ID code: '1HJB' 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' --------------------------------------------------------------------------------- 11 C1' A I 2 beta 7 12 10 32 C1' A I 3 beta 28 33 31 53 C1' G I 4 beta 49 54 52 75 C1' A I 5 beta 71 76 74 96 C1' T I 6 beta 92 97 95 116 C1' T I 7 beta 112 117 115 136 C1' T I 8 beta 132 137 135 156 C1' C I 9 beta 152 157 155 175 C1' C I 10 beta 171 176 174 194 C1' A I 11 beta 190 195 193 215 C1' A I 12 beta 211 216 214 236 C1' A I 13 beta 232 237 235 257 C1' C I 14 beta 253 258 256 276 C1' T I 15 beta 272 277 275 296 C1' C I 16 beta 292 297 295 315 C1' T I 17 beta 311 316 314 335 C1' G I 18 beta 331 336 334 357 C1' T I 19 beta 353 358 356 377 C1' G I 20 beta 373 378 376 399 C1' G I 21 beta 395 400 398 421 C1' T I 22 beta 417 422 420 441 C1' T I 23 beta 437 442 440 461 C1' G I 24 beta 457 462 460 483 C1' C I 25 beta 479 484 482 502 C1' G I 26 beta 498 503 501 525 C1' C J 2 beta 521 526 524 544 C1' G J 3 beta 540 545 543 566 C1' C J 4 beta 562 567 565 585 C1' A J 5 beta 581 586 584 606 C1' A J 6 beta 602 607 605 627 C1' C J 7 beta 623 628 626 646 C1' C J 8 beta 642 647 645 665 C1' A J 9 beta 661 666 664 686 C1' C J 10 beta 682 687 685 705 C1' A J 11 beta 701 706 704 726 C1' G J 12 beta 722 727 725 748 C1' A J 13 beta 744 749 747 769 C1' G J 14 beta 765 770 768 791 C1' T J 15 beta 787 792 790 811 C1' T J 16 beta 807 812 810 831 C1' T J 17 beta 827 832 830 851 C1' G J 18 beta 847 852 850 873 C1' G J 19 beta 869 874 872 895 C1' A J 20 beta 891 896 894 916 C1' A J 21 beta 912 917 915 937 C1' A J 22 beta 933 938 936 958 C1' T J 23 beta 954 959 957 978 C1' C J 24 beta 974 979 977 997 C1' T J 25 beta 993 998 996 1017 C1' T J 26 beta 1013 1018 1016 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A I 2 11 8 31 C2' A I 3 32 29 52 C2' G I 4 53 50 74 C2' A I 5 75 72 95 C2' T I 6 96 93 115 C2' T I 7 116 113 135 C2' T I 8 136 133 155 C2' C I 9 156 153 174 C2' C I 10 175 172 193 C2' A I 11 194 191 214 C2' A I 12 215 212 235 C2' A I 13 236 233 256 C2' C I 14 257 254 275 C2' T I 15 276 273 295 C2' C I 16 296 293 314 C2' T I 17 315 312 334 C2' G I 18 335 332 356 C2' T I 19 357 354 376 C2' G I 20 377 374 398 C2' G I 21 399 396 420 C2' T I 22 421 418 440 C2' T I 23 441 438 460 C2' G I 24 461 458 482 C2' C I 25 483 480 501 C2' G I 26 502 499 524 C2' C J 2 525 522 543 C2' G J 3 544 541 565 C2' C J 4 566 563 584 C2' A J 5 585 582 605 C2' A J 6 606 603 626 C2' C J 7 627 624 645 C2' C J 8 646 643 664 C2' A J 9 665 662 685 C2' C J 10 686 683 704 C2' A J 11 705 702 725 C2' G J 12 726 723 747 C2' A J 13 748 745 768 C2' G J 14 769 766 790 C2' T J 15 791 788 810 C2' T J 16 811 808 830 C2' T J 17 831 828 850 C2' G J 18 851 848 872 C2' G J 19 873 870 894 C2' A J 20 895 892 915 C2' A J 21 916 913 936 C2' A J 22 937 934 957 C2' T J 23 958 955 977 C2' C J 24 978 975 996 C2' T J 25 997 994 1016 C2' T J 26 1017 1014 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A I 2 OK 6 9 10 29 C3' A I 3 OK 27 30 31 50 C3' G I 4 OK 48 51 52 72 C3' A I 5 OK 70 73 74 93 C3' T I 6 OK 91 94 95 113 C3' T I 7 OK 111 114 115 133 C3' T I 8 OK 131 134 135 153 C3' C I 9 OK 151 154 155 172 C3' C I 10 OK 170 173 174 191 C3' A I 11 OK 189 192 193 