ID code: '2L8W' 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' C A 2 alpha beta 36 56 42 39 72 C1' G A 3 alpha beta 67 90 73 70 106 C1' C A 4 alpha beta 101 121 107 104 137 C1' U A 5 alpha beta 132 152 138 135 167 C1' G A 6 alpha beta 162 185 168 165 201 C1' C A 7 alpha beta 196 216 202 199 232 C1' G A 8 alpha beta 227 250 233 230 266 C1' G A 9 alpha beta 261 285 267 264 299 C1' C B 10 alpha beta 294 314 300 297 331 C1' C B 11 alpha beta 326 346 332 329 362 C1' G B 12 alpha beta 357 380 363 360 396 C1' C B 13 alpha beta 391 411 397 394 427 C1' U B 14 alpha beta 422 442 428 425 457 C1' G B 15 alpha beta 452 475 458 455 491 C1' C B 16 alpha beta 486 506 492 489 522 C1' G B 17 alpha beta 517 540 523 520 556 C1' G B 18 alpha beta 551 575 557 554 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 2 OK OK 41 37 54 40 70 C2' G A 3 OK OK 72 68 88 71 104 C2' C A 4 OK OK 106 102 119 105 135 C2' U A 5 OK OK 137 133 150 136 165 C2' G A 6 OK OK 167 163 183 166 199 C2' C A 7 OK OK 201 197 214 200 230 C2' G A 8 OK OK 232 228 248 231 264 C2' G A 9 OK OK 266 262 283 265 297 C2' C B 10 OK OK 299 295 312 298 329 C2' C B 11 OK OK 331 327 344 330 360 C2' G B 12 OK OK 362 358 378 361 394 C2' C B 13 OK OK 396 392 409 395 425 C2' U B 14 OK OK 427 423 440 426 455 C2' G B 15 OK OK 457 453 473 456 489 C2' C B 16 OK OK 491 487 504 490 520 C2' G B 17 OK OK 522 518 538 521 554 C2' G B 18 OK OK 556 552 573 555 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' C A 2 OK OK 35 53 38 39 68 C3' G A 3 OK OK 66 87 69 70 102 C3' C A 4 OK OK 100 118 103 104 133 C3' U A 5 OK OK 131 149 134 135 163 C3' G A 6 OK OK 161 182 164 165 197 C3' C A 7 OK OK 195 213 198 199 228 C3' G A 8 OK OK 226 247 229 230 262 C3' G A 9 OK OK 260 281 263 264 295 C3' C B 10 OK OK 293 311 296 297 327 C3' C B 11 OK OK 325 343 328 329 358 C3' G B 12 OK OK 356 377 359 360 392 C3' C B 13 OK OK 390 408 393 394 423 C3' U B 14 OK OK 421 439 424 425 453 C3' G B 15 OK OK 451 472 454 455 487 C3' C B 16 OK OK 485 503 488 489 518 C3' G B 17 OK OK 516 537 519 520 552 C3' G B 18 OK OK 550 571 553 554 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' C A 2 OK OK 37 52 34 36 66 C4' G A 3 OK OK 68 86 65 67 100 C4' C A 4 OK OK 102 117 99 101 131 C4' U A 5 OK OK 133 148 130 132 161 C4' G A 6 OK OK 163 181 160 162 195 C4' C A 7 OK OK 197 212 194 196 226 C4' G A 8 OK OK 228 246 225 227 260 C4' G A 9 OK OK 262 280 259 261 293 C4' C B 10 OK OK 295 310 292 294 325 C4' C B 11 OK OK 327 342 324 326 356 C4' G B 12 OK OK 358 376 355 357 390 C4' C B 13 OK OK 392 407 389 391 421 C4' U B 14 OK OK 423 438 420 422 451 C4' G B 15 OK OK 453 471 450 452 485 C4' C B 16 OK OK 487 502 484 486 516 C4' G B 17 OK OK 518 536 515 517 550 C4' G B 18 OK OK 552 570 549 551 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 2 OK OK 33 50 51 35 65 C5' G A 3 OK OK 64 84 85 66 99 C5' C A 4 OK OK 98 115 116 100 130 C5' U A 5 OK OK 129 146 147 131 160 C5' G A 6 OK OK 159 179 180 161 194 C5' C A 7 OK OK 193 210 211 195 225 C5' G A 8 OK OK 224 244 245 226 259 C5' G A 9 OK OK 258 278 279 260 292 C5' C B 10 OK OK 291 308 309 293 324 C5' C B 11 OK OK 323 340 341 325 355 C5' G B 12 OK OK 354 374 375 356 389 C5' C B 13 OK OK 388 405 406 390 420 C5' U B 14 OK OK 419 436 437 421 450 C5' G B 15 OK OK 449 469 470 451 484 C5' C B 16 OK OK 483 500 501 485 515 C5' G B 17 OK OK 514 534 535 516 549 C5' G B 18 OK OK 548 568 569 550 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P C A 2 distorted distorted 6 31 32 33 61 P G A 3 distorted distorted 38 62 63 64 95 P C A 4 distorted distorted 69 96 97 98 126 P U A 5 distorted distorted 103 127 128 129 156 P G A 6 distorted distorted 134 157 158 159 190 P C A 7 distorted distorted 164 191 192 193 221 P G A 8 distorted distorted 198 222 223 224 255 P G A 9 distorted distorted 229 256 257 258 320 P C B 11 distorted distorted 296 321 322 323 351 P G B 12 distorted distorted 328 352 353 354 385 P C B 13 distorted distorted 359 386 387 388 416 P U B 14 distorted distorted 393 417 418 419 446 P G B 15 distorted distorted 424 447 448 449 480 P C B 16 distorted distorted 454 481 482 483 511 P G B 17 distorted distorted 488 512 513 514 545 P G B 18 distorted distorted 519 546 547 548 ---------------------------------------------------------------------------------