ID code: '1M5X' 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 C 501 beta 4 9 7 30 C1' C C 502 beta 26 31 29 49 C1' A C 503 beta 45 50 48 70 C1' G C 504 beta 66 71 69 92 C1' A C 505 beta 88 93 91 113 C1' A C 506 beta 109 114 112 134 C1' C C 507 beta 130 135 133 153 C1' G C 508 beta 149 154 152 175 C1' T C 509 beta 171 176 174 195 C1' C C 510 beta 191 196 194 214 C1' G C 511 beta 210 215 213 236 C1' T C 512 beta 232 237 235 256 C1' G C 513 beta 252 257 255 278 C1' A C 514 beta 274 279 277 299 C1' G C 515 beta 295 300 298 321 C1' A C 516 beta 317 322 320 342 C1' C C 517 beta 338 343 341 361 C1' A C 518 beta 357 362 360 382 C1' G C 519 beta 378 383 381 404 C1' T C 520 beta 400 405 403 424 C1' T C 521 beta 420 425 423 444 C1' C C 522 beta 440 445 443 463 C1' C C 523 beta 459 464 462 482 C1' G C 524 beta 478 483 481 502 C1' C D 551 beta 498 503 501 521 C1' G D 552 beta 517 522 520 543 C1' G D 553 beta 539 544 542 565 C1' A D 554 beta 561 566 564 586 C1' A D 555 beta 582 587 585 607 C1' C D 556 beta 603 608 606 626 C1' T D 557 beta 622 627 625 646 C1' G D 558 beta 642 647 645 668 C1' T D 559 beta 664 669 667 688 C1' C D 560 beta 684 689 687 707 C1' T D 561 beta 703 708 706 727 C1' C D 562 beta 723 728 726 746 C1' A D 563 beta 742 747 745 767 C1' C D 564 beta 763 768 766 786 C1' G D 565 beta 782 787 785 808 C1' A D 566 beta 804 809 807 829 C1' C D 567 beta 825 830 828 848 C1' G D 568 beta 844 849 847 870 C1' T D 569 beta 866 871 869 890 C1' T D 570 beta 886 891 889 910 C1' C D 571 beta 906 911 909 929 C1' T D 572 beta 925 930 928 949 C1' G D 573 beta 945 950 948 971 C1' C D 574 beta 967 972 970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 501 8 5 29 C2' C C 502 30 27 48 C2' A C 503 49 46 69 C2' G C 504 70 67 91 C2' A C 505 92 89 112 C2' A C 506 113 110 133 C2' C C 507 134 131 152 C2' G C 508 153 150 174 C2' T C 509 175 172 194 C2' C C 510 195 192 213 C2' G C 511 214 211 235 C2' T C 512 236 233 255 C2' G C 513 256 253 277 C2' A C 514 278 275 298 C2' G C 515 299 296 320 C2' A C 516 321 318 341 C2' C C 517 342 339 360 C2' A C 518 361 358 381 C2' G C 519 382 379 403 C2' T C 520 404 401 423 C2' T C 521 424 421 443 C2' C C 522 444 441 462 C2' C C 523 463 460 481 C2' G C 524 482 479 501 C2' C D 551 502 499 520 C2' G D 552 521 518 542 C2' G D 553 543 540 564 C2' A D 554 565 562 585 C2' A D 555 586 583 606 C2' C D 556 607 604 625 C2' T D 557 626 623 645 C2' G D 558 646 643 667 C2' T D 559 668 665 687 C2' C D 560 688 685 706 C2' T D 561 707 704 726 C2' C D 562 727 724 745 C2' A D 563 746 743 766 C2' C D 564 767 764 785 C2' G D 565 786 783 807 C2' A D 566 808 805 828 C2' C D 567 829 826 847 C2' G D 568 848 845 869 C2' T D 569 870 867 889 C2' T D 570 890 887 909 C2' C D 571 910 907 928 C2' T D 572 929 926 948 C2' G D 573 949 946 970 C2' C D 574 971 968 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 501 OK 3 6 7 27 C3' C C 502 OK 25 28 29 46 C3' A C 503 OK 44 47 48 67 C3' G C 504 OK 65 68 69 89 C3' A C 505 OK 87 90 91 110 C3' A C 506 OK 108 111 112 131 C3' C C 507 OK 129 132 133 150 C3' G C 508 OK 148 151 152 172 C3' T C 509 OK 170 173 174 192 C3' C C 510 OK 190 193 194 211 