ID code: '1XHP' 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 43 C1' A A 2 alpha beta 38 60 44 41 76 C1' G A 3 alpha beta 71 94 77 74 110 C1' C A 4 alpha beta 105 125 111 108 141 C1' A A 5 alpha beta 136 158 142 139 174 C1' G A 6 alpha beta 169 192 175 172 208 C1' U A 7 alpha beta 203 223 209 206 238 C1' U A 8 alpha beta 233 253 239 236 268 C1' C A 9 alpha beta 263 283 269 266 299 C1' C A 10 alpha beta 294 314 300 297 330 C1' C A 11 alpha beta 325 345 331 328 361 C1' C A 12 alpha beta 356 376 362 359 392 C1' U A 13 alpha beta 387 407 393 390 422 C1' G A 14 alpha beta 417 440 423 420 456 C1' C A 15 alpha beta 451 471 457 454 487 C1' A A 16 alpha beta 482 504 488 485 520 C1' U A 17 alpha beta 515 535 521 518 550 C1' A A 18 alpha beta 545 567 551 548 583 C1' A A 19 alpha beta 578 600 584 581 616 C1' G A 20 alpha beta 611 634 617 614 650 C1' G A 21 alpha beta 645 668 651 648 684 C1' A A 22 alpha beta 679 701 685 682 717 C1' U A 23 alpha beta 712 732 718 715 747 C1' G A 24 alpha beta 742 765 748 745 781 C1' A A 25 alpha beta 776 798 782 779 814 C1' A A 26 alpha beta 809 831 815 812 847 C1' C A 27 alpha beta 842 862 848 845 878 C1' C A 28 alpha beta 873 893 879 876 909 C1' G A 29 alpha beta 904 927 910 907 943 C1' U A 30 alpha beta 938 958 944 941 973 C1' U A 31 alpha beta 968 988 974 971 1003 C1' C A 32 alpha beta 998 1019 1004 1001 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' A A 2 OK OK 43 39 58 42 74 C2' G A 3 OK OK 76 72 92 75 108 C2' C A 4 OK OK 110 106 123 109 139 C2' A A 5 OK OK 141 137 156 140 172 C2' G A 6 OK OK 174 170 190 173 206 C2' U A 7 OK OK 208 204 221 207 236 C2' U A 8 OK OK 238 234 251 237 266 C2' C A 9 OK OK 268 264 281 267 297 C2' C A 10 OK OK 299 295 312 298 328 C2' C A 11 OK OK 330 326 343 329 359 C2' C A 12 OK OK 361 357 374 360 390 C2' U A 13 OK OK 392 388 405 391 420 C2' G A 14 OK OK 422 418 438 421 454 C2' C A 15 OK OK 456 452 469 455 485 C2' A A 16 OK OK 487 483 502 486 518 C2' U A 17 OK OK 520 516 533 519 548 C2' A A 18 OK OK 550 546 565 549 581 C2' A A 19 OK OK 583 579 598 582 614 C2' G A 20 OK OK 616 612 632 615 648 C2' G A 21 OK OK 650 646 666 649 682 C2' A A 22 OK OK 684 680 699 683 715 C2' U A 23 OK OK 717 713 730 716 745 C2' G A 24 OK OK 747 743 763 746 779 C2' A A 25 OK OK 781 777 796 780 812 C2' A A 26 OK OK 814 810 829 813 845 C2' C A 27 OK OK 847 843 860 846 876 C2' C A 28 OK OK 878 874 891 877 907 C2' G A 29 OK OK 909 905 925 908 941 C2' U A 30 OK OK 943 939 956 942 971 C2' U A 31 OK OK 973 969 986 972 1001 C2' C A 32 OK OK 1003 999 1017 1002 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' A A 2 OK OK 37 57 40 41 72 C3' G A 3 OK OK 70 91 73 74 106 C3' C A 4 OK OK 104 122 107 108 137 C3' A A 5 OK OK 135 155 138 139 170 C3' G A 6 OK OK 168 189 171 172 204 C3' U A 7 OK OK 202 220 205 206 234 C3' U A 8 OK OK 232 250 235 236 264 C3' C A 9 OK OK 262 280 265 266 295 C3' C A 10 OK OK 293 311 296 297 326 C3' C A 11 OK OK 324 342 327 328 357 C3' C A 12 OK OK 355 373 358 359 388 C3' U A 13 OK OK 386 404 389 390 418 C3' G A 14 OK OK 416 437 419 420 452 C3' C A 15 OK OK 450 468 453 454 483 C3' A A 16 OK OK 481 501 484 485 516 C3' U A 17 OK OK 514 532 517 518 546 C3' A A 18 OK OK 544 564 547 548 579 C3' A A 19 OK OK 577 597 580 581 612 C3' G A 20 OK OK 610 631 613 614 646 C3' G A 21 OK OK 644 665 647 648 680 C3' A A 22 OK OK 678 698 681 682 713 C3' U A 23 OK OK 711 729 714 715 743 C3' G A 24 OK OK 741 762 744 745 777 C3' A A 25 OK OK 775 795 778 779 810 C3' A A 26 OK OK 808 828 811 812 843 C3' C A 27 OK OK 841 859 844 845 874 C3' C A 28 OK OK 872 890 875 876 905 C3' G A 29 OK OK 903 924 906 907 939 C3' U A 30 OK OK 937 955 940 941 969 C3' U A 31 OK OK 967 985 970 971 999 C3' C A 32 OK OK 997 1015 1000 1001 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' A A 2 OK OK 39 56 36 38 70 C4' G A 3 OK OK 72 90 69 71 104 C4' C A 4 OK OK 106 121 