ID code: '2KPD' 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' U A 6 alpha beta 167 187 173 170 202 C1' C A 7 alpha beta 197 217 203 200 233 C1' A A 8 alpha beta 228 250 234 231 266 C1' G A 9 alpha beta 261 284 267 264 300 C1' U A 10 alpha beta 295 315 301 298 330 C1' U A 11 alpha beta 325 345 331 328 360 C1' U A 12 alpha beta 355 375 361 358 390 C1' G A 13 alpha beta 385 408 391 388 424 C1' C A 14 alpha beta 419 439 425 422 455 C1' U A 15 alpha beta 450 470 456 453 485 C1' C A 16 alpha beta 480 500 486 483 516 C1' A A 17 alpha beta 511 534 517 514 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 6 OK OK 172 168 185 171 200 C2' C A 7 OK OK 202 198 215 201 231 C2' A A 8 OK OK 233 229 248 232 264 C2' G A 9 OK OK 266 262 282 265 298 C2' U A 10 OK OK 300 296 313 299 328 C2' U A 11 OK OK 330 326 343 329 358 C2' U A 12 OK OK 360 356 373 359 388 C2' G A 13 OK OK 390 386 406 389 422 C2' C A 14 OK OK 424 420 437 423 453 C2' U A 15 OK OK 455 451 468 454 483 C2' C A 16 OK OK 485 481 498 484 514 C2' A A 17 OK OK 516 512 532 515 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 6 OK OK 166 184 169 170 198 C3' C A 7 OK OK 196 214 199 200 229 C3' A A 8 OK OK 227 247 230 231 262 C3' G A 9 OK OK 260 281 263 264 296 C3' U A 10 OK OK 294 312 297 298 326 C3' U A 11 OK OK 324 342 327 328 356 C3' U A 12 OK OK 354 372 357 358 386 C3' G A 13 OK OK 384 405 387 388 420 C3' C A 14 OK OK 418 436 421 422 451 C3' U A 15 OK OK 449 467 452 453 481 C3' C A 16 OK OK 479 497 482 483 512 C3' A A 17 OK OK 510 530 513 514 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 6 OK OK 168 183 165 167 196 C4' C A 7 OK OK 198 213 195 197 227 C4' A A 8 OK OK 229 246 226 228 260 C4' G A 9 OK OK 262 280 259 261 294 C4' U A 10 OK OK 296 311 293 295 324 C4' U A 11 OK OK 326 341 323 325 354 C4' U A 12 OK OK 356 371 353 355 384 C4' G A 13 OK OK 386 404 383 385 418 C4' C A 14 OK OK 420 435 417 419 449 C4' U A 15 OK OK 451 466 448 450 479 C4' C A 16 OK OK 481 496 478 480 510 C4' A A 17 OK OK 512 529 509 511 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 6 OK OK 164 181 182 166 195 C5' C A 7 OK OK 194 211 212 196 226 C5' A A 8 OK OK 225 244 245 227 259 C5' G A 9 OK OK 258 278 279 260 293 C5' U A 10 OK OK 292 309 310 294 323 C5' U A 11 OK OK 322 339 340 324 353 C5' U A 12 OK OK 352 369 370 354 383 C5' G A 13 OK OK 382 402 403 384 417 C5' C A 14 OK OK 416 433 434 418 448 C5' U A 15 OK OK 447 464 465 449 478 C5' C A 16 OK OK 477 494 495 479 509 C5' A A 17 OK OK 508 527 528 510 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 6 distorted distorted 138 162 163 164 191 P C A 7 distorted distorted 169 192 193 194 222 P A A 8 distorted distorted 199 223 224 225 255 P G A 9 distorted distorted 230 256 257 258 289 P U A 10 distorted distorted 263 290 291 292 319 P U A 11 distorted distorted 297 320 321 322 349 P U A 12 distorted distorted 327 350 351 352 379 P G A 13 distorted distorted 357 380 381 382 413 P C A 14 distorted distorted 387 414 415 416 444 P U A 15 distorted distorted 421 445 446 447 474 P C A 16 distorted distorted 452 475 476 477 505 P A A 17 distorted distorted 482 506 507 508 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