ID code: '1ELH' 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' --------------------------------------------------------------------------------- 9 C1' U A -1 alpha beta 4 24 10 7 40 C1' U A 1 alpha beta 35 55 41 38 70 C1' G A 2 alpha beta 65 88 71 68 104 C1' C A 3 alpha beta 99 119 105 102 135 C1' C A 4 alpha beta 130 150 136 133 166 C1' U A 5 alpha beta 161 181 167 164 196 C1' G A 6 alpha beta 191 214 197 194 230 C1' G A 7 alpha beta 225 248 231 228 264 C1' C A 8 alpha beta 259 279 265 262 295 C1' G A 9 alpha beta 290 313 296 293 329 C1' G A 10 alpha beta 324 347 330 327 363 C1' C A 11 alpha beta 358 379 364 361 393 C1' A B 8 alpha beta 388 410 394 391 427 C1' A B 9 alpha beta 422 444 428 425 460 C1' C B 10 alpha beta 455 475 461 458 491 C1' U B 11 alpha beta 486 506 492 489 521 C1' G B 12 alpha beta 516 539 522 519 555 C1' C B 13 alpha beta 550 570 556 553 586 C1' C B 14 alpha beta 581 601 587 584 617 C1' A B 15 alpha beta 612 634 618 615 650 C1' G B 16 alpha beta 645 668 651 648 684 C1' G B 17 alpha beta 679 702 685 682 718 C1' C B 18 alpha beta 713 733 719 716 749 C1' A B 19 alpha beta 744 766 750 747 782 C1' U B 20 alpha beta 777 798 783 780 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A -1 OK OK 9 5 22 8 38 C2' U A 1 OK OK 40 36 53 39 68 C2' G A 2 OK OK 70 66 86 69 102 C2' C A 3 OK OK 104 100 117 103 133 C2' C A 4 OK OK 135 131 148 134 164 C2' U A 5 OK OK 166 162 179 165 194 C2' G A 6 OK OK 196 192 212 195 228 C2' G A 7 OK OK 230 226 246 229 262 C2' C A 8 OK OK 264 260 277 263 293 C2' G A 9 OK OK 295 291 311 294 327 C2' G A 10 OK OK 329 325 345 328 361 C2' C A 11 OK OK 363 359 377 362 391 C2' A B 8 OK OK 393 389 408 392 425 C2' A B 9 OK OK 427 423 442 426 458 C2' C B 10 OK OK 460 456 473 459 489 C2' U B 11 OK OK 491 487 504 490 519 C2' G B 12 OK OK 521 517 537 520 553 C2' C B 13 OK OK 555 551 568 554 584 C2' C B 14 OK OK 586 582 599 585 615 C2' A B 15 OK OK 617 613 632 616 648 C2' G B 16 OK OK 650 646 666 649 682 C2' G B 17 OK OK 684 680 700 683 716 C2' C B 18 OK OK 718 714 731 717 747 C2' A B 19 OK OK 749 745 764 748 780 C2' U B 20 OK OK 782 778 796 781 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A -1 OK OK 3 21 6 7 36 C3' U A 1 OK OK 34 52 37 38 66 C3' G A 2 OK OK 64 85 67 68 100 C3' C A 3 OK OK 98 116 101 102 131 C3' C A 4 OK OK 129 147 132 133 162 C3' U A 5 OK OK 160 178 163 164 192 C3' G A 6 OK OK 190 211 193 194 226 C3' G A 7 OK OK 224 245 227 228 260 C3' C A 8 OK OK 258 276 261 262 291 C3' G A 9 OK OK 289 310 292 293 325 C3' G A 10 OK OK 323 344 326 327 359 C3' C A 11 OK OK 357 375 360 361 389 C3' A B 8 OK OK 387 407 390 391 423 C3' A B 9 OK OK 421 441 424 425 456 C3' C B 10 OK OK 454 472 457 458 487 C3' U B 11 OK OK 485 503 488 489 517 C3' G B 12 OK OK 515 536 518 519 551 C3' C B 13 OK OK 549 567 552 553 582 C3' C B 14 OK OK 580 598 583 584 613 C3' A B 15 OK OK 611 631 614 615 646 C3' G B 16 OK OK 644 665 647 648 680 C3' G B 17 OK OK 678 699 681 682 714 C3' C B 18 OK OK 712 730 715 716 745 C3' A B 19 OK OK 743 763 746 747 778 C3' U B 20 OK OK 776 794 779 780 