ID code: '2MER' 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 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' C A 3 alpha beta 75 95 81 78 111 C1' C A 4 alpha beta 106 126 112 109 142 C1' G A 5 alpha beta 137 160 143 140 173 C1' PSU A 6 alpha beta 179 188 169 174 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' A A 8 alpha beta 234 256 240 237 272 C1' C A 9 alpha beta 267 287 273 270 300 C1' PSU A 10 alpha beta 306 315 296 301 333 C1' A A 11 alpha beta 328 350 334 331 363 C1' PSU A 12 alpha beta 369 378 359 364 396 C1' A A 13 alpha beta 391 413 397 394 429 C1' A A 14 alpha beta 424 446 430 427 462 C1' C A 15 alpha beta 457 477 463 460 493 C1' G A 16 alpha beta 488 511 494 491 527 C1' G A 17 alpha beta 522 545 528 525 561 C1' U A 18 alpha beta 556 576 562 559 591 C1' C A 19 alpha beta 586 607 592 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 44 C2' G A 2 OK OK 46 42 62 45 78 C2' C A 3 OK OK 80 76 93 79 109 C2' C A 4 OK OK 111 107 124 110 140 C2' G A 5 OK OK 142 138 158 141 174 C2' PSU A 6 OK OK 173 176 189 175 204 C2' A A 7 OK OK 206 202 221 205 237 C2' A A 8 OK OK 239 235 254 238 270 C2' C A 9 OK OK 272 268 285 271 301 C2' PSU A 10 OK OK 300 303 316 302 331 C2' A A 11 OK OK 333 329 348 332 364 C2' PSU A 12 OK OK 363 366 379 365 394 C2' A A 13 OK OK 396 392 411 395 427 C2' A A 14 OK OK 429 425 444 428 460 C2' C A 15 OK OK 462 458 475 461 491 C2' G A 16 OK OK 493 489 509 492 525 C2' G A 17 OK OK 527 523 543 526 559 C2' U A 18 OK OK 561 557 574 560 589 C2' C A 19 OK OK 591 587 605 590 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' C A 3 OK OK 74 92 77 78 107 C3' C A 4 OK OK 105 123 108 109 138 C3' G A 5 OK OK 136 157 139 140 176 C3' PSU A 6 OK OK 177 191 178 174 202 C3' A A 7 OK OK 200 220 203 204 235 C3' A A 8 OK OK 233 253 236 237 268 C3' C A 9 OK OK 266 284 269 270 303 C3' PSU A 10 OK OK 304 318 305 301 329 C3' A A 11 OK OK 327 347 330 331 366 C3' PSU A 12 OK OK 367 381 368 364 392 C3' A A 13 OK OK 390 410 393 394 425 C3' A A 14 OK OK 423 443 426 427 458 C3' C A 15 OK OK 456 474 459 460 489 C3' G A 16 OK OK 487 508 490 491 523 C3' G A 17 OK OK 521 542 524 525 557 C3' U A 18 OK OK 555 573 558 559 587 C3' C A 19 OK OK 585 603 588 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' C A 3 OK OK 76 91 73 75 105 C4' C A 4 OK OK 107 122 104 106 136 C4' G A 5 OK OK 138 156 135 137 177 C4' PSU A 6 OK OK 176 192 180 179 200 C4' A A 7 OK OK 202 219 199 201 233 C4' A A 8 OK OK 235 252 232 234 266 C4' C A 9 OK OK 268 283 265 267 304 C4' PSU A 10 OK OK 303 319 307 306 327 C4' A A 11 OK OK 329 346 326 328 367 C4' PSU A 12 OK OK 366 382 370 369 390 C4' A A 13 OK OK 392 409 389 391 423 C4' A A 14 OK OK 425 442 422 424 456 C4' C A 15 OK OK 458 473 455 457 487 C4' G A 16 OK OK 489 507 486 488 521 C4' G A 17 OK OK 523 541 520 522 555 C4' U A 18 OK OK 557 572 554 556 585 C4' C A 19 OK OK 587 602 584 586 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 39 C5' G A 2 OK OK 38 58 59 40 73 C5' C A 3 OK OK 72 89 90 74 104 C5' C A 4 OK OK 103 120 121 105 135 C5' G A 5 OK OK 134 154 155 136 180 C5' PSU A 6 OK OK 181 193 194 177 199 C5' A A 7 OK OK 198 217 218 200 232 C5' A A 8 OK OK 231 250 251 233 265 C5' C A 9 OK OK 264 281 282 266 307 C5' PSU A 10 OK OK 308 320 321 304 326 C5' A A 11 OK OK 325 344 345 327 370 C5' PSU A 12 OK OK 371 383 384 367 389 C5' A A 13 OK OK 388 407 408 390 422 C5' A A 14 OK OK 421 440 441 423 455 C5' C A 15 OK OK 454 471 472 456 486 C5' G A 16 OK OK 485 505 506 487 520 C5' G A 17 OK OK 519 539 540 521 554 C5' U A 18 OK OK 553 570 571 555 584 C5' C A 19 OK OK 583 600 601 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P C A 3 distorted distorted 43 70 71 72 100 P C A 4 distorted distorted 77 101 102 103 131 P G A 5 distorted distorted 108 132 133 134 182 P PSU A 6 distorted distorted 139 183 184 181 195 P A A 7 distorted distorted 178 196 197 198 228 P A A 8 distorted distorted 203 229 230 231 261 P C A 9 distorted distorted 236 262 263 264 309 P PSU A 10 distorted distorted 269 310 311 308 322 P A A 11 distorted distorted 305 323 324 325 372 P PSU A 12 distorted distorted 330 373 374 371 385 P A A 13 distorted distorted 368 386 387 388 418 P A A 14 distorted distorted 393 419 420 421 451 P C A 15 distorted distorted 426 452 453 454 482 P G A 16 distorted distorted 459 483 484 485 516 P G A 17 distorted distorted 490 517 518 519 550 P U A 18 distorted distorted 524 551 552 553 580 P C A 19 distorted distorted 558 581 582 583 ---------------------------------------------------------------------------------