ID code: '1YXP' 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' C A 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' 5BU A 3 beta 44 50 47 70 C1' G A 4 beta 65 71 68 93 C1' C A 5 beta 88 94 91 113 C1' U A 6 beta 108 114 111 133 C1' G A 7 beta 128 134 131 156 C1' A A 8 beta 151 157 154 178 C1' A A 9 beta 173 179 176 200 C1' G A 10 beta 195 201 198 223 C1' U A 11 beta 218 224 221 243 C1' G A 12 beta 238 244 241 266 C1' C A 13 beta 261 267 264 286 C1' A A 14 beta 281 287 284 308 C1' C A 15 beta 303 309 306 328 C1' A A 16 beta 323 329 326 350 C1' C A 17 beta 345 351 348 370 C1' A A 18 beta 365 371 368 392 C1' G A 19 beta 387 393 390 415 C1' C A 20 beta 410 416 413 435 C1' A A 21 beta 430 436 433 457 C1' A A 22 beta 452 458 455 479 C1' G A 23 beta 474 480 477 500 C1' C B 1 beta 495 501 498 520 C1' U B 2 beta 515 521 518 540 C1' 5BU B 3 beta 535 541 538 561 C1' G B 4 beta 556 562 559 584 C1' C B 5 beta 579 585 582 604 C1' U B 6 beta 599 605 602 624 C1' G B 7 beta 619 625 622 647 C1' A B 8 beta 642 648 645 669 C1' A B 9 beta 664 670 667 691 C1' G B 10 beta 686 692 689 714 C1' U B 11 beta 709 715 712 734 C1' G B 12 beta 729 735 732 757 C1' C B 13 beta 752 758 755 777 C1' A B 14 beta 772 778 775 799 C1' C B 15 beta 794 800 797 819 C1' A B 16 beta 814 820 817 841 C1' C B 17 beta 836 842 839 861 C1' A B 18 beta 856 862 859 883 C1' G B 19 beta 878 884 881 906 C1' C B 20 beta 901 907 904 926 C1' A B 21 beta 921 927 924 948 C1' A B 22 beta 943 949 946 970 C1' G B 23 beta 965 971 968 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' 5BU A 3 OK 49 45 48 68 C2' G A 4 OK 70 66 69 91 C2' C A 5 OK 93 89 92 111 C2' U A 6 OK 113 109 112 131 C2' G A 7 OK 133 129 132 154 C2' A A 8 OK 156 152 155 176 C2' A A 9 OK 178 174 177 198 C2' G A 10 OK 200 196 199 221 C2' U A 11 OK 223 219 222 241 C2' G A 12 OK 243 239 242 264 C2' C A 13 OK 266 262 265 284 C2' A A 14 OK 286 282 285 306 C2' C A 15 OK 308 304 307 326 C2' A A 16 OK 328 324 327 348 C2' C A 17 OK 350 346 349 368 C2' A A 18 OK 370 366 369 390 C2' G A 19 OK 392 388 391 413 C2' C A 20 OK 415 411 414 433 C2' A A 21 OK 435 431 434 455 C2' A A 22 OK 457 453 456 477 C2' G A 23 OK 479 475 478 498 C2' C B 1 OK 500 496 499 518 C2' U B 2 OK 520 516 519 538 C2' 5BU B 3 OK 540 536 539 559 C2' G B 4 OK 561 557 560 582 C2' C B 5 OK 584 580 583 602 C2' U B 6 OK 604 600 603 622 C2' G B 7 OK 624 620 623 645 C2' A B 8 OK 647 643 646 667 C2' A B 9 OK 669 665 668 689 C2' G B 10 OK 691 687 690 712 C2' U B 11 OK 714 710 713 732 C2' G B 12 OK 734 730 733 755 C2' C B 13 OK 757 753 756 775 C2' A B 14 OK 777 773 776 797 C2' C B 15 OK 799 795 798 817 C2' A B 16 OK 819 815 818 839 C2' C B 17 OK 841 837 840 859 C2' A B 18 OK 861 857 860 881 C2' G B 19 OK 883 879 882 904 C2' C B 20 OK 906 902 905 924 C2' A B 21 OK 926 922 925 946 C2' A B 22 OK 948 944 947 968 C2' G B 23 OK 970 966 969 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' 5BU A 3 OK 43 46 47 66 C3' G