ID code: '2KPC' 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' U A 1 alpha beta 4 24 10 7 40 C1' G A 2 alpha beta 35 58 41 38 74 C1' A A 3 alpha beta 69 91 75 72 107 C1' G A 4 alpha beta 102 125 108 105 141 C1' C A 5 alpha beta 136 156 142 139 172 C1' A A 6 alpha beta 167 189 173 170 205 C1' C A 7 alpha beta 200 220 206 203 236 C1' A A 8 alpha beta 231 253 237 234 269 C1' G A 9 alpha beta 264 287 270 267 303 C1' U A 10 alpha beta 298 318 304 301 333 C1' U A 11 alpha beta 328 348 334 331 363 C1' U A 12 alpha beta 358 378 364 361 393 C1' G A 13 alpha beta 388 411 394 391 427 C1' C A 14 alpha beta 422 442 428 425 458 C1' U A 15 alpha beta 453 473 459 456 488 C1' C A 16 alpha beta 483 503 489 486 519 C1' A A 17 alpha beta 514 537 520 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK OK 9 5 22 8 38 C2' G A 2 OK OK 40 36 56 39 72 C2' A A 3 OK OK 74 70 89 73 105 C2' G A 4 OK OK 107 103 123 106 139 C2' C A 5 OK OK 141 137 154 140 170 C2' A A 6 OK OK 172 168 187 171 203 C2' C A 7 OK OK 205 201 218 204 234 C2' A A 8 OK OK 236 232 251 235 267 C2' G A 9 OK OK 269 265 285 268 301 C2' U A 10 OK OK 303 299 316 302 331 C2' U A 11 OK OK 333 329 346 332 361 C2' U A 12 OK OK 363 359 376 362 391 C2' G A 13 OK OK 393 389 409 392 425 C2' C A 14 OK OK 427 423 440 426 456 C2' U A 15 OK OK 458 454 471 457 486 C2' C A 16 OK OK 488 484 501 487 517 C2' A A 17 OK OK 519 515 535 518 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK OK 3 21 6 7 36 C3' G A 2 OK OK 34 55 37 38 70 C3' A A 3 OK OK 68 88 71 72 103 C3' G A 4 OK OK 101 122 104 105 137 C3' C A 5 OK OK 135 153 138 139 168 C3' A A 6 OK OK 166 186 169 170 201 C3' C A 7 OK OK 199 217 202 203 232 C3' A A 8 OK OK 230 250 233 234 265 C3' G A 9 OK OK 263 284 266 267 299 C3' U A 10 OK OK 297 315 300 301 329 C3' U A 11 OK OK 327 345 330 331 359 C3' U A 12 OK OK 357 375 360 361 389 C3' G A 13 OK OK 387 408 390 391 423 C3' C A 14 OK OK 421 439 424 425 454 C3' U A 15 OK OK 452 470 455 456 484 C3' C A 16 OK OK 482 500 485 486 515 C3' A A 17 OK OK 513 533 516 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK OK 5 20 2 4 34 C4' G A 2 OK OK 36 54 33 35 68 C4' A A 3 OK OK 70 87 67 69 101 C4' G A 4 OK OK 103 121 100 102 135 C4' C A 5 OK OK 137 152 134 136 166 C4' A A 6 OK OK 168 185 165 167 199 C4' C A 7 OK OK 201 216 198 200 230 C4' A A 8 OK OK 232 249 229 231 263 C4' G A 9 OK OK 265 283 262 264 297 C4' U A 10 OK OK 299 314 296 298 327 C4' U A 11 OK OK 329 344 326 328 357 C4' U A 12 OK OK 359 374 356 358 387 C4' G A 13 OK OK 389 407 386 388 421 C4' C A 14 OK OK 423 438 420 422 452 C4' U A 15 OK OK 454 469 451 453 482 C4' C A 16 OK OK 484 499 481 483 513 C4' A A 17 OK OK 515 532 512 514 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 OK OK 1 18 19 3 33 C5' G A 2 OK OK 32 52 53 34 67 C5' A A 3 OK OK 66 85 86 68 100 C5' G A 4 OK OK 99 119 120 101 134 C5' C A 5 OK OK 133 150 151 135 165 C5' A A 6 OK OK 164 183 184 166 198 C5' C A 7 OK OK 197 214 215 199 229 C5' A A 8 OK OK 228 247 248 230 262 C5' G A 9 OK OK 261 281 282 263 296 C5' U A 10 OK OK 295 312 313 297 326 C5' U A 11 OK OK 325 342 343 327 356 C5' U A 12 OK OK 355 372 373 357 386 C5' G A 13 OK OK 385 405 406 387 420 C5' C A 14 OK OK 419 436 437 421 451 C5' U A 15 OK OK 450 467 468 452 481 C5' C A 16 OK OK 480 497 498 482 512 C5' A A 17 OK OK 511 530 531 513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P G A 2 distorted distorted 6 30 31 32 63 P A A 3 distorted distorted 37 64 65 66 96 P G A 4 distorted distorted 71 97 98 99 130 P C A 5 distorted distorted 104 131 132 133 161 P A A 6 distorted distorted 138 162 163 164 194 P C A 7 distorted distorted 169 195 196 197 225 P A A 8 distorted distorted 202 226 227 228 258 P G A 9 distorted distorted 233 259 260 261 292 P U A 10 distorted distorted 266 293 294 295 322 P U A 11 distorted distorted 300 323 324 325 352 P U A 12 distorted distorted 330 353 354 355 382 P G A 13 distorted distorted 360 383 384 385 416 P C A 14 distorted distorted 390 417 418 419 447 P U A 15 distorted distorted 424 448 449 450 477 P C A 16 distorted distorted 455 478 479 480 508 P A A 17 distorted distorted 485 509 510 511 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