ID code: '1D66' 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 1 beta 4 9 7 27 C1' C D 2 beta 23 28 26 46 C1' G D 3 beta 42 47 45 68 C1' G D 4 beta 64 69 67 90 C1' A D 5 beta 86 91 89 111 C1' G D 6 beta 107 112 110 133 C1' G D 7 beta 129 134 132 155 C1' A D 8 beta 151 156 154 176 C1' C D 9 beta 172 177 175 195 C1' A D 10 beta 191 196 194 216 C1' G D 11 beta 212 217 215 238 C1' T D 12 beta 234 239 237 258 C1' C D 13 beta 254 259 257 277 C1' C D 14 beta 273 278 276 296 C1' T D 15 beta 292 297 295 316 C1' C D 16 beta 312 317 315 335 C1' C D 17 beta 331 336 334 354 C1' G D 18 beta 350 355 353 376 C1' G D 19 beta 372 377 375 396 C1' C E 20 beta 392 397 395 415 C1' C E 21 beta 411 416 414 434 C1' G E 22 beta 430 435 433 456 C1' G E 23 beta 452 457 455 478 C1' A E 24 beta 474 479 477 499 C1' G E 25 beta 495 500 498 521 C1' G E 26 beta 517 522 520 543 C1' A E 27 beta 539 544 542 564 C1' C E 28 beta 560 565 563 583 C1' T E 29 beta 579 584 582 603 C1' G E 30 beta 599 604 602 625 C1' T E 31 beta 621 626 624 645 C1' C E 32 beta 641 646 644 664 C1' C E 33 beta 660 665 663 683 C1' T E 34 beta 679 684 682 703 C1' C E 35 beta 699 704 702 722 C1' C E 36 beta 718 723 721 741 C1' G E 37 beta 737 742 740 763 C1' G E 38 beta 759 764 762 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C D 1 8 5 26 C2' C D 2 27 24 45 C2' G D 3 46 43 67 C2' G D 4 68 65 89 C2' A D 5 90 87 110 C2' G D 6 111 108 132 C2' G D 7 133 130 154 C2' A D 8 155 152 175 C2' C D 9 176 173 194 C2' A D 10 195 192 215 C2' G D 11 216 213 237 C2' T D 12 238 235 257 C2' C D 13 258 255 276 C2' C D 14 277 274 295 C2' T D 15 296 293 315 C2' C D 16 316 313 334 C2' C D 17 335 332 353 C2' G D 18 354 351 375 C2' G D 19 376 373 395 C2' C E 20 396 393 414 C2' C E 21 415 412 433 C2' G E 22 434 431 455 C2' G E 23 456 453 477 C2' A E 24 478 475 498 C2' G E 25 499 496 520 C2' G E 26 521 518 542 C2' A E 27 543 540 563 C2' C E 28 564 561 582 C2' T E 29 583 580 602 C2' G E 30 603 600 624 C2' T E 31 625 622 644 C2' C E 32 645 642 663 C2' C E 33 664 661 682 C2' T E 34 683 680 702 C2' C E 35 703 700 721 C2' C E 36 722 719 740 C2' G E 37 741 738 762 C2' G E 38 763 760 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C D 1 OK 3 6 7 24 C3' C D 2 OK 22 25 26 43 C3' G D 3 OK 41 44 45 65 C3' G D 4 OK 63 66 67 87 C3' A D 5 OK 85 88 89 108 C3' G D 6 OK 106 109 110 130 C3' G D 7 OK 128 131 132 152 C3' A D 8 OK 150 153 154 173 C3' C D 9 OK 171 174 175 192 C3' A D 10 OK 190 193 194 213 C3' G D 11 OK 211 214 215 235 C3' T D 12 OK 233 236 237 255 C3' C D 13 OK 253 256 257 274 C3' C D 14 OK 272 275 276 293 C3' T D 15 OK 291 294 295 313 C3' C D 16 OK 311 314 315 332 C3' C D 17 OK 330 333 334 351 C3' G D 18 OK 349 352 353 373 C3' G D 19 OK 371 374 375 393 C3' C E 20 OK 391 394 395 412 C3' C E 21 OK 410 413 414 431 C3' G E 22 OK 429 432 433 453 C3' G E 23 OK 451 454 455 475 C3' A E 24 OK 473 476 477 496 C3' G E 25 OK 494 497 498 518 C3' G E 26 OK 516 519 520 540 C3' A E 27 OK 538 541 542 561 C3' C E 28 OK 559 562 563 580 C3' T E 29 OK 578 581 582 600 C3' G E 30 OK 598 601 602 622 C3' T E 31 OK 620 623 624 642 C3' C E 32 OK 640 643 644 661 C3' C E 33 OK 659 662 663 680 C3' T E 34 OK 678 681 682 700 C3' C E 35 OK 698 701 702 719 C3' C E 36 OK 717 720 721 738 C3' G E 37 OK 736 739 740 760 C3' G E 38 OK 758 761 762 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C D 1 OK 5 2 4 22 