ID code: '2ISO' 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' DC T 6 beta 104 109 107 127 C1' DG T 7 beta 123 128 126 149 C1' DC T 8 beta 145 150 148 168 C1' DG T 9 beta 164 169 167 190 C1' DC T 10 beta 186 191 189 209 C1' DA T 11 beta 205 210 208 230 C1' DT T 12 beta 226 231 229 250 C1' DC T 13 beta 246 251 249 269 C1' DA T 14 beta 265 270 268 290 C1' DG T 15 beta 286 291 289 312 C1' DC T 16 beta 308 313 311 329 C1' DG P 1 beta 325 330 328 351 C1' DC P 2 beta 347 352 350 370 C1' DT P 3 beta 366 371 369 390 C1' DG P 4 beta 386 391 389 412 C1' DA P 5 beta 408 413 411 433 C1' DT P 6 beta 429 434 432 453 C1' DG P 7 beta 449 454 452 475 C1' DC P 8 beta 471 476 474 494 C1' DG P 9 beta 490 495 493 514 C1' DOC P 10 beta 518 506 515 536 C1' DG D 1 beta 532 537 535 558 C1' DT D 2 beta 554 559 557 578 C1' DC D 3 beta 574 579 577 597 C1' DG D 4 beta 593 598 596 619 C1' DG D 5 beta 615 620 618 3284 C1' GFF A 338 beta 3283 3285 3296 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' DC T 6 108 105 126 C2' DG T 7 127 124 148 C2' DC T 8 149 146 167 C2' DG T 9 168 165 189 C2' DC T 10 190 187 208 C2' DA T 11 209 206 229 C2' DT T 12 230 227 249 C2' DC T 13 250 247 268 C2' DA T 14 269 266 289 C2' DG T 15 290 287 311 C2' DC T 16 312 309 328 C2' DG P 1 329 326 350 C2' DC P 2 351 348 369 C2' DT P 3 370 367 389 C2' DG P 4 390 387 411 C2' DA P 5 412 409 432 C2' DT P 6 433 430 452 C2' DG P 7 453 450 474 C2' DC P 8 475 472 493 C2' DG P 9 494 491 515 C2' DOC P 10 514 516 535 C2' DG D 1 536 533 557 C2' DT D 2 558 555 577 C2' DC D 3 578 575 596 C2' DG D 4 597 594 618 C2' DG D 5 619 616 3296 C2' GFF A 338 3284 3297 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DC T 6 OK 103 106 107 124 C3' DG T 7 OK 122 125 126 146 C3' DC T 8 OK 144 147 148 165 C3' DG T 9 OK 163 166 167 187 C3' DC T 10 OK 185 188 189 206 C3' DA T 11 OK 204 207 208 227 C3' DT T 12 OK 225 228 229 247 C3' DC T 13 OK 245 248 249 266 C3' DA T 14 OK 264 267 268 287 C3' DG T 15 OK 285 288 289 309 C3' DC T 16 OK 307 310 311 326 C3' DG P 1 OK 324 327 328 348 C3' DC P 2 OK 346 349 350 367 C3' DT P 3 OK 365 368 369 387 C3' DG P 4 OK 385 388 389 409 C3' DA P 5 OK 407 410 411 430 C3' DT P 6 OK 428 431 432 450 C3' DG P 7 OK 448 451 452 472 C3' DC P 8 OK 470 473 474 491 C3' DG P 9 OK 489 492 493 516 C3' DOC P 10 517 515 533 C3' DG D 1 OK 531 534 535 555 C3' DT D 2 OK 553 556 557 575 C3' DC D 3 OK 573 576 577 594 C3' DG D 4 OK 592 595 596 616 C3' DG D 5 OK 614 617 618 3297 C3' GFF A 338 OK 3282 3298 3296 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DC T 6 OK 105 102 104 122 C4' DG T 7 OK 124 121 123 144 C4' DC T 8 OK 146 143 145 163 C4' DG T 9 OK 165 162 164 185 C4' DC T 10 OK 187 184 186 204 C4' DA T 11 OK 206 203 205 225 C4' DT T 12 OK 227 224 226 245 C4' DC T 13 OK 247 244 246 264 C4' DA T 14 OK 266 263 265 285 C4' DG T 15 OK 287 284 286 307 C4' DC T 16 OK 309 306 308 324 C4' DG P 1 OK 326 323 325 346 C4' DC P 2 OK 348 345 347 365 C4' DT P 3 OK 367 364 366 385 C4' DG P 4 OK 387 384 386 407 C4' DA P 5 OK 409 406 408 428 C4' DT P 6 OK 430 427 429 448 C4' DG P 7 OK 450 447 449 470 C4' DC P 8 OK 472 469 471 489 C4' DG P 9 OK 491 488 490 517 C4' DOC P 10 OK 516 519 518 531 C4' DG D 1 OK 533 530 532 553 C4' DT D 2 OK 555 552 554 573 C4' DC D 3 OK 575 572 574 592 C4' DG D 4 OK 594 591 593 614 C4' DG D 5 OK 616 613 615 3282 C4' GFF A 338 OK 3297 3281 3283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DC T 6 101 103 121 C5' DG T 7 120 122 143 C5' DC T 8 142 144 162 C5' DG T 9 161 163 184 C5' DC T 10 183 185 203 C5' DA T 11 202 204 224 C5' DT T 12 223 225 244 C5' DC T 13 243 245 263 C5' DA T 14 262 264 284 C5' DG T 15 283 285 306 C5' DC T 16 305 307 323 C5' DG P 1 322 324 345 C5' DC P 2 344 346 364 C5' DT P 3 363 365 384 C5' DG P 4 383 385 406 C5' DA P 5 405 407 427 C5' DT P 6 426 428 447 C5' DG P 7 446 448 469 C5' DC P 8 468 470 488 C5' DG P 9 487 489 519 C5' DOC P 10 520 517 530 C5' DG D 1 529 531 552 C5' DT D 2 551 553 572 C5' DC D 3 571 573 591 C5' DG D 4 590 592 613 C5' DG D 5 612 614 3281 C5' GFF A 338 3270 3282 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 DC T 6 distorted distorted 87 99 100 101 117 P DG T 7 distorted distorted 106 118 119 120 139 P DC T 8 distorted distorted 125 140 141 142 158 P DG T 9 distorted distorted 147 159 160 161 180 P DC T 10 distorted distorted 166 181 182 183 199 P DA T 11 distorted distorted 188 200 201 202 220 P DT T 12 distorted distorted 207 221 222 223 240 P DC T 13 distorted distorted 228 241 242 243 259 P DA T 14 distorted distorted 248 260 261 262 280 P DG T 15 distorted distorted 267 281 282 283 302 P DC T 16 distorted distorted 288 303 304 305 341 P DC P 2 distorted distorted 327 342 343 344 360 P DT P 3 distorted distorted 349 361 362 363 380 P DG P 4 distorted distorted 368 381 382 383 402 P DA P 5 distorted distorted 388 403 404 405 423 P DT P 6 distorted distorted 410 424 425 426 443 P DG P 7 distorted distorted 431 444 445 446 465 P DC P 8 distorted distorted 451 466 467 468 484 P DG P 9 distorted distorted 473 485 486 487 521 P DOC P 10 distorted distorted 492 522 523 520 526 P DG D 1 OK OK 527 528 529 548 P DT D 2 distorted distorted 534 549 550 551 568 P DC D 3 distorted distorted 556 569 570 571 587 P DG D 4 distorted distorted 576 588 589 590 609 P DG D 5 distorted distorted 595 610 611 612 ---------------------------------------------------------------------------------