ID code: '2NCI' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 alpha beta 3 23 9 6 39 C1' G A 2 alpha beta 34 57 40 37 73 C1' A A 3 alpha beta 68 90 74 71 106 C1' C A 4 alpha beta 101 121 107 104 137 C1' G A 5 alpha beta 132 155 138 135 171 C1' U A 6 alpha beta 166 186 172 169 201 C1' U A 7 alpha beta 196 216 202 199 231 C1' A A 8 alpha beta 226 248 232 229 264 C1' A A 9 alpha beta 259 281 265 262 297 C1' A A 10 alpha beta 292 314 298 295 330 C1' A A 11 alpha beta 325 347 331 328 363 C1' G A 12 alpha beta 358 381 364 361 397 C1' G A 13 alpha beta 392 415 398 395 431 C1' C A 14 alpha beta 426 446 432 429 462 C1' U A 15 alpha beta 457 477 463 460 492 C1' U A 16 alpha beta 487 507 493 490 522 C1' C A 17 alpha beta 517 537 523 520 553 C1' G A 18 alpha beta 548 571 554 551 587 C1' G A 19 alpha beta 582 605 588 585 621 C1' C A 20 alpha beta 616 636 622 619 652 C1' C A 21 alpha beta 647 667 653 650 683 C1' U A 22 alpha beta 678 698 684 681 713 C1' A A 23 alpha beta 708 730 714 711 746 C1' C A 24 alpha beta 741 761 747 744 777 C1' G A 25 alpha beta 772 795 778 775 811 C1' U A 26 alpha beta 806 826 812 809 841 C1' C A 27 alpha beta 836 856 842 839 872 C1' C A 28 alpha beta 867 887 873 870 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6 C2' G A 1 OK OK 8 4 22 7 37 C2' G A 2 OK OK 39 35 55 38 71 C2' A A 3 OK OK 73 69 88 72 104 C2' C A 4 OK OK 106 102 119 105 135 C2' G A 5 OK OK 137 133 153 136 169 C2' U A 6 OK OK 171 167 184 170 199 C2' U A 7 OK OK 201 197 214 200 229 C2' A A 8 OK OK 231 227 246 230 262 C2' A A 9 OK OK 264 260 279 263 295 C2' A A 10 OK OK 297 293 312 296 328 C2' A A 11 OK OK 330 326 345 329 361 C2' G A 12 OK OK 363 359 379 362 395 C2' G A 13 OK OK 397 393 413 396 429 C2' C A 14 OK OK 431 427 444 430 460 C2' U A 15 OK OK 462 458 475 461 490 C2' U A 16 OK OK 492 488 505 491 520 C2' C A 17 OK OK 522 518 535 521 551 C2' G A 18 OK OK 553 549 569 552 585 C2' G A 19 OK OK 587 583 603 586 619 C2' C A 20 OK OK 621 617 634 620 650 C2' C A 21 OK OK 652 648 665 651 681 C2' U A 22 OK OK 683 679 696 682 711 C2' A A 23 OK OK 713 709 728 712 744 C2' C A 24 OK OK 746 742 759 745 775 C2' G A 25 OK OK 777 773 793 776 809 C2' U A 26 OK OK 811 807 824 810 839 C2' C A 27 OK OK 841 837 854 840 870 C2' C A 28 OK OK 872 868 885 871 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4 C3' G A 1 OK OK 2 21 5 6 35 C3' G A 2 OK OK 33 54 36 37 69 C3' A A 3 OK OK 67 87 70 71 102 C3' C A 4 OK OK 100 118 103 104 133 C3' G A 5 OK OK 131 152 134 135 167 C3' U A 6 OK OK 165 183 168 169 197 C3' U A 7 OK OK 195 213 198 199 227 C3' A A 8 OK OK 225 245 228 229 260 C3' A A 9 OK OK 258 278 261 262 293 C3' A A 10 OK OK 291 311 294 295 326 C3' A A 11 OK OK 324 344 327 328 359 C3' G A 12 OK OK 357 378 360 361 393 C3' G A 13 OK OK 391 412 394 395 427 C3' C A 14 OK OK 425 443 428 429 458 C3' U A 15 OK OK 456 474 459 460 488 C3' U A 16 OK OK 486 504 489 490 518 C3' C A 17 OK OK 516 534 519 520 549 C3' G A 18 OK OK 547 568 550 551 583 C3' G A 19 OK OK 581 602 584 585 617 C3' C A 20 OK OK 615 633 618 619 648 C3' C A 21 OK OK 646 664 649 650 679 C3' U A 22 OK OK 677 695 680 681 709 C3' A A 23 OK OK 707 727 710 711 742 C3' C A 24 OK OK 740 758 743 744 773 C3' G A 25 OK OK 771 792 774 775 807 C3' U A 26 OK OK 805 823 808 809 837 C3' C A 27 OK OK 835 853 838 839 868 C3' C A 28 OK OK 866 884 869 870 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2 C4' G A 1 OK OK 4 20 1 3 33 C4' G A 2 OK OK 35 53 