OK OK 674 694 695 676 709 C5' U A 23 OK OK 708 725 726 710 739 C5' U A 24 OK OK 738 755 756 740 769 C5' A A 25 OK OK 768 787 788 770 802 C5' C A 26 OK OK 801 818 819 803 833 C5' C A 27 OK OK 832 849 850 834 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P A A 4 distorted distorted 75 98 99 100 130 P A A 5 distorted distorted 105 131 132 133 163 P C A 6 distorted distorted 138 164 165 166 194 P A A 7 distorted distorted 171 195 196 197 227 P A A 8 distorted distorted 202 228 229 230 260 P U A 9 distorted distorted 235 261 262 263 290 P A A 10 distorted distorted 268 291 292 293 323 P U A 11 distorted distorted 298 324 325 326 353 P G A 12 distorted distorted 331 354 355 356 387 P C A 13 distorted distorted 361 388 389 390 418 P U A 14 distorted distorted 395 419 420 421 448 P A A 15 distorted distorted 426 449 450 451 481 P A A 16 distorted distorted 456 482 483 484 514 P A A 17 distorted distorted 489 515 516 517 547 P U A 18 distorted distorted 522 548 549 550 577 P G A 19 distorted distorted 555 578 579 580 611 P U A 20 distorted distorted 585 612 613 614 641 P U A 21 distorted distorted 619 642 643 644 671 P G A 22 distorted distorted 649 672 673 674 705 P U A 23 distorted distorted 679 706 707 708 735 P U A 24 distorted distorted 713 736 737 738 765 P A A 25 distorted distorted 743 766 767 768 798 P C A 26 distorted distorted 773 799 800 801 829 P C A 27 distorted distorted 806 830 831 832 ---------------------------------------------------------------------------------