ID code: '3TD1' 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' --------------------------------------------------------------------------------- 12 C1' U A 2 beta 7 13 10 32 C1' G A 3 beta 27 33 30 55 C1' C A 4 beta 50 56 53 75 C1' G A 5 beta 70 76 73 98 C1' U A 6 beta 93 99 96 118 C1' C A 7 beta 113 119 116 138 C1' G A 8 beta 133 139 136 161 C1' C A 9 beta 156 162 159 181 C1' G A 10 beta 176 182 179 204 C1' 5BU A 11 beta 199 205 202 225 C1' C A 12 beta 220 226 223 245 C1' G A 13 beta 240 246 243 268 C1' A A 14 beta 263 269 266 290 C1' C A 15 beta 285 291 288 310 C1' G A 16 beta 305 311 308 333 C1' A A 17 beta 328 334 331 355 C1' A A 18 beta 350 356 353 377 C1' G A 19 beta 372 378 375 400 C1' U A 20 beta 395 401 398 420 C1' C A 21 beta 415 421 418 440 C1' G A 22 beta 435 441 438 463 C1' C A 23 beta 458 464 461 481 C1' U B 24 beta 476 482 479 501 C1' U B 25 beta 496 502 499 521 C1' G B 26 beta 516 522 519 544 C1' C B 27 beta 539 545 542 564 C1' G B 28 beta 559 565 562 587 C1' U B 29 beta 582 588 585 607 C1' C B 30 beta 602 608 605 627 C1' G B 31 beta 622 628 625 650 C1' C B 32 beta 645 651 648 670 C1' G B 33 beta 665 671 668 693 C1' 5BU B 34 beta 688 694 691 714 C1' C B 35 beta 709 715 712 734 C1' G B 36 beta 729 735 732 757 C1' A B 37 beta 752 758 755 779 C1' C B 38 beta 774 780 777 799 C1' G B 39 beta 794 800 797 822 C1' A B 40 beta 817 823 820 844 C1' A B 41 beta 839 845 842 866 C1' G B 42 beta 861 867 864 889 C1' U B 43 beta 884 890 887 909 C1' C B 44 beta 904 910 907 929 C1' G B 45 beta 924 930 927 952 C1' C B 46 beta 947 953 950 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U A 2 OK 12 8 11 30 C2' G A 3 OK 32 28 31 53 C2' C A 4 OK 55 51 54 73 C2' G A 5 OK 75 71 74 96 C2' U A 6 OK 98 94 97 116 C2' C A 7 OK 118 114 117 136 C2' G A 8 OK 138 134 137 159 C2' C A 9 OK 161 157 160 179 C2' G A 10 OK 181 177 180 202 C2' 5BU A 11 OK 204 200 203 223 C2' C A 12 OK 225 221 224 243 C2' G A 13 OK 245 241 244 266 C2' A A 14 OK 268 264 267 288 C2' C A 15 OK 290 286 289 308 C2' G A 16 OK 310 306 309 331 C2' A A 17 OK 333 329 332 353 C2' A A 18 OK 355 351 354 375 C2' G A 19 OK 377 373 376 398 C2' U A 20 OK 400 396 399 418 C2' C A 21 OK 420 416 419 438 C2' G A 22 OK 440 436 439 461 C2' C A 23 OK 463 459 462 479 C2' U B 24 OK 481 477 480 499 C2' U B 25 OK 501 497 500 519 C2' G B 26 OK 521 517 520 542 C2' C B 27 OK 544 540 543 562 C2' G B 28 OK 564 560 563 585 C2' U B 29 OK 587 583 586 605 C2' C B 30 OK 607 603 606 625 C2' G B 31 OK 627 623 626 648 C2' C B 32 OK 650 646 649 668 C2' G B 33 OK 670 666 669 691 C2' 5BU B 34 OK 693 689 692 712 C2' C B 35 OK 714 710 713 732 C2' G B 36 OK 734 730 733 755 C2' A B 37 OK 757 753 756 777 C2' C B 38 OK 779 775 778 797 C2' G B 39 OK 799 795 798 820 C2' A B 40 OK 822 818 821 842 C2' A B 41 OK 844 840 843 864 C2' G B 42 OK 866 862 865 887 C2' U B 43 OK 889 885 888 907 C2' C B 44 OK 909 905 908 927 C2' G B 45 OK 929 925 928 950 C2' C B 46 OK 952 948 951 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U A 