ID code: '1G9Y' 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' C C 401 beta 4 9 7 27 C1' G C 402 beta 23 28 26 49 C1' A C 403 beta 45 50 48 70 C1' A C 404 beta 66 71 69 91 C1' A C 405 beta 87 92 90 112 C1' C C 406 beta 108 113 111 131 C1' T C 407 beta 127 132 130 151 C1' G C 408 beta 147 152 150 173 C1' T C 409 beta 169 174 172 193 C1' C C 410 beta 189 194 192 212 C1' T C 411 beta 208 213 211 232 C1' C C 412 beta 228 233 231 251 C1' A C 413 beta 247 252 250 272 C1' C C 414 beta 268 273 271 291 C1' G C 415 beta 287 292 290 313 C1' A C 416 beta 309 314 312 334 C1' C C 417 beta 330 335 333 353 C1' G C 418 beta 349 354 352 375 C1' T C 419 beta 371 376 374 395 C1' T C 420 beta 391 396 394 415 C1' T C 421 beta 411 416 414 435 C1' T C 422 beta 431 436 434 455 C1' G C 423 beta 451 456 454 477 C1' C C 424 beta 473 478 476 494 C1' G D 501 beta 490 495 493 516 C1' C D 502 beta 512 517 515 535 C1' A D 503 beta 531 536 534 556 C1' A D 504 beta 552 557 555 577 C1' A D 505 beta 573 578 576 598 C1' A D 506 beta 594 599 597 619 C1' C D 507 beta 615 620 618 638 C1' G D 508 beta 634 639 637 660 C1' T D 509 beta 656 661 659 680 C1' C D 510 beta 676 681 679 699 C1' G D 511 beta 695 700 698 721 C1' T D 512 beta 717 722 720 741 C1' G D 513 beta 737 742 740 763 C1' A D 514 beta 759 764 762 784 C1' G D 515 beta 780 785 783 806 C1' A D 516 beta 802 807 805 827 C1' C D 517 beta 823 828 826 846 C1' A D 518 beta 842 847 845 867 C1' G D 519 beta 863 868 866 889 C1' T D 520 beta 885 890 888 909 C1' T D 521 beta 905 910 908 929 C1' T D 522 beta 925 930 928 949 C1' C D 523 beta 945 950 948 968 C1' G D 524 beta 964 969 967 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C C 401 8 5 26 C2' G C 402 27 24 48 C2' A C 403 49 46 69 C2' A C 404 70 67 90 C2' A C 405 91 88 111 C2' C C 406 112 109 130 C2' T C 407 131 128 150 C2' G C 408 151 148 172 C2' T C 409 173 170 192 C2' C C 410 193 190 211 C2' T C 411 212 209 231 C2' C C 412 232 229 250 C2' A C 413 251 248 271 C2' C C 414 272 269 290 C2' G C 415 291 288 312 C2' A C 416 313 310 333 C2' C C 417 334 331 352 C2' G C 418 353 350 374 C2' T C 419 375 372 394 C2' T C 420 395 392 414 C2' T C 421 415 412 434 C2' T C 422 435 432 454 C2' G C 423 455 452 476 C2' C C 424 477 474 493 C2' G D 501 494 491 515 C2' C D 502 516 513 534 C2' A D 503 535 532 555 C2' A D 504 556 553 576 C2' A D 505 577 574 597 C2' A D 506 598 595 618 C2' C D 507 619 616 637 C2' G D 508 638 635 659 C2' T D 509 660 657 679 C2' C D 510 680 677 698 C2' G D 511 699 696 720 C2' T D 512 721 718 740 C2' G D 513 741 738 762 C2' A D 514 763 760 783 C2' G D 515 784 781 805 C2' A D 516 806 803 826 C2' C D 517 827 824 845 C2' A D 518 846 843 866 C2' G D 519 867 864 888 C2' T D 520 889 886 908 C2' T D 521 909 906 928 C2' T D 522 929 926 948 C2' C D 523 949 946 967 C2' G D 524 968 965 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C C 401 OK 3 6 7 24 C3' G C 402 OK 22 25 26 46 C3' A C 403 OK 44 47 48 67 C3' A C 404 OK 65 68 69 88 C3' A C 405 OK 86 89 90 109 C3' C C 406 OK 107 110 111 128 C3' T C 407 OK 126 129 130 148 C3' G C 408 OK 146 149 150 170 C3' T C 409 OK 168 171 172 190 C3' C C 410 OK 188 191 192 