C3' G C 511 OK 209 212 213 233 C3' T C 512 OK 231 234 235 253 C3' G C 513 OK 251 254 255 275 C3' A C 514 OK 273 276 277 296 C3' G C 515 OK 294 297 298 318 C3' A C 516 OK 316 319 320 339 C3' C C 517 OK 337 340 341 358 C3' A C 518 OK 356 359 360 379 C3' G C 519 OK 377 380 381 401 C3' T C 520 OK 399 402 403 421 C3' T C 521 OK 419 422 423 441 C3' C C 522 OK 439 442 443 460 C3' C C 523 OK 458 461 462 479 C3' G C 524 OK 477 480 481 499 C3' C D 551 OK 497 500 501 518 C3' G D 552 OK 516 519 520 540 C3' G D 553 OK 538 541 542 562 C3' A D 554 OK 560 563 564 583 C3' A D 555 OK 581 584 585 604 C3' C D 556 OK 602 605 606 623 C3' T D 557 OK 621 624 625 643 C3' G D 558 OK 641 644 645 665 C3' T D 559 OK 663 666 667 685 C3' C D 560 OK 683 686 687 704 C3' T D 561 OK 702 705 706 724 C3' C D 562 OK 722 725 726 743 C3' A D 563 OK 741 744 745 764 C3' C D 564 OK 762 765 766 783 C3' G D 565 OK 781 784 785 805 C3' A D 566 OK 803 806 807 826 C3' C D 567 OK 824 827 828 845 C3' G D 568 OK 843 846 847 867 C3' T D 569 OK 865 868 869 887 C3' T D 570 OK 885 888 889 907 C3' C D 571 OK 905 908 909 926 C3' T D 572 OK 924 927 928 946 C3' G D 573 OK 944 947 948 968 C3' C D 574 OK 966 969 970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 501 OK 5 2 4 25 C4' C C 502 OK 27 24 26 44 C4' A C 503 OK 46 43 45 65 C4' G C 504 OK 67 64 66 87 C4' A C 505 OK 89 86 88 108 C4' A C 506 OK 110 107 109 129 C4' C C 507 OK 131 128 130 148 C4' G C 508 OK 150 147 149 170 C4' T C 509 OK 172 169 171 190 C4' C C 510 OK 192 189 191 209 C4' G C 511 OK 211 208 210 231 C4' T C 512 OK 233 230 232 251 C4' G C 513 OK 253 250 252 273 C4' A C 514 OK 275 272 274 294 C4' G C 515 OK 296 293 295 316 C4' A C 516 OK 318 315 317 337 C4' C C 517 OK 339 336 338 356 C4' A C 518 OK 358 355 357 377 C4' G C 519 OK 379 376 378 399 C4' T C 520 OK 401 398 400 419 C4' T C 521 OK 421 418 420 439 C4' C C 522 OK 441 438 440 458 C4' C C 523 OK 460 457 459 477 C4' G C 524 OK 479 476 478 497 C4' C D 551 OK 499 496 498 516 C4' G D 552 OK 518 515 517 538 C4' G D 553 OK 540 537 539 560 C4' A D 554 OK 562 559 561 581 C4' A D 555 OK 583 580 582 602 C4' C D 556 OK 604 601 603 621 C4' T D 557 OK 623 620 622 641 C4' G D 558 OK 643 640 642 663 C4' T D 559 OK 665 662 664 683 C4' C D 560 OK 685 682 684 702 C4' T D 561 OK 704 701 703 722 C4' C D 562 OK 724 721 723 741 C4' A D 563 OK 743 740 742 762 C4' C D 564 OK 764 761 763 781 C4' G D 565 OK 783 780 782 803 C4' A D 566 OK 805 802 804 824 C4' C D 567 OK 826 823 825 843 C4' G D 568 OK 845 842 844 865 C4' T D 569 OK 867 864 866 885 C4' T D 570 OK 887 884 886 905 C4' C D 571 OK 907 904 906 924 C4' T D 572 OK 926 923 925 944 C4' G D 573 OK 946 943 945 966 C4' C D 574 OK 968 965 967 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 501 1 3 24 C5' C C 502 23 25 43 C5' A C 503 42 44 64 C5' G C 504 63 65 86 C5' A C 505 85 87 107 C5' A C 506 106 108 128 C5' C C 507 127 129 147 C5' G C 508 146 148 169 C5' T C 509 168 170 189 C5' C C 510 188 190 208 C5' G C 511 207 209 230 C5' T C 512 229 231 250 C5' G C 513 249 251 272 C5' A C 514 271 273 293 C5' G C 515 292 294 315 C5' A C 516 314 316 336 C5' C C 517 335 337 355 C5' A C 518 