ID code: '1JEY' 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 C 1 beta 4 9 7 30 C1' T C 2 beta 26 31 29 50 C1' T C 3 beta 46 51 49 70 C1' T C 4 beta 66 71 69 90 C1' T C 5 beta 86 91 89 110 C1' T C 6 beta 106 111 109 130 C1' A C 7 beta 126 131 129 151 C1' G C 8 beta 147 152 150 173 C1' T C 9 beta 169 174 172 193 C1' T C 10 beta 189 194 192 213 C1' T C 11 beta 209 214 212 233 C1' A C 12 beta 229 234 232 254 C1' T C 13 beta 250 255 253 274 C1' T C 14 beta 270 275 273 295 C1' A D 21 beta 291 296 294 316 C1' A D 22 beta 312 317 315 337 C1' T D 23 beta 333 338 336 357 C1' A D 24 beta 353 358 356 378 C1' A D 25 beta 374 379 377 399 C1' A D 26 beta 395 400 398 420 C1' C D 27 beta 416 421 419 439 C1' T D 28 beta 435 440 438 459 C1' A D 29 beta 455 460 458 480 C1' A D 30 beta 476 481 479 501 C1' A D 31 beta 497 502 500 522 C1' A D 32 beta 518 523 521 543 C1' A D 33 beta 539 544 542 564 C1' C D 34 beta 560 565 563 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 1 8 5 29 C2' T C 2 30 27 49 C2' T C 3 50 47 69 C2' T C 4 70 67 89 C2' T C 5 90 87 109 C2' T C 6 110 107 129 C2' A C 7 130 127 150 C2' G C 8 151 148 172 C2' T C 9 173 170 192 C2' T C 10 193 190 212 C2' T C 11 213 210 232 C2' A C 12 233 230 253 C2' T C 13 254 251 273 C2' T C 14 274 271 294 C2' A D 21 295 292 315 C2' A D 22 316 313 336 C2' T D 23 337 334 356 C2' A D 24 357 354 377 C2' A D 25 378 375 398 C2' A D 26 399 396 419 C2' C D 27 420 417 438 C2' T D 28 439 436 458 C2' A D 29 459 456 479 C2' A D 30 480 477 500 C2' A D 31 501 498 521 C2' A D 32 522 519 542 C2' A D 33 543 540 563 C2' C D 34 564 561 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 1 OK 3 6 7 27 C3' T C 2 OK 25 28 29 47 C3' T C 3 OK 45 48 49 67 C3' T C 4 OK 65 68 69 87 C3' T C 5 OK 85 88 89 107 C3' T C 6 OK 105 108 109 127 C3' A C 7 OK 125 128 129 148 C3' G C 8 OK 146 149 150 170 C3' T C 9 OK 168 171 172 190 C3' T C 10 OK 188 191 192 210 C3' T C 11 OK 208 211 212 230 C3' A C 12 OK 228 231 232 251 C3' T C 13 OK 249 252 253 271 C3' T C 14 OK 269 272 273 292 C3' A D 21 OK 290 293 294 313 C3' A D 22 OK 311 314 315 334 C3' T D 23 OK 332 335 336 354 C3' A D 24 OK 352 355 356 375 C3' A D 25 OK 373 376 377 396 C3' A D 26 OK 394 397 398 417 C3' C D 27 OK 415 418 419 436 C3' T D 28 OK 434 437 438 456 C3' A D 29 OK 454 457 458 477 C3' A D 30 OK 475 478 479 498 C3' A D 31 OK 496 499 500 519 C3' A D 32 OK 517 520 521 540 C3' A D 33 OK 538 541 542 561 C3' C D 34 OK 559 562 563 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 1 OK 5 2 4 25 C4' T C 2 OK 27 24 26 45 C4' T C 3 OK 47 44 46 65 C4' T C 4 OK 67 64 66 85 C4' T C 5 OK 87 84 86 105 C4' T C 6 OK 107 104 106 125 C4' A C 7 OK 127 124 126 146 C4' G C 8 OK 148 145 147 168 C4' T C 9 OK 170 167 169 188 C4' T C 10 OK 190 187 189 208 C4' T C 11 OK 210 207 209 228 C4' A C 12 OK 230 227 229 249 C4' T C 13 OK 251 248 250 269 C4' T C 14 OK 271 268 270 290 C4' A D 21 OK 292 289 291 311 C4' A D 22 OK 313 310 312 332 C4' T D 23 OK 334 331 333 352 C4' A D 24 OK 354 351 353 373 C4' A D 25 OK 375 372 374 394 C4' A D 26 OK 396 393 395 415 C4' C D 27 OK 417 414 416 434 C4' T D 28 OK 436 433 435 454 C4' A D 29 OK 456 453 455 475 C4' A D 30 OK 477 474 476 496 C4' A D 31 OK 498 495 497 517 C4' A D 32 OK 519 516 518 538 C4' A D 33 OK 540 537 539 559 C4' C D 34 OK 561 558 560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 1 1 3 24 C5' T C 2 23 25 44 C5' T C 3 43 45 64 C5' T C 4 63 65 84 C5' T C 5 83 85 104 C5' T C 6 103 105 124 C5' A C 7 123 125 145 C5' G C 8 144 146 167 C5' T C 9 166 168 187 C5' T C 10 186 188 207 C5' T C 11 206 208 227 C5' A C 12 226 228 248 C5' T C 13 247 249 268 C5' T C 14 267 269 289 C5' A D 21 288 290 310 C5' A D 22 309 311 331 C5' T D 23 330 332 351 C5' A D 24 350 352 372 C5' A D 25 371 373 393 C5' A D 26 392 394 414 C5' C D 27 413 415 433 C5' T D 28 432 434 453 C5' A D 29 452 454 474 C5' A D 30 473 475 495 C5' A D 31 494 496 516 C5' A D 32 515 517 537 C5' A D 33 536 538 558 C5' C D 34 557 559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P T C 2 distorted distorted 6 21 22 23 40 P T C 3 distorted distorted 28 41 42 43 60 P T C 4 distorted distorted 48 61 62 63 80 P T C 5 distorted distorted 68 81 82 83 100 P T C 6 distorted distorted 88 101 102 103 120 P A C 7 distorted distorted 108 121 122 123 141 P G C 8 distorted distorted 128 142 143 144 163 P T C 9 distorted distorted 149 164 165 166 183 P T C 10 distorted distorted 171 184 185 186 203 P T C 11 distorted distorted 191 204 205 206 223 P A C 12 distorted distorted 211 224 225 226 244 P T C 13 distorted distorted 231 245 246 247 264 P T C 14 distorted distorted 252 265 266 267 285 P A D 21 distorted distorted 286 287 288 306 P A D 22 distorted distorted 293 307 308 309 327 P T D 23 distorted distorted 314 328 329 330 347 P A D 24 distorted distorted 335 348 349 350 368 P A D 25 distorted distorted 355 369 370 371 389 P A D 26 distorted distorted 376 390 391 392 410 P C D 27 distorted distorted 397 411 412 413 429 P T D 28 distorted distorted 418 430 431 432 449 P A D 29 distorted distorted 437 450 451 452 470 P A D 30 distorted distorted 457 471 472 473 491 P A D 31 distorted distorted 478 492 493 494 512 P A D 32 distorted distorted 499 513 514 515 533 P A D 33 distorted distorted 520 534 535 536 554 P C D 34 distorted distorted 541 555 556 557 ---------------------------------------------------------------------------------