ID code: '1K6O' 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 D 101 beta 4 9 7 27 C1' A D 102 beta 23 28 26 48 C1' C D 103 beta 44 49 47 67 C1' A D 104 beta 63 68 66 88 C1' G D 105 beta 84 89 87 110 C1' G D 106 beta 106 111 109 132 C1' A D 107 beta 128 133 131 153 C1' T D 108 beta 149 154 152 173 C1' G D 109 beta 169 174 172 195 C1' T D 110 beta 191 196 194 215 C1' C D 111 beta 211 216 214 234 C1' C D 112 beta 230 235 233 253 C1' A D 113 beta 249 254 252 274 C1' T D 114 beta 270 275 273 294 C1' A D 115 beta 290 295 293 315 C1' T D 116 beta 311 316 314 335 C1' T D 117 beta 331 336 334 355 C1' A D 118 beta 351 356 354 376 C1' G D 119 beta 372 377 375 398 C1' G D 120 beta 394 399 397 420 C1' A D 121 beta 416 421 419 441 C1' C D 122 beta 437 442 440 460 C1' A D 123 beta 456 461 459 479 C1' T E 201 beta 475 480 478 499 C1' G E 202 beta 495 500 498 521 C1' T E 203 beta 517 522 520 541 C1' C E 204 beta 537 542 540 560 C1' C E 205 beta 556 561 559 579 C1' T E 206 beta 575 580 578 599 C1' A E 207 beta 595 600 598 620 C1' A E 208 beta 616 621 619 641 C1' T E 209 beta 637 642 640 661 C1' A E 210 beta 657 662 660 682 C1' T E 211 beta 678 683 681 702 C1' G E 212 beta 698 703 701 724 C1' G E 213 beta 720 725 723 746 C1' A E 214 beta 742 747 745 767 C1' C E 215 beta 763 768 766 786 C1' A E 216 beta 782 787 785 807 C1' T E 217 beta 803 808 806 827 C1' C E 218 beta 823 828 826 846 C1' C E 219 beta 842 847 845 865 C1' T E 220 beta 861 866 864 885 C1' G E 221 beta 881 886 884 907 C1' T E 222 beta 903 908 906 927 C1' G E 223 beta 923 928 926 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C D 101 8 5 26 C2' A D 102 27 24 47 C2' C D 103 48 45 66 C2' A D 104 67 64 87 C2' G D 105 88 85 109 C2' G D 106 110 107 131 C2' A D 107 132 129 152 C2' T D 108 153 150 172 C2' G D 109 173 170 194 C2' T D 110 195 192 214 C2' C D 111 215 212 233 C2' C D 112 234 231 252 C2' A D 113 253 250 273 C2' T D 114 274 271 293 C2' A D 115 294 291 314 C2' T D 116 315 312 334 C2' T D 117 335 332 354 C2' A D 118 355 352 375 C2' G D 119 376 373 397 C2' G D 120 398 395 419 C2' A D 121 420 417 440 C2' C D 122 441 438 459 C2' A D 123 460 457 478 C2' T E 201 479 476 498 C2' G E 202 499 496 520 C2' T E 203 521 518 540 C2' C E 204 541 538 559 C2' C E 205 560 557 578 C2' T E 206 579 576 598 C2' A E 207 599 596 619 C2' A E 208 620 617 640 C2' T E 209 641 638 660 C2' A E 210 661 658 681 C2' T E 211 682 679 701 C2' G E 212 702 699 723 C2' G E 213 724 721 745 C2' A E 214 746 743 766 C2' C E 215 767 764 785 C2' A E 216 786 783 806 C2' T E 217 807 804 826 C2' C E 218 827 824 845 C2' C E 219 846 843 864 C2' T E 220 865 862 884 C2' G E 221 885 882 906 C2' T E 222 907 904 926 C2' G E 223 927 924 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C D 101 OK 3 6 7 24 C3' A D 102 OK 22 25 26 45 C3' C D 103 OK 43 46 47 64 C3' A D 104 OK 62 65 66 85 C3' G D 105 OK 83 86 87 107 C3' G D 106 OK 105 108 109 129 C3' A D 107 OK 127 130 131 150 C3' T D 108 OK 148 151 152 170 C3' G D 109 OK 168 171 172 192 C3' T D 110 OK 