ID code: '2RP1' 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' --------------------------------------------------------------------------------- 12 C1' U A 4 alpha beta 7 27 13 10 42 C1' C A 5 alpha beta 37 57 43 40 73 C1' C A 6 alpha beta 68 88 74 71 104 C1' G A 7 alpha beta 99 122 105 102 138 C1' G A 8 alpha beta 133 156 139 136 172 C1' U A 9 alpha beta 167 187 173 170 202 C1' CH A 10 alpha beta 197 217 203 200 234 C1' G A 11 alpha beta 229 252 235 232 268 C1' A A 12 alpha beta 263 285 269 266 301 C1' C A 13 alpha beta 296 316 302 299 332 C1' U A 14 alpha beta 327 347 333 330 362 C1' C A 15 alpha beta 357 377 363 360 393 C1' C A 16 alpha beta 388 408 394 391 424 C1' G A 17 alpha beta 419 442 425 422 458 C1' G A 18 alpha beta 453 476 459 456 492 C1' A A 19 alpha beta 487 509 493 490 525 C1' G A 20 alpha beta 520 543 526 523 559 C1' A A 21 alpha beta 554 576 560 557 592 C1' A A 22 alpha beta 587 609 593 590 625 C1' A A 23 alpha beta 620 642 626 623 658 C1' C A 24 alpha beta 653 673 659 656 689 C1' A A 25 alpha beta 684 706 690 687 722 C1' A A 26 alpha beta 717 739 723 720 755 C1' A A 27 alpha beta 750 772 756 753 788 C1' G A 28 alpha beta 783 806 789 786 822 C1' U A 29 alpha beta 817 837 823 820 852 C1' C A 30 alpha beta 847 867 853 850 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U A 4 OK OK 12 8 25 11 40 C2' C A 5 OK OK 42 38 55 41 71 C2' C A 6 OK OK 73 69 86 72 102 C2' G A 7 OK OK 104 100 120 103 136 C2' G A 8 OK OK 138 134 154 137 170 C2' U A 9 OK OK 172 168 185 171 200 C2' CH A 10 OK OK 202 198 215 201 232 C2' G A 11 OK OK 234 230 250 233 266 C2' A A 12 OK OK 268 264 283 267 299 C2' C A 13 OK OK 301 297 314 300 330 C2' U A 14 OK OK 332 328 345 331 360 C2' C A 15 OK OK 362 358 375 361 391 C2' C A 16 OK OK 393 389 406 392 422 C2' G A 17 OK OK 424 420 440 423 456 C2' G A 18 OK OK 458 454 474 457 490 C2' A A 19 OK OK 492 488 507 491 523 C2' G A 20 OK OK 525 521 541 524 557 C2' A A 21 OK OK 559 555 574 558 590 C2' A A 22 OK OK 592 588 607 591 623 C2' A A 23 OK OK 625 621 640 624 656 C2' C A 24 OK OK 658 654 671 657 687 C2' A A 25 OK OK 689 685 704 688 720 C2' A A 26 OK OK 722 718 737 721 753 C2' A A 27 OK OK 755 751 770 754 786 C2' G A 28 OK OK 788 784 804 787 820 C2' U A 29 OK OK 822 818 835 821 850 C2' C A 30 OK OK 852 848 865 851 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U A 4 OK OK 6 24 9 10 38 C3' C A 5 OK OK 36 54 39 40 69 C3' C A 6 OK OK 67 85 70 71 100 C3' G A 7 OK OK 98 119 101 102 134 C3' G A 8 OK OK 132 153 135 136 168 C3' U A 9 OK OK 166 184 169 170 198 C3' CH A 10 OK OK 196 214 199 200 230 C3' G A 11 OK OK 228 249 231 232 264 C3' A A 12 OK OK 262 282 265 266 297 C3' C A 13 OK OK 295 313 298 299 328 C3' U A 14 OK OK 326 344 329 330 358 C3' C A 15 OK OK 356 374 359 360 389 C3' C A 16 OK OK 387 405 390 391 420 C3' G A 17 OK OK 418 439 421 422 454 C3' G A 18 OK OK 452 473 455 456 488 C3' A A 19 OK OK 486 506 489 490 521 C3' G A 20 OK OK 519 540 522 523 555 C3' A A 21 OK OK 553 573 556 557 588 C3' A A 22 OK OK 586 606 589 590 621 C3' A A 23 OK OK 619 639 622 623 654 C3' C A 24 OK OK 652 670 655 656 685 C3' A A 25 OK OK 683 703 686 687 718 C3' A A 26 OK OK 716 736 719 720 751 C3' A A 27 OK OK 749 769 752 753 784 C3' G A 28 OK OK 782 803 785 786 818 C3' U A 29 OK OK 816 834 819 820 848 C3' C A 30 OK OK 846 864 849 850 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U A 4 OK OK 8 