ID code: '1LB2' 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 M 33 beta 4 9 7 27 C1' T M 32 beta 23 28 26 47 C1' T M 31 beta 43 48 46 67 C1' T M 30 beta 63 68 66 87 C1' T M 29 beta 83 88 86 107 C1' T M 28 beta 103 108 106 127 C1' T M 27 beta 123 128 126 147 C1' C M 26 beta 143 148 146 166 C1' C M 25 beta 162 167 165 185 C1' T M 24 beta 181 186 184 205 C1' A M 23 beta 201 206 204 226 C1' A M 22 beta 222 227 225 247 C1' A M 21 beta 243 248 246 268 C1' A M 20 beta 264 269 267 289 C1' T M 19 beta 285 290 288 309 C1' G M 18 beta 305 310 308 331 C1' T M 17 beta 327 332 330 351 C1' G M 16 beta 347 352 350 373 C1' A M 15 beta 369 374 372 394 C1' T M 14 beta 390 395 393 415 C1' A L 14 beta 411 416 414 436 C1' T L 15 beta 432 437 435 456 C1' C L 16 beta 452 457 455 475 C1' A L 17 beta 471 476 474 496 C1' C L 18 beta 492 497 495 515 C1' A L 19 beta 511 516 514 536 C1' T L 20 beta 532 537 535 556 C1' T L 21 beta 552 557 555 576 C1' T L 22 beta 572 577 575 596 C1' T L 23 beta 592 597 595 616 C1' A L 24 beta 612 617 615 637 C1' G L 25 beta 633 638 636 659 C1' G L 26 beta 655 660 658 681 C1' A L 27 beta 677 682 680 702 C1' A L 28 beta 698 703 701 723 C1' A L 29 beta 719 724 722 744 C1' A L 30 beta 740 745 743 765 C1' A L 31 beta 761 766 764 786 C1' A L 32 beta 782 787 785 807 C1' G L 33 beta 803 808 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C M 33 8 5 26 C2' T M 32 27 24 46 C2' T M 31 47 44 66 C2' T M 30 67 64 86 C2' T M 29 87 84 106 C2' T M 28 107 104 126 C2' T M 27 127 124 146 C2' C M 26 147 144 165 C2' C M 25 166 163 184 C2' T M 24 185 182 204 C2' A M 23 205 202 225 C2' A M 22 226 223 246 C2' A M 21 247 244 267 C2' A M 20 268 265 288 C2' T M 19 289 286 308 C2' G M 18 309 306 330 C2' T M 17 331 328 350 C2' G M 16 351 348 372 C2' A M 15 373 370 393 C2' T M 14 394 391 414 C2' A L 14 415 412 435 C2' T L 15 436 433 455 C2' C L 16 456 453 474 C2' A L 17 475 472 495 C2' C L 18 496 493 514 C2' A L 19 515 512 535 C2' T L 20 536 533 555 C2' T L 21 556 553 575 C2' T L 22 576 573 595 C2' T L 23 596 593 615 C2' A L 24 616 613 636 C2' G L 25 637 634 658 C2' G L 26 659 656 680 C2' A L 27 681 678 701 C2' A L 28 702 699 722 C2' A L 29 723 720 743 C2' A L 30 744 741 764 C2' A L 31 765 762 785 C2' A L 32 786 783 806 C2' G L 33 807 804 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C M 33 OK 3 6 7 24 C3' T M 32 OK 22 25 26 44 C3' T M 31 OK 42 45 46 64 C3' T M 30 OK 62 65 66 84 C3' T M 29 OK 82 85 86 104 C3' T M 28 OK 102 105 106 124 C3' T M 27 OK 122 125 126 144 C3' C M 26 OK 142 145 146 163 C3' C M 25 OK 161 164 165 182 C3' T M 24 OK 180 183 184 202 C3' A M 23 OK 200 203 204 223 C3' A M 22 OK 221 224 225 244 C3' A M 21 OK 242 245 246 265 C3' A M 20 OK 263 266 267 286 C3' T M 19 OK 284 287 288 306 C3' G M 18 OK 304 307 308 328 C3' T M 17 OK 326 329 330 348 C3' G M 16 OK 346 349 350 370 C3' A M 15 OK 368 371 372 391 C3' T M 14 OK 389 392 393 412 C3' A L 14 OK 410 413 414 433 C3' T L 15 OK 431 434 435 453 C3' C L 16 OK 451 454 455 472 C3' A L 17 OK 470 473 474 493 C3' C L 18 OK 491 494 495 512 C3' A L 19 OK 510 513 514 533 C3' T L 20 OK 531 534 535 553 C3' T L 21 OK 551 554 555 573 C3' T L 22 OK 571 574 575 593 C3' T L 23 OK 591 594 595 613 C3' A L 24 OK 611 614 615 634 C3' G L 25 OK 632 635 636 656 C3' G L 26 OK 654 657 658 678 C3' A L 27 OK 676 679 680 699 C3' A L 28 OK 697 700 701 720 C3' A L 29 OK 718 721 722 741 C3' A L 30 OK 739 742 743 762 C3' A L 31 OK 760 763 764 783 C3' A L 32 OK 781 784 785 804 C3' G L 33 OK 802 805 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C M 33 OK 5 2 4 22 C4' T M 32 OK 24 21 23 42 C4' T M 31 OK 44 41 43 62 C4' T M 30 OK 64 61 63 82 C4' T M 29 OK 84 81 83 102 C4' T M 28 OK 104 101 103 122 C4' T M 27 OK 124 121 123 142 C4' C M 26 OK 144 141 143 161 C4' C M 25 OK 163 160 162 180 C4' T M 24 OK 182 179 181 200 C4' A M 23 OK 202 199 