ID code: '2KEZ' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' U A 4 alpha beta 103 123 109 106 138 C1' C A 5 alpha beta 133 153 139 136 169 C1' C A 6 alpha beta 164 184 170 167 200 C1' C A 7 alpha beta 195 215 201 198 231 C1' C A 8 alpha beta 226 246 232 229 262 C1' U A 9 alpha beta 257 277 263 260 292 C1' G A 10 alpha beta 287 310 293 290 326 C1' C A 11 alpha beta 321 341 327 324 357 C1' A A 12 alpha beta 352 374 358 355 390 C1' U A 13 alpha beta 385 405 391 388 420 C1' A A 14 alpha beta 415 437 421 418 453 C1' A A 15 alpha beta 448 470 454 451 486 C1' G A 16 alpha beta 481 504 487 484 520 C1' G A 17 alpha beta 515 538 521 518 554 C1' A A 18 alpha beta 549 571 555 552 587 C1' U A 19 alpha beta 582 602 588 585 617 C1' G A 20 alpha beta 612 635 618 615 651 C1' A A 21 alpha beta 646 668 652 649 684 C1' A A 22 alpha beta 679 701 685 682 717 C1' C A 23 alpha beta 712 732 718 715 748 C1' C A 24 alpha beta 743 764 749 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' U A 4 OK OK 108 104 121 107 136 C2' C A 5 OK OK 138 134 151 137 167 C2' C A 6 OK OK 169 165 182 168 198 C2' C A 7 OK OK 200 196 213 199 229 C2' C A 8 OK OK 231 227 244 230 260 C2' U A 9 OK OK 262 258 275 261 290 C2' G A 10 OK OK 292 288 308 291 324 C2' C A 11 OK OK 326 322 339 325 355 C2' A A 12 OK OK 357 353 372 356 388 C2' U A 13 OK OK 390 386 403 389 418 C2' A A 14 OK OK 420 416 435 419 451 C2' A A 15 OK OK 453 449 468 452 484 C2' G A 16 OK OK 486 482 502 485 518 C2' G A 17 OK OK 520 516 536 519 552 C2' A A 18 OK OK 554 550 569 553 585 C2' U A 19 OK OK 587 583 600 586 615 C2' G A 20 OK OK 617 613 633 616 649 C2' A A 21 OK OK 651 647 666 650 682 C2' A A 22 OK OK 684 680 699 683 715 C2' C A 23 OK OK 717 713 730 716 746 C2' C A 24 OK OK 748 744 762 747 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' U A 4 OK OK 102 120 105 106 134 C3' C A 5 OK OK 132 150 135 136 165 C3' C A 6 OK OK 163 181 166 167 196 C3' C A 7 OK OK 194 212 197 198 227 C3' C A 8 OK OK 225 243 228 229 258 C3' U A 9 OK OK 256 274 259 260 288 C3' G A 10 OK OK 286 307 289 290 322 C3' C A 11 OK OK 320 338 323 324 353 C3' A A 12 OK OK 351 371 354 355 386 C3' U A 13 OK OK 384 402 387 388 416 C3' A A 14 OK OK 414 434 417 418 449 C3' A A 15 OK OK 447 467 450 451 482 C3' G A 16 OK OK 480 501 483 484 516 C3' G A 17 OK OK 514 535 517 518 550 C3' A A 18 OK OK 548 568 551 552 583 C3' U A 19 OK OK 581 599 584 585 613 C3' G A 20 OK OK 611 632 614 615 647 C3' A A 21 OK OK 645 665 648 649 680 C3' A A 22 OK OK 678 698 681 682 713 C3' C A 23 OK OK 711 729 714 715 744 C3' C A 24 OK OK 742 760 745 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' U A 4 OK OK 104 119 101 103 132 C4' C A 5 OK OK 134 149 131 133 163 C4' C A 6 OK OK 165 180 162 164 194 C4' C A 7 OK OK 196 211 193 195 225 C4' C A 8 OK OK 227 242 224 226 256 C4' U A 9 OK OK 258 273 255 257 286 C4' G A 10 OK OK 288 306 285 287 320 C4' C A 11 OK OK 322 337 319 321 351 C4' A A 12 OK OK 353 370 350 352 384 C4' U A 13 OK OK 386 401 383 385 414 C4' A A 14 OK OK 416 433 413 415 447 C4' A A 15 OK OK 449 466 446 448 480 C4' G A 16 OK OK 482 500 479 481 514 C4' G A 17 OK OK 516 534 513 515 548 C4' A A 18 OK OK 550 567 547 549 581 C4' U A 19 OK OK 583 598 580 582 611 C4' G A 20 OK OK 613 631 610 612 645 C4' A A 21 OK OK 647 664 644 646 678 C4' A A 22 OK OK 680 697 677 679 711 C4' C A 23 OK OK 713 728 710 712 742 C4' C A 24 OK OK 744 759 741 743 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' U A 4 OK OK 100 117 118 102 131 C5' C A 5 OK OK 130 147 148 132 162 C5' C A 6 OK OK 161 178 179 163 193 C5' C A 7 OK OK 192 209 210 194 224 C5' C A 8 OK OK 223 240 241 225 255 C5' U A 9 OK OK 254 271 272 256 285 C5' G A 10 OK OK 284 304 305 286 319 C5' C A 11 OK OK 318 335 336 320 350 C5' A A 12 OK OK 349 368 369 351 383 C5' U A 13 OK OK 382 399 400 384 413 C5' A A 14 OK OK 412 431 432 414 446 C5' A A 15 OK OK 445 464 465 447 479 C5' G A 16 OK OK 478 498 499 480 513 C5' G A 17 OK OK 512 532 533 514 547 C5' A A 18 OK OK 546 565 566 548 580 C5' U A 19 OK OK 579 596 597 581 610 C5' G A 20 OK OK 609 629 630 611 644 C5' A A 21 OK OK 643 662 663 645 677 C5' A A 22 OK OK 676 695 696 678 710 C5' C A 23 OK OK 709 726 727 711 741 C5' C A 24 OK OK 740 757 758 742 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P U A 4 distorted distorted 75 98 99 100 127 P C A 5 distorted distorted 105 128 129 130 158 P C A 6 distorted distorted 135 159 160 161 189 P C A 7 distorted distorted 166 190 191 192 220 P C A 8 distorted distorted 197 221 222 223 251 P U A 9 distorted distorted 228 252 253 254 281 P G A 10 distorted distorted 259 282 283 284 315 P C A 11 distorted distorted 289 316 317 318 346 P A A 12 distorted distorted 323 347 348 349 379 P U A 13 distorted distorted 354 380 381 382 409 P A A 14 distorted distorted 387 410 411 412 442 P A A 15 distorted distorted 417 443 444 445 475 P G A 16 distorted distorted 450 476 477 478 509 P G A 17 distorted distorted 483 510 511 512 543 P A A 18 distorted distorted 517 544 545 546 576 P U A 19 distorted distorted 551 577 578 579 606 P G A 20 distorted distorted 584 607 608 609 640 P A A 21 distorted distorted 614 641 642 643 673 P A A 22 distorted distorted 648 674 675 676 706 P C A 23 distorted distorted 681 707 708 709 737 P C A 24 distorted distorted 714 738 739 740 ---------------------------------------------------------------------------------