ID code: 'PDT013' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 beta 4 9 7 30 C1' A A 2 beta 26 31 29 51 C1' C A 3 beta 47 52 50 70 C1' T A 4 beta 66 71 69 90 C1' A A 5 beta 86 91 89 111 C1' A A 6 beta 107 112 110 132 C1' G A 7 beta 128 133 131 154 C1' T A 8 beta 150 155 153 174 C1' C A 9 beta 170 175 173 193 C1' A A 10 beta 189 194 192 214 C1' A A 11 beta 210 215 213 235 C1' C A 12 beta 231 236 234 254 C1' C A 13 beta 250 255 253 271 C1' G B 21 beta 267 272 270 293 C1' G B 22 beta 289 294 292 315 C1' T B 23 beta 311 316 314 335 C1' T B 24 beta 331 336 334 355 C1' G B 25 beta 351 356 354 377 C1' A B 26 beta 373 378 376 398 C1' C B 27 beta 394 399 397 417 C1' T B 28 beta 413 418 416 437 C1' T B 29 beta 433 438 436 457 C1' A B 30 beta 453 458 456 478 C1' G B 31 beta 474 479 477 500 C1' T B 32 beta 496 501 499 520 C1' C B 33 beta 516 521 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 29 C2' A A 2 30 27 50 C2' C A 3 51 48 69 C2' T A 4 70 67 89 C2' A A 5 90 87 110 C2' A A 6 111 108 131 C2' G A 7 132 129 153 C2' T A 8 154 151 173 C2' C A 9 174 171 192 C2' A A 10 193 190 213 C2' A A 11 214 211 234 C2' C A 12 235 232 253 C2' C A 13 254 251 270 C2' G B 21 271 268 292 C2' G B 22 293 290 314 C2' T B 23 315 312 334 C2' T B 24 335 332 354 C2' G B 25 355 352 376 C2' A B 26 377 374 397 C2' C B 27 398 395 416 C2' T B 28 417 414 436 C2' T B 29 437 434 456 C2' A B 30 457 454 477 C2' G B 31 478 475 499 C2' T B 32 500 497 519 C2' C B 33 520 517 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 27 C3' A A 2 OK 25 28 29 48 C3' C A 3 OK 46 49 50 67 C3' T A 4 OK 65 68 69 87 C3' A A 5 OK 85 88 89 108 C3' A A 6 OK 106 109 110 129 C3' G A 7 OK 127 130 131 151 C3' T A 8 OK 149 152 153 171 C3' C A 9 OK 169 172 173 190 C3' A A 10 OK 188 191 192 211 C3' A A 11 OK 209 212 213 232 C3' C A 12 OK 230 233 234 251 C3' C A 13 OK 249 252 253 268 C3' G B 21 OK 266 269 270 290 C3' G B 22 OK 288 291 292 312 C3' T B 23 OK 310 313 314 332 C3' T B 24 OK 330 333 334 352 C3' G B 25 OK 350 353 354 374 C3' A B 26 OK 372 375 376 395 C3' C B 27 OK 393 396 397 414 C3' T B 28 OK 412 415 416 434 C3' T B 29 OK 432 435 436 454 C3' A B 30 OK 452 455 456 475 C3' G B 31 OK 473 476 477 497 C3' T B 32 OK 495 498 499 517 C3' C B 33 OK 515 518 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 25 C4' A A 2 OK 27 24 26 46 C4' C A 3 OK 48 45 47 65 C4' T A 4 OK 67 64 66 85 C4' A A 5 OK 87 84 86 106 C4' A A 6 OK 108 105 107 127 C4' G A 7 OK 129 126 128 149 C4' T A 8 OK 151 148 150 169 C4' C A 9 OK 171 168 170 188 C4' A A 10 OK 190 187 189 209 C4' A A 11 OK 211 208 210 230 C4' C A 12 OK 232 229 231 249 C4' C A 13 OK 251 248 250 266 C4' G B 21 OK 268 265 267 288 C4' G B 22 OK 290 287 289 310 C4' T B 23 OK 312 309 311 330 C4' T B 24 OK 332 329 331 350 C4' G B 25 OK 352 349 351 372 C4' A B 26 OK 374 371 373 393 C4' C B 27 OK 395 392 394 412 C4' T B 28 OK 414 411 413 432 C4' T B 29 OK 434 431 433 452 C4' A B 30 OK 454 451 453 473 C4' G B 31 OK 475 472 474 495 C4' T B 32 OK 497 494 496 515 C4' C B 33 OK 517 514 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 24 C5' A A 2 23 25 45 C5' C A 3 44 46 64 C5' T A 4 63 65 84 C5' A A 5 83 85 105 C5' A A 6 104 106 126 C5' G A 7 125 127 148 C5' T A 8 147 149 168 C5' C A 9 167 169 187 C5' A A 10 186 188 208 C5' A A 11 207 209 229 C5' C A 12 228 230 248 C5' C A 13 247 249 265 C5' G B 21 264 266 287 C5' G B 22 286 288 309 C5' T B 23 308 310 329 C5' T B 24 328 330 349 C5' G B 25 348 350 371 C5' A B 26 370 372 392 C5' C B 27 391 393 411 C5' T B 28 410 412 431 C5' T B 29 430 432 451 C5' A B 30 450 452 472 C5' G B 31 471 473 494 C5' T B 32 493 495 514 C5' C B 33 513 515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A A 2 distorted distorted 6 21 22 23 41 P C A 3 distorted distorted 28 42 43 44 60 P T A 4 distorted distorted 49 61 62 63 80 P A A 5 distorted distorted 68 81 82 83 101 P A A 6 distorted distorted 88 102 103 104 122 P G A 7 distorted distorted 109 123 124 125 144 P T A 8 distorted distorted 130 145 146 147 164 P C A 9 distorted distorted 152 165 166 167 183 P A A 10 distorted distorted 172 184 185 186 204 P A A 11 distorted distorted 191 205 206 207 225 P C A 12 distorted distorted 212 226 227 228 244 P C A 13 distorted distorted 233 245 246 247 283 P G B 22 distorted distorted 269 284 285 286 305 P T B 23 distorted distorted 291 306 307 308 325 P T B 24 distorted distorted 313 326 327 328 345 P G B 25 distorted distorted 333 346 347 348 367 P A B 26 distorted distorted 353 368 369 370 388 P C B 27 distorted distorted 375 389 390 391 407 P T B 28 distorted distorted 396 408 409 410 427 P T B 29 distorted distorted 415 428 429 430 447 P A B 30 distorted distorted 435 448 449 450 468 P G B 31 distorted distorted 455 469 470 471 490 P T B 32 distorted distorted 476 491 492 493 510 P C B 33 distorted distorted 498 511 512 513 ---------------------------------------------------------------------------------