23 5 7 36 C4' C A 5 OK OK 38 53 35 37 67 C4' C A 6 OK OK 69 84 66 68 98 C4' G A 7 OK OK 100 118 97 99 132 C4' G A 8 OK OK 134 152 131 133 166 C4' U A 9 OK OK 168 183 165 167 196 C4' CH A 10 OK OK 198 213 195 197 228 C4' G A 11 OK OK 230 248 227 229 262 C4' A A 12 OK OK 264 281 261 263 295 C4' C A 13 OK OK 297 312 294 296 326 C4' U A 14 OK OK 328 343 325 327 356 C4' C A 15 OK OK 358 373 355 357 387 C4' C A 16 OK OK 389 404 386 388 418 C4' G A 17 OK OK 420 438 417 419 452 C4' G A 18 OK OK 454 472 451 453 486 C4' A A 19 OK OK 488 505 485 487 519 C4' G A 20 OK OK 521 539 518 520 553 C4' A A 21 OK OK 555 572 552 554 586 C4' A A 22 OK OK 588 605 585 587 619 C4' A A 23 OK OK 621 638 618 620 652 C4' C A 24 OK OK 654 669 651 653 683 C4' A A 25 OK OK 685 702 682 684 716 C4' A A 26 OK OK 718 735 715 717 749 C4' A A 27 OK OK 751 768 748 750 782 C4' G A 28 OK OK 784 802 781 783 816 C4' U A 29 OK OK 818 833 815 817 846 C4' C A 30 OK OK 848 863 845 847 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U A 4 OK OK 4 21 22 6 35 C5' C A 5 OK OK 34 51 52 36 66 C5' C A 6 OK OK 65 82 83 67 97 C5' G A 7 OK OK 96 116 117 98 131 C5' G A 8 OK OK 130 150 151 132 165 C5' U A 9 OK OK 164 181 182 166 195 C5' CH A 10 OK OK 194 211 212 196 227 C5' G A 11 OK OK 226 246 247 228 261 C5' A A 12 OK OK 260 279 280 262 294 C5' C A 13 OK OK 293 310 311 295 325 C5' U A 14 OK OK 324 341 342 326 355 C5' C A 15 OK OK 354 371 372 356 386 C5' C A 16 OK OK 385 402 403 387 417 C5' G A 17 OK OK 416 436 437 418 451 C5' G A 18 OK OK 450 470 471 452 485 C5' A A 19 OK OK 484 503 504 486 518 C5' G A 20 OK OK 517 537 538 519 552 C5' A A 21 OK OK 551 570 571 553 585 C5' A A 22 OK OK 584 603 604 586 618 C5' A A 23 OK OK 617 636 637 619 651 C5' C A 24 OK OK 650 667 668 652 682 C5' A A 25 OK OK 681 700 701 683 715 C5' A A 26 OK OK 714 733 734 716 748 C5' A A 27 OK OK 747 766 767 749 781 C5' G A 28 OK OK 780 800 801 782 815 C5' U A 29 OK OK 814 831 832 816 845 C5' C A 30 OK OK 844 861 862 846 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U A 4 OK OK 2 3 4 31 P C A 5 distorted distorted 9 32 33 34 62 P C A 6 distorted distorted 39 63 64 65 93 P G A 7 distorted distorted 70 94 95 96 127 P G A 8 distorted distorted 101 128 129 130 161 P U A 9 distorted distorted 135 162 163 164 191 P CH A 10 distorted distorted 169 192 193 194 223 P G A 11 distorted distorted 199 224 225 226 257 P A A 12 distorted distorted 231 258 259 260 290 P C A 13 distorted distorted 265 291 292 293 321 P U A 14 distorted distorted 298 322 323 324 351 P C A 15 distorted distorted 329 352 353 354 382 P C A 16 distorted distorted 359 383 384 385 413 P G A 17 distorted distorted 390 414 415 416 447 P G A 18 distorted distorted 421 448 449 450 481 P A A 19 distorted distorted 455 482 483 484 514 P G A 20 distorted distorted 489 515 516 517 548 P A A 21 distorted distorted 522 549 550 551 581 P A A 22 distorted distorted 556 582 583 584 614 P A A 23 distorted distorted 589 615 616 617 647 P C A 24 distorted distorted 622 648 649 650 678 P A A 25 distorted distorted 655 679 680 681 711 P A A 26 distorted distorted 686 712 713 714 744 P A A 27 distorted distorted 719 745 746 747 777 P G A 28 distorted distorted 752 778 779 780 811 P U A 29 distorted distorted 785 812 813 814 841 P C A 30 distorted distorted 819 842 843 844 ---------------------------------------------------------------------------------