2 OK 6 9 10 28 C3' G A 3 OK 26 29 30 51 C3' C A 4 OK 49 52 53 71 C3' G A 5 OK 69 72 73 94 C3' U A 6 OK 92 95 96 114 C3' C A 7 OK 112 115 116 134 C3' G A 8 OK 132 135 136 157 C3' C A 9 OK 155 158 159 177 C3' G A 10 OK 175 178 179 200 C3' 5BU A 11 OK 198 201 202 221 C3' C A 12 OK 219 222 223 241 C3' G A 13 OK 239 242 243 264 C3' A A 14 OK 262 265 266 286 C3' C A 15 OK 284 287 288 306 C3' G A 16 OK 304 307 308 329 C3' A A 17 OK 327 330 331 351 C3' A A 18 OK 349 352 353 373 C3' G A 19 OK 371 374 375 396 C3' U A 20 OK 394 397 398 416 C3' C A 21 OK 414 417 418 436 C3' G A 22 OK 434 437 438 459 C3' C A 23 OK 457 460 461 477 C3' U B 24 OK 475 478 479 497 C3' U B 25 OK 495 498 499 517 C3' G B 26 OK 515 518 519 540 C3' C B 27 OK 538 541 542 560 C3' G B 28 OK 558 561 562 583 C3' U B 29 OK 581 584 585 603 C3' C B 30 OK 601 604 605 623 C3' G B 31 OK 621 624 625 646 C3' C B 32 OK 644 647 648 666 C3' G B 33 OK 664 667 668 689 C3' 5BU B 34 OK 687 690 691 710 C3' C B 35 OK 708 711 712 730 C3' G B 36 OK 728 731 732 753 C3' A B 37 OK 751 754 755 775 C3' C B 38 OK 773 776 777 795 C3' G B 39 OK 793 796 797 818 C3' A B 40 OK 816 819 820 840 C3' A B 41 OK 838 841 842 862 C3' G B 42 OK 860 863 864 885 C3' U B 43 OK 883 886 887 905 C3' C B 44 OK 903 906 907 925 C3' G B 45 OK 923 926 927 948 C3' C B 46 OK 946 949 950 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U A 2 OK 8 5 7 26 C4' G A 3 OK 28 25 27 49 C4' C A 4 OK 51 48 50 69 C4' G A 5 OK 71 68 70 92 C4' U A 6 OK 94 91 93 112 C4' C A 7 OK 114 111 113 132 C4' G A 8 OK 134 131 133 155 C4' C A 9 OK 157 154 156 175 C4' G A 10 OK 177 174 176 198 C4' 5BU A 11 OK 200 197 199 219 C4' C A 12 OK 221 218 220 239 C4' G A 13 OK 241 238 240 262 C4' A A 14 OK 264 261 263 284 C4' C A 15 OK 286 283 285 304 C4' G A 16 OK 306 303 305 327 C4' A A 17 OK 329 326 328 349 C4' A A 18 OK 351 348 350 371 C4' G A 19 OK 373 370 372 394 C4' U A 20 OK 396 393 395 414 C4' C A 21 OK 416 413 415 434 C4' G A 22 OK 436 433 435 457 C4' C A 23 OK 459 456 458 475 C4' U B 24 OK 477 474 476 495 C4' U B 25 OK 497 494 496 515 C4' G B 26 OK 517 514 516 538 C4' C B 27 OK 540 537 539 558 C4' G B 28 OK 560 557 559 581 C4' U B 29 OK 583 580 582 601 C4' C B 30 OK 603 600 602 621 C4' G B 31 OK 623 620 622 644 C4' C B 32 OK 646 643 645 664 C4' G B 33 OK 666 663 665 687 C4' 5BU B 34 OK 689 686 688 708 C4' C B 35 OK 710 707 709 728 C4' G B 36 OK 730 727 729 751 C4' A B 37 OK 753 750 752 773 C4' C B 38 OK 775 772 774 793 C4' G B 39 OK 795 792 794 816 C4' A B 40 OK 818 815 817 838 C4' A B 41 OK 840 837 839 860 C4' G B 42 OK 862 859 861 883 C4' U B 43 OK 885 882 884 903 C4' C B 44 OK 905 902 904 923 C4' G B 45 OK 925 922 924 946 C4' C B 46 OK 948 945 947 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U A 2 4 6 25 C5' G A 3 24 26 48 C5' C A 4 47 49 68 C5' G A 5 67 69 91 C5' U A 6 90 92 111 C5' C A 7 110 112 131 C5' G A 8 130 132 154 C5' C A 9 153 155 174 C5' G A 10 173 175 197 C5' 5BU A 11 196 198 218 C5' C A 12 217 219 238 C5' G A 13 237 239 261 C5' A A 14 