ID code: '1AC3' 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' DC A 1 alpha beta 4 23 9 7 39 C1' DG A 2 alpha beta 35 57 40 38 72 C1' DC A 3 alpha beta 68 87 73 71 102 C1' DG A 4 alpha beta 98 120 103 101 135 C1' DT A 5 alpha beta 131 151 136 134 167 C1' TSP A 6 alpha beta 163 183 168 166 197 C1' TCP A 7 alpha beta 193 215 198 196 231 C1' DT A 8 alpha beta 227 247 232 230 263 C1' DG A 9 alpha beta 259 281 264 262 296 C1' DC A 10 alpha beta 292 311 297 295 326 C1' DG A 11 alpha beta 322 344 327 325 359 C1' DC A 12 alpha beta 355 375 360 358 389 C1' G B 13 alpha beta 384 407 390 387 424 C1' C B 14 alpha beta 419 439 425 422 455 C1' G B 15 alpha beta 450 473 456 453 489 C1' C B 16 alpha beta 484 504 490 487 520 C1' A B 17 alpha beta 515 537 521 518 553 C1' A B 18 alpha beta 548 570 554 551 586 C1' A B 19 alpha beta 581 603 587 584 619 C1' A B 20 alpha beta 614 636 620 617 652 C1' C B 21 alpha beta 647 667 653 650 683 C1' G B 22 alpha beta 678 701 684 681 717 C1' C B 23 alpha beta 712 732 718 715 748 C1' G B 24 alpha beta 743 767 749 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DC A 1 OK OK 8 5 21 22 38 C2' DG A 2 OK OK 39 36 55 56 71 C2' DC A 3 OK OK 72 69 85 86 101 C2' DG A 4 OK OK 102 99 118 119 134 C2' DT A 5 OK OK 135 132 149 150 166 C2' TSP A 6 OK OK 167 164 181 182 196 C2' TCP A 7 OK OK 197 194 213 214 230 C2' DT A 8 OK OK 231 228 245 246 262 C2' DG A 9 OK OK 263 260 279 280 295 C2' DC A 10 OK OK 296 293 309 310 325 C2' DG A 11 OK OK 326 323 342 343 358 C2' DC A 12 OK OK 359 356 373 374 387 C2' G B 13 OK OK 389 385 405 388 422 C2' C B 14 OK OK 424 420 437 423 453 C2' G B 15 OK OK 455 451 471 454 487 C2' C B 16 OK OK 489 485 502 488 518 C2' A B 17 OK OK 520 516 535 519 551 C2' A B 18 OK OK 553 549 568 552 584 C2' A B 19 OK OK 586 582 601 585 617 C2' A B 20 OK OK 619 615 634 618 650 C2' C B 21 OK OK 652 648 665 651 681 C2' G B 22 OK OK 683 679 699 682 715 C2' C B 23 OK OK 717 713 730 716 746 C2' G B 24 OK OK 748 744 765 747 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC A 1 OK OK 3 20 6 7 36 C3' DG A 2 OK OK 34 54 37 38 69 C3' DC A 3 OK OK 67 84 70 71 99 C3' DG A 4 OK OK 97 117 100 101 132 C3' DT A 5 OK OK 130 148 133 134 164 C3' TSP A 6 OK 162 180 166 194 C3' TCP A 7 OK OK 192 212 195 196 228 C3' DT A 8 OK OK 226 244 229 230 260 C3' DG A 9 OK OK 258 278 261 262 293 C3' DC A 10 OK OK 291 308 294 295 323 C3' DG A 11 OK OK 321 341 324 325 356 C3' DC A 12 OK OK 354 371 357 358 385 C3' G B 13 OK OK 383 404 386 387 420 C3' C B 14 OK OK 418 436 421 422 451 C3' G B 15 OK OK 449 470 452 453 485 C3' C B 16 OK OK 483 501 486 487 516 C3' A B 17 OK OK 514 534 517 518 549 C3' A B 18 OK OK 547 567 550 551 582 C3' A B 19 OK OK 580 600 583 584 615 C3' A B 20 OK OK 613 633 616 617 648 C3' C B 21 OK OK 646 664 649 650 679 C3' G B 22 OK OK 677 698 680 681 713 C3' C B 23 OK OK 711 729 714 715 744 C3' G B 24 OK OK 742 763 745 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC