ID code: '1MA7' 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' A C 1 beta 4 9 7 29 C1' T C 2 beta 25 30 28 49 C1' A C 3 beta 45 50 48 70 C1' A C 4 beta 66 71 69 91 C1' C C 5 beta 87 92 90 110 C1' T C 6 beta 106 111 109 130 C1' T C 7 beta 126 131 129 150 C1' A C 8 beta 146 151 149 171 C1' G C 9 beta 167 172 170 193 C1' T C 10 beta 189 194 192 213 C1' A C 11 beta 209 214 212 234 C1' T C 12 beta 230 235 233 254 C1' A C 13 beta 250 255 253 275 C1' A C 14 beta 271 276 274 296 C1' T C 15 beta 292 297 295 316 C1' G C 16 beta 312 317 315 339 C1' C D 19 beta 335 340 338 358 C1' A D 20 beta 354 359 357 379 C1' T D 21 beta 375 380 378 399 C1' T D 22 beta 395 400 398 419 C1' A D 23 beta 415 420 418 440 C1' T D 24 beta 436 441 439 460 C1' A D 25 beta 456 461 459 481 C1' C D 26 beta 477 482 480 500 C1' T D 27 beta 496 501 499 520 C1' A D 28 beta 516 521 519 541 C1' A D 29 beta 537 542 540 562 C1' G D 30 beta 558 563 561 584 C1' T D 31 beta 580 585 583 604 C1' T D 32 beta 600 605 603 624 C1' A D 33 beta 620 625 623 645 C1' T D 34 beta 641 646 644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A C 1 8 5 28 C2' T C 2 29 26 48 C2' A C 3 49 46 69 C2' A C 4 70 67 90 C2' C C 5 91 88 109 C2' T C 6 110 107 129 C2' T C 7 130 127 149 C2' A C 8 150 147 170 C2' G C 9 171 168 192 C2' T C 10 193 190 212 C2' A C 11 213 210 233 C2' T C 12 234 231 253 C2' A C 13 254 251 274 C2' A C 14 275 272 295 C2' T C 15 296 293 315 C2' G C 16 316 313 338 C2' C D 19 339 336 357 C2' A D 20 358 355 378 C2' T D 21 379 376 398 C2' T D 22 399 396 418 C2' A D 23 419 416 439 C2' T D 24 440 437 459 C2' A D 25 460 457 480 C2' C D 26 481 478 499 C2' T D 27 500 497 519 C2' A D 28 520 517 540 C2' A D 29 541 538 561 C2' G D 30 562 559 583 C2' T D 31 584 581 603 C2' T D 32 604 601 623 C2' A D 33 624 621 644 C2' T D 34 645 642 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A C 1 OK 3 6 7 26 C3' T C 2 OK 24 27 28 46 C3' A C 3 OK 44 47 48 67 C3' A C 4 OK 65 68 69 88 C3' C C 5 OK 86 89 90 107 C3' T C 6 OK 105 108 109 127 C3' T C 7 OK 125 128 129 147 C3' A C 8 OK 145 148 149 168 C3' G C 9 OK 166 169 170 190 C3' T C 10 OK 188 191 192 210 C3' A C 11 OK 208 211 212 231 C3' T C 12 OK 229 232 233 251 C3' A C 13 OK 249 252 253 272 C3' A C 14 OK 270 273 274 293 C3' T C 15 OK 291 294 295 313 C3' G C 16 OK 311 314 315 336 C3' C D 19 OK 334 337 338 355 C3' A D 20 OK 353 356 357 376 C3' T D 21 OK 374 377 378 396 C3' T D 22 OK 394 397 398 416 C3' A D 23 OK 414 417 418 437 C3' T D 24 OK 435 438 439 457 C3' A D 25 OK 455 458 459 478 C3' C D 26 OK 476 479 480 497 C3' T D 27 OK 495 498 499 517 C3' A D 28 OK 515 518 519 538 C3' A D 29 OK 536 539 540 559 C3' G D 30 OK 557 560 561 581 C3' T D 31 OK 579 582 583 601 C3' T D 32 OK 599 602 603 621 C3' A D 33 OK 619 622 623 642 C3' T D 34 OK 640 643 644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A C 1 OK 5 2 4 24 C4' T C 2 OK 26 23 25 44 C4' A C 3 OK 46 43 45 65 C4' A C 4 OK 67 64 66 86 C4' C C 5 OK 88 85 87 105 C4' T C 6 OK 107 104 106 125 C4' T C 7 OK 127 124 126 145 C4' A C 8 OK 147 144 146 166 C4' G C 9 OK 168 165 