32 34 67 C4' A A 3 OK OK 69 86 66 68 100 C4' C A 4 OK OK 102 117 99 101 131 C4' G A 5 OK OK 133 151 130 132 165 C4' U A 6 OK OK 167 182 164 166 195 C4' U A 7 OK OK 197 212 194 196 225 C4' A A 8 OK OK 227 244 224 226 258 C4' A A 9 OK OK 260 277 257 259 291 C4' A A 10 OK OK 293 310 290 292 324 C4' A A 11 OK OK 326 343 323 325 357 C4' G A 12 OK OK 359 377 356 358 391 C4' G A 13 OK OK 393 411 390 392 425 C4' C A 14 OK OK 427 442 424 426 456 C4' U A 15 OK OK 458 473 455 457 486 C4' U A 16 OK OK 488 503 485 487 516 C4' C A 17 OK OK 518 533 515 517 547 C4' G A 18 OK OK 549 567 546 548 581 C4' G A 19 OK OK 583 601 580 582 615 C4' C A 20 OK OK 617 632 614 616 646 C4' C A 21 OK OK 648 663 645 647 677 C4' U A 22 OK OK 679 694 676 678 707 C4' A A 23 OK OK 709 726 706 708 740 C4' C A 24 OK OK 742 757 739 741 771 C4' G A 25 OK OK 773 791 770 772 805 C4' U A 26 OK OK 807 822 804 806 835 C4' C A 27 OK OK 837 852 834 836 866 C4' C A 28 OK OK 868 883 865 867 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1 C5' G A 1 2 32 C5' G A 2 OK OK 31 51 52 33 66 C5' A A 3 OK OK 65 84 85 67 99 C5' C A 4 OK OK 98 115 116 100 130 C5' G A 5 OK OK 129 149 150 131 164 C5' U A 6 OK OK 163 180 181 165 194 C5' U A 7 OK OK 193 210 211 195 224 C5' A A 8 OK OK 223 242 243 225 257 C5' A A 9 OK OK 256 275 276 258 290 C5' A A 10 OK OK 289 308 309 291 323 C5' A A 11 OK OK 322 341 342 324 356 C5' G A 12 OK OK 355 375 376 357 390 C5' G A 13 OK OK 389 409 410 391 424 C5' C A 14 OK OK 423 440 441 425 455 C5' U A 15 OK OK 454 471 472 456 485 C5' U A 16 OK OK 484 501 502 486 515 C5' C A 17 OK OK 514 531 532 516 546 C5' G A 18 OK OK 545 565 566 547 580 C5' G A 19 OK OK 579 599 600 581 614 C5' C A 20 OK OK 613 630 631 615 645 C5' C A 21 OK OK 644 661 662 646 676 C5' U A 22 OK OK 675 692 693 677 706 C5' A A 23 OK OK 705 724 725 707 739 C5' C A 24 OK OK 738 755 756 740 770 C5' G A 25 OK OK 769 789 790 771 804 C5' U A 26 OK OK 803 820 821 805 834 C5' C A 27 OK OK 833 850 851 835 865 C5' C A 28 OK OK 864 881 882 866 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 28 P G A 2 distorted distorted 5 29 30 31 62 P A A 3 distorted distorted 36 63 64 65 95 P C A 4 distorted distorted 70 96 97 98 126 P G A 5 distorted distorted 103 127 128 129 160 P U A 6 distorted distorted 134 161 162 163 190 P U A 7 distorted distorted 168 191 192 193 220 P A A 8 distorted distorted 198 221 222 223 253 P A A 9 distorted distorted 228 254 255 256 286 P A A 10 distorted distorted 261 287 288 289 319 P A A 11 distorted distorted 294 320 321 322 352 P G A 12 distorted distorted 327 353 354 355 386 P G A 13 distorted distorted 360 387 388 389 420 P C A 14 distorted distorted 394 421 422 423 451 P U A 15 distorted distorted 428 452 453 454 481 P U A 16 distorted distorted 459 482 483 484 511 P C A 17 distorted distorted 489 512 513 514 542 P G A 18 distorted distorted 519 543 544 545 576 P G A 19 distorted distorted 550 577 578 579 610 P C A 20 distorted distorted 584 611 612 613 641 P C A 21 distorted distorted 618 642 643 644 672 P U A 22 distorted distorted 649 673 674 675 702 P A A 23 distorted distorted 680 703 704 705 735 P C A 24 distorted distorted 710 736 737 738 766 P G A 25 distorted distorted 743 767 768 769 800 P U A 26 distorted distorted 774 801 802 803 830 P C A 27 distorted distorted 808 831 832 833 861 P C A 28 distorted distorted 838 862 863 864 ---------------------------------------------------------------------------------