212 C3' A I 12 OK 210 213 214 233 C3' A I 13 OK 231 234 235 254 C3' C I 14 OK 252 255 256 273 C3' T I 15 OK 271 274 275 293 C3' C I 16 OK 291 294 295 312 C3' T I 17 OK 310 313 314 332 C3' G I 18 OK 330 333 334 354 C3' T I 19 OK 352 355 356 374 C3' G I 20 OK 372 375 376 396 C3' G I 21 OK 394 397 398 418 C3' T I 22 OK 416 419 420 438 C3' T I 23 OK 436 439 440 458 C3' G I 24 OK 456 459 460 480 C3' C I 25 OK 478 481 482 499 C3' G I 26 OK 497 500 501 522 C3' C J 2 OK 520 523 524 541 C3' G J 3 OK 539 542 543 563 C3' C J 4 OK 561 564 565 582 C3' A J 5 OK 580 583 584 603 C3' A J 6 OK 601 604 605 624 C3' C J 7 OK 622 625 626 643 C3' C J 8 OK 641 644 645 662 C3' A J 9 OK 660 663 664 683 C3' C J 10 OK 681 684 685 702 C3' A J 11 OK 700 703 704 723 C3' G J 12 OK 721 724 725 745 C3' A J 13 OK 743 746 747 766 C3' G J 14 OK 764 767 768 788 C3' T J 15 OK 786 789 790 808 C3' T J 16 OK 806 809 810 828 C3' T J 17 OK 826 829 830 848 C3' G J 18 OK 846 849 850 870 C3' G J 19 OK 868 871 872 892 C3' A J 20 OK 890 893 894 913 C3' A J 21 OK 911 914 915 934 C3' A J 22 OK 932 935 936 955 C3' T J 23 OK 953 956 957 975 C3' C J 24 OK 973 976 977 994 C3' T J 25 OK 992 995 996 1014 C3' T J 26 OK 1012 1015 1016 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A I 2 OK 8 5 7 27 C4' A I 3 OK 29 26 28 48 C4' G I 4 OK 50 47 49 70 C4' A I 5 OK 72 69 71 91 C4' T I 6 OK 93 90 92 111 C4' T I 7 OK 113 110 112 131 C4' T I 8 OK 133 130 132 151 C4' C I 9 OK 153 150 152 170 C4' C I 10 OK 172 169 171 189 C4' A I 11 OK 191 188 190 210 C4' A I 12 OK 212 209 211 231 C4' A I 13 OK 233 230 232 252 C4' C I 14 OK 254 251 253 271 C4' T I 15 OK 273 270 272 291 C4' C I 16 OK 293 290 292 310 C4' T I 17 OK 312 309 311 330 C4' G I 18 OK 332 329 331 352 C4' T I 19 OK 354 351 353 372 C4' G I 20 OK 374 371 373 394 C4' G I 21 OK 396 393 395 416 C4' T I 22 OK 418 415 417 436 C4' T I 23 OK 438 435 437 456 C4' G I 24 OK 458 455 457 478 C4' C I 25 OK 480 477 479 497 C4' G I 26 OK 499 496 498 520 C4' C J 2 OK 522 519 521 539 C4' G J 3 OK 541 538 540 561 C4' C J 4 OK 563 560 562 580 C4' A J 5 OK 582 579 581 601 C4' A J 6 OK 603 600 602 622 C4' C J 7 OK 624 621 623 641 C4' C J 8 OK 643 640 642 660 C4' A J 9 OK 662 659 661 681 C4' C J 10 OK 683 680 682 700 C4' A J 11 OK 702 699 701 721 C4' G J 12 OK 723 720 722 743 C4' A J 13 OK 745 742 744 764 C4' G J 14 OK 766 763 765 786 C4' T J 15 OK 788 785 787 806 C4' T J 16 OK 808 805 807 826 C4' T J 17 OK 828 825 827 846 C4' G J 18 OK 848 845 847 868 C4' G J 19 OK 870 867 869 890 C4' A J 20 OK 892 889 891 911 C4' A J 21 OK 913 910 912 932 C4' A J 22 OK 934 931 933 953 C4' T J 23 OK 955 952 954 973 C4' C J 24 OK 975 972 974 992 C4' T J 25 OK 994 991 993 1012 C4' T J 26 OK 1014 1011 1013 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A I 2 4 6 26 C5' A I 3 25 27 47 C5' G I 4 46 48 69 C5' A I 5 68 70 90 C5' T I 6 89 91 110 C5' T I 7 109 111 130 C5' T I 8 129 131 150 C5' C I 9 149 151 169 C5' C I 10 168 170 188 C5' A I 11 187 189 209 C5' A I 12 208 210 230 C5' A I 13 229 231 251 C5' C I 14 250 252 270 C5' T I 15 269 271 290 C5' C I 16 289 291 309 C5' T I 17 308 310 329 C5' G I 18 328 330 351 C5' T I 19 350 352 371 C5' G I 20 370 372 393 C5' G I 21 392 394 415 C5' T I 