167 188 C4' T C 10 OK 190 187 189 208 C4' A C 11 OK 210 207 209 229 C4' T C 12 OK 231 228 230 249 C4' A C 13 OK 251 248 250 270 C4' A C 14 OK 272 269 271 291 C4' T C 15 OK 293 290 292 311 C4' G C 16 OK 313 310 312 334 C4' C D 19 OK 336 333 335 353 C4' A D 20 OK 355 352 354 374 C4' T D 21 OK 376 373 375 394 C4' T D 22 OK 396 393 395 414 C4' A D 23 OK 416 413 415 435 C4' T D 24 OK 437 434 436 455 C4' A D 25 OK 457 454 456 476 C4' C D 26 OK 478 475 477 495 C4' T D 27 OK 497 494 496 515 C4' A D 28 OK 517 514 516 536 C4' A D 29 OK 538 535 537 557 C4' G D 30 OK 559 556 558 579 C4' T D 31 OK 581 578 580 599 C4' T D 32 OK 601 598 600 619 C4' A D 33 OK 621 618 620 640 C4' T D 34 OK 642 639 641 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A C 1 1 3 23 C5' T C 2 22 24 43 C5' A C 3 42 44 64 C5' A C 4 63 65 85 C5' C C 5 84 86 104 C5' T C 6 103 105 124 C5' T C 7 123 125 144 C5' A C 8 143 145 165 C5' G C 9 164 166 187 C5' T C 10 186 188 207 C5' A C 11 206 208 228 C5' T C 12 227 229 248 C5' A C 13 247 249 269 C5' A C 14 268 270 290 C5' T C 15 289 291 310 C5' G C 16 309 311 333 C5' C D 19 332 334 352 C5' A D 20 351 353 373 C5' T D 21 372 374 393 C5' T D 22 392 394 413 C5' A D 23 412 414 434 C5' T D 24 433 435 454 C5' A D 25 453 455 475 C5' C D 26 474 476 494 C5' T D 27 493 495 514 C5' A D 28 513 515 535 C5' A D 29 534 536 556 C5' G D 30 555 557 578 C5' T D 31 577 579 598 C5' T D 32 597 599 618 C5' A D 33 617 619 639 C5' T D 34 638 640 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P T C 2 distorted distorted 6 20 21 22 39 P A C 3 distorted distorted 27 40 41 42 60 P A C 4 distorted distorted 47 61 62 63 81 P C C 5 distorted distorted 68 82 83 84 100 P T C 6 distorted distorted 89 101 102 103 120 P T C 7 distorted distorted 108 121 122 123 140 P A C 8 distorted distorted 128 141 142 143 161 P G C 9 distorted distorted 148 162 163 164 183 P T C 10 distorted distorted 169 184 185 186 203 P A C 11 distorted distorted 191 204 205 206 224 P T C 12 distorted distorted 211 225 226 227 244 P A C 13 distorted distorted 232 245 246 247 265 P A C 14 distorted distorted 252 266 267 268 286 P T C 15 distorted distorted 273 287 288 289 306 P G C 16 distorted distorted 294 307 308 309 329 P C D 19 distorted distorted 330 331 332 348 P A D 20 distorted distorted 337 349 350 351 369 P T D 21 distorted distorted 356 370 371 372 389 P T D 22 distorted distorted 377 390 391 392 409 P A D 23 distorted distorted 397 410 411 412 430 P T D 24 distorted distorted 417 431 432 433 450 P A D 25 distorted distorted 438 451 452 453 471 P C D 26 distorted distorted 458 472 473 474 490 P T D 27 distorted distorted 479 491 492 493 510 P A D 28 distorted distorted 498 511 512 513 531 P A D 29 distorted distorted 518 532 533 534 552 P G D 30 distorted distorted 539 553 554 555 574 P T D 31 distorted distorted 560 575 576 577 594 P T D 32 distorted distorted 582 595 596 597 614 P A D 33 distorted distorted 602 615 616 617 635 P T D 34 distorted distorted 622 636 637 638 ---------------------------------------------------------------------------------