ID code: '2JWV' 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' U A 3 alpha beta 72 92 78 75 107 C1' A A 4 alpha beta 102 124 108 105 140 C1' C A 5 alpha beta 135 155 141 138 171 C1' U A 6 alpha beta 166 186 172 169 201 C1' U A 7 alpha beta 196 216 202 199 231 C1' G A 8 alpha beta 226 249 232 229 265 C1' A A 9 alpha beta 260 282 266 263 298 C1' A A 10 alpha beta 293 315 299 296 331 C1' A A 11 alpha beta 326 348 332 329 364 C1' C A 12 alpha beta 359 379 365 362 395 C1' U A 13 alpha beta 390 410 396 393 425 C1' G A 14 alpha beta 420 443 426 423 459 C1' U A 15 alpha beta 454 474 460 457 489 C1' A A 16 alpha beta 484 506 490 487 522 C1' A A 17 alpha beta 517 539 523 520 555 C1' G A 18 alpha beta 550 573 556 553 589 C1' G A 19 alpha beta 584 607 590 587 623 C1' U A 20 alpha beta 618 638 624 621 653 C1' U A 21 alpha beta 648 668 654 651 683 C1' G A 22 alpha beta 678 701 684 681 717 C1' G A 23 alpha beta 712 735 718 715 751 C1' C A 24 alpha beta 746 766 752 749 782 C1' G A 25 alpha beta 777 800 783 780 816 C1' U A 26 alpha beta 811 831 817 814 846 C1' A A 27 alpha beta 841 863 847 844 879 C1' U A 28 alpha beta 874 894 880 877 909 C1' C A 29 alpha beta 904 925 910 907 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 77 73 90 76 105 C2' A A 4 OK OK 107 103 122 106 138 C2' C A 5 OK OK 140 136 153 139 169 C2' U A 6 OK OK 171 167 184 170 199 C2' U A 7 OK OK 201 197 214 200 229 C2' G A 8 OK OK 231 227 247 230 263 C2' A A 9 OK OK 265 261 280 264 296 C2' A A 10 OK OK 298 294 313 297 329 C2' A A 11 OK OK 331 327 346 330 362 C2' C A 12 OK OK 364 360 377 363 393 C2' U A 13 OK OK 395 391 408 394 423 C2' G A 14 OK OK 425 421 441 424 457 C2' U A 15 OK OK 459 455 472 458 487 C2' A A 16 OK OK 489 485 504 488 520 C2' A A 17 OK OK 522 518 537 521 553 C2' G A 18 OK OK 555 551 571 554 587 C2' G A 19 OK OK 589 585 605 588 621 C2' U A 20 OK OK 623 619 636 622 651 C2' U A 21 OK OK 653 649 666 652 681 C2' G A 22 OK OK 683 679 699 682 715 C2' G A 23 OK OK 717 713 733 716 749 C2' C A 24 OK OK 751 747 764 750 780 C2' G A 25 OK OK 782 778 798 781 814 C2' U A 26 OK OK 816 812 829 815 844 C2' A A 27 OK OK 846 842 861 845 877 C2' U A 28 OK OK 879 875 892 878 907 C2' C A 29 OK OK 909 905 923 908 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 71 89 74 75 103 C3' A A 4 OK OK 101 121 104 105 136 C3' C A 5 OK OK 134 152 137 138 167 C3' U A 6 OK OK 165 183 168 169 197 C3' U A 7 OK OK 195 213 198 199 227 C3' G A 8 OK OK 225 246 228 229 261 C3' A A 9 OK OK 259 279 262 263 294 C3' A A 10 OK OK 292 312 295 296 327 C3' A A 11 OK OK 325 345 328 329 360 C3' C A 12 OK OK 358 376 361 362 391 C3' U A 13 OK OK 389 407 392 393 421 C3' G A 14 OK OK 419 440 422 423 455 C3' U A 15 OK OK 453 471 456 457 485 C3' A A 16 OK OK 483 503 486 487 518 C3' A A 17 OK OK 516 536 519 520 551 C3' G A 18 OK OK 549 570 552 553 585 C3' G A 19 OK OK 583 604 586 587 619 C3' U A 20 OK OK 617 635 620 621 649 C3' U A 21 OK OK 647 665 650 651 679 C3' G A 22 OK OK 677 698 680 681 713 C3' G A 23 OK OK 711 732 714 715 747 C3' C A 24 OK OK 745 763 748 749 778 C3' G A 25 OK OK 776 797 779 780 812 C3' U A 26 OK OK 810 828 813 814 842 C3' A A 27 OK OK 840 860 843 844 875 C3' U A 28 OK OK 873 891 876 877 905 C3' C A 29 OK OK 903 921 906 907 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 73 88 70 72 101 C4' A A 4 OK OK 103 120 100 102 134 C4' C A 5 OK OK 136 