190 193 194 212 C3' C D 111 OK 210 213 214 231 C3' C D 112 OK 229 232 233 250 C3' A D 113 OK 248 251 252 271 C3' T D 114 OK 269 272 273 291 C3' A D 115 OK 289 292 293 312 C3' T D 116 OK 310 313 314 332 C3' T D 117 OK 330 333 334 352 C3' A D 118 OK 350 353 354 373 C3' G D 119 OK 371 374 375 395 C3' G D 120 OK 393 396 397 417 C3' A D 121 OK 415 418 419 438 C3' C D 122 OK 436 439 440 457 C3' A D 123 OK 455 458 459 476 C3' T E 201 OK 474 477 478 496 C3' G E 202 OK 494 497 498 518 C3' T E 203 OK 516 519 520 538 C3' C E 204 OK 536 539 540 557 C3' C E 205 OK 555 558 559 576 C3' T E 206 OK 574 577 578 596 C3' A E 207 OK 594 597 598 617 C3' A E 208 OK 615 618 619 638 C3' T E 209 OK 636 639 640 658 C3' A E 210 OK 656 659 660 679 C3' T E 211 OK 677 680 681 699 C3' G E 212 OK 697 700 701 721 C3' G E 213 OK 719 722 723 743 C3' A E 214 OK 741 744 745 764 C3' C E 215 OK 762 765 766 783 C3' A E 216 OK 781 784 785 804 C3' T E 217 OK 802 805 806 824 C3' C E 218 OK 822 825 826 843 C3' C E 219 OK 841 844 845 862 C3' T E 220 OK 860 863 864 882 C3' G E 221 OK 880 883 884 904 C3' T E 222 OK 902 905 906 924 C3' G E 223 OK 922 925 926 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C D 101 OK 5 2 4 22 C4' A D 102 OK 24 21 23 43 C4' C D 103 OK 45 42 44 62 C4' A D 104 OK 64 61 63 83 C4' G D 105 OK 85 82 84 105 C4' G D 106 OK 107 104 106 127 C4' A D 107 OK 129 126 128 148 C4' T D 108 OK 150 147 149 168 C4' G D 109 OK 170 167 169 190 C4' T D 110 OK 192 189 191 210 C4' C D 111 OK 212 209 211 229 C4' C D 112 OK 231 228 230 248 C4' A D 113 OK 250 247 249 269 C4' T D 114 OK 271 268 270 289 C4' A D 115 OK 291 288 290 310 C4' T D 116 OK 312 309 311 330 C4' T D 117 OK 332 329 331 350 C4' A D 118 OK 352 349 351 371 C4' G D 119 OK 373 370 372 393 C4' G D 120 OK 395 392 394 415 C4' A D 121 OK 417 414 416 436 C4' C D 122 OK 438 435 437 455 C4' A D 123 OK 457 454 456 474 C4' T E 201 OK 476 473 475 494 C4' G E 202 OK 496 493 495 516 C4' T E 203 OK 518 515 517 536 C4' C E 204 OK 538 535 537 555 C4' C E 205 OK 557 554 556 574 C4' T E 206 OK 576 573 575 594 C4' A E 207 OK 596 593 595 615 C4' A E 208 OK 617 614 616 636 C4' T E 209 OK 638 635 637 656 C4' A E 210 OK 658 655 657 677 C4' T E 211 OK 679 676 678 697 C4' G E 212 OK 699 696 698 719 C4' G E 213 OK 721 718 720 741 C4' A E 214 OK 743 740 742 762 C4' C E 215 OK 764 761 763 781 C4' A E 216 OK 783 780 782 802 C4' T E 217 OK 804 801 803 822 C4' C E 218 OK 824 821 823 841 C4' C E 219 OK 843 840 842 860 C4' T E 220 OK 862 859 861 880 C4' G E 221 OK 882 879 881 902 C4' T E 222 OK 904 901 903 922 C4' G E 223 OK 924 921 923 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C D 101 1 3 21 C5' A D 102 20 22 42 C5' C D 103 41 43 61 C5' A D 104 60 62 82 C5' G D 105 81 83 104 C5' G D 106 103 105 126 C5' A D 107 125 127 147 C5' T D 108 146 148 167 C5' G D 109 166 168 189 C5' T D 110 188 190 209 C5' C D 111 208 210 228 C5' C D 112 227 229 247 C5' A D 113 246 248 268 C5' T D 114 267 269 288 C5' A D 115 287 289 309 C5' T D 116 308 310 329 C5' T D 117 