A 1 OK OK 5 19 2 4 34 C4' DG A 2 OK OK 36 53 33 35 67 C4' DC A 3 OK OK 69 83 66 68 97 C4' DG A 4 OK OK 99 116 96 98 130 C4' DT A 5 OK OK 132 147 129 131 162 C4' TSP A 6 OK OK 164 179 161 163 192 C4' TCP A 7 OK OK 194 211 191 193 226 C4' DT A 8 OK OK 228 243 225 227 258 C4' DG A 9 OK OK 260 277 257 259 291 C4' DC A 10 OK OK 293 307 290 292 321 C4' DG A 11 OK OK 323 340 320 322 354 C4' DC A 12 OK OK 356 370 353 355 383 C4' G B 13 OK OK 385 403 382 384 418 C4' C B 14 OK OK 420 435 417 419 449 C4' G B 15 OK OK 451 469 448 450 483 C4' C B 16 OK OK 485 500 482 484 514 C4' A B 17 OK OK 516 533 513 515 547 C4' A B 18 OK OK 549 566 546 548 580 C4' A B 19 OK OK 582 599 579 581 613 C4' A B 20 OK OK 615 632 612 614 646 C4' C B 21 OK OK 648 663 645 647 677 C4' G B 22 OK OK 679 697 676 678 711 C4' C B 23 OK OK 713 728 710 712 742 C4' G B 24 OK OK 744 762 741 743 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC A 1 OK OK 1 17 18 3 33 C5' DG A 2 OK OK 32 51 52 34 66 C5' DC A 3 OK OK 65 81 82 67 96 C5' DG A 4 OK OK 95 114 115 97 129 C5' DT A 5 OK OK 128 145 146 130 161 C5' TSP A 6 OK OK 160 177 178 162 191 C5' TCP A 7 OK OK 190 209 210 192 225 C5' DT A 8 OK OK 224 241 242 226 257 C5' DG A 9 OK OK 256 275 276 258 290 C5' DC A 10 OK OK 289 305 306 291 320 C5' DG A 11 OK OK 319 338 339 321 353 C5' DC A 12 OK OK 352 368 369 354 382 C5' G B 13 OK OK 381 401 402 383 417 C5' C B 14 OK OK 416 433 434 418 448 C5' G B 15 OK OK 447 467 468 449 482 C5' C B 16 OK OK 481 498 499 483 513 C5' A B 17 OK OK 512 531 532 514 546 C5' A B 18 OK OK 545 564 565 547 579 C5' A B 19 OK OK 578 597 598 580 612 C5' A B 20 OK OK 611 630 631 613 645 C5' C B 21 OK OK 644 661 662 646 676 C5' G B 22 OK OK 675 695 696 677 710 C5' C B 23 OK OK 709 726 727 711 741 C5' G B 24 OK OK 740 760 761 742 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P DG A 2 distorted distorted 6 30 31 32 62 P DC A 3 distorted distorted 37 63 64 65 92 P DG A 4 distorted distorted 70 93 94 95 125 P DT A 5 distorted distorted 100 126 127 128 157 P TSP A 6 distorted distorted 133 158 159 160 221 P DT A 8 distorted distorted 195 222 223 224 253 P DG A 9 distorted distorted 229 254 255 256 286 P DC A 10 distorted distorted 261 287 288 289 316 P DG A 11 distorted distorted 294 317 318 319 349 P DC A 12 distorted distorted 324 350 351 352 413 P C B 14 distorted distorted 386 414 415 416 444 P G B 15 distorted distorted 421 445 446 447 478 P C B 16 distorted distorted 452 479 480 481 509 P A B 17 distorted distorted 486 510 511 512 542 P A B 18 distorted distorted 517 543 544 545 575 P A B 19 distorted distorted 550 576 577 578 608 P A B 20 distorted distorted 583 609 610 611 641 P C B 21 distorted distorted 616 642 643 644 672 P G B 22 distorted distorted 649 673 674 675 706 P C B 23 distorted distorted 680 707 708 709 737 P G B 24 distorted distorted 714 738 739 740 ---------------------------------------------------------------------------------