151 133 135 165 C4' U A 6 OK OK 167 182 164 166 195 C4' U A 7 OK OK 197 212 194 196 225 C4' G A 8 OK OK 227 245 224 226 259 C4' A A 9 OK OK 261 278 258 260 292 C4' A A 10 OK OK 294 311 291 293 325 C4' A A 11 OK OK 327 344 324 326 358 C4' C A 12 OK OK 360 375 357 359 389 C4' U A 13 OK OK 391 406 388 390 419 C4' G A 14 OK OK 421 439 418 420 453 C4' U A 15 OK OK 455 470 452 454 483 C4' A A 16 OK OK 485 502 482 484 516 C4' A A 17 OK OK 518 535 515 517 549 C4' G A 18 OK OK 551 569 548 550 583 C4' G A 19 OK OK 585 603 582 584 617 C4' U A 20 OK OK 619 634 616 618 647 C4' U A 21 OK OK 649 664 646 648 677 C4' G A 22 OK OK 679 697 676 678 711 C4' G A 23 OK OK 713 731 710 712 745 C4' C A 24 OK OK 747 762 744 746 776 C4' G A 25 OK OK 778 796 775 777 810 C4' U A 26 OK OK 812 827 809 811 840 C4' A A 27 OK OK 842 859 839 841 873 C4' U A 28 OK OK 875 890 872 874 903 C4' C A 29 OK OK 905 920 902 904 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 69 86 87 71 100 C5' A A 4 OK OK 99 118 119 101 133 C5' C A 5 OK OK 132 149 150 134 164 C5' U A 6 OK OK 163 180 181 165 194 C5' U A 7 OK OK 193 210 211 195 224 C5' G A 8 OK OK 223 243 244 225 258 C5' A A 9 OK OK 257 276 277 259 291 C5' A A 10 OK OK 290 309 310 292 324 C5' A A 11 OK OK 323 342 343 325 357 C5' C A 12 OK OK 356 373 374 358 388 C5' U A 13 OK OK 387 404 405 389 418 C5' G A 14 OK OK 417 437 438 419 452 C5' U A 15 OK OK 451 468 469 453 482 C5' A A 16 OK OK 481 500 501 483 515 C5' A A 17 OK OK 514 533 534 516 548 C5' G A 18 OK OK 547 567 568 549 582 C5' G A 19 OK OK 581 601 602 583 616 C5' U A 20 OK OK 615 632 633 617 646 C5' U A 21 OK OK 645 662 663 647 676 C5' G A 22 OK OK 675 695 696 677 710 C5' G A 23 OK OK 709 729 730 711 744 C5' C A 24 OK OK 743 760 761 745 775 C5' G A 25 OK OK 774 794 795 776 809 C5' U A 26 OK OK 808 825 826 810 839 C5' A A 27 OK OK 838 857 858 840 872 C5' U A 28 OK OK 871 888 889 873 902 C5' C A 29 OK OK 901 918 919 903 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P U A 3 distorted distorted 41 67 68 69 96 P A A 4 distorted distorted 74 97 98 99 129 P C A 5 distorted distorted 104 130 131 132 160 P U A 6 distorted distorted 137 161 162 163 190 P U A 7 distorted distorted 168 191 192 193 220 P G A 8 distorted distorted 198 221 222 223 254 P A A 9 distorted distorted 228 255 256 257 287 P A A 10 distorted distorted 262 288 289 290 320 P A A 11 distorted distorted 295 321 322 323 353 P C A 12 distorted distorted 328 354 355 356 384 P U A 13 distorted distorted 361 385 386 387 414 P G A 14 distorted distorted 392 415 416 417 448 P U A 15 distorted distorted 422 449 450 451 478 P A A 16 distorted distorted 456 479 480 481 511 P A A 17 distorted distorted 486 512 513 514 544 P G A 18 distorted distorted 519 545 546 547 578 P G A 19 distorted distorted 552 579 580 581 612 P U A 20 distorted distorted 586 613 614 615 642 P U A 21 distorted distorted 620 643 644 645 672 P G A 22 distorted distorted 650 673 674 675 706 P G A 23 distorted distorted 680 707 708 709 740 P C A 24 distorted distorted 714 741 742 743 771 P G A 25 distorted distorted 748 772 773 774 805 P U A 26 distorted distorted 779 806 807 808 835 P A A 27 distorted distorted 813 836 837 838 868 P U A 28 distorted distorted 843 869 870 871 898 P C A 29 distorted distorted 876 899 900 901 ---------------------------------------------------------------------------------