ID code: '1NH2' 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' T E 1 beta 4 9 7 28 C1' G E 2 beta 24 29 27 50 C1' T E 3 beta 46 51 49 70 C1' A E 4 beta 66 71 69 90 C1' 5IU E 5 beta 95 81 91 111 C1' G E 6 beta 107 112 110 133 C1' T E 7 beta 129 134 132 153 C1' A E 8 beta 149 154 152 174 C1' T E 9 beta 170 175 173 194 C1' A E 10 beta 190 195 193 214 C1' 5IU E 11 beta 219 205 215 235 C1' A E 12 beta 231 236 234 256 C1' A E 13 beta 252 257 255 277 C1' A E 14 beta 273 278 276 298 C1' A E 15 beta 294 299 297 319 C1' C E 16 beta 315 320 318 336 C1' G F 1 beta 332 337 335 358 C1' T F 2 beta 354 359 357 378 C1' T F 3 beta 374 379 377 398 C1' T F 4 beta 394 399 397 418 C1' T F 5 beta 414 419 417 438 C1' A F 6 beta 434 439 437 459 C1' T F 7 beta 455 460 458 479 C1' A F 8 beta 475 480 478 500 C1' T F 9 beta 496 501 499 520 C1' A F 10 beta 516 521 519 541 C1' C F 11 beta 537 542 540 560 C1' A F 12 beta 556 561 559 581 C1' T F 13 beta 577 582 580 601 C1' A F 14 beta 597 602 600 622 C1' C F 15 beta 618 623 621 641 C1' A F 16 beta 637 642 640 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' T E 1 8 5 27 C2' G E 2 28 25 49 C2' T E 3 50 47 69 C2' A E 4 70 67 91 C2' 5IU E 5 90 92 110 C2' G E 6 111 108 132 C2' T E 7 133 130 152 C2' A E 8 153 150 173 C2' T E 9 174 171 193 C2' A E 10 194 191 215 C2' 5IU E 11 214 216 234 C2' A E 12 235 232 255 C2' A E 13 256 253 276 C2' A E 14 277 274 297 C2' A E 15 298 295 318 C2' C E 16 319 316 335 C2' G F 1 336 333 357 C2' T F 2 358 355 377 C2' T F 3 378 375 397 C2' T F 4 398 395 417 C2' T F 5 418 415 437 C2' A F 6 438 435 458 C2' T F 7 459 456 478 C2' A F 8 479 476 499 C2' T F 9 500 497 519 C2' A F 10 520 517 540 C2' C F 11 541 538 559 C2' A F 12 560 557 580 C2' T F 13 581 578 600 C2' A F 14 601 598 621 C2' C F 15 622 619 640 C2' A F 16 641 638 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' T E 1 OK 3 6 7 25 C3' G E 2 OK 23 26 27 47 C3' T E 3 OK 45 48 49 67 C3' A E 4 OK 65 68 69 92 C3' 5IU E 5 OK 93 94 91 108 C3' G E 6 OK 106 109 110 130 C3' T E 7 OK 128 131 132 150 C3' A E 8 OK 148 151 152 171 C3' T E 9 OK 169 172 173 191 C3' A E 10 OK 189 192 193 216 C3' 5IU E 11 OK 217 218 215 232 C3' A E 12 OK 230 233 234 253 C3' A E 13 OK 251 254 255 274 C3' A E 14 OK 272 275 276 295 C3' A E 15 OK 293 296 297 316 C3' C E 16 OK 314 317 318 333 C3' G F 1 OK 331 334 335 355 C3' T F 2 OK 353 356 357 375 C3' T F 3 OK 373 376 377 395 C3' T F 4 OK 393 396 397 415 C3' T F 5 OK 413 416 417 435 C3' A F 6 OK 433 436 437 456 C3' T F 7 OK 454 457 458 476 C3' A F 8 OK 474 477 478 497 C3' T F 9 OK 495 498 499 517 C3' A F 10 OK 515 518 519 538 C3' C F 11 OK 536 539 540 557 C3' A F 12 OK 555 558 559 578 C3' T F 13 OK 576 579 580 598 C3' A F 14 OK 596 599 600 619 C3' C F 15 OK 617 620 621 638 C3' A F 16 OK 636 639 640 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' T E 1 OK 5 2 4 23 C4' G E 2 OK 25 22 24 45 C4' T E 3 OK 47 44 46 65 C4' A E 4 OK 67 64 66 93 C4' 5IU E 5 OK 92 96 95 106 C4' G E 6 OK 108 105 107 128 C4' T E 7 OK 130 127 129 148 C4' A E 8 