ID code: '1WKS' 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' C A 3 alpha beta 73 93 79 76 109 C1' U A 4 alpha beta 104 124 110 107 139 C1' U A 5 alpha beta 134 154 140 137 169 C1' U A 6 alpha beta 164 184 170 167 199 C1' G A 7 alpha beta 194 217 200 197 233 C1' G A 8 alpha beta 228 251 234 231 267 C1' A A 9 alpha beta 262 284 268 265 300 C1' U A 10 alpha beta 295 315 301 298 330 C1' A A 11 alpha beta 325 347 331 328 363 C1' A A 12 alpha beta 358 380 364 361 396 C1' A A 13 alpha beta 391 413 397 394 429 C1' A A 14 alpha beta 424 446 430 427 462 C1' G A 15 alpha beta 457 480 463 460 496 C1' C A 16 alpha beta 491 511 497 494 527 C1' C A 17 alpha beta 522 543 528 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' U A 4 OK OK 109 105 122 108 137 C2' U A 5 OK OK 139 135 152 138 167 C2' U A 6 OK OK 169 165 182 168 197 C2' G A 7 OK OK 199 195 215 198 231 C2' G A 8 OK OK 233 229 249 232 265 C2' A A 9 OK OK 267 263 282 266 298 C2' U A 10 OK OK 300 296 313 299 328 C2' A A 11 OK OK 330 326 345 329 361 C2' A A 12 OK OK 363 359 378 362 394 C2' A A 13 OK OK 396 392 411 395 427 C2' A A 14 OK OK 429 425 444 428 460 C2' G A 15 OK OK 462 458 478 461 494 C2' C A 16 OK OK 496 492 509 495 525 C2' C A 17 OK OK 527 523 541 526 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' U A 4 OK OK 103 121 106 107 135 C3' U A 5 OK OK 133 151 136 137 165 C3' U A 6 OK OK 163 181 166 167 195 C3' G A 7 OK OK 193 214 196 197 229 C3' G A 8 OK OK 227 248 230 231 263 C3' A A 9 OK OK 261 281 264 265 296 C3' U A 10 OK OK 294 312 297 298 326 C3' A A 11 OK OK 324 344 327 328 359 C3' A A 12 OK OK 357 377 360 361 392 C3' A A 13 OK OK 390 410 393 394 425 C3' A A 14 OK OK 423 443 426 427 458 C3' G A 15 OK OK 456 477 459 460 492 C3' C A 16 OK OK 490 508 493 494 523 C3' C A 17 OK OK 521 539 524 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' U A 4 OK OK 105 120 102 104 133 C4' U A 5 OK OK 135 150 132 134 163 C4' U A 6 OK OK 165 180 162 164 193 C4' G A 7 OK OK 195 213 192 194 227 C4' G A 8 OK OK 229 247 226 228 261 C4' A A 9 OK OK 263 280 260 262 294 C4' U A 10 OK OK 296 311 293 295 324 C4' A A 11 OK OK 326 343 323 325 357 C4' A A 12 OK OK 359 376 356 358 390 C4' A A 13 OK OK 392 409 389 391 423 C4' A A 14 OK OK 425 442 422 424 456 C4' G A 15 OK OK 458 476 455 457 490 C4' C A 16 OK OK 492 507 489 491 521 C4' C A 17 OK OK 523 538 520 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' U A 4 OK OK 101 118 119 103 132 C5' U A 5 OK OK 131 148 149 133 162 C5' U A 6 OK OK 161 178 179 163 192 C5' G A 7 OK OK 191 211 212 193 226 C5' G A 8 OK OK 225 245 246 227 260 C5' A A 9 OK OK 259 278 279 261 293 C5' U A 10 OK OK 292 309 310 294 323 C5' A A 11 OK OK 322 341 342 324 356 C5' A A 12 OK OK 355 374 375 357 389 C5' A A 13 OK OK 388 407 408 390 422 C5' A A 14 OK OK 421 440 441 423 455 C5' G A 15 OK OK 454 474 475 456 489 C5' C A 16 OK OK 488 505 506 490 520 C5' C A 17 OK OK 519 536 537 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P U A 4 distorted distorted 75 99 100 101 128 P U A 5 distorted distorted 106 129 130 131 158 P U A 6 distorted distorted 136 159 160 161 188 P G A 7 distorted distorted 166 189 190 191 222 P G A 8 distorted distorted 196 223 224 225 256 P A A 9 distorted distorted 230 257 258 259 289 P U A 10 distorted distorted 264 290 291 292 319 P A A 11 distorted distorted 297 320 321 322 352 P A A 12 distorted distorted 327 353 354 355 385 P A A 13 distorted distorted 360 386 387 388 418 P A A 14 distorted distorted 393 419 420 421 451 P G A 15 distorted distorted 426 452 453 454 485 P C A 16 distorted distorted 459 486 487 488 516 P C A 17 distorted distorted 493 517 518 519 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