ID code: '2FMP' 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' DC T 1 beta 4 9 7 27 C1' DC T 2 beta 23 28 26 46 C1' DG T 3 beta 42 47 45 68 C1' DA T 4 beta 64 69 67 89 C1' DC T 5 beta 85 90 88 108 C1' DG T 6 beta 104 109 107 130 C1' DG T 7 beta 126 131 129 152 C1' DC T 8 beta 148 153 151 171 C1' DG T 9 beta 167 172 170 193 C1' DC T 10 beta 189 194 192 212 C1' DA T 11 beta 208 213 211 233 C1' DT T 12 beta 229 234 232 253 C1' DC T 13 beta 249 254 252 272 C1' DA T 14 beta 268 273 271 293 C1' DG T 15 beta 289 294 292 315 C1' DC T 16 beta 311 316 314 332 C1' DG P 1 beta 328 333 331 354 C1' DC P 2 beta 350 355 353 373 C1' DT P 3 beta 369 374 372 393 C1' DG P 4 beta 389 394 392 415 C1' DA P 5 beta 411 416 414 436 C1' DT P 6 beta 432 437 435 456 C1' DG P 7 beta 452 457 455 478 C1' DC P 8 beta 474 479 477 497 C1' DG P 9 beta 493 498 496 517 C1' DOC P 10 beta 521 509 518 539 C1' DG D 1 beta 535 540 538 561 C1' DT D 2 beta 557 562 560 663 C1' DG D 5 beta 659 664 662 3408 C1' DCT A1338 beta 3412 3400 3409 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DC T 1 8 5 26 C2' DC T 2 27 24 45 C2' DG T 3 46 43 67 C2' DA T 4 68 65 88 C2' DC T 5 89 86 107 C2' DG T 6 108 105 129 C2' DG T 7 130 127 151 C2' DC T 8 152 149 170 C2' DG T 9 171 168 192 C2' DC T 10 193 190 211 C2' DA T 11 212 209 232 C2' DT T 12 233 230 252 C2' DC T 13 253 250 271 C2' DA T 14 272 269 292 C2' DG T 15 293 290 314 C2' DC T 16 315 312 331 C2' DG P 1 332 329 353 C2' DC P 2 354 351 372 C2' DT P 3 373 370 392 C2' DG P 4 393 390 414 C2' DA P 5 415 412 435 C2' DT P 6 436 433 455 C2' DG P 7 456 453 477 C2' DC P 8 478 475 496 C2' DG P 9 497 494 518 C2' DOC P 10 517 519 538 C2' DG D 1 539 536 560 C2' DT D 2 561 558 662 C2' DG D 5 663 660 3409 C2' DCT A1338 3408 3410 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC T 1 OK 3 6 7 24 C3' DC T 2 OK 22 25 26 43 C3' DG T 3 OK 41 44 45 65 C3' DA T 4 OK 63 66 67 86 C3' DC T 5 OK 84 87 88 105 C3' DG T 6 OK 103 106 107 127 C3' DG T 7 OK 125 128 129 149 C3' DC T 8 OK 147 150 151 168 C3' DG T 9 OK 166 169 170 190 C3' DC T 10 OK 188 191 192 209 C3' DA T 11 OK 207 210 211 230 C3' DT T 12 OK 228 231 232 250 C3' DC T 13 OK 248 251 252 269 C3' DA T 14 OK 267 270 271 290 C3' DG T 15 OK 288 291 292 312 C3' DC T 16 OK 310 313 314 329 C3' DG P 1 OK 327 330 331 351 C3' DC P 2 OK 349 352 353 370 C3' DT P 3 OK 368 371 372 390 C3' DG P 4 OK 388 391 392 412 C3' DA P 5 OK 410 413 414 433 C3' DT P 6 OK 431 434 435 453 C3' DG P 7 OK 451 454 455 475 C3' DC P 8 OK 473 476 477 494 C3' DG P 9 OK 492 495 496 519 C3' DOC P 10 520 518 536 C3' DG D 1 OK 534 537 538 558 C3' DT D 2 OK 556 559 560 660 C3' DG D 5 OK 658 661 662 3410 C3' DCT A1338 3411 3409 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC T 1 OK 5 2 4 22 C4' DC T 2 OK 24 21 23 41 C4' DG T 3 OK 43 40 42 63 C4' DA T 4 OK 65 62 64 84 C4' DC T 5 OK 86 83 85 103 C4' DG T 6 OK 105 102 104 125 C4' DG T 7 OK 127 124 126 147 C4' DC