ID code: '1QWA' 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' A A 3 alpha beta 73 95 79 76 111 C1' U A 4 alpha beta 106 126 112 109 141 C1' G A 5 alpha beta 136 159 142 139 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' C A 7 alpha beta 201 221 207 204 237 C1' U A 8 alpha beta 232 252 238 235 267 C1' C A 9 alpha beta 262 282 268 265 298 C1' C A 10 alpha beta 293 313 299 296 329 C1' C A 11 alpha beta 324 344 330 327 360 C1' G A 12 alpha beta 355 378 361 358 394 C1' A A 13 alpha beta 389 411 395 392 427 C1' G A 14 alpha beta 422 445 428 425 461 C1' U A 15 alpha beta 456 476 462 459 491 C1' G A 16 alpha beta 486 509 492 489 525 C1' C A 17 alpha beta 520 540 526 523 556 C1' A A 18 alpha beta 551 573 557 554 589 C1' U A 19 alpha beta 584 604 590 587 619 C1' C A 20 alpha beta 614 634 620 617 650 C1' C A 21 alpha beta 645 666 651 648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' U A 4 OK OK 111 107 124 110 139 C2' G A 5 OK OK 141 137 157 140 173 C2' C A 6 OK OK 175 171 188 174 204 C2' C A 7 OK OK 206 202 219 205 235 C2' U A 8 OK OK 237 233 250 236 265 C2' C A 9 OK OK 267 263 280 266 296 C2' C A 10 OK OK 298 294 311 297 327 C2' C A 11 OK OK 329 325 342 328 358 C2' G A 12 OK OK 360 356 376 359 392 C2' A A 13 OK OK 394 390 409 393 425 C2' G A 14 OK OK 427 423 443 426 459 C2' U A 15 OK OK 461 457 474 460 489 C2' G A 16 OK OK 491 487 507 490 523 C2' C A 17 OK OK 525 521 538 524 554 C2' A A 18 OK OK 556 552 571 555 587 C2' U A 19 OK OK 589 585 602 588 617 C2' C A 20 OK OK 619 615 632 618 648 C2' C A 21 OK OK 650 646 664 649 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' U A 4 OK OK 105 123 108 109 137 C3' G A 5 OK OK 135 156 138 139 171 C3' C A 6 OK OK 169 187 172 173 202 C3' C A 7 OK OK 200 218 203 204 233 C3' U A 8 OK OK 231 249 234 235 263 C3' C A 9 OK OK 261 279 264 265 294 C3' C A 10 OK OK 292 310 295 296 325 C3' C A 11 OK OK 323 341 326 327 356 C3' G A 12 OK OK 354 375 357 358 390 C3' A A 13 OK OK 388 408 391 392 423 C3' G A 14 OK OK 421 442 424 425 457 C3' U A 15 OK OK 455 473 458 459 487 C3' G A 16 OK OK 485 506 488 489 521 C3' C A 17 OK OK 519 537 522 523 552 C3' A A 18 OK OK 550 570 553 554 585 C3' U A 19 OK OK 583 601 586 587 615 C3' C A 20 OK OK 613 631 616 617 646 C3' C A 21 OK OK 644 662 647 648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' U A 4 OK OK 107 122 104 106 135 C4' G A 5 OK OK 137 155 134 136 169 C4' C A 6 OK OK 171 186 168 170 200 C4' C A 7 OK OK 202 217 199 201 231 C4' U A 8 OK OK 233 248 230 232 261 C4' C A 9 OK OK 263 278 260 262 292 C4' C A 10 OK OK 294 309 291 293 323 C4' C A 11 OK OK 325 340 322 324 354 C4' G A 12 OK OK 356 374 353 355 388 C4' A A 13 OK OK 390 407 387 389 421 C4' G A 14 OK OK 423 441 420 422 455 C4' U A 15 OK OK 457 472 454 456 485 C4' G A 16 OK OK 487 505 484 486 519 C4' C A 17 OK OK 521 536 518 520 550 C4' A A 18 OK OK 552 569 549 551 583 C4' U A 19 OK OK 585 600 582 584 613 C4' C A 20 OK OK 615 630 612 614 644 C4' C A 21 OK OK 646 661 643 645 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' U A 4 OK OK 103 120 121 105 134 C5' G A 5 OK OK 133 153 154 135 168 C5' C A 6 OK OK 167 184 185 169 199 C5' C A 7 OK OK 198 215 216 200 230 C5' U A 8 OK OK 229 246 247 231 260 C5' C A 9 OK OK 259 276 277 261 291 C5' C A 10 OK OK 290 307 308 292 322 C5' C A 11 OK OK 321 338 339 323 353 C5' G A 12 OK OK 352 372 373 354 387 C5' A A 13 OK OK 386 405 406 388 420 C5' G A 14 OK OK 419 439 440 421 454 C5' U A 15 OK OK 453 470 471 455 484 C5' G A 16 OK OK 483 503 504 485 518 C5' C A 17 OK OK 517 534 535 519 549 C5' A A 18 OK OK 548 567 568 550 582 C5' U A 19 OK OK 581 598 599 583 612 C5' C A 20 OK OK 611 628 629 613 643 C5' C A 21 OK OK 642 659 660 644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P U A 4 distorted distorted 75 101 102 103 130 P G A 5 distorted distorted 108 131 132 133 164 P C A 6 distorted distorted 138 165 166 167 195 P C A 7 distorted distorted 172 196 197 198 226 P U A 8 distorted distorted 203 227 228 229 256 P C A 9 distorted distorted 234 257 258 259 287 P C A 10 distorted distorted 264 288 289 290 318 P C A 11 distorted distorted 295 319 320 321 349 P G A 12 distorted distorted 326 350 351 352 383 P A A 13 distorted distorted 357 384 385 386 416 P G A 14 distorted distorted 391 417 418 419 450 P U A 15 distorted distorted 424 451 452 453 480 P G A 16 distorted distorted 458 481 482 483 514 P C A 17 distorted distorted 488 515 516 517 545 P A A 18 distorted distorted 522 546 547 548 578 P U A 19 distorted distorted 553 579 580 581 608 P C A 20 distorted distorted 586 609 610 611 639 P C A 21 distorted distorted 616 640 641 642 ---------------------------------------------------------------------------------