354 356 376 C5' G C 519 375 377 398 C5' T C 520 397 399 418 C5' T C 521 417 419 438 C5' C C 522 437 439 457 C5' C C 523 456 458 476 C5' G C 524 475 477 496 C5' C D 551 495 497 515 C5' G D 552 514 516 537 C5' G D 553 536 538 559 C5' A D 554 558 560 580 C5' A D 555 579 581 601 C5' C D 556 600 602 620 C5' T D 557 619 621 640 C5' G D 558 639 641 662 C5' T D 559 661 663 682 C5' C D 560 681 683 701 C5' T D 561 700 702 721 C5' C D 562 720 722 740 C5' A D 563 739 741 761 C5' C D 564 760 762 780 C5' G D 565 779 781 802 C5' A D 566 801 803 823 C5' C D 567 822 824 842 C5' G D 568 841 843 864 C5' T D 569 863 865 884 C5' T D 570 883 885 904 C5' C D 571 903 905 923 C5' T D 572 922 924 943 C5' G D 573 942 944 965 C5' C D 574 964 966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C C 502 distorted distorted 6 21 22 23 39 P A C 503 distorted distorted 28 40 41 42 60 P G C 504 distorted distorted 47 61 62 63 82 P A C 505 distorted distorted 68 83 84 85 103 P A C 506 distorted distorted 90 104 105 106 124 P C C 507 distorted distorted 111 125 126 127 143 P G C 508 distorted distorted 132 144 145 146 165 P T C 509 distorted distorted 151 166 167 168 185 P C C 510 distorted distorted 173 186 187 188 204 P G C 511 distorted distorted 193 205 206 207 226 P T C 512 distorted distorted 212 227 228 229 246 P G C 513 distorted distorted 234 247 248 249 268 P A C 514 distorted distorted 254 269 270 271 289 P G C 515 distorted distorted 276 290 291 292 311 P A C 516 distorted distorted 297 312 313 314 332 P C C 517 distorted distorted 319 333 334 335 351 P A C 518 distorted distorted 340 352 353 354 372 P G C 519 distorted distorted 359 373 374 375 394 P T C 520 distorted distorted 380 395 396 397 414 P T C 521 distorted distorted 402 415 416 417 434 P C C 522 distorted distorted 422 435 436 437 453 P C C 523 distorted distorted 442 454 455 456 472 P G C 524 distorted distorted 461 473 474 475 511 P G D 552 distorted distorted 500 512 513 514 533 P G D 553 distorted distorted 519 534 535 536 555 P A D 554 distorted distorted 541 556 557 558 576 P A D 555 distorted distorted 563 577 578 579 597 P C D 556 distorted distorted 584 598 599 600 616 P T D 557 distorted distorted 605 617 618 619 636 P G D 558 distorted distorted 624 637 638 639 658 P T D 559 distorted distorted 644 659 660 661 678 P C D 560 distorted distorted 666 679 680 681 697 P T D 561 distorted distorted 686 698 699 700 717 P C D 562 distorted distorted 705 718 719 720 736 P A D 563 distorted distorted 725 737 738 739 757 P C D 564 distorted distorted 744 758 759 760 776 P G D 565 distorted distorted 765 777 778 779 798 P A D 566 distorted distorted 784 799 800 801 819 P C D 567 distorted distorted 806 820 821 822 838 P G D 568 distorted distorted 827 839 840 841 860 P T D 569 distorted distorted 846 861 862 863 880 P T D 570 distorted distorted 868 881 882 883 900 P C D 571 distorted distorted 888 901 902 903 919 P T D 572 distorted distorted 908 920 921 922 939 P G D 573 distorted distorted 927 940 941 942 961 P C D 574 distorted distorted 947 962 963 964 ---------------------------------------------------------------------------------