103 105 135 C4' A A 5 OK OK 137 154 134 136 168 C4' G A 6 OK OK 170 188 167 169 202 C4' U A 7 OK OK 204 219 201 203 232 C4' U A 8 OK OK 234 249 231 233 262 C4' C A 9 OK OK 264 279 261 263 293 C4' C A 10 OK OK 295 310 292 294 324 C4' C A 11 OK OK 326 341 323 325 355 C4' C A 12 OK OK 357 372 354 356 386 C4' U A 13 OK OK 388 403 385 387 416 C4' G A 14 OK OK 418 436 415 417 450 C4' C A 15 OK OK 452 467 449 451 481 C4' A A 16 OK OK 483 500 480 482 514 C4' U A 17 OK OK 516 531 513 515 544 C4' A A 18 OK OK 546 563 543 545 577 C4' A A 19 OK OK 579 596 576 578 610 C4' G A 20 OK OK 612 630 609 611 644 C4' G A 21 OK OK 646 664 643 645 678 C4' A A 22 OK OK 680 697 677 679 711 C4' U A 23 OK OK 713 728 710 712 741 C4' G A 24 OK OK 743 761 740 742 775 C4' A A 25 OK OK 777 794 774 776 808 C4' A A 26 OK OK 810 827 807 809 841 C4' C A 27 OK OK 843 858 840 842 872 C4' C A 28 OK OK 874 889 871 873 903 C4' G A 29 OK OK 905 923 902 904 937 C4' U A 30 OK OK 939 954 936 938 967 C4' U A 31 OK OK 969 984 966 968 997 C4' C A 32 OK OK 999 1014 996 998 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 36 C5' A A 2 OK OK 35 54 55 37 69 C5' G A 3 OK OK 68 88 89 70 103 C5' C A 4 OK OK 102 119 120 104 134 C5' A A 5 OK OK 133 152 153 135 167 C5' G A 6 OK OK 166 186 187 168 201 C5' U A 7 OK OK 200 217 218 202 231 C5' U A 8 OK OK 230 247 248 232 261 C5' C A 9 OK OK 260 277 278 262 292 C5' C A 10 OK OK 291 308 309 293 323 C5' C A 11 OK OK 322 339 340 324 354 C5' C A 12 OK OK 353 370 371 355 385 C5' U A 13 OK OK 384 401 402 386 415 C5' G A 14 OK OK 414 434 435 416 449 C5' C A 15 OK OK 448 465 466 450 480 C5' A A 16 OK OK 479 498 499 481 513 C5' U A 17 OK OK 512 529 530 514 543 C5' A A 18 OK OK 542 561 562 544 576 C5' A A 19 OK OK 575 594 595 577 609 C5' G A 20 OK OK 608 628 629 610 643 C5' G A 21 OK OK 642 662 663 644 677 C5' A A 22 OK OK 676 695 696 678 710 C5' U A 23 OK OK 709 726 727 711 740 C5' G A 24 OK OK 739 759 760 741 774 C5' A A 25 OK OK 773 792 793 775 807 C5' A A 26 OK OK 806 825 826 808 840 C5' C A 27 OK OK 839 856 857 841 871 C5' C A 28 OK OK 870 887 888 872 902 C5' G A 29 OK OK 901 921 922 903 936 C5' U A 30 OK OK 935 952 953 937 966 C5' U A 31 OK OK 965 982 983 967 996 C5' C A 32 OK OK 995 1012 1013 997 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P A A 2 distorted distorted 6 33 34 35 65 P G A 3 distorted distorted 40 66 67 68 99 P C A 4 distorted distorted 73 100 101 102 130 P A A 5 distorted distorted 107 131 132 133 163 P G A 6 distorted distorted 138 164 165 166 197 P U A 7 distorted distorted 171 198 199 200 227 P U A 8 distorted distorted 205 228 229 230 257 P C A 9 distorted distorted 235 258 259 260 288 P C A 10 distorted distorted 265 289 290 291 319 P C A 11 distorted distorted 296 320 321 322 350 P C A 12 distorted distorted 327 351 352 353 381 P U A 13 distorted distorted 358 382 383 384 411 P G A 14 distorted distorted 389 412 413 414 445 P C A 15 distorted distorted 419 446 447 448 476 P A A 16 distorted distorted 453 477 478 479 509 P U A 17 distorted distorted 484 510 511 512 539 P A A 18 distorted distorted 517 540 541 542 572 P A A 19 distorted distorted 547 573 574 575 605 P G A 20 distorted distorted 580 606 607 608 639 P G A 21 distorted distorted 613 640 641 642 673 P A A 22 distorted distorted 647 674 675 676 706 P U A 23 distorted distorted 681 707 708 709 736 P G A 24 distorted distorted 714 737 738 739 770 P A A 25 distorted distorted 744 771 772 773 803 P A A 26 distorted distorted 778 804 805 806 836 P C A 27 distorted distorted 811 837 838 839 867 P C A 28 distorted distorted 844 868 869 870 898 P G A 29 distorted distorted 875 899 900 901 932 P U A 30 distorted distorted 906 933 934 935 962 P U A 31 distorted distorted 940 963 964 965 992 P C A 32 distorted distorted 970 993 994 995 ---------------------------------------------------------------------------------