201 221 C4' A M 22 OK 223 220 222 242 C4' A M 21 OK 244 241 243 263 C4' A M 20 OK 265 262 264 284 C4' T M 19 OK 286 283 285 304 C4' G M 18 OK 306 303 305 326 C4' T M 17 OK 328 325 327 346 C4' G M 16 OK 348 345 347 368 C4' A M 15 OK 370 367 369 389 C4' T M 14 OK 391 388 390 410 C4' A L 14 OK 412 409 411 431 C4' T L 15 OK 433 430 432 451 C4' C L 16 OK 453 450 452 470 C4' A L 17 OK 472 469 471 491 C4' C L 18 OK 493 490 492 510 C4' A L 19 OK 512 509 511 531 C4' T L 20 OK 533 530 532 551 C4' T L 21 OK 553 550 552 571 C4' T L 22 OK 573 570 572 591 C4' T L 23 OK 593 590 592 611 C4' A L 24 OK 613 610 612 632 C4' G L 25 OK 634 631 633 654 C4' G L 26 OK 656 653 655 676 C4' A L 27 OK 678 675 677 697 C4' A L 28 OK 699 696 698 718 C4' A L 29 OK 720 717 719 739 C4' A L 30 OK 741 738 740 760 C4' A L 31 OK 762 759 761 781 C4' A L 32 OK 783 780 782 802 C4' G L 33 OK 804 801 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C M 33 1 3 21 C5' T M 32 20 22 41 C5' T M 31 40 42 61 C5' T M 30 60 62 81 C5' T M 29 80 82 101 C5' T M 28 100 102 121 C5' T M 27 120 122 141 C5' C M 26 140 142 160 C5' C M 25 159 161 179 C5' T M 24 178 180 199 C5' A M 23 198 200 220 C5' A M 22 219 221 241 C5' A M 21 240 242 262 C5' A M 20 261 263 283 C5' T M 19 282 284 303 C5' G M 18 302 304 325 C5' T M 17 324 326 345 C5' G M 16 344 346 367 C5' A M 15 366 368 388 C5' T M 14 387 389 409 C5' A L 14 408 410 430 C5' T L 15 429 431 450 C5' C L 16 449 451 469 C5' A L 17 468 470 490 C5' C L 18 489 491 509 C5' A L 19 508 510 530 C5' T L 20 529 531 550 C5' T L 21 549 551 570 C5' T L 22 569 571 590 C5' T L 23 589 591 610 C5' A L 24 609 611 631 C5' G L 25 630 632 653 C5' G L 26 652 654 675 C5' A L 27 674 676 696 C5' A L 28 695 697 717 C5' A L 29 716 718 738 C5' A L 30 737 739 759 C5' A L 31 758 760 780 C5' A L 32 779 781 801 C5' G L 33 800 802 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P T M 32 distorted distorted 6 18 19 20 37 P T M 31 distorted distorted 25 38 39 40 57 P T M 30 distorted distorted 45 58 59 60 77 P T M 29 distorted distorted 65 78 79 80 97 P T M 28 distorted distorted 85 98 99 100 117 P T M 27 distorted distorted 105 118 119 120 137 P C M 26 distorted distorted 125 138 139 140 156 P C M 25 distorted distorted 145 157 158 159 175 P T M 24 distorted distorted 164 176 177 178 195 P A M 23 distorted distorted 183 196 197 198 216 P A M 22 distorted distorted 203 217 218 219 237 P A M 21 distorted distorted 224 238 239 240 258 P A M 20 distorted distorted 245 259 260 261 279 P T M 19 distorted distorted 266 280 281 282 299 P G M 18 distorted distorted 287 300 301 302 321 P T M 17 distorted distorted 307 322 323 324 341 P G M 16 distorted distorted 329 342 343 344 363 P A M 15 distorted distorted 349 364 365 366 384 P T M 14 distorted distorted 371 385 386 387 405 P A L 14 distorted distorted 406 407 408 426 P T L 15 distorted distorted 413 427 428 429 446 P C L 16 distorted distorted 434 447 448 449 465 P A L 17 distorted distorted 454 466 467 468 486 P C L 18 distorted distorted 473 487 488 489 505 P A L 19 distorted distorted 494 506 507 508 526 P T L 20 distorted distorted 513 527 528 529 546 P T L 21 distorted distorted 534 547 548 549 566 P T L 22 distorted distorted 554 567 568 569 586 P T L 23 distorted distorted 574 587 588 589 606 P A L 24 distorted distorted 594 607 608 609 627 P G L 25 distorted distorted 614 628 629 630 649 P G L 26 distorted distorted 635 650 651 652 671 P A L 27 distorted distorted 657 672 673 674 692 P A L 28 distorted distorted 679 693 694 695 713 P A L 29 distorted distorted 700 714 715 716 734 P A L 30 distorted distorted 721 735 736 737 755 P A L 31 distorted distorted 742 756 757 758 776 P A L 32 distorted distorted 763 777 778 779 797 P G L 33 distorted distorted 784 798 799 800 ---------------------------------------------------------------------------------