ID code: '1KML' 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 A 1 alpha beta 4 24 9 7 42 C1' T A 2 alpha beta 38 58 43 41 74 C1' G A 3 alpha beta 70 90 75 73 106 C1' G A 4 alpha beta 102 122 107 105 139 C1' C A 5 alpha beta 135 152 140 138 169 C1' G A 6 alpha beta 165 185 170 168 201 C1' G A 7 alpha beta 197 217 202 200 234 C1' C A 8 alpha beta 230 247 235 233 264 C1' G A 9 alpha beta 260 280 265 263 296 C1' G A 10 alpha beta 292 312 297 295 329 C1' C A 11 alpha beta 325 342 330 328 359 C1' C A 12 alpha beta 355 373 360 358 388 C1' G B 1 alpha beta 384 404 389 387 422 C1' G B 2 alpha beta 418 438 423 421 455 C1' C B 3 alpha beta 451 468 456 454 485 C1' C B 4 alpha beta 481 498 486 484 515 C1' G B 5 alpha beta 511 531 516 514 548 C1' C B 6 alpha beta 544 561 549 547 578 C1' C B 7 alpha beta 574 591 579 577 608 C1' G B 8 alpha beta 604 624 609 607 641 C1' C B 9 alpha beta 637 654 642 640 671 C1' C B 10 alpha beta 667 684 672 670 701 C1' A B 11 alpha beta 697 716 702 700 733 C1' C B 12 alpha beta 729 747 734 732 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 30 31 41 C2' T A 2 OK OK 42 39 56 57 73 C2' G A 3 OK OK 74 71 95 94 105 C2' G A 4 OK OK 106 103 127 128 138 C2' C A 5 OK OK 139 136 157 158 168 C2' G A 6 OK OK 169 166 190 189 200 C2' G A 7 OK OK 201 198 222 223 233 C2' C A 8 OK OK 234 231 252 253 263 C2' G A 9 OK OK 264 261 285 284 295 C2' G A 10 OK OK 296 293 317 318 328 C2' C A 11 OK OK 329 326 347 348 358 C2' C A 12 OK OK 359 356 379 378 387 C2' G B 1 OK OK 388 385 410 411 421 C2' G B 2 OK OK 422 419 443 444 454 C2' C B 3 OK OK 455 452 473 474 484 C2' C B 4 OK OK 485 482 503 504 514 C2' G B 5 OK OK 515 512 536 537 547 C2' C B 6 OK OK 548 545 566 567 577 C2' C B 7 OK OK 578 575 596 597 607 C2' G B 8 OK OK 608 605 629 630 640 C2' C B 9 OK OK 641 638 659 660 670 C2' C B 10 OK OK 671 668 689 690 700 C2' A B 11 OK OK 701 698 721 722 732 C2' C B 12 OK OK 733 730 752 753 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 23 6 7 39 C3' T A 2 OK OK 37 55 40 41 71 C3' G A 3 OK OK 69 89 72 73 103 C3' G A 4 OK OK 101 121 104 105 136 C3' C A 5 OK OK 134 151 137 138 166 C3' G A 6 OK OK 164 184 167 168 198 C3' G A 7 OK OK 196 216 199 200 231 C3' C A 8 OK OK 229 246 232 233 261 C3' G A 9 OK OK 259 279 262 263 293 C3' G A 10 OK OK 291 311 294 295 326 C3' C A 11 OK OK 324 341 327 328 356 C3' C A 12 OK OK 354 371 357 358 385 C3' G B 1 OK OK 383 403 386 387 419 C3' G B 2 OK OK 417 437 420 421 452 C3' C B 3 OK OK 450 467 453 454 482 C3' C B 4 OK OK 480 497 483 484 512 C3' G B 5 OK OK 510 530 513 514 545 C3' C B 6 OK OK 543 560 546 547 575 C3' C B 7 OK OK 573 590 576 577 605 C3' G B 8 OK OK 603 623 606 607 638 C3' C B 9 OK OK 636 653 639 640 668 C3' C B 10 OK OK 666 683 669 670 698 C3' A B 11 OK OK 696 715 699 700 730 C3' C B 12 OK OK 728 745 731 732 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 22 2 4 37 C4' T A 