ID code: '1SCL' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' U A 4 alpha beta 107 127 113 110 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' C A 8 alpha beta 232 252 238 235 268 C1' A A 9 alpha beta 263 285 269 266 301 C1' G A 10 alpha beta 296 319 302 299 335 C1' U A 11 alpha beta 330 350 336 333 365 C1' A A 12 alpha beta 360 382 366 363 398 C1' C A 13 alpha beta 393 413 399 396 429 C1' G A 14 alpha beta 424 447 430 427 463 C1' A A 15 alpha beta 458 480 464 461 496 C1' G A 16 alpha beta 491 514 497 494 530 C1' A A 17 alpha beta 525 547 531 528 563 C1' G A 18 alpha beta 558 581 564 561 597 C1' G A 19 alpha beta 592 615 598 595 631 C1' A A 20 alpha beta 626 648 632 629 664 C1' A A 21 alpha beta 659 681 665 662 697 C1' C A 22 alpha beta 692 712 698 695 728 C1' C A 23 alpha beta 723 743 729 726 759 C1' G A 24 alpha beta 754 777 760 757 793 C1' C A 25 alpha beta 788 808 794 791 824 C1' A A 26 alpha beta 819 841 825 822 857 C1' C A 27 alpha beta 852 872 858 855 888 C1' C A 28 alpha beta 883 903 889 886 919 C1' C A 29 alpha beta 914 935 920 917 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' U A 4 OK OK 112 108 125 111 140 C2' G A 5 OK OK 142 138 158 141 174 C2' C A 6 OK OK 176 172 189 175 205 C2' U A 7 OK OK 207 203 220 206 235 C2' C A 8 OK OK 237 233 250 236 266 C2' A A 9 OK OK 268 264 283 267 299 C2' G A 10 OK OK 301 297 317 300 333 C2' U A 11 OK OK 335 331 348 334 363 C2' A A 12 OK OK 365 361 380 364 396 C2' C A 13 OK OK 398 394 411 397 427 C2' G A 14 OK OK 429 425 445 428 461 C2' A A 15 OK OK 463 459 478 462 494 C2' G A 16 OK OK 496 492 512 495 528 C2' A A 17 OK OK 530 526 545 529 561 C2' G A 18 OK OK 563 559 579 562 595 C2' G A 19 OK OK 597 593 613 596 629 C2' A A 20 OK OK 631 627 646 630 662 C2' A A 21 OK OK 664 660 679 663 695 C2' C A 22 OK OK 697 693 710 696 726 C2' C A 23 OK OK 728 724 741 727 757 C2' G A 24 OK OK 759 755 775 758 791 C2' C A 25 OK OK 793 789 806 792 822 C2' A A 26 OK OK 824 820 839 823 855 C2' C A 27 OK OK 857 853 870 856 886 C2' C A 28 OK OK 888 884 901 887 917 C2' C A 29 OK OK 919 915 933 918 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' U A 4 OK OK 106 124 109 110 138 C3' G A 5 OK OK 136 157 139 140 172 C3' C A 6 OK OK 170 188 173 174 203 C3' U A 7 OK OK 201 219 204 205 233 C3' C A 8 OK OK 231 249 234 235 264 C3' A A 9 OK OK 262 282 265 266 297 C3' G A 10 OK OK 295 316 298 299 331 C3' U A 11 OK OK 329 347 332 333 361 C3' A A 12 OK OK 359 379 362 363 394 C3' C A 13 OK OK 392 410 395 396 425 C3' G A 14 OK OK 423 444 426 427 459 C3' A A 15 OK OK 457 477 460 461 492 C3' G A 16 OK OK 490 511 493 494 526 C3' A A 17 OK OK 524 544 527 528 559 C3' G A 18 OK OK 557 578 560 561 593 C3' G A 19 OK OK 591 612 594 595 627 C3' A A 20 OK OK 625 645 628 629 660 C3' A A 21 OK OK 658 678 661 662 693 C3' C A 22 OK OK 691 709 694 695 724 C3' C A 23 OK OK 722 740 725 726 755 C3' G A 24 OK OK 753 774 756 757 789 C3' C A 25 OK OK 787 805 790 791 820 C3' A A 26 OK OK 818 838 821 822 853 C3' C A 27 OK OK 851 869 854 855 884 C3' C A 28 OK OK 882 900 885 886 915 C3' C A 29 OK OK 913 931 916 917 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' U A 4 OK OK 108 123 105 107 136 C4' G A 5 OK OK 138 156 135 137 170 C4' C A 6 OK OK 172 187 169 171 201 C4' U