ID code: '2KVN' 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' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' U A 6 alpha beta 170 190 176 173 205 C1' U A 7 alpha beta 200 220 206 203 235 C1' G A 8 alpha beta 230 253 236 233 269 C1' A A 9 alpha beta 264 286 270 267 302 C1' G A 10 alpha beta 297 320 303 300 336 C1' U A 11 alpha beta 331 351 337 334 366 C1' U A 12 alpha beta 361 381 367 364 396 C1' C A 13 alpha beta 391 411 397 394 427 C1' A A 14 alpha beta 422 444 428 425 460 C1' C A 15 alpha beta 455 475 461 458 491 C1' C A 16 alpha beta 486 506 492 489 522 C1' A A 17 alpha beta 517 540 523 520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' A A 5 OK OK 142 138 157 141 173 C2' U A 6 OK OK 175 171 188 174 203 C2' U A 7 OK OK 205 201 218 204 233 C2' G A 8 OK OK 235 231 251 234 267 C2' A A 9 OK OK 269 265 284 268 300 C2' G A 10 OK OK 302 298 318 301 334 C2' U A 11 OK OK 336 332 349 335 364 C2' U A 12 OK OK 366 362 379 365 394 C2' C A 13 OK OK 396 392 409 395 425 C2' A A 14 OK OK 427 423 442 426 458 C2' C A 15 OK OK 460 456 473 459 489 C2' C A 16 OK OK 491 487 504 490 520 C2' A A 17 OK OK 522 518 538 521 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' A A 5 OK OK 136 156 139 140 171 C3' U A 6 OK OK 169 187 172 173 201 C3' U A 7 OK OK 199 217 202 203 231 C3' G A 8 OK OK 229 250 232 233 265 C3' A A 9 OK OK 263 283 266 267 298 C3' G A 10 OK OK 296 317 299 300 332 C3' U A 11 OK OK 330 348 333 334 362 C3' U A 12 OK OK 360 378 363 364 392 C3' C A 13 OK OK 390 408 393 394 423 C3' A A 14 OK OK 421 441 424 425 456 C3' C A 15 OK OK 454 472 457 458 487 C3' C A 16 OK OK 485 503 488 489 518 C3' A A 17 OK OK 516 536 519 520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' A A 5 OK OK 138 155 135 137 169 C4' U A 6 OK OK 171 186 168 170 199 C4' U A 7 OK OK 201 216 198 200 229 C4' G A 8 OK OK 231 249 228 230 263 C4' A A 9 OK OK 265 282 262 264 296 C4' G A 10 OK OK 298 316 295 297 330 C4' U A 11 OK OK 332 347 329 331 360 C4' U A 12 OK OK 362 377 359 361 390 C4' C A 13 OK OK 392 407 389 391 421 C4' A A 14 OK OK 423 440 420 422 454 C4' C A 15 OK OK 456 471 453 455 485 C4' C A 16 OK OK 487 502 484 486 516 C4' A A 17 OK OK 518 535 515 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' A A 5 OK OK 134 153 154 136 168 C5' U A 6 OK OK 167 184 185 169 198 C5' U A 7 OK OK 197 214 215 199 228 C5' G A 8 OK OK 227 247 248 229 262 C5' A A 9 OK OK 261 280 281 263 295 C5' G A 10 OK OK 294 314 315 296 329 C5' U A 11 OK OK 328 345 346 330 359 C5' U A 12 OK OK 358 375 376 360 389 C5' C A 13 OK OK 388 405 406 390 420 C5' A A 14 OK OK 419 438 439 421 453 C5' C A 15 OK OK 452 469 470 454 484 C5' C A 16 OK OK 483 500 501 485 515 C5' A A 17 OK OK 514 533 534 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P A A 5 distorted distorted 105 132 133 134 164 P U A 6 distorted distorted 139 165 166 167 194 P U A 7 distorted distorted 172 195 196 197 224 P G A 8 distorted distorted 202 225 226 227 258 P A A 9 distorted distorted 232 259 260 261 291 P G A 10 distorted distorted 266 292 293 294 325 P U A 11 distorted distorted 299 326 327 328 355 P U A 12 distorted distorted 333 356 357 358 385 P C A 13 distorted distorted 363 386 387 388 416 P A A 14 distorted distorted 393 417 418 419 449 P C A 15 distorted distorted 424 450 451 452 480 P C A 16 distorted distorted 457 481 482 483 511 P A A 17 distorted distorted 488 512 513 514 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