ID code: '1C4L' 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' G A 2 alpha beta 36 59 42 39 75 C1' A A 3 alpha beta 70 92 76 73 108 C1' C A 4 alpha beta 103 123 109 106 139 C1' U A 5 alpha beta 134 154 140 137 169 C1' C A 6 alpha beta 164 184 170 167 200 C1' A A 7 alpha beta 195 217 201 198 233 C1' G A 8 alpha beta 228 251 234 231 267 C1' G A 9 alpha beta 262 286 268 265 300 C1' C B 10 alpha beta 295 315 301 298 332 C1' C B 11 alpha beta 327 347 333 330 363 C1' U B 12 alpha beta 358 378 364 361 393 C1' G B 13 alpha beta 388 411 394 391 427 C1' C B 14 alpha beta 422 442 428 425 458 C1' G B 15 alpha beta 453 476 459 456 492 C1' U B 16 alpha beta 487 507 493 490 522 C1' C B 17 alpha beta 517 537 523 520 553 C1' G B 18 alpha beta 548 572 554 551 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 41 37 57 40 73 C2' A A 3 OK OK 75 71 90 74 106 C2' C A 4 OK OK 108 104 121 107 137 C2' U A 5 OK OK 139 135 152 138 167 C2' C A 6 OK OK 169 165 182 168 198 C2' A A 7 OK OK 200 196 215 199 231 C2' G A 8 OK OK 233 229 249 232 265 C2' G A 9 OK OK 267 263 284 266 298 C2' C B 10 OK OK 300 296 313 299 330 C2' C B 11 OK OK 332 328 345 331 361 C2' U B 12 OK OK 363 359 376 362 391 C2' G B 13 OK OK 393 389 409 392 425 C2' C B 14 OK OK 427 423 440 426 456 C2' G B 15 OK OK 458 454 474 457 490 C2' U B 16 OK OK 492 488 505 491 520 C2' C B 17 OK OK 522 518 535 521 551 C2' G B 18 OK OK 553 549 570 552 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' G A 2 OK OK 35 56 38 39 71 C3' A A 3 OK OK 69 89 72 73 104 C3' C A 4 OK OK 102 120 105 106 135 C3' U A 5 OK OK 133 151 136 137 165 C3' C A 6 OK OK 163 181 166 167 196 C3' A A 7 OK OK 194 214 197 198 229 C3' G A 8 OK OK 227 248 230 231 263 C3' G A 9 OK OK 261 282 264 265 296 C3' C B 10 OK OK 294 312 297 298 328 C3' C B 11 OK OK 326 344 329 330 359 C3' U B 12 OK OK 357 375 360 361 389 C3' G B 13 OK OK 387 408 390 391 423 C3' C B 14 OK OK 421 439 424 425 454 C3' G B 15 OK OK 452 473 455 456 488 C3' U B 16 OK OK 486 504 489 490 518 C3' C B 17 OK OK 516 534 519 520 549 C3' G B 18 OK OK 547 568 550 551 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' G A 2 OK OK 37 55 34 36 69 C4' A A 3 OK OK 71 88 68 70 102 C4' C A 4 OK OK 104 119 101 103 133 C4' U A 5 OK OK 135 150 132 134 163 C4' C A 6 OK OK 165 180 162 164 194 C4' A A 7 OK OK 196 213 193 195 227 C4' G A 8 OK OK 229 247 226 228 261 C4' G A 9 OK OK 263 281 260 262 294 C4' C B 10 OK OK 296 311 293 295 326 C4' C B 11 OK OK 328 343 325 327 357 C4' U B 12 OK OK 359 374 356 358 387 C4' G B 13 OK OK 389 407 386 388 421 C4' C B 14 OK OK 423 438 420 422 452 C4' G B 15 OK OK 454 472 451 453 486 C4' U B 16 OK OK 488 503 485 487 516 C4' C B 17 OK OK 518 533 515 517 547 C4' G B 18 OK OK 549 567 546 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 33 53 54 35 68 C5' A A 3 OK OK 67 86 87 69 101 C5' C A 4 OK OK 100 117 118 102 132 C5' U A 5 OK OK 131 148 149 133 162 C5' C A 6 OK OK 161 178 179 163 193 C5' A A 7 OK OK 192 211 212 194 226 C5' G A 8 OK OK 225 245 246 227 260 C5' G A 9 OK OK 259 279 280 261 293 C5' C B 10 OK OK 292 309 310 294 325 C5' C B 11 OK OK 324 341 342 326 356 C5' U B 12 OK OK 355 372 373 357 386 C5' G B 13 OK OK 385 405 406 387 420 C5' C B 14 OK OK 419 436 437 421 451 C5' G B 15 OK OK 450 470 471 452 485 C5' U B 16 OK OK 484 501 502 486 515 C5' C B 17 OK OK 514 531 532 516 546 C5' G B 18 OK OK 545 565 566 547 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P G A 2 distorted distorted 6 31 32 33 64 P A A 3 distorted distorted 38 65 66 67 97 P C A 4 distorted distorted 72 98 99 100 128 P U A 5 distorted distorted 105 129 130 131 158 P C A 6 distorted distorted 136 159 160 161 189 P A A 7 distorted distorted 166 190 191 192 222 P G A 8 distorted distorted 197 223 224 225 256 P G A 9 distorted distorted 230 257 258 259 321 P C B 11 distorted distorted 297 322 323 324 352 P U B 12 distorted distorted 329 353 354 355 382 P G B 13 distorted distorted 360 383 384 385 416 P C B 14 distorted distorted 390 417 418 419 447 P G B 15 distorted distorted 424 448 449 450 481 P U B 16 distorted distorted 455 482 483 484 511 P C B 17 distorted distorted 489 512 513 514 542 P G B 18 distorted distorted 519 543 544 545 ---------------------------------------------------------------------------------