ID code: '1L3L' 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' G E 1 beta 4 9 7 30 C1' A E 2 beta 26 31 29 51 C1' T E 3 beta 47 52 50 71 C1' G E 4 beta 67 72 70 93 C1' T E 5 beta 89 94 92 113 C1' G E 6 beta 109 114 112 135 C1' C E 7 beta 131 136 134 154 C1' A E 8 beta 150 155 153 175 C1' G E 9 beta 171 176 174 197 C1' A E 10 beta 193 198 196 218 C1' T E 11 beta 214 219 217 238 C1' C E 12 beta 234 239 237 257 C1' T E 13 beta 253 258 256 277 C1' G E 14 beta 273 278 276 299 C1' C E 15 beta 295 300 298 318 C1' A E 16 beta 314 319 317 339 C1' C E 17 beta 335 340 338 358 C1' A E 18 beta 354 359 357 379 C1' T E 19 beta 375 380 378 399 C1' C E 20 beta 395 400 398 416 C1' G G 1 beta 412 417 415 438 C1' A G 2 beta 434 439 437 459 C1' T G 3 beta 455 460 458 479 C1' G G 4 beta 475 480 478 501 C1' T G 5 beta 497 502 500 521 C1' G G 6 beta 517 522 520 543 C1' C G 7 beta 539 544 542 562 C1' A G 8 beta 558 563 561 583 C1' G G 9 beta 579 584 582 605 C1' A G 10 beta 601 606 604 626 C1' T G 11 beta 622 627 625 646 C1' C G 12 beta 642 647 645 665 C1' T G 13 beta 661 666 664 685 C1' G G 14 beta 681 686 684 707 C1' C G 15 beta 703 708 706 726 C1' A G 16 beta 722 727 725 747 C1' C G 17 beta 743 748 746 766 C1' A G 18 beta 762 767 765 787 C1' T G 19 beta 783 788 786 807 C1' C G 20 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' G E 1 8 5 29 C2' A E 2 30 27 50 C2' T E 3 51 48 70 C2' G E 4 71 68 92 C2' T E 5 93 90 112 C2' G E 6 113 110 134 C2' C E 7 135 132 153 C2' A E 8 154 151 174 C2' G E 9 175 172 196 C2' A E 10 197 194 217 C2' T E 11 218 215 237 C2' C E 12 238 235 256 C2' T E 13 257 254 276 C2' G E 14 277 274 298 C2' C E 15 299 296 317 C2' A E 16 318 315 338 C2' C E 17 339 336 357 C2' A E 18 358 355 378 C2' T E 19 379 376 398 C2' C E 20 399 396 415 C2' G G 1 416 413 437 C2' A G 2 438 435 458 C2' T G 3 459 456 478 C2' G G 4 479 476 500 C2' T G 5 501 498 520 C2' G G 6 521 518 542 C2' C G 7 543 540 561 C2' A G 8 562 559 582 C2' G G 9 583 580 604 C2' A G 10 605 602 625 C2' T G 11 626 623 645 C2' C G 12 646 643 664 C2' T G 13 665 662 684 C2' G G 14 685 682 706 C2' C G 15 707 704 725 C2' A G 16 726 723 746 C2' C G 17 747 744 765 C2' A G 18 766 763 786 C2' T G 19 787 784 806 C2' C G 20 807 804 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G E 1 OK 3 6 7 27 C3' A E 2 OK 25 28 29 48 C3' T E 3 OK 46 49 50 68 C3' G E 4 OK 66 69 70 90 C3' T E 5 OK 88 91 92 110 C3' G E 6 OK 108 111 112 132 C3' C E 7 OK 130 133 134 151 C3' A E 8 OK 149 152 153 172 C3' G E 9 OK 170 173 174 194 C3' A E 10 OK 192 195 196 215 C3' T E 11 OK 213 216 217 235 C3' C E 12 OK 233 236 237 254 C3' T E 13 OK 252 255 256 274 C3' G E 14 OK 272 275 276 296 C3' C E 15 OK 294 297 298 315 C3' A E 16 OK 313 316 317 336 C3' C E 17 OK 334 337 338 355 C3' A E 18 OK 353 356 357 376 C3' T E 19 OK 374 377 378 396 C3' C E 20 OK 394 397 398 413 C3' G G 1 OK 411 414 415 435 C3' A G 2 OK 433 436 437 456 C3' T G 3 OK 454 457 458 476 C3' G G 4 OK 474 477 478 498 C3' T G 5 OK 496 499 500 518 C3' G G 6 OK 516 519 520 540 C3' C G 7 OK 538 541 542 559 C3' A G 8 OK 557 560 561 580 C3' G G 9 OK 578 581 582 602 C3' A G 10 OK 600 603 604 623 C3' T G 11 OK 621 624 625 643 C3' C G 12 OK 641 644 645 662 C3' T G 13 OK 660 663 664 682 C3' G G 14 OK 680 683 684 704 C3' C G 15 OK 702 705 706 723 C3' A G 16 OK 721 724 725 744 C3' C G 17 OK 742 745 746 763 C3' A G 18 OK 761 764 765 784 C3' T G 19 OK 782 785 786 804 C3' C G 20 OK 802 805 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G E 1 OK 5 2 4 25 C4' A E 2 OK 27 24 26 46 C4' T E 3 OK 48 45 47 66 C4' G E 4 OK 68 65 67 88 C4' T E 5 OK 90 87 89 108 C4' G E 6 OK 110 107 109 130 C4' C E 7 OK 132 129 131 149 C4' A E 8 OK 151 148 150 170 C4' G E 9 OK 172 169 171 192 C4' A E 10 OK 194 191 193 213 C4' T E 11 OK 