ID code: '2CGP' 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' --------------------------------------------------------------------------------- 765 C1' A B 534 beta 761 766 764 786 C1' T B 535 beta 782 787 785 806 C1' T B 536 beta 802 807 805 826 C1' A B 537 beta 822 827 825 847 C1' A B 538 beta 843 848 846 868 C1' T B 539 beta 864 869 867 888 C1' G B 540 beta 884 889 887 910 C1' T B 541 beta 906 911 909 930 C1' G B 542 beta 926 931 929 952 C1' A B 543 beta 948 953 951 973 C1' C B 544 beta 969 974 972 992 C1' A B 545 beta 988 993 991 1013 C1' T B 546 beta 1009 1014 1012 1033 C1' A B 547 beta 1029 1034 1032 1054 C1' T B 548 beta 1050 1055 1053 8 C1' G A 503 beta 4 9 7 30 C1' T A 504 beta 26 31 29 50 C1' C A 505 beta 46 51 49 69 C1' A A 506 beta 65 70 68 90 C1' C A 507 beta 86 91 89 109 C1' A A 508 beta 105 110 108 130 C1' T A 509 beta 126 131 129 150 C1' T A 510 beta 146 151 149 170 C1' A A 511 beta 166 171 169 191 C1' A A 512 beta 187 192 190 212 C1' T A 513 beta 208 213 211 455 C1' A B 534 beta 451 456 454 476 C1' T B 535 beta 472 477 475 496 C1' T B 536 beta 492 497 495 516 C1' A B 537 beta 512 517 515 537 C1' A B 538 beta 533 538 536 558 C1' T B 539 beta 554 559 557 578 C1' G B 540 beta 574 579 577 600 C1' T B 541 beta 596 601 599 620 C1' G B 542 beta 616 621 619 642 C1' A B 543 beta 638 643 641 663 C1' C B 544 beta 659 664 662 682 C1' A B 545 beta 678 683 681 703 C1' T B 546 beta 699 704 702 723 C1' A B 547 beta 719 724 722 744 C1' T B 548 beta 740 745 743 230 C1' G A 503 beta 226 231 229 252 C1' T A 504 beta 248 253 251 272 C1' C A 505 beta 268 273 271 291 C1' A A 506 beta 287 292 290 312 C1' C A 507 beta 308 313 311 331 C1' A A 508 beta 327 332 330 352 C1' T A 509 beta 348 353 351 372 C1' T A 510 beta 368 373 371 392 C1' A A 511 beta 388 393 391 413 C1' A A 512 beta 409 414 412 434 C1' T A 513 beta 430 435 433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 764 C2' A B 534 765 762 785 C2' T B 535 786 783 805 C2' T B 536 806 803 825 C2' A B 537 826 823 846 C2' A B 538 847 844 867 C2' T B 539 868 865 887 C2' G B 540 888 885 909 C2' T B 541 910 907 929 C2' G B 542 930 927 951 C2' A B 543 952 949 972 C2' C B 544 973 970 991 C2' A B 545 992 989 1012 C2' T B 546 1013 1010 1032 C2' A B 547 1033 1030 1053 C2' T B 548 1054 1051 7 C2' G A 503 8 5 29 C2' T A 504 30 27 49 C2' C A 505 50 47 68 C2' A A 506 69 66 89 C2' C A 507 90 87 108 C2' A A 508 109 106 129 C2' T A 509 130 127 149 C2' T A 510 150 147 169 C2' A A 511 170 167 190 C2' A A 512 191 188 211 C2' T A 513 212 209 454 C2' A B 534 455 452 475 C2' T B 535 476 473 495 C2' T B 536 496 493 515 C2' A B 537 516 513 536 C2' A B 538 537 534 557 C2' T B 539 558 555 577 C2' G B 540 578 575 599 C2' T B 541 600 597 619 C2' G B 542 620 617 641 C2' A B 543 642 639 662 C2' C B 544 663 660 681 C2' A B 545 682 679 702 C2' T B 546 703 700 722 C2' A B 547 723 720 743 C2' T B 548 744 741 229 C2' G A 503 230 227 251 C2' T A 504 252 249 271 C2' C A 505 272 269 290 C2' A A 506 291 288 311 C2' C A 507 312 309 330 C2' A A 508 331 328 351 C2' T A 509 352 349 371 C2' T A 510 372 369 391 C2' A A 511 392 389 412 C2' A A 512 413 410 433 C2' T A 513 434 431 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 762 C3' A B 534 OK 760 763 764 783 C3' T B 535 OK 781 784 785 803 C3' T B 536 OK 801 804 805 823 C3' A B 537 OK 821 824 