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A -1 OK OK 5 20 2 4 34 C4' U A 1 OK OK 36 51 33 35 64 C4' G A 2 OK OK 66 84 63 65 98 C4' C A 3 OK OK 100 115 97 99 129 C4' C A 4 OK OK 131 146 128 130 160 C4' U A 5 OK OK 162 177 159 161 190 C4' G A 6 OK OK 192 210 189 191 224 C4' G A 7 OK OK 226 244 223 225 258 C4' C A 8 OK OK 260 275 257 259 289 C4' G A 9 OK OK 291 309 288 290 323 C4' G A 10 OK OK 325 343 322 324 357 C4' C A 11 OK OK 359 374 356 358 387 C4' A B 8 OK OK 389 406 386 388 421 C4' A B 9 OK OK 423 440 420 422 454 C4' C B 10 OK OK 456 471 453 455 485 C4' U B 11 OK OK 487 502 484 486 515 C4' G B 12 OK OK 517 535 514 516 549 C4' C B 13 OK OK 551 566 548 550 580 C4' C B 14 OK OK 582 597 579 581 611 C4' A B 15 OK OK 613 630 610 612 644 C4' G B 16 OK OK 646 664 643 645 678 C4' G B 17 OK OK 680 698 677 679 712 C4' C B 18 OK OK 714 729 711 713 743 C4' A B 19 OK OK 745 762 742 744 776 C4' U B 20 OK OK 778 793 775 777 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A -1 OK OK 1 18 19 3 33 C5' U A 1 OK OK 32 49 50 34 63 C5' G A 2 OK OK 62 82 83 64 97 C5' C A 3 OK OK 96 113 114 98 128 C5' C A 4 OK OK 127 144 145 129 159 C5' U A 5 OK OK 158 175 176 160 189 C5' G A 6 OK OK 188 208 209 190 223 C5' G A 7 OK OK 222 242 243 224 257 C5' C A 8 OK OK 256 273 274 258 288 C5' G A 9 OK OK 287 307 308 289 322 C5' G A 10 OK OK 321 341 342 323 356 C5' C A 11 OK OK 355 372 373 357 386 C5' A B 8 OK OK 385 404 405 387 420 C5' A B 9 OK OK 419 438 439 421 453 C5' C B 10 OK OK 452 469 470 454 484 C5' U B 11 OK OK 483 500 501 485 514 C5' G B 12 OK OK 513 533 534 515 548 C5' C B 13 OK OK 547 564 565 549 579 C5' C B 14 OK OK 578 595 596 580 610 C5' A B 15 OK OK 609 628 629 611 643 C5' G B 16 OK OK 642 662 663 644 677 C5' G B 17 OK OK 676 696 697 678 711 C5' C B 18 OK OK 710 727 728 712 742 C5' A B 19 OK OK 741 760 761 743 775 C5' U B 20 OK OK 774 791 792 776 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P U A 1 distorted distorted 6 30 31 32 59 P G A 2 distorted distorted 37 60 61 62 93 P C A 3 distorted distorted 67 94 95 96 124 P C A 4 distorted distorted 101 125 126 127 155 P U A 5 distorted distorted 132 156 157 158 185 P G A 6 distorted distorted 163 186 187 188 219 P G A 7 distorted distorted 193 220 221 222 253 P C A 8 distorted distorted 227 254 255 256 284 P G A 9 distorted distorted 261 285 286 287 318 P G A 10 distorted distorted 292 319 320 321 352 P C A 11 distorted distorted 326 353 354 355 416 P A B 9 distorted distorted 390 417 418 419 449 P C B 10 distorted distorted 424 450 451 452 480 P U B 11 distorted distorted 457 481 482 483 510 P G B 12 distorted distorted 488 511 512 513 544 P C B 13 distorted distorted 518 545 546 547 575 P C B 14 distorted distorted 552 576 577 578 606 P A B 15 distorted distorted 583 607 608 609 639 P G B 16 distorted distorted 614 640 641 642 673 P G B 17 distorted distorted 647 674 675 676 707 P C B 18 distorted distorted 681 708 709 710 738 P A B 19 distorted distorted 715 739 740 741 771 P U B 20 distorted distorted 746 772 773 774 ---------------------------------------------------------------------------------