ID code: '1BVJ' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 alpha beta 7 29 13 10 45 C1' G A 2 alpha beta 40 62 46 43 78 C1' C A 3 alpha beta 73 92 79 76 108 C1' G A 4 alpha beta 103 125 109 106 141 C1' A A 5 alpha beta 136 157 142 139 173 C1' C A 6 alpha beta 168 187 174 171 203 C1' G A 7 alpha beta 198 220 204 201 236 C1' G A 8 alpha beta 231 253 237 234 269 C1' U A 9 alpha beta 264 283 270 267 298 C1' G A 10 alpha beta 293 315 299 296 331 C1' U A 11 alpha beta 326 345 332 329 360 C1' A A 12 alpha beta 355 376 361 358 392 C1' A A 13 alpha beta 387 408 393 390 424 C1' A A 14 alpha beta 419 440 425 422 456 C1' A A 15 alpha beta 451 472 457 454 488 C1' A A 16 alpha beta 483 504 489 486 520 C1' U A 17 alpha beta 515 534 521 518 549 C1' C A 18 alpha beta 544 563 550 547 579 C1' U A 19 alpha beta 574 593 580 577 608 C1' C A 20 alpha beta 603 622 609 606 638 C1' G A 21 alpha beta 633 655 639 636 671 C1' C A 22 alpha beta 666 685 672 669 701 C1' C A 23 alpha beta 696 715 702 699 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 43 C2' G A 2 OK OK 45 41 61 44 76 C2' C A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 139 C2' A A 5 OK OK 141 137 156 140 171 C2' C A 6 OK OK 173 169 186 172 201 C2' G A 7 OK OK 203 199 219 202 234 C2' G A 8 OK OK 236 232 252 235 267 C2' U A 9 OK OK 269 265 282 268 296 C2' G A 10 OK OK 298 294 314 297 329 C2' U A 11 OK OK 331 327 344 330 358 C2' A A 12 OK OK 360 356 375 359 390 C2' A A 13 OK OK 392 388 407 391 422 C2' A A 14 OK OK 424 420 439 423 454 C2' A A 15 OK OK 456 452 471 455 486 C2' A A 16 OK OK 488 484 503 487 518 C2' U A 17 OK OK 520 516 533 519 547 C2' C A 18 OK OK 549 545 562 548 577 C2' U A 19 OK OK 579 575 592 578 606 C2' C A 20 OK OK 608 604 621 607 636 C2' G A 21 OK OK 638 634 654 637 669 C2' C A 22 OK OK 671 667 684 670 699 C2' C A 23 OK OK 701 697 714 700 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 41 C3' G A 2 OK OK 39 60 42 43 74 C3' C A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 137 C3' A A 5 OK OK 135 155 138 139 169 C3' C A 6 OK OK 167 185 170 171 199 C3' G A 7 OK OK 197 218 200 201 232 C3' G A 8 OK OK 230 251 233 234 265 C3' U A 9 OK OK 263 281 266 267 294 C3' G A 10 OK OK 292 313 295 296 327 C3' U A 11 OK OK 325 343 328 329 356 C3' A A 12 OK OK 354 374 357 358 388 C3' A A 13 OK OK 386 406 389 390 420 C3' A A 14 OK OK 418 438 421 422 452 C3' A A 15 OK OK 450 470 453 454 484 C3' A A 16 OK OK 482 502 485 486 516 C3' U A 17 OK OK 514 532 517 518 545 C3' C A 18 OK OK 543 561 546 547 575 C3' U A 19 OK OK 573 591 576 577 604 C3' C A 20 OK OK 602 620 605 606 634 C3' G A 21 OK OK 632 653 635 636 667 C3' C A 22 OK OK 665 683 668 669 697 C3' C A 23 OK OK 695 713 698 699 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 39 C4' G A 2 OK OK 41 59 38 40 72 C4' C A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 135 C4' A A 5 OK OK 137 154 134 136 167 C4' C A 6 OK OK 169 184 166 168 197 C4' G A 7 OK OK 199 217 196 198 230 C4' G A 8 OK OK 232 250 229 231 263 C4' U A 9 OK OK 265 280 262 264 292 C4' G A 10 OK OK 294 312 291 293 325 C4' U A 11 OK OK 327 342 324 326 354 C4' A A 12 OK OK 356 373 353 355 386 C4' A A 13 OK OK 388 405 385 387 418 C4' A A 14 OK OK 420 437 417 419 450 C4' A A 15 OK OK 452 469 449 451 482 C4' A A 16 OK OK 484 501 481 483 514 C4' U A 17 OK OK 516 531 513 515 543 C4' C A 18 OK OK 545 560 542 544 573 C4' U A 19 OK OK 575 590 572 574 602 C4' C A 20 OK OK 604 619 601 603 632 C4' G A 21 OK OK 634 652 631 633 665 C4' C A 22 OK OK 667 682 664 666 695 C4' C A 23 OK OK 697 712 694 696 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 38 C5' G A 2 OK OK 37 57 58 39 71 C5' C A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 134 C5' A A 5 OK OK 133 152 153 135 166 C5' C A 6 OK OK 165 182 183 167 196 C5' G A 7 OK OK 195 215 216 197 229 C5' G A 8 OK OK 228 248 249 230 262 C5' U A 9 OK OK 261 278 279 263 291 C5' G A 10 OK OK 290 310 311 292 324 C5' U A 11 OK OK 323 340 341 325 353 C5' A A 12 OK OK 352 371 372 354 385 C5' A A 13 OK OK 384 403 404 386 417 C5' A A 14 OK OK 416 435 436 418 449 C5' A A 15 OK OK 448 467 468 450 481 C5' A A 16 OK OK 480 499 500 482 513 C5' U A 17 OK OK 512 529 530 514 542 C5' C A 18 OK OK 541 558 559 543 572 C5' U A 19 OK OK 571 588 589 573 601 C5' C A 20 OK OK 600 617 618 602 631 C5' G A 21 OK OK 630 650 651 632 664 C5' C A 22 OK OK 663 680 681 665 694 C5' C A 23 OK OK 693 710 711 695 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 OK OK 2 3 4 34 P G A 2 distorted distorted 9 35 36 37 67 P C A 3 distorted distorted 42 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 130 P A A 5 distorted distorted 105 131 132 133 162 P C A 6 distorted distorted 138 163 164 165 192 P G A 7 distorted distorted 170 193 194 195 225 P G A 8 distorted distorted 200 226 227 228 258 P U A 9 distorted distorted 233 259 260 261 287 P G A 10 distorted distorted 266 288 289 290 320 P U A 11 distorted distorted 295 321 322 323 349 P A A 12 distorted distorted 328 350 351 352 381 P A A 13 distorted distorted 357 382 383 384 413 P A A 14 distorted distorted 389 414 415 416 445 P A A 15 distorted distorted 421 446 447 448 477 P A A 16 distorted distorted 453 478 479 480 509 P U A 17 distorted distorted 485 510 511 512 538 P C A 18 distorted distorted 517 539 540 541 568 P U A 19 distorted distorted 546 569 570 571 597 P C A 20 distorted distorted 576 598 599 600 627 P G A 21 distorted distorted 605 628 629 630 660 P C A 22 distorted distorted 635 661 662 663 690 P C A 23 distorted distorted 668 691 692 693 ---------------------------------------------------------------------------------