328 330 349 C5' A D 118 348 350 370 C5' G D 119 369 371 392 C5' G D 120 391 393 414 C5' A D 121 413 415 435 C5' C D 122 434 436 454 C5' A D 123 453 455 473 C5' T E 201 472 474 493 C5' G E 202 492 494 515 C5' T E 203 514 516 535 C5' C E 204 534 536 554 C5' C E 205 553 555 573 C5' T E 206 572 574 593 C5' A E 207 592 594 614 C5' A E 208 613 615 635 C5' T E 209 634 636 655 C5' A E 210 654 656 676 C5' T E 211 675 677 696 C5' G E 212 695 697 718 C5' G E 213 717 719 740 C5' A E 214 739 741 761 C5' C E 215 760 762 780 C5' A E 216 779 781 801 C5' T E 217 800 802 821 C5' C E 218 820 822 840 C5' C E 219 839 841 859 C5' T E 220 858 860 879 C5' G E 221 878 880 901 C5' T E 222 900 902 921 C5' G E 223 920 922 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A D 102 distorted distorted 6 18 19 20 38 P C D 103 distorted distorted 25 39 40 41 57 P A D 104 distorted distorted 46 58 59 60 78 P G D 105 distorted distorted 65 79 80 81 100 P G D 106 distorted distorted 86 101 102 103 122 P A D 107 distorted distorted 108 123 124 125 143 P T D 108 distorted distorted 130 144 145 146 163 P G D 109 distorted distorted 151 164 165 166 185 P T D 110 distorted distorted 171 186 187 188 205 P C D 111 distorted distorted 193 206 207 208 224 P C D 112 distorted distorted 213 225 226 227 243 P A D 113 distorted distorted 232 244 245 246 264 P T D 114 distorted distorted 251 265 266 267 284 P A D 115 distorted distorted 272 285 286 287 305 P T D 116 distorted distorted 292 306 307 308 325 P T D 117 distorted distorted 313 326 327 328 345 P A D 118 distorted distorted 333 346 347 348 366 P G D 119 distorted distorted 353 367 368 369 388 P G D 120 distorted distorted 374 389 390 391 410 P A D 121 distorted distorted 396 411 412 413 431 P C D 122 distorted distorted 418 432 433 434 450 P A D 123 distorted distorted 439 451 452 453 489 P G E 202 distorted distorted 477 490 491 492 511 P T E 203 distorted distorted 497 512 513 514 531 P C E 204 distorted distorted 519 532 533 534 550 P C E 205 distorted distorted 539 551 552 553 569 P T E 206 distorted distorted 558 570 571 572 589 P A E 207 distorted distorted 577 590 591 592 610 P A E 208 distorted distorted 597 611 612 613 631 P T E 209 distorted distorted 618 632 633 634 651 P A E 210 distorted distorted 639 652 653 654 672 P T E 211 distorted distorted 659 673 674 675 692 P G E 212 distorted distorted 680 693 694 695 714 P G E 213 distorted distorted 700 715 716 717 736 P A E 214 distorted distorted 722 737 738 739 757 P C E 215 distorted distorted 744 758 759 760 776 P A E 216 distorted distorted 765 777 778 779 797 P T E 217 distorted distorted 784 798 799 800 817 P C E 218 distorted distorted 805 818 819 820 836 P C E 219 distorted distorted 825 837 838 839 855 P T E 220 distorted distorted 844 856 857 858 875 P G E 221 distorted distorted 863 876 877 878 897 P T E 222 distorted distorted 883 898 899 900 917 P G E 223 distorted distorted 905 918 919 920 ---------------------------------------------------------------------------------