22 414 416 435 C5' T I 23 434 436 455 C5' G I 24 454 456 477 C5' C I 25 476 478 496 C5' G I 26 495 497 519 C5' C J 2 518 520 538 C5' G J 3 537 539 560 C5' C J 4 559 561 579 C5' A J 5 578 580 600 C5' A J 6 599 601 621 C5' C J 7 620 622 640 C5' C J 8 639 641 659 C5' A J 9 658 660 680 C5' C J 10 679 681 699 C5' A J 11 698 700 720 C5' G J 12 719 721 742 C5' A J 13 741 743 763 C5' G J 14 762 764 785 C5' T J 15 784 786 805 C5' T J 16 804 806 825 C5' T J 17 824 826 845 C5' G J 18 844 846 867 C5' G J 19 866 868 889 C5' A J 20 888 890 910 C5' A J 21 909 911 931 C5' A J 22 930 932 952 C5' T J 23 951 953 972 C5' C J 24 971 973 991 C5' T J 25 990 992 1011 C5' T J 26 1010 1012 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A I 2 distorted distorted 2 3 4 22 P A I 3 distorted distorted 9 23 24 25 43 P G I 4 distorted distorted 30 44 45 46 65 P A I 5 distorted distorted 51 66 67 68 86 P T I 6 distorted distorted 73 87 88 89 106 P T I 7 distorted distorted 94 107 108 109 126 P T I 8 distorted distorted 114 127 128 129 146 P C I 9 distorted distorted 134 147 148 149 165 P C I 10 distorted distorted 154 166 167 168 184 P A I 11 distorted distorted 173 185 186 187 205 P A I 12 distorted distorted 192 206 207 208 226 P A I 13 distorted distorted 213 227 228 229 247 P C I 14 distorted distorted 234 248 249 250 266 P T I 15 distorted distorted 255 267 268 269 286 P C I 16 distorted distorted 274 287 288 289 305 P T I 17 distorted distorted 294 306 307 308 325 P G I 18 distorted distorted 313 326 327 328 347 P T I 19 distorted distorted 333 348 349 350 367 P G I 20 distorted distorted 355 368 369 370 389 P G I 21 distorted distorted 375 390 391 392 411 P T I 22 distorted distorted 397 412 413 414 431 P T I 23 distorted distorted 419 432 433 434 451 P G I 24 distorted distorted 439 452 453 454 473 P C I 25 distorted distorted 459 474 475 476 492 P G I 26 distorted distorted 481 493 494 495 515 P C J 2 distorted distorted 516 517 518 534 P G J 3 distorted distorted 523 535 536 537 556 P C J 4 distorted distorted 542 557 558 559 575 P A J 5 distorted distorted 564 576 577 578 596 P A J 6 distorted distorted 583 597 598 599 617 P C J 7 distorted distorted 604 618 619 620 636 P C J 8 distorted distorted 625 637 638 639 655 P A J 9 distorted distorted 644 656 657 658 676 P C J 10 distorted distorted 663 677 678 679 695 P A J 11 distorted distorted 684 696 697 698 716 P G J 12 distorted distorted 703 717 718 719 738 P A J 13 distorted distorted 724 739 740 741 759 P G J 14 distorted distorted 746 760 761 762 781 P T J 15 distorted distorted 767 782 783 784 801 P T J 16 distorted distorted 789 802 803 804 821 P T J 17 distorted distorted 809 822 823 824 841 P G J 18 distorted distorted 829 842 843 844 863 P G J 19 distorted distorted 849 864 865 866 885 P A J 20 distorted distorted 871 886 887 888 906 P A J 21 distorted distorted 893 907 908 909 927 P A J 22 distorted distorted 914 928 929 930 948 P T J 23 distorted distorted 935 949 950 951 968 P C J 24 distorted distorted 956 969 970 971 987 P T J 25 distorted distorted 976 988 989 990 1007 P T J 26 distorted distorted 995 1008 1009 1010 ---------------------------------------------------------------------------------