215 212 214 233 C4' C E 12 OK 235 232 234 252 C4' T E 13 OK 254 251 253 272 C4' G E 14 OK 274 271 273 294 C4' C E 15 OK 296 293 295 313 C4' A E 16 OK 315 312 314 334 C4' C E 17 OK 336 333 335 353 C4' A E 18 OK 355 352 354 374 C4' T E 19 OK 376 373 375 394 C4' C E 20 OK 396 393 395 411 C4' G G 1 OK 413 410 412 433 C4' A G 2 OK 435 432 434 454 C4' T G 3 OK 456 453 455 474 C4' G G 4 OK 476 473 475 496 C4' T G 5 OK 498 495 497 516 C4' G G 6 OK 518 515 517 538 C4' C G 7 OK 540 537 539 557 C4' A G 8 OK 559 556 558 578 C4' G G 9 OK 580 577 579 600 C4' A G 10 OK 602 599 601 621 C4' T G 11 OK 623 620 622 641 C4' C G 12 OK 643 640 642 660 C4' T G 13 OK 662 659 661 680 C4' G G 14 OK 682 679 681 702 C4' C G 15 OK 704 701 703 721 C4' A G 16 OK 723 720 722 742 C4' C G 17 OK 744 741 743 761 C4' A G 18 OK 763 760 762 782 C4' T G 19 OK 784 781 783 802 C4' C G 20 OK 804 801 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G E 1 1 3 24 C5' A E 2 23 25 45 C5' T E 3 44 46 65 C5' G E 4 64 66 87 C5' T E 5 86 88 107 C5' G E 6 106 108 129 C5' C E 7 128 130 148 C5' A E 8 147 149 169 C5' G E 9 168 170 191 C5' A E 10 190 192 212 C5' T E 11 211 213 232 C5' C E 12 231 233 251 C5' T E 13 250 252 271 C5' G E 14 270 272 293 C5' C E 15 292 294 312 C5' A E 16 311 313 333 C5' C E 17 332 334 352 C5' A E 18 351 353 373 C5' T E 19 372 374 393 C5' C E 20 392 394 410 C5' G G 1 409 411 432 C5' A G 2 431 433 453 C5' T G 3 452 454 473 C5' G G 4 472 474 495 C5' T G 5 494 496 515 C5' G G 6 514 516 537 C5' C G 7 536 538 556 C5' A G 8 555 557 577 C5' G G 9 576 578 599 C5' A G 10 598 600 620 C5' T G 11 619 621 640 C5' C G 12 639 641 659 C5' T G 13 658 660 679 C5' G G 14 678 680 701 C5' C G 15 700 702 720 C5' A G 16 719 721 741 C5' C G 17 740 742 760 C5' A G 18 759 761 781 C5' T G 19 780 782 801 C5' C G 20 800 802 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A E 2 distorted distorted 6 21 22 23 41 P T E 3 distorted distorted 28 42 43 44 61 P G E 4 distorted distorted 49 62 63 64 83 P T E 5 distorted distorted 69 84 85 86 103 P G E 6 distorted distorted 91 104 105 106 125 P C E 7 distorted distorted 111 126 127 128 144 P A E 8 distorted distorted 133 145 146 147 165 P G E 9 distorted distorted 152 166 167 168 187 P A E 10 distorted distorted 173 188 189 190 208 P T E 11 distorted distorted 195 209 210 211 228 P C E 12 distorted distorted 216 229 230 231 247 P T E 13 distorted distorted 236 248 249 250 267 P G E 14 distorted distorted 255 268 269 270 289 P C E 15 distorted distorted 275 290 291 292 308 P A E 16 distorted distorted 297 309 310 311 329 P C E 17 distorted distorted 316 330 331 332 348 P A E 18 distorted distorted 337 349 350 351 369 P T E 19 distorted distorted 356 370 371 372 389 P C E 20 distorted distorted 377 390 391 392 428 P A G 2 distorted distorted 414 429 430 431 449 P T G 3 distorted distorted 436 450 451 452 469 P G G 4 distorted distorted 457 470 471 472 491 P T G 5 distorted distorted 477 492 493 494 511 P G G 6 distorted distorted 499 512 513 514 533 P C G 7 distorted distorted 519 534 535 536 552 P A G 8 distorted distorted 541 553 554 555 573 P G G 9 distorted distorted 560 574 575 576 595 P A G 10 distorted distorted 581 596 597 598 616 P T G 11 distorted distorted 603 617 618 619 636 P C G 12 distorted distorted 624 637 638 639 655 P T G 13 distorted distorted 644 656 657 658 675 P G G 14 distorted distorted 663 676 677 678 697 P C G 15 distorted distorted 683 698 699 700 716 P A G 16 distorted distorted 705 717 718 719 737 P C G 17 distorted distorted 724 738 739 740 756 P A G 18 distorted distorted 745 757 758 759 777 P T G 19 distorted distorted 764 778 779 780 797 P C G 20 distorted distorted 785 798 799 800 ---------------------------------------------------------------------------------