825 844 C3' A B 538 OK 842 845 846 865 C3' T B 539 OK 863 866 867 885 C3' G B 540 OK 883 886 887 907 C3' T B 541 OK 905 908 909 927 C3' G B 542 OK 925 928 929 949 C3' A B 543 OK 947 950 951 970 C3' C B 544 OK 968 971 972 989 C3' A B 545 OK 987 990 991 1010 C3' T B 546 OK 1008 1011 1012 1030 C3' A B 547 OK 1028 1031 1032 1051 C3' T B 548 OK 1049 1052 1053 5 C3' G A 503 OK 3 6 7 27 C3' T A 504 OK 25 28 29 47 C3' C A 505 OK 45 48 49 66 C3' A A 506 OK 64 67 68 87 C3' C A 507 OK 85 88 89 106 C3' A A 508 OK 104 107 108 127 C3' T A 509 OK 125 128 129 147 C3' T A 510 OK 145 148 149 167 C3' A A 511 OK 165 168 169 188 C3' A A 512 OK 186 189 190 209 C3' T A 513 OK 207 210 211 452 C3' A B 534 OK 450 453 454 473 C3' T B 535 OK 471 474 475 493 C3' T B 536 OK 491 494 495 513 C3' A B 537 OK 511 514 515 534 C3' A B 538 OK 532 535 536 555 C3' T B 539 OK 553 556 557 575 C3' G B 540 OK 573 576 577 597 C3' T B 541 OK 595 598 599 617 C3' G B 542 OK 615 618 619 639 C3' A B 543 OK 637 640 641 660 C3' C B 544 OK 658 661 662 679 C3' A B 545 OK 677 680 681 700 C3' T B 546 OK 698 701 702 720 C3' A B 547 OK 718 721 722 741 C3' T B 548 OK 739 742 743 227 C3' G A 503 OK 225 228 229 249 C3' T A 504 OK 247 250 251 269 C3' C A 505 OK 267 270 271 288 C3' A A 506 OK 286 289 290 309 C3' C A 507 OK 307 310 311 328 C3' A A 508 OK 326 329 330 349 C3' T A 509 OK 347 350 351 369 C3' T A 510 OK 367 370 371 389 C3' A A 511 OK 387 390 391 410 C3' A A 512 OK 408 411 412 431 C3' T A 513 OK 429 432 433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 760 C4' A B 534 OK 762 759 761 781 C4' T B 535 OK 783 780 782 801 C4' T B 536 OK 803 800 802 821 C4' A B 537 OK 823 820 822 842 C4' A B 538 OK 844 841 843 863 C4' T B 539 OK 865 862 864 883 C4' G B 540 OK 885 882 884 905 C4' T B 541 OK 907 904 906 925 C4' G B 542 OK 927 924 926 947 C4' A B 543 OK 949 946 948 968 C4' C B 544 OK 970 967 969 987 C4' A B 545 OK 989 986 988 1008 C4' T B 546 OK 1010 1007 1009 1028 C4' A B 547 OK 1030 1027 1029 1049 C4' T B 548 OK 1051 1048 1050 3 C4' G A 503 OK 5 2 4 25 C4' T A 504 OK 27 24 26 45 C4' C A 505 OK 47 44 46 64 C4' A A 506 OK 66 63 65 85 C4' C A 507 OK 87 84 86 104 C4' A A 508 OK 106 103 105 125 C4' T A 509 OK 127 124 126 145 C4' T A 510 OK 147 144 146 165 C4' A A 511 OK 167 164 166 186 C4' A A 512 OK 188 185 187 207 C4' T A 513 OK 209 206 208 450 C4' A B 534 OK 452 449 451 471 C4' T B 535 OK 473 470 472 491 C4' T B 536 OK 493 490 492 511 C4' A B 537 OK 513 510 512 532 C4' A B 538 OK 534 531 533 553 C4' T B 539 OK 555 552 554 573 C4' G B 540 OK 575 572 574 595 C4' T B 541 OK 597 594 596 615 C4' G B 542 OK 617 614 616 637 C4' A B 543 OK 639 636 638 658 C4' C B 544 OK 660 657 659 677 C4' A B 545 OK 679 676 678 698 C4' T B 546 OK 700 697 699 718 C4' A B 547 OK 720 717 719 739 C4' T B 548 OK 741 738 740 225 C4' G A 503 OK 227 224 226 247 C4' T A 504 OK 249 246 248 267 C4' C A 505 OK 269 266 268 286 C4' A A 506 OK 288 285 287 307 C4' C A 507 OK 309 306 308 326 C4' A A 508 OK 328 325 327 347 C4' T A 509 OK 349 346 348 367 C4' T A 510 OK 369 366 368 387 C4' A A 511 OK 389 386 388 408 C4' A A 512 OK 410 407 409 429 C4' T A 513 OK 431 428 430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 759 C5' A B 534 758 760 780 C5' T B 535 779 781 800 C5' T B 536 799 801 820 C5' A B 537 819 821 841 C5' A B 538 840 842 862 C5' T B 539 