OK 150 147 149 169 C4' T E 9 OK 171 168 170 189 C4' A E 10 OK 191 188 190 217 C4' 5IU E 11 OK 216 220 219 230 C4' A E 12 OK 232 229 231 251 C4' A E 13 OK 253 250 252 272 C4' A E 14 OK 274 271 273 293 C4' A E 15 OK 295 292 294 314 C4' C E 16 OK 316 313 315 331 C4' G F 1 OK 333 330 332 353 C4' T F 2 OK 355 352 354 373 C4' T F 3 OK 375 372 374 393 C4' T F 4 OK 395 392 394 413 C4' T F 5 OK 415 412 414 433 C4' A F 6 OK 435 432 434 454 C4' T F 7 OK 456 453 455 474 C4' A F 8 OK 476 473 475 495 C4' T F 9 OK 497 494 496 515 C4' A F 10 OK 517 514 516 536 C4' C F 11 OK 538 535 537 555 C4' A F 12 OK 557 554 556 576 C4' T F 13 OK 578 575 577 596 C4' A F 14 OK 598 595 597 617 C4' C F 15 OK 619 616 618 636 C4' A F 16 OK 638 635 637 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' T E 1 1 3 22 C5' G E 2 21 23 44 C5' T E 3 43 45 64 C5' A E 4 63 65 96 C5' 5IU E 5 97 93 105 C5' G E 6 104 106 127 C5' T E 7 126 128 147 C5' A E 8 146 148 168 C5' T E 9 167 169 188 C5' A E 10 187 189 220 C5' 5IU E 11 221 217 229 C5' A E 12 228 230 250 C5' A E 13 249 251 271 C5' A E 14 270 272 292 C5' A E 15 291 293 313 C5' C E 16 312 314 330 C5' G F 1 329 331 352 C5' T F 2 351 353 372 C5' T F 3 371 373 392 C5' T F 4 391 393 412 C5' T F 5 411 413 432 C5' A F 6 431 433 453 C5' T F 7 452 454 473 C5' A F 8 472 474 494 C5' T F 9 493 495 514 C5' A F 10 513 515 535 C5' C F 11 534 536 554 C5' A F 12 553 555 575 C5' T F 13 574 576 595 C5' A F 14 594 596 616 C5' C F 15 615 617 635 C5' A F 16 634 636 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G E 2 distorted distorted 6 19 20 21 40 P T E 3 distorted distorted 26 41 42 43 60 P A E 4 distorted distorted 48 61 62 63 98 P 5IU E 5 OK OK 68 99 100 97 101 P G E 6 distorted distorted 94 102 103 104 123 P T E 7 distorted distorted 109 124 125 126 143 P A E 8 distorted distorted 131 144 145 146 164 P T E 9 distorted distorted 151 165 166 167 184 P A E 10 distorted distorted 172 185 186 187 222 P 5IU E 11 OK OK 192 223 224 221 225 P A E 12 distorted distorted 218 226 227 228 246 P A E 13 distorted distorted 233 247 248 249 267 P A E 14 distorted distorted 254 268 269 270 288 P A E 15 distorted distorted 275 289 290 291 309 P C E 16 distorted distorted 296 310 311 312 348 P T F 2 distorted distorted 334 349 350 351 368 P T F 3 distorted distorted 356 369 370 371 388 P T F 4 distorted distorted 376 389 390 391 408 P T F 5 distorted distorted 396 409 410 411 428 P A F 6 distorted distorted 416 429 430 431 449 P T F 7 distorted distorted 436 450 451 452 469 P A F 8 distorted distorted 457 470 471 472 490 P T F 9 distorted distorted 477 491 492 493 510 P A F 10 distorted distorted 498 511 512 513 531 P C F 11 distorted distorted 518 532 533 534 550 P A F 12 distorted distorted 539 551 552 553 571 P T F 13 distorted distorted 558 572 573 574 591 P A F 14 distorted distorted 579 592 593 594 612 P C F 15 distorted distorted 599 613 614 615 631 P A F 16 distorted distorted 620 632 633 634 ---------------------------------------------------------------------------------