260 262 283 C5' C A 15 282 284 303 C5' G A 16 302 304 326 C5' A A 17 325 327 348 C5' A A 18 347 349 370 C5' G A 19 369 371 393 C5' U A 20 392 394 413 C5' C A 21 412 414 433 C5' G A 22 432 434 456 C5' C A 23 455 457 474 C5' U B 24 473 475 494 C5' U B 25 493 495 514 C5' G B 26 513 515 537 C5' C B 27 536 538 557 C5' G B 28 556 558 580 C5' U B 29 579 581 600 C5' C B 30 599 601 620 C5' G B 31 619 621 643 C5' C B 32 642 644 663 C5' G B 33 662 664 686 C5' 5BU B 34 685 687 707 C5' C B 35 706 708 727 C5' G B 36 726 728 750 C5' A B 37 749 751 772 C5' C B 38 771 773 792 C5' G B 39 791 793 815 C5' A B 40 814 816 837 C5' A B 41 836 838 859 C5' G B 42 858 860 882 C5' U B 43 881 883 902 C5' C B 44 901 903 922 C5' G B 45 921 923 945 C5' C B 46 944 946 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U A 2 distorted distorted 2 3 4 21 P G A 3 distorted distorted 9 22 23 24 44 P C A 4 distorted distorted 29 45 46 47 64 P G A 5 distorted distorted 52 65 66 67 87 P U A 6 distorted distorted 72 88 89 90 107 P C A 7 distorted distorted 95 108 109 110 127 P G A 8 distorted distorted 115 128 129 130 150 P C A 9 distorted distorted 135 151 152 153 170 P G A 10 distorted distorted 158 171 172 173 193 P 5BU A 11 distorted distorted 178 194 195 196 214 P C A 12 distorted distorted 201 215 216 217 234 P G A 13 distorted distorted 222 235 236 237 257 P A A 14 distorted distorted 242 258 259 260 279 P C A 15 distorted distorted 265 280 281 282 299 P G A 16 distorted distorted 287 300 301 302 322 P A A 17 distorted distorted 307 323 324 325 344 P A A 18 distorted distorted 330 345 346 347 366 P G A 19 distorted distorted 352 367 368 369 389 P U A 20 distorted distorted 374 390 391 392 409 P C A 21 distorted distorted 397 410 411 412 429 P G A 22 distorted distorted 417 430 431 432 452 P C A 23 distorted distorted 437 453 454 455 490 P U B 25 distorted distorted 478 491 492 493 510 P G B 26 distorted distorted 498 511 512 513 533 P C B 27 distorted distorted 518 534 535 536 553 P G B 28 distorted distorted 541 554 555 556 576 P U B 29 distorted distorted 561 577 578 579 596 P C B 30 distorted distorted 584 597 598 599 616 P G B 31 distorted distorted 604 617 618 619 639 P C B 32 distorted distorted 624 640 641 642 659 P G B 33 distorted distorted 647 660 661 662 682 P 5BU B 34 distorted distorted 667 683 684 685 703 P C B 35 distorted distorted 690 704 705 706 723 P G B 36 distorted distorted 711 724 725 726 746 P A B 37 distorted distorted 731 747 748 749 768 P C B 38 distorted distorted 754 769 770 771 788 P G B 39 distorted distorted 776 789 790 791 811 P A B 40 distorted distorted 796 812 813 814 833 P A B 41 distorted distorted 819 834 835 836 855 P G B 42 distorted distorted 841 856 857 858 878 P U B 43 distorted distorted 863 879 880 881 898 P C B 44 distorted distorted 886 899 900 901 918 P G B 45 distorted distorted 906 919 920 921 941 P C B 46 distorted distorted 926 942 943 944 ---------------------------------------------------------------------------------