T 8 OK 149 146 148 166 C4' DG T 9 OK 168 165 167 188 C4' DC T 10 OK 190 187 189 207 C4' DA T 11 OK 209 206 208 228 C4' DT T 12 OK 230 227 229 248 C4' DC T 13 OK 250 247 249 267 C4' DA T 14 OK 269 266 268 288 C4' DG T 15 OK 290 287 289 310 C4' DC T 16 OK 312 309 311 327 C4' DG P 1 OK 329 326 328 349 C4' DC P 2 OK 351 348 350 368 C4' DT P 3 OK 370 367 369 388 C4' DG P 4 OK 390 387 389 410 C4' DA P 5 OK 412 409 411 431 C4' DT P 6 OK 433 430 432 451 C4' DG P 7 OK 453 450 452 473 C4' DC P 8 OK 475 472 474 492 C4' DG P 9 OK 494 491 493 520 C4' DOC P 10 OK 519 522 521 534 C4' DG D 1 OK 536 533 535 556 C4' DT D 2 OK 558 555 557 658 C4' DG D 5 OK 660 657 659 3411 C4' DCT A1338 OK 3410 3413 3412 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC T 1 1 3 21 C5' DC T 2 20 22 40 C5' DG T 3 39 41 62 C5' DA T 4 61 63 83 C5' DC T 5 82 84 102 C5' DG T 6 101 103 124 C5' DG T 7 123 125 146 C5' DC T 8 145 147 165 C5' DG T 9 164 166 187 C5' DC T 10 186 188 206 C5' DA T 11 205 207 227 C5' DT T 12 226 228 247 C5' DC T 13 246 248 266 C5' DA T 14 265 267 287 C5' DG T 15 286 288 309 C5' DC T 16 308 310 326 C5' DG P 1 325 327 348 C5' DC P 2 347 349 367 C5' DT P 3 366 368 387 C5' DG P 4 386 388 409 C5' DA P 5 408 410 430 C5' DT P 6 429 431 450 C5' DG P 7 449 451 472 C5' DC P 8 471 473 491 C5' DG P 9 490 492 522 C5' DOC P 10 523 520 533 C5' DG D 1 532 534 555 C5' DT D 2 554 556 657 C5' DG D 5 656 658 3413 C5' DCT A1338 3414 3411 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P DC T 2 distorted distorted 6 18 19 20 36 P DG T 3 distorted distorted 25 37 38 39 58 P DA T 4 distorted distorted 44 59 60 61 79 P DC T 5 distorted distorted 66 80 81 82 98 P DG T 6 distorted distorted 87 99 100 101 120 P DG T 7 distorted distorted 106 121 122 123 142 P DC T 8 distorted distorted 128 143 144 145 161 P DG T 9 distorted distorted 150 162 163 164 183 P DC T 10 distorted distorted 169 184 185 186 202 P DA T 11 distorted distorted 191 203 204 205 223 P DT T 12 distorted distorted 210 224 225 226 243 P DC T 13 distorted distorted 231 244 245 246 262 P DA T 14 distorted distorted 251 263 264 265 283 P DG T 15 distorted distorted 270 284 285 286 305 P DC T 16 distorted distorted 291 306 307 308 344 P DC P 2 distorted distorted 330 345 346 347 363 P DT P 3 distorted distorted 352 364 365 366 383 P DG P 4 distorted distorted 371 384 385 386 405 P DA P 5 distorted distorted 391 406 407 408 426 P DT P 6 distorted distorted 413 427 428 429 446 P DG P 7 distorted distorted 434 447 448 449 468 P DC P 8 distorted distorted 454 469 470 471 487 P DG P 9 distorted distorted 476 488 489 490 524 P DOC P 10 distorted distorted 495 525 526 523 529 P DG D 1 distorted distorted 530 531 532 551 P DT D 2 distorted distorted 537 552 553 554 571 P DC D 3 559 572 P DC D 3 559 609 P DG D 4 610 P DG D 4 653 P DG D 5 distorted distorted 654 655 656 ---------------------------------------------------------------------------------