209 C3' T C 411 OK 207 210 211 229 C3' C C 412 OK 227 230 231 248 C3' A C 413 OK 246 249 250 269 C3' C C 414 OK 267 270 271 288 C3' G C 415 OK 286 289 290 310 C3' A C 416 OK 308 311 312 331 C3' C C 417 OK 329 332 333 350 C3' G C 418 OK 348 351 352 372 C3' T C 419 OK 370 373 374 392 C3' T C 420 OK 390 393 394 412 C3' T C 421 OK 410 413 414 432 C3' T C 422 OK 430 433 434 452 C3' G C 423 OK 450 453 454 474 C3' C C 424 OK 472 475 476 491 C3' G D 501 OK 489 492 493 513 C3' C D 502 OK 511 514 515 532 C3' A D 503 OK 530 533 534 553 C3' A D 504 OK 551 554 555 574 C3' A D 505 OK 572 575 576 595 C3' A D 506 OK 593 596 597 616 C3' C D 507 OK 614 617 618 635 C3' G D 508 OK 633 636 637 657 C3' T D 509 OK 655 658 659 677 C3' C D 510 OK 675 678 679 696 C3' G D 511 OK 694 697 698 718 C3' T D 512 OK 716 719 720 738 C3' G D 513 OK 736 739 740 760 C3' A D 514 OK 758 761 762 781 C3' G D 515 OK 779 782 783 803 C3' A D 516 OK 801 804 805 824 C3' C D 517 OK 822 825 826 843 C3' A D 518 OK 841 844 845 864 C3' G D 519 OK 862 865 866 886 C3' T D 520 OK 884 887 888 906 C3' T D 521 OK 904 907 908 926 C3' T D 522 OK 924 927 928 946 C3' C D 523 OK 944 947 948 965 C3' G D 524 OK 963 966 967 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C C 401 OK 5 2 4 22 C4' G C 402 OK 24 21 23 44 C4' A C 403 OK 46 43 45 65 C4' A C 404 OK 67 64 66 86 C4' A C 405 OK 88 85 87 107 C4' C C 406 OK 109 106 108 126 C4' T C 407 OK 128 125 127 146 C4' G C 408 OK 148 145 147 168 C4' T C 409 OK 170 167 169 188 C4' C C 410 OK 190 187 189 207 C4' T C 411 OK 209 206 208 227 C4' C C 412 OK 229 226 228 246 C4' A C 413 OK 248 245 247 267 C4' C C 414 OK 269 266 268 286 C4' G C 415 OK 288 285 287 308 C4' A C 416 OK 310 307 309 329 C4' C C 417 OK 331 328 330 348 C4' G C 418 OK 350 347 349 370 C4' T C 419 OK 372 369 371 390 C4' T C 420 OK 392 389 391 410 C4' T C 421 OK 412 409 411 430 C4' T C 422 OK 432 429 431 450 C4' G C 423 OK 452 449 451 472 C4' C C 424 OK 474 471 473 489 C4' G D 501 OK 491 488 490 511 C4' C D 502 OK 513 510 512 530 C4' A D 503 OK 532 529 531 551 C4' A D 504 OK 553 550 552 572 C4' A D 505 OK 574 571 573 593 C4' A D 506 OK 595 592 594 614 C4' C D 507 OK 616 613 615 633 C4' G D 508 OK 635 632 634 655 C4' T D 509 OK 657 654 656 675 C4' C D 510 OK 677 674 676 694 C4' G D 511 OK 696 693 695 716 C4' T D 512 OK 718 715 717 736 C4' G D 513 OK 738 735 737 758 C4' A D 514 OK 760 757 759 779 C4' G D 515 OK 781 778 780 801 C4' A D 516 OK 803 800 802 822 C4' C D 517 OK 824 821 823 841 C4' A D 518 OK 843 840 842 862 C4' G D 519 OK 864 861 863 884 C4' T D 520 OK 886 883 885 904 C4' T D 521 OK 906 903 905 924 C4' T D 522 OK 926 923 925 944 C4' C D 523 OK 946 943 945 963 C4' G D 524 OK 965 962 964 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C C 401 1 3 21 C5' G C 402 20 22 43 C5' A C 403 42 44 64 C5' A C 404 63 65 85 C5' A C 405 84 86 106 C5' C C 406 105 107 125 C5' T C 407 124 126 145 C5' G C 408 144 146 167 C5' T C 409 166 168 187 C5' C C 410 186 188 206 C5' T C 411 205 207 226 C5' C C 412 225 227 245 C5' A C 413 244 246 266 C5' C C 414 265 267 285 C5' G C 415 284 286 307 C5' A C 416 306 308 328 C5' C C 417 327 329 347 C5' G C 