861 863 882 C5' G B 540 881 883 904 C5' T B 541 903 905 924 C5' G B 542 923 925 946 C5' A B 543 945 947 967 C5' C B 544 966 968 986 C5' A B 545 985 987 1007 C5' T B 546 1006 1008 1027 C5' A B 547 1026 1028 1048 C5' T B 548 1047 1049 2 C5' G A 503 1 3 24 C5' T A 504 23 25 44 C5' C A 505 43 45 63 C5' A A 506 62 64 84 C5' C A 507 83 85 103 C5' A A 508 102 104 124 C5' T A 509 123 125 144 C5' T A 510 143 145 164 C5' A A 511 163 165 185 C5' A A 512 184 186 206 C5' T A 513 205 207 449 C5' A B 534 448 450 470 C5' T B 535 469 471 490 C5' T B 536 489 491 510 C5' A B 537 509 511 531 C5' A B 538 530 532 552 C5' T B 539 551 553 572 C5' G B 540 571 573 594 C5' T B 541 593 595 614 C5' G B 542 613 615 636 C5' A B 543 635 637 657 C5' C B 544 656 658 676 C5' A B 545 675 677 697 C5' T B 546 696 698 717 C5' A B 547 716 718 738 C5' T B 548 737 739 224 C5' G A 503 223 225 246 C5' T A 504 245 247 266 C5' C A 505 265 267 285 C5' A A 506 284 286 306 C5' C A 507 305 307 325 C5' A A 508 324 326 346 C5' T A 509 345 347 366 C5' T A 510 365 367 386 C5' A A 511 385 387 407 C5' A A 512 406 408 428 C5' T A 513 427 429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 776 P T B 535 distorted distorted 763 777 778 779 796 P T B 536 distorted distorted 784 797 798 799 816 P A B 537 distorted distorted 804 817 818 819 837 P A B 538 distorted distorted 824 838 839 840 858 P T B 539 distorted distorted 845 859 860 861 878 P G B 540 distorted distorted 866 879 880 881 900 P T B 541 OK OK 886 901 902 903 920 P G B 542 OK OK 908 921 922 923 942 P A B 543 OK OK 928 943 944 945 963 P C B 544 OK OK 950 964 965 966 982 P A B 545 OK OK 971 983 984 985 1003 P T B 546 OK OK 990 1004 1005 1006 1023 P A B 547 OK OK 1011 1024 1025 1026 1044 P T B 548 OK OK 1031 1045 1046 1047 20 P T A 504 OK OK 6 21 22 23 40 P C A 505 OK OK 28 41 42 43 59 P A A 506 OK OK 48 60 61 62 80 P C A 507 distorted distorted 67 81 82 83 99 P A A 508 distorted distorted 88 100 101 102 120 P T A 509 distorted distorted 107 121 122 123 140 P T A 510 distorted distorted 128 141 142 143 160 P A A 511 distorted distorted 148 161 162 163 181 P A A 512 distorted distorted 168 182 183 184 202 P T A 513 distorted distorted 189 203 204 205 466 P T B 535 distorted distorted 453 467 468 469 486 P T B 536 distorted distorted 474 487 488 489 506 P A B 537 distorted distorted 494 507 508 509 527 P A B 538 distorted distorted 514 528 529 530 548 P T B 539 distorted distorted 535 549 550 551 568 P G B 540 distorted distorted 556 569 570 571 590 P T B 541 OK OK 576 591 592 593 610 P G B 542 OK OK 598 611 612 613 632 P A B 543 OK OK 618 633 634 635 653 P C B 544 OK OK 640 654 655 656 672 P A B 545 OK OK 661 673 674 675 693 P T B 546 OK OK 680 694 695 696 713 P A B 547 OK OK 701 714 715 716 734 P T B 548 OK OK 721 735 736 737 242 P T A 504 OK OK 228 243 244 245 262 P C A 505 OK OK 250 263 264 265 281 P A A 506 OK OK 270 282 283 284 302 P C A 507 distorted distorted 289 303 304 305 321 P A A 508 distorted distorted 310 322 323 324 342 P T A 509 distorted distorted 329 343 344 345 362 P T A 510 distorted distorted 350 363 364 365 382 P A A 511 distorted distorted 370 383 384 385 403 P A A 512 distorted distorted 390 404 405 406 424 P T A 513 distorted distorted 411 425 426 427 ---------------------------------------------------------------------------------