A 4 OK 64 67 68 89 C3' C A 5 OK 87 90 91 109 C3' U A 6 OK 107 110 111 129 C3' G A 7 OK 127 130 131 152 C3' A A 8 OK 150 153 154 174 C3' A A 9 OK 172 175 176 196 C3' G A 10 OK 194 197 198 219 C3' U A 11 OK 217 220 221 239 C3' G A 12 OK 237 240 241 262 C3' C A 13 OK 260 263 264 282 C3' A A 14 OK 280 283 284 304 C3' C A 15 OK 302 305 306 324 C3' A A 16 OK 322 325 326 346 C3' C A 17 OK 344 347 348 366 C3' A A 18 OK 364 367 368 388 C3' G A 19 OK 386 389 390 411 C3' C A 20 OK 409 412 413 431 C3' A A 21 OK 429 432 433 453 C3' A A 22 OK 451 454 455 475 C3' G A 23 OK 473 476 477 496 C3' C B 1 OK 494 497 498 516 C3' U B 2 OK 514 517 518 536 C3' 5BU B 3 OK 534 537 538 557 C3' G B 4 OK 555 558 559 580 C3' C B 5 OK 578 581 582 600 C3' U B 6 OK 598 601 602 620 C3' G B 7 OK 618 621 622 643 C3' A B 8 OK 641 644 645 665 C3' A B 9 OK 663 666 667 687 C3' G B 10 OK 685 688 689 710 C3' U B 11 OK 708 711 712 730 C3' G B 12 OK 728 731 732 753 C3' C B 13 OK 751 754 755 773 C3' A B 14 OK 771 774 775 795 C3' C B 15 OK 793 796 797 815 C3' A B 16 OK 813 816 817 837 C3' C B 17 OK 835 838 839 857 C3' A B 18 OK 855 858 859 879 C3' G B 19 OK 877 880 881 902 C3' C B 20 OK 900 903 904 922 C3' A B 21 OK 920 923 924 944 C3' A B 22 OK 942 945 946 966 C3' G B 23 OK 964 967 968 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' 5BU A 3 OK 45 42 44 64 C4' G A 4 OK 66 63 65 87 C4' C A 5 OK 89 86 88 107 C4' U A 6 OK 109 106 108 127 C4' G A 7 OK 129 126 128 150 C4' A A 8 OK 152 149 151 172 C4' A A 9 OK 174 171 173 194 C4' G A 10 OK 196 193 195 217 C4' U A 11 OK 219 216 218 237 C4' G A 12 OK 239 236 238 260 C4' C A 13 OK 262 259 261 280 C4' A A 14 OK 282 279 281 302 C4' C A 15 OK 304 301 303 322 C4' A A 16 OK 324 321 323 344 C4' C A 17 OK 346 343 345 364 C4' A A 18 OK 366 363 365 386 C4' G A 19 OK 388 385 387 409 C4' C A 20 OK 411 408 410 429 C4' A A 21 OK 431 428 430 451 C4' A A 22 OK 453 450 452 473 C4' G A 23 OK 475 472 474 494 C4' C B 1 OK 496 493 495 514 C4' U B 2 OK 516 513 515 534 C4' 5BU B 3 OK 536 533 535 555 C4' G B 4 OK 557 554 556 578 C4' C B 5 OK 580 577 579 598 C4' U B 6 OK 600 597 599 618 C4' G B 7 OK 620 617 619 641 C4' A B 8 OK 643 640 642 663 C4' A B 9 OK 665 662 664 685 C4' G B 10 OK 687 684 686 708 C4' U B 11 OK 710 707 709 728 C4' G B 12 OK 730 727 729 751 C4' C B 13 OK 753 750 752 771 C4' A B 14 OK 773 770 772 793 C4' C B 15 OK 795 792 794 813 C4' A B 16 OK 815 812 814 835 C4' C B 17 OK 837 834 836 855 C4' A B 18 OK 857 854 856 877 C4' G B 19 OK 879 876 878 900 C4' C B 20 OK 902 899 901 920 C4' A B 21 OK 922 919 921 942 C4' A B 22 OK 944 941 943 964 C4' G B 23 OK 966 963 965 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' U A 2 21 23 42 C5' 5BU A 3 41 43 63 C5' G A 4 62 64 86 C5' C A 5 85 87 106 C5' U A 6 105 107 126 C5' G A 7 125 127 149 C5' A A 8 148 150 171 C5' A A 9 170 172 193 C5' G A 10 192 194 216 C5' U A 11 215 217 236 C5' G A 12 235 237 259 C5' C A 13 258 260 279 C5' A A 14 278 280 301 