418 346 348 369 C5' T C 419 368 370 389 C5' T C 420 388 390 409 C5' T C 421 408 410 429 C5' T C 422 428 430 449 C5' G C 423 448 450 471 C5' C C 424 470 472 488 C5' G D 501 487 489 510 C5' C D 502 509 511 529 C5' A D 503 528 530 550 C5' A D 504 549 551 571 C5' A D 505 570 572 592 C5' A D 506 591 593 613 C5' C D 507 612 614 632 C5' G D 508 631 633 654 C5' T D 509 653 655 674 C5' C D 510 673 675 693 C5' G D 511 692 694 715 C5' T D 512 714 716 735 C5' G D 513 734 736 757 C5' A D 514 756 758 778 C5' G D 515 777 779 800 C5' A D 516 799 801 821 C5' C D 517 820 822 840 C5' A D 518 839 841 861 C5' G D 519 860 862 883 C5' T D 520 882 884 903 C5' T D 521 902 904 923 C5' T D 522 922 924 943 C5' C D 523 942 944 962 C5' G D 524 961 963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P G C 402 distorted distorted 6 18 19 20 39 P A C 403 distorted distorted 25 40 41 42 60 P A C 404 distorted distorted 47 61 62 63 81 P A C 405 distorted distorted 68 82 83 84 102 P C C 406 distorted distorted 89 103 104 105 121 P T C 407 distorted distorted 110 122 123 124 141 P G C 408 distorted distorted 129 142 143 144 163 P T C 409 distorted distorted 149 164 165 166 183 P C C 410 distorted distorted 171 184 185 186 202 P T C 411 distorted distorted 191 203 204 205 222 P C C 412 distorted distorted 210 223 224 225 241 P A C 413 distorted distorted 230 242 243 244 262 P C C 414 distorted distorted 249 263 264 265 281 P G C 415 distorted distorted 270 282 283 284 303 P A C 416 distorted distorted 289 304 305 306 324 P C C 417 distorted distorted 311 325 326 327 343 P G C 418 distorted distorted 332 344 345 346 365 P T C 419 distorted distorted 351 366 367 368 385 P T C 420 distorted distorted 373 386 387 388 405 P T C 421 distorted distorted 393 406 407 408 425 P T C 422 distorted distorted 413 426 427 428 445 P G C 423 distorted distorted 433 446 447 448 467 P C C 424 distorted distorted 453 468 469 470 506 P C D 502 distorted distorted 492 507 508 509 525 P A D 503 distorted distorted 514 526 527 528 546 P A D 504 distorted distorted 533 547 548 549 567 P A D 505 distorted distorted 554 568 569 570 588 P A D 506 distorted distorted 575 589 590 591 609 P C D 507 distorted distorted 596 610 611 612 628 P G D 508 distorted distorted 617 629 630 631 650 P T D 509 distorted distorted 636 651 652 653 670 P C D 510 distorted distorted 658 671 672 673 689 P G D 511 distorted distorted 678 690 691 692 711 P T D 512 distorted distorted 697 712 713 714 731 P G D 513 distorted distorted 719 732 733 734 753 P A D 514 distorted distorted 739 754 755 756 774 P G D 515 distorted distorted 761 775 776 777 796 P A D 516 distorted distorted 782 797 798 799 817 P C D 517 distorted distorted 804 818 819 820 836 P A D 518 distorted distorted 825 837 838 839 857 P G D 519 distorted distorted 844 858 859 860 879 P T D 520 distorted distorted 865 880 881 882 899 P T D 521 distorted distorted 887 900 901 902 919 P T D 522 distorted distorted 907 920 921 922 939 P C D 523 distorted distorted 927 940 941 942 958 P G D 524 distorted distorted 947 959 960 961 ---------------------------------------------------------------------------------