2 OK OK 39 54 36 38 69 C4' G A 3 OK OK 71 88 68 70 101 C4' G A 4 OK OK 103 120 100 102 134 C4' C A 5 OK OK 136 150 133 135 164 C4' G A 6 OK OK 166 183 163 165 196 C4' G A 7 OK OK 198 215 195 197 229 C4' C A 8 OK OK 231 245 228 230 259 C4' G A 9 OK OK 261 278 258 260 291 C4' G A 10 OK OK 293 310 290 292 324 C4' C A 11 OK OK 326 340 323 325 354 C4' C A 12 OK OK 356 370 353 355 383 C4' G B 1 OK OK 385 402 382 384 417 C4' G B 2 OK OK 419 436 416 418 450 C4' C B 3 OK OK 452 466 449 451 480 C4' C B 4 OK OK 482 496 479 481 510 C4' G B 5 OK OK 512 529 509 511 543 C4' C B 6 OK OK 545 559 542 544 573 C4' C B 7 OK OK 575 589 572 574 603 C4' G B 8 OK OK 605 622 602 604 636 C4' C B 9 OK OK 638 652 635 637 666 C4' C B 10 OK OK 668 682 665 667 696 C4' A B 11 OK OK 698 714 695 697 728 C4' C B 12 OK OK 730 744 727 729 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 20 21 3 36 C5' T A 2 OK OK 35 52 53 37 68 C5' G A 3 OK OK 67 86 87 69 100 C5' G A 4 OK OK 99 118 119 101 133 C5' C A 5 OK OK 132 148 149 134 163 C5' G A 6 OK OK 162 181 182 164 195 C5' G A 7 OK OK 194 213 214 196 228 C5' C A 8 OK OK 227 243 244 229 258 C5' G A 9 OK OK 257 276 277 259 290 C5' G A 10 OK OK 289 308 309 291 323 C5' C A 11 OK OK 322 338 339 324 353 C5' C A 12 OK OK 352 368 369 354 382 C5' G B 1 OK OK 381 400 401 383 416 C5' G B 2 OK OK 415 434 435 417 449 C5' C B 3 OK OK 448 464 465 450 479 C5' C B 4 OK OK 478 494 495 480 509 C5' G B 5 OK OK 508 527 528 510 542 C5' C B 6 OK OK 541 557 558 543 572 C5' C B 7 OK OK 571 587 588 573 602 C5' G B 8 OK OK 601 620 621 603 635 C5' C B 9 OK OK 634 650 651 636 665 C5' C B 10 OK OK 664 680 681 666 695 C5' A B 11 OK OK 694 712 713 696 727 C5' C B 12 OK OK 726 742 743 728 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P T A 2 distorted distorted 6 33 34 35 64 P G A 3 distorted distorted 40 65 66 67 96 P G A 4 distorted distorted 72 97 98 99 129 P C A 5 distorted distorted 104 130 131 132 159 P G A 6 distorted distorted 137 160 161 162 191 P G A 7 distorted distorted 167 192 193 194 224 P C A 8 distorted distorted 199 225 226 227 254 P G A 9 distorted distorted 232 255 256 257 286 P G A 10 distorted distorted 262 287 288 289 319 P C A 11 distorted distorted 294 320 321 322 349 P C A 12 distorted distorted 327 350 351 352 412 P G B 2 distorted distorted 386 413 414 415 445 P C B 3 distorted distorted 420 446 447 448 475 P C B 4 distorted distorted 453 476 477 478 505 P G B 5 distorted distorted 483 506 507 508 538 P C B 6 distorted distorted 513 539 540 541 568 P C B 7 distorted distorted 546 569 570 571 598 P G B 8 distorted distorted 576 599 600 601 631 P C B 9 distorted distorted 606 632 633 634 661 P C B 10 distorted distorted 639 662 663 664 691 P A B 11 distorted distorted 669 692 693 694 723 P C B 12 distorted distorted 699 724 725 726 ---------------------------------------------------------------------------------