ID code: '2LBK' 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' C A 5 alpha beta 140 160 146 143 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' U A 8 alpha beta 232 252 238 235 267 C1' C A 9 alpha beta 262 282 268 265 298 C1' C A 10 alpha beta 293 313 299 296 329 C1' C A 11 alpha beta 324 344 330 327 360 C1' G A 12 alpha beta 355 378 361 358 394 C1' G A 13 alpha beta 389 412 395 392 428 C1' U A 14 alpha beta 423 443 429 426 458 C1' C A 15 alpha beta 453 473 459 456 489 C1' U A 16 alpha beta 484 504 490 487 519 C1' C A 17 alpha beta 514 535 520 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 5 OK OK 145 141 158 144 174 C2' C A 6 OK OK 176 172 189 175 205 C2' U A 7 OK OK 207 203 220 206 235 C2' U A 8 OK OK 237 233 250 236 265 C2' C A 9 OK OK 267 263 280 266 296 C2' C A 10 OK OK 298 294 311 297 327 C2' C A 11 OK OK 329 325 342 328 358 C2' G A 12 OK OK 360 356 376 359 392 C2' G A 13 OK OK 394 390 410 393 426 C2' U A 14 OK OK 428 424 441 427 456 C2' C A 15 OK OK 458 454 471 457 487 C2' U A 16 OK OK 489 485 502 488 517 C2' C A 17 OK OK 519 515 533 518 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 5 OK OK 139 157 142 143 172 C3' C A 6 OK OK 170 188 173 174 203 C3' U A 7 OK OK 201 219 204 205 233 C3' U A 8 OK OK 231 249 234 235 263 C3' C A 9 OK OK 261 279 264 265 294 C3' C A 10 OK OK 292 310 295 296 325 C3' C A 11 OK OK 323 341 326 327 356 C3' G A 12 OK OK 354 375 357 358 390 C3' G A 13 OK OK 388 409 391 392 424 C3' U A 14 OK OK 422 440 425 426 454 C3' C A 15 OK OK 452 470 455 456 485 C3' U A 16 OK OK 483 501 486 487 515 C3' C A 17 OK OK 513 531 516 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 5 OK OK 141 156 138 140 170 C4' C A 6 OK OK 172 187 169 171 201 C4' U A 7 OK OK 203 218 200 202 231 C4' U A 8 OK OK 233 248 230 232 261 C4' C A 9 OK OK 263 278 260 262 292 C4' C A 10 OK OK 294 309 291 293 323 C4' C A 11 OK OK 325 340 322 324 354 C4' G A 12 OK OK 356 374 353 355 388 C4' G A 13 OK OK 390 408 387 389 422 C4' U A 14 OK OK 424 439 421 423 452 C4' C A 15 OK OK 454 469 451 453 483 C4' U A 16 OK OK 485 500 482 484 513 C4' C A 17 OK OK 515 530 512 514 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 5 OK OK 137 154 155 139 169 C5' C A 6 OK OK 168 185 186 170 200 C5' U A 7 OK OK 199 216 217 201 230 C5' U A 8 OK OK 229 246 247 231 260 C5' C A 9 OK OK 259 276 277 261 291 C5' C A 10 OK OK 290 307 308 292 322 C5' C A 11 OK OK 321 338 339 323 353 C5' G A 12 OK OK 352 372 373 354 387 C5' G A 13 OK OK 386 406 407 388 421 C5' U A 14 OK OK 420 437 438 422 451 C5' C A 15 OK OK 450 467 468 452 482 C5' U A 16 OK OK 481 498 499 483 512 C5' C A 17 OK OK 511 528 529 513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 C A 5 distorted distorted 109 135 136 137 165 P C A 6 distorted distorted 142 166 167 168 196 P U A 7 distorted distorted 173 197 198 199 226 P U A 8 distorted distorted 204 227 228 229 256 P C A 9 distorted distorted 234 257 258 259 287 P C A 10 distorted distorted 264 288 289 290 318 P C A 11 distorted distorted 295 319 320 321 349 P G A 12 distorted distorted 326 350 351 352 383 P G A 13 distorted distorted 357 384 385 386 417 P U A 14 distorted distorted 391 418 419 420 447 P C A 15 distorted distorted 425 448 449 450 478 P U A 16 distorted distorted 455 479 480 481 508 P C A 17 distorted distorted 486 509 510 511 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