ID code: '1HLX' 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' G A 3 alpha beta 73 96 79 76 112 C1' A A 4 alpha beta 107 129 113 110 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' A A 6 alpha beta 170 192 176 173 208 C1' A A 7 alpha beta 203 225 209 206 241 C1' C A 8 alpha beta 236 256 242 239 272 C1' U A 9 alpha beta 267 287 273 270 302 C1' U A 10 alpha beta 297 317 303 300 332 C1' C A 11 alpha beta 327 347 333 330 363 C1' G A 12 alpha beta 358 381 364 361 397 C1' G A 13 alpha beta 392 415 398 395 431 C1' U A 14 alpha beta 426 446 432 429 461 C1' U A 15 alpha beta 456 476 462 459 491 C1' G A 16 alpha beta 486 509 492 489 525 C1' U A 17 alpha beta 520 540 526 523 555 C1' C A 18 alpha beta 550 570 556 553 586 C1' C A 19 alpha beta 581 601 587 584 617 C1' C A 20 alpha beta 612 633 618 615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' A A 4 OK OK 112 108 127 111 143 C2' U A 5 OK OK 145 141 158 144 173 C2' A A 6 OK OK 175 171 190 174 206 C2' A A 7 OK OK 208 204 223 207 239 C2' C A 8 OK OK 241 237 254 240 270 C2' U A 9 OK OK 272 268 285 271 300 C2' U A 10 OK OK 302 298 315 301 330 C2' C A 11 OK OK 332 328 345 331 361 C2' G A 12 OK OK 363 359 379 362 395 C2' G A 13 OK OK 397 393 413 396 429 C2' U A 14 OK OK 431 427 444 430 459 C2' U A 15 OK OK 461 457 474 460 489 C2' G A 16 OK OK 491 487 507 490 523 C2' U A 17 OK OK 525 521 538 524 553 C2' C A 18 OK OK 555 551 568 554 584 C2' C A 19 OK OK 586 582 599 585 615 C2' C A 20 OK OK 617 613 631 616 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' A A 4 OK OK 106 126 109 110 141 C3' U A 5 OK OK 139 157 142 143 171 C3' A A 6 OK OK 169 189 172 173 204 C3' A A 7 OK OK 202 222 205 206 237 C3' C A 8 OK OK 235 253 238 239 268 C3' U A 9 OK OK 266 284 269 270 298 C3' U A 10 OK OK 296 314 299 300 328 C3' C A 11 OK OK 326 344 329 330 359 C3' G A 12 OK OK 357 378 360 361 393 C3' G A 13 OK OK 391 412 394 395 427 C3' U A 14 OK OK 425 443 428 429 457 C3' U A 15 OK OK 455 473 458 459 487 C3' G A 16 OK OK 485 506 488 489 521 C3' U A 17 OK OK 519 537 522 523 551 C3' C A 18 OK OK 549 567 552 553 582 C3' C A 19 OK OK 580 598 583 584 613 C3' C A 20 OK OK 611 629 614 615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' A A 4 OK OK 108 125 105 107 139 C4' U A 5 OK OK 141 156 138 140 169 C4' A A 6 OK OK 171 188 168 170 202 C4' A A 7 OK OK 204 221 201 203 235 C4' C A 8 OK OK 237 252 234 236 266 C4' U A 9 OK OK 268 283 265 267 296 C4' U A 10 OK OK 298 313 295 297 326 C4' C A 11 OK OK 328 343 325 327 357 C4' G A 12 OK OK 359 377 356 358 391 C4' G A 13 OK OK 393 411 390 392 425 C4' U A 14 OK OK 427 442 424 426 455 C4' U A 15 OK OK 457 472 454 456 485 C4' G A 16 OK OK 487 505 484 486 519 C4' U A 17 OK OK 521 536 518 520 549 C4' C A 18 OK OK 551 566 548 550 580 C4' C A 19 OK OK 582 597 579 581 611 C4' C A 20 OK OK 613 628 610 612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' A A 4 OK OK 104 123 124 106 138 C5' U A 5 OK OK 137 154 155 139 168 C5' A A 6 OK OK 167 186 187 169 201 C5' A A 7 OK OK 200 219 220 202 234 C5' C A 8 OK OK 233 250 251 235 265 C5' U A 9 OK OK 264 281 282 266 295 C5' U A 10 OK OK 294 311 312 296 325 C5' C A 11 OK OK 324 341 342 326 356 C5' G A 12 OK OK 355 375 376 357 390 C5' G A 13 OK OK 389 409 410 391 424 C5' U A 14 OK OK 423 440 441 425 454 C5' U A 15 OK OK 453 470 471 455 484 C5' G A 16 OK OK 483 503 504 485 518 C5' U A 17 OK OK 517 534 535 519 548 C5' C A 18 OK OK 547 564 565 549 579 C5' C A 19 OK OK 578 595 596 580 610 C5' C A 20 OK OK 609 626 627 611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P A A 4 distorted distorted 75 102 103 104 134 P U A 5 distorted distorted 109 135 136 137 164 P A A 6 distorted distorted 142 165 166 167 197 P A A 7 distorted distorted 172 198 199 200 230 P C A 8 distorted distorted 205 231 232 233 261 P U A 9 distorted distorted 238 262 263 264 291 P U A 10 distorted distorted 269 292 293 294 321 P C A 11 distorted distorted 299 322 323 324 352 P G A 12 distorted distorted 329 353 354 355 386 P G A 13 distorted distorted 360 387 388 389 420 P U A 14 distorted distorted 394 421 422 423 450 P U A 15 distorted distorted 428 451 452 453 480 P G A 16 distorted distorted 458 481 482 483 514 P U A 17 distorted distorted 488 515 516 517 544 P C A 18 distorted distorted 522 545 546 547 575 P C A 19 distorted distorted 552 576 577 578 606 P C A 20 distorted distorted 583 607 608 609 ---------------------------------------------------------------------------------