ID code: '1K2G' 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' C A 1 alpha beta 4 24 10 7 41 C1' A A 2 alpha beta 36 58 42 39 74 C1' G A 3 alpha beta 69 92 75 72 108 C1' A A 4 alpha beta 103 125 109 106 141 C1' C A 5 alpha beta 136 156 142 139 172 C1' U A 6 alpha beta 167 187 173 170 202 C1' U A 7 alpha beta 197 217 203 200 232 C1' C A 8 alpha beta 227 247 233 230 263 C1' G A 9 alpha beta 258 281 264 261 297 C1' G A 10 alpha beta 292 315 298 295 331 C1' U A 11 alpha beta 326 346 332 329 361 C1' C A 12 alpha beta 356 376 362 359 392 C1' G A 13 alpha beta 387 410 393 390 426 C1' C A 14 alpha beta 421 441 427 424 457 C1' A A 15 alpha beta 452 474 458 455 490 C1' G A 16 alpha beta 485 508 491 488 524 C1' A A 17 alpha beta 519 541 525 522 557 C1' G A 18 alpha beta 552 575 558 555 591 C1' A A 19 alpha beta 586 608 592 589 624 C1' U A 20 alpha beta 619 639 625 622 654 C1' G A 21 alpha beta 649 672 655 652 688 C1' G A 22 alpha beta 683 707 689 686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK OK 9 5 22 8 39 C2' A A 2 OK OK 41 37 56 40 72 C2' G A 3 OK OK 74 70 90 73 106 C2' A A 4 OK OK 108 104 123 107 139 C2' C A 5 OK OK 141 137 154 140 170 C2' U A 6 OK OK 172 168 185 171 200 C2' U A 7 OK OK 202 198 215 201 230 C2' C A 8 OK OK 232 228 245 231 261 C2' G A 9 OK OK 263 259 279 262 295 C2' G A 10 OK OK 297 293 313 296 329 C2' U A 11 OK OK 331 327 344 330 359 C2' C A 12 OK OK 361 357 374 360 390 C2' G A 13 OK OK 392 388 408 391 424 C2' C A 14 OK OK 426 422 439 425 455 C2' A A 15 OK OK 457 453 472 456 488 C2' G A 16 OK OK 490 486 506 489 522 C2' A A 17 OK OK 524 520 539 523 555 C2' G A 18 OK OK 557 553 573 556 589 C2' A A 19 OK OK 591 587 606 590 622 C2' U A 20 OK OK 624 620 637 623 652 C2' G A 21 OK OK 654 650 670 653 686 C2' G A 22 OK OK 688 684 705 687 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' A A 2 OK OK 35 55 38 39 70 C3' G A 3 OK OK 68 89 71 72 104 C3' A A 4 OK OK 102 122 105 106 137 C3' C A 5 OK OK 135 153 138 139 168 C3' U A 6 OK OK 166 184 169 170 198 C3' U A 7 OK OK 196 214 199 200 228 C3' C A 8 OK OK 226 244 229 230 259 C3' G A 9 OK OK 257 278 260 261 293 C3' G A 10 OK OK 291 312 294 295 327 C3' U A 11 OK OK 325 343 328 329 357 C3' C A 12 OK OK 355 373 358 359 388 C3' G A 13 OK OK 386 407 389 390 422 C3' C A 14 OK OK 420 438 423 424 453 C3' A A 15 OK OK 451 471 454 455 486 C3' G A 16 OK OK 484 505 487 488 520 C3' A A 17 OK OK 518 538 521 522 553 C3' G A 18 OK OK 551 572 554 555 587 C3' A A 19 OK OK 585 605 588 589 620 C3' U A 20 OK OK 618 636 621 622 650 C3' G A 21 OK OK 648 669 651 652 684 C3' G A 22 OK OK 682 703 685 686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' A A 2 OK OK 37 54 34 36 68 C4' G A 3 OK OK 70 88 67 69 102 C4' A A 4 OK OK 104 121 101 103 135 C4' C A 5 OK OK 137 152 134 136 166 C4' U A 6 OK OK 168 183 165 167 196 C4' U A 7 OK OK 198 213 195 197 226 C4' C A 8 OK OK 228 243 225 227 257 C4' G A 9 OK OK 259 277 256 258 291 C4' G A 10 OK OK 293 311 290 292 325 C4' U A 11 OK OK 327 342 324 326 355 C4' C A 12 OK OK 357 372 354 356 386 C4' G A 13 OK OK 388 406 385 387 420 C4' C A 14 OK OK 422 437 419 421 451 C4' A A 15 OK OK 453 470 450 452 484 C4' G A 16 OK OK 486 504 483 485 518 C4' A A 17 OK OK 520 537 517 519 551 C4' G A 18 OK OK 553 571 550 552 585 C4' A A 19 OK OK 587 604 584 586 618 C4' U A 20 OK OK 620 635 617 619 648 C4' G A 21 OK OK 650 668 647 649 682 C4' G A 22 OK OK 684 702 681 683 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 34 C5' A A 2 OK OK 33 52 53 35 67 C5' G A 3 OK OK 66 86 87 68 101 C5' A A 4 OK OK 100 119 120 102 134 C5' C A 5 OK OK 133 150 151 135 165 C5' U A 6 OK OK 164 181 182 166 195 C5' U A 7 OK OK 194 211 212 196 225 C5' C A 8 OK OK 224 241 242 226 256 C5' G A 9 OK OK 255 275 276 257 290 C5' G A 10 OK OK 289 309 310 291 324 C5' U A 11 OK OK 323 340 341 325 354 C5' C A 12 OK OK 353 370 371 355 385 C5' G A 13 OK OK 384 404 405 386 419 C5' C A 14 OK OK 418 435 436 420 450 C5' A A 15 OK OK 449 468 469 451 483 C5' G A 16 OK OK 482 502 503 484 517 C5' A A 17 OK OK 516 535 536 518 550 C5' G A 18 OK OK 549 569 570 551 584 C5' A A 19 OK OK 583 602 603 585 617 C5' U A 20 OK OK 616 633 634 618 647 C5' G A 21 OK OK 646 666 667 648 681 C5' G A 22 OK OK 680 700 701 682 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P A A 2 distorted distorted 6 31 32 33 63 P G A 3 distorted distorted 38 64 65 66 97 P A A 4 distorted distorted 71 98 99 100 130 P C A 5 distorted distorted 105 131 132 133 161 P U A 6 distorted distorted 138 162 163 164 191 P U A 7 distorted distorted 169 192 193 194 221 P C A 8 distorted distorted 199 222 223 224 252 P G A 9 distorted distorted 229 253 254 255 286 P G A 10 distorted distorted 260 287 288 289 320 P U A 11 distorted distorted 294 321 322 323 350 P C A 12 distorted distorted 328 351 352 353 381 P G A 13 distorted distorted 358 382 383 384 415 P C A 14 distorted distorted 389 416 417 418 446 P A A 15 distorted distorted 423 447 448 449 479 P G A 16 distorted distorted 454 480 481 482 513 P A A 17 distorted distorted 487 514 515 516 546 P G A 18 distorted distorted 521 547 548 549 580 P A A 19 distorted distorted 554 581 582 583 613 P U A 20 distorted distorted 588 614 615 616 643 P G A 21 distorted distorted 621 644 645 646 677 P G A 22 distorted distorted 651 678 679 680 ---------------------------------------------------------------------------------