A 7 OK OK 203 218 200 202 231 C4' C A 8 OK OK 233 248 230 232 262 C4' A A 9 OK OK 264 281 261 263 295 C4' G A 10 OK OK 297 315 294 296 329 C4' U A 11 OK OK 331 346 328 330 359 C4' A A 12 OK OK 361 378 358 360 392 C4' C A 13 OK OK 394 409 391 393 423 C4' G A 14 OK OK 425 443 422 424 457 C4' A A 15 OK OK 459 476 456 458 490 C4' G A 16 OK OK 492 510 489 491 524 C4' A A 17 OK OK 526 543 523 525 557 C4' G A 18 OK OK 559 577 556 558 591 C4' G A 19 OK OK 593 611 590 592 625 C4' A A 20 OK OK 627 644 624 626 658 C4' A A 21 OK OK 660 677 657 659 691 C4' C A 22 OK OK 693 708 690 692 722 C4' C A 23 OK OK 724 739 721 723 753 C4' G A 24 OK OK 755 773 752 754 787 C4' C A 25 OK OK 789 804 786 788 818 C4' A A 26 OK OK 820 837 817 819 851 C4' C A 27 OK OK 853 868 850 852 882 C4' C A 28 OK OK 884 899 881 883 913 C4' C A 29 OK OK 915 930 912 914 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' U A 4 OK OK 104 121 122 106 135 C5' G A 5 OK OK 134 154 155 136 169 C5' C A 6 OK OK 168 185 186 170 200 C5' U A 7 OK OK 199 216 217 201 230 C5' C A 8 OK OK 229 246 247 231 261 C5' A A 9 OK OK 260 279 280 262 294 C5' G A 10 OK OK 293 313 314 295 328 C5' U A 11 OK OK 327 344 345 329 358 C5' A A 12 OK OK 357 376 377 359 391 C5' C A 13 OK OK 390 407 408 392 422 C5' G A 14 OK OK 421 441 442 423 456 C5' A A 15 OK OK 455 474 475 457 489 C5' G A 16 OK OK 488 508 509 490 523 C5' A A 17 OK OK 522 541 542 524 556 C5' G A 18 OK OK 555 575 576 557 590 C5' G A 19 OK OK 589 609 610 591 624 C5' A A 20 OK OK 623 642 643 625 657 C5' A A 21 OK OK 656 675 676 658 690 C5' C A 22 OK OK 689 706 707 691 721 C5' C A 23 OK OK 720 737 738 722 752 C5' G A 24 OK OK 751 771 772 753 786 C5' C A 25 OK OK 785 802 803 787 817 C5' A A 26 OK OK 816 835 836 818 850 C5' C A 27 OK OK 849 866 867 851 881 C5' C A 28 OK OK 880 897 898 882 912 C5' C A 29 OK OK 911 928 929 913 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P U A 4 distorted distorted 75 102 103 104 131 P G A 5 distorted distorted 109 132 133 134 165 P C A 6 distorted distorted 139 166 167 168 196 P U A 7 distorted distorted 173 197 198 199 226 P C A 8 distorted distorted 204 227 228 229 257 P A A 9 distorted distorted 234 258 259 260 290 P G A 10 distorted distorted 265 291 292 293 324 P U A 11 distorted distorted 298 325 326 327 354 P A A 12 distorted distorted 332 355 356 357 387 P C A 13 distorted distorted 362 388 389 390 418 P G A 14 distorted distorted 395 419 420 421 452 P A A 15 distorted distorted 426 453 454 455 485 P G A 16 distorted distorted 460 486 487 488 519 P A A 17 distorted distorted 493 520 521 522 552 P G A 18 distorted distorted 527 553 554 555 586 P G A 19 distorted distorted 560 587 588 589 620 P A A 20 distorted distorted 594 621 622 623 653 P A A 21 distorted distorted 628 654 655 656 686 P C A 22 distorted distorted 661 687 688 689 717 P C A 23 distorted distorted 694 718 719 720 748 P G A 24 distorted distorted 725 749 750 751 782 P C A 25 distorted distorted 756 783 784 785 813 P A A 26 distorted distorted 790 814 815 816 846 P C A 27 distorted distorted 821 847 848 849 877 P C A 28 distorted distorted 854 878 879 880 908 P C A 29 distorted distorted 885 909 910 911 ---------------------------------------------------------------------------------