C4' C D 2 OK 24 21 23 41 C4' G D 3 OK 43 40 42 63 C4' G D 4 OK 65 62 64 85 C4' A D 5 OK 87 84 86 106 C4' G D 6 OK 108 105 107 128 C4' G D 7 OK 130 127 129 150 C4' A D 8 OK 152 149 151 171 C4' C D 9 OK 173 170 172 190 C4' A D 10 OK 192 189 191 211 C4' G D 11 OK 213 210 212 233 C4' T D 12 OK 235 232 234 253 C4' C D 13 OK 255 252 254 272 C4' C D 14 OK 274 271 273 291 C4' T D 15 OK 293 290 292 311 C4' C D 16 OK 313 310 312 330 C4' C D 17 OK 332 329 331 349 C4' G D 18 OK 351 348 350 371 C4' G D 19 OK 373 370 372 391 C4' C E 20 OK 393 390 392 410 C4' C E 21 OK 412 409 411 429 C4' G E 22 OK 431 428 430 451 C4' G E 23 OK 453 450 452 473 C4' A E 24 OK 475 472 474 494 C4' G E 25 OK 496 493 495 516 C4' G E 26 OK 518 515 517 538 C4' A E 27 OK 540 537 539 559 C4' C E 28 OK 561 558 560 578 C4' T E 29 OK 580 577 579 598 C4' G E 30 OK 600 597 599 620 C4' T E 31 OK 622 619 621 640 C4' C E 32 OK 642 639 641 659 C4' C E 33 OK 661 658 660 678 C4' T E 34 OK 680 677 679 698 C4' C E 35 OK 700 697 699 717 C4' C E 36 OK 719 716 718 736 C4' G E 37 OK 738 735 737 758 C4' G E 38 OK 760 757 759 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C D 1 1 3 21 C5' C D 2 20 22 40 C5' G D 3 39 41 62 C5' G D 4 61 63 84 C5' A D 5 83 85 105 C5' G D 6 104 106 127 C5' G D 7 126 128 149 C5' A D 8 148 150 170 C5' C D 9 169 171 189 C5' A D 10 188 190 210 C5' G D 11 209 211 232 C5' T D 12 231 233 252 C5' C D 13 251 253 271 C5' C D 14 270 272 290 C5' T D 15 289 291 310 C5' C D 16 309 311 329 C5' C D 17 328 330 348 C5' G D 18 347 349 370 C5' G D 19 369 371 390 C5' C E 20 389 391 409 C5' C E 21 408 410 428 C5' G E 22 427 429 450 C5' G E 23 449 451 472 C5' A E 24 471 473 493 C5' G E 25 492 494 515 C5' G E 26 514 516 537 C5' A E 27 536 538 558 C5' C E 28 557 559 577 C5' T E 29 576 578 597 C5' G E 30 596 598 619 C5' T E 31 618 620 639 C5' C E 32 638 640 658 C5' C E 33 657 659 677 C5' T E 34 676 678 697 C5' C E 35 696 698 716 C5' C E 36 715 717 735 C5' G E 37 734 736 757 C5' G E 38 756 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P C D 2 OK OK 6 18 19 20 36 P G D 3 OK OK 25 37 38 39 58 P G D 4 OK OK 44 59 60 61 80 P A D 5 OK OK 66 81 82 83 101 P G D 6 OK OK 88 102 103 104 123 P G D 7 OK OK 109 124 125 126 145 P A D 8 OK OK 131 146 147 148 166 P C D 9 OK OK 153 167 168 169 185 P A D 10 OK OK 174 186 187 188 206 P G D 11 OK OK 193 207 208 209 228 P T D 12 OK OK 214 229 230 231 248 P C D 13 OK OK 236 249 250 251 267 P C D 14 OK OK 256 268 269 270 286 P T D 15 OK OK 275 287 288 289 306 P C D 16 OK OK 294 307 308 309 325 P C D 17 OK OK 314 326 327 328 344 P G D 18 OK OK 333 345 346 347 366 P G D 19 OK OK 352 367 368 369 405 P C E 21 OK OK 394 406 407 408 424 P G E 22 OK OK 413 425 426 427 446 P G E 23 OK OK 432 447 448 449 468 P A E 24 OK OK 454 469 470 471 489 P G E 25 OK OK 476 490 491 492 511 P G E 26 OK OK 497 512 513 514 533 P A E 27 OK OK 519 534 535 536 554 P C E 28 OK OK 541 555 556 557 573 P T E 29 OK OK 562 574 575 576 593 P G E 30 distorted distorted 581 594 595 596 615 P T E 31 OK OK 601 616 617 618 635 P C E 32 OK OK 623 636 637 638 654 P C E 33 OK OK 643 655 656 657 673 P T E 34 OK OK 662 674 675 676 693 P C E 35 OK OK 681 694 695 696 712 P C E 36 OK OK 701 713 714 715 731 P G E 37 OK OK 720 732 733 734 753 P G E 38 distorted distorted 739 754 755 756 ---------------------------------------------------------------------------------