C5' C A 15 300 302 321 C5' A A 16 320 322 343 C5' C A 17 342 344 363 C5' A A 18 362 364 385 C5' G A 19 384 386 408 C5' C A 20 407 409 428 C5' A A 21 427 429 450 C5' A A 22 449 451 472 C5' G A 23 471 473 493 C5' C B 1 492 494 513 C5' U B 2 512 514 533 C5' 5BU B 3 532 534 554 C5' G B 4 553 555 577 C5' C B 5 576 578 597 C5' U B 6 596 598 617 C5' G B 7 616 618 640 C5' A B 8 639 641 662 C5' A B 9 661 663 684 C5' G B 10 683 685 707 C5' U B 11 706 708 727 C5' G B 12 726 728 750 C5' C B 13 749 751 770 C5' A B 14 769 771 792 C5' C B 15 791 793 812 C5' A B 16 811 813 834 C5' C B 17 833 835 854 C5' A B 18 853 855 876 C5' G B 19 875 877 899 C5' C B 20 898 900 919 C5' A B 21 918 920 941 C5' A B 22 940 942 963 C5' G B 23 962 964 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P 5BU A 3 distorted distorted 26 39 40 41 59 P G A 4 distorted distorted 46 60 61 62 82 P C A 5 distorted distorted 67 83 84 85 102 P U A 6 distorted distorted 90 103 104 105 122 P G A 7 distorted distorted 110 123 124 125 145 P A A 8 distorted distorted 130 146 147 148 167 P A A 9 distorted distorted 153 168 169 170 189 P G A 10 distorted distorted 175 190 191 192 212 P U A 11 distorted distorted 197 213 214 215 232 P G A 12 distorted distorted 220 233 234 235 255 P C A 13 distorted distorted 240 256 257 258 275 P A A 14 distorted distorted 263 276 277 278 297 P C A 15 distorted distorted 283 298 299 300 317 P A A 16 distorted distorted 305 318 319 320 339 P C A 17 distorted distorted 325 340 341 342 359 P A A 18 distorted distorted 347 360 361 362 381 P G A 19 distorted distorted 367 382 383 384 404 P C A 20 distorted distorted 389 405 406 407 424 P A A 21 distorted distorted 412 425 426 427 446 P A A 22 distorted distorted 432 447 448 449 468 P G A 23 distorted distorted 454 469 470 471 509 P U B 2 distorted distorted 497 510 511 512 529 P 5BU B 3 distorted distorted 517 530 531 532 550 P G B 4 distorted distorted 537 551 552 553 573 P C B 5 distorted distorted 558 574 575 576 593 P U B 6 distorted distorted 581 594 595 596 613 P G B 7 distorted distorted 601 614 615 616 636 P A B 8 distorted distorted 621 637 638 639 658 P A B 9 distorted distorted 644 659 660 661 680 P G B 10 distorted distorted 666 681 682 683 703 P U B 11 distorted distorted 688 704 705 706 723 P G B 12 distorted distorted 711 724 725 726 746 P C B 13 distorted distorted 731 747 748 749 766 P A B 14 distorted distorted 754 767 768 769 788 P C B 15 distorted distorted 774 789 790 791 808 P A B 16 distorted distorted 796 809 810 811 830 P C B 17 distorted distorted 816 831 832 833 850 P A B 18 distorted distorted 838 851 852 853 872 P G B 19 distorted distorted 858 873 874 875 895 P C B 20 distorted distorted 880 896 897 898 915 P A B 21 distorted distorted 903 916 917 918 937 P A B 22 distorted distorted 923 938 939 940 959 P G B 23 distorted distorted 945 960 961 962 ---------------------------------------------------------------------------------