ID code: '1OH5' 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 E 1 beta 4 9 7 29 C1' G E 2 beta 25 30 28 51 C1' C E 3 beta 47 52 50 70 C1' T E 4 beta 66 71 69 90 C1' G E 5 beta 86 91 89 112 C1' C E 6 beta 108 113 111 131 C1' C E 7 beta 127 132 130 150 C1' A E 8 beta 146 151 149 171 C1' C E 9 beta 167 172 170 190 C1' G E 10 beta 186 191 189 212 C1' C E 11 beta 208 213 211 231 C1' A E 12 beta 227 232 230 252 C1' C E 13 beta 248 253 251 271 C1' C E 14 beta 267 272 270 290 C1' A E 15 beta 286 291 289 311 C1' G E 16 beta 307 312 310 333 C1' T E 17 beta 329 334 332 351 C1' A F 14 beta 347 352 350 372 C1' C F 15 beta 368 373 371 391 C1' T F 16 beta 387 392 390 411 C1' G F 17 beta 407 412 410 433 C1' G F 18 beta 429 434 432 455 C1' T F 19 beta 451 456 454 475 C1' G F 20 beta 471 476 474 497 C1' C F 21 beta 493 498 496 516 C1' A F 22 beta 512 517 515 537 C1' T F 23 beta 533 538 536 557 C1' G F 24 beta 553 558 556 579 C1' G F 25 beta 575 580 578 601 C1' C F 26 beta 597 602 600 620 C1' A F 27 beta 616 621 619 641 C1' G F 28 beta 637 642 640 663 C1' C F 29 beta 659 664 662 682 C1' T F 30 beta 678 683 681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A E 1 8 5 28 C2' G E 2 29 26 50 C2' C E 3 51 48 69 C2' T E 4 70 67 89 C2' G E 5 90 87 111 C2' C E 6 112 109 130 C2' C E 7 131 128 149 C2' A E 8 150 147 170 C2' C E 9 171 168 189 C2' G E 10 190 187 211 C2' C E 11 212 209 230 C2' A E 12 231 228 251 C2' C E 13 252 249 270 C2' C E 14 271 268 289 C2' A E 15 290 287 310 C2' G E 16 311 308 332 C2' T E 17 333 330 350 C2' A F 14 351 348 371 C2' C F 15 372 369 390 C2' T F 16 391 388 410 C2' G F 17 411 408 432 C2' G F 18 433 430 454 C2' T F 19 455 452 474 C2' G F 20 475 472 496 C2' C F 21 497 494 515 C2' A F 22 516 513 536 C2' T F 23 537 534 556 C2' G F 24 557 554 578 C2' G F 25 579 576 600 C2' C F 26 601 598 619 C2' A F 27 620 617 640 C2' G F 28 641 638 662 C2' C F 29 663 660 681 C2' T F 30 682 679 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A E 1 OK 3 6 7 26 C3' G E 2 OK 24 27 28 48 C3' C E 3 OK 46 49 50 67 C3' T E 4 OK 65 68 69 87 C3' G E 5 OK 85 88 89 109 C3' C E 6 OK 107 110 111 128 C3' C E 7 OK 126 129 130 147 C3' A E 8 OK 145 148 149 168 C3' C E 9 OK 166 169 170 187 C3' G E 10 OK 185 188 189 209 C3' C E 11 OK 207 210 211 228 C3' A E 12 OK 226 229 230 249 C3' C E 13 OK 247 250 251 268 C3' C E 14 OK 266 269 270 287 C3' A E 15 OK 285 288 289 308 C3' G E 16 OK 306 309 310 330 C3' T E 17 OK 328 331 332 348 C3' A F 14 OK 346 349 350 369 C3' C F 15 OK 367 370 371 388 C3' T F 16 OK 386 389 390 408 C3' G F 17 OK 406 409 410 430 C3' G F 18 OK 428 431 432 452 C3' T F 19 OK 450 453 454 472 C3' G F 20 OK 470 473 474 494 C3' C F 21 OK 492 495 496 513 C3' A F 22 OK 511 514 515 534 C3' T F 23 OK 532 535 536 554 C3' G F 24 OK 552 555 556 576 C3' G F 25 OK 574 577 578 598 C3' C F 26 OK 596 599 600 617 C3' A F 27 OK 615 618 619 638 C3' G F 28 OK 636 639 640 660 C3' C F 29 OK 658 661 662 679 C3' T F 30 OK 677 680 681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A E 1 OK 5 2 4 24 C4' G E 2 OK 26 23 25 46 C4' C E 3 OK 48 45 47 65 C4' T E 4 OK 67 64 66 85 C4' G E 5 OK 87 84 86 107 C4' C E 6 OK 109 106 108 126 C4' C E 7 OK 128 125 127 145 C4' A E 8 OK 147 144 146 166 C4' C E 9 OK 168 165 167 185 C4' G E 10 OK 187 184 186 207 C4' C E 11 OK 209 206 208 226 C4' A E 12 OK 228 225 227 247 C4' C E 13 OK 249 246 248 266 C4' C E 14 OK 268 265 267 285 C4' A E 15 OK 287 284 286 306 C4' G E 16 OK 308 305 307 328 C4' T E 17 OK 330 327 329 346 C4' A F 14 OK 348 345 347 367 C4' C F 15 OK 369 366 368 386 C4' T F 16 OK 388 385 387 406 C4' G F 17 OK 408 405 407 428 C4' G F 18 OK 430 427 429 450 C4' T F 19 OK 452 449 451 470 C4' G F 20 OK 472 469 471 492 C4' C F 21 OK 494 491 493 511 C4' A F 22 OK 513 510 512 532 C4' T F 23 OK 534 531 533 552 C4' G F 24 OK 554 551 553 574 C4' G F 25 OK 576 573 575 596 C4' C F 26 OK 598 595 597 615 C4' A F 27 OK 617 614 616 636 C4' G F 28 OK 638 635 637 658 C4' C F 29 OK 660 657 659 677 C4' T F 30 OK 679 676 678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A E 1 1 3 23 C5' G E 2 22 24 45 C5' C E 3 44 46 64 C5' T E 4 63 65 84 C5' G E 5 83 85 106 C5' C E 6 105 107 125 C5' C E 7 124 126 144 C5' A E 8 143 145 165 C5' C E 9 164 166 184 C5' G E 10 183 185 206 C5' C E 11 205 207 225 C5' A E 12 224 226 246 C5' C E 13 245 247 265 C5' C E 14 264 266 284 C5' A E 15 283 285 305 C5' G E 16 304 306 327 C5' T E 17 326 328 345 C5' A F 14 344 346 366 C5' C F 15 365 367 385 C5' T F 16 384 386 405 C5' G F 17 404 406 427 C5' G F 18 426 428 449 C5' T F 19 448 450 469 C5' G F 20 468 470 491 C5' C F 21 490 492 510 C5' A F 22 509 511 531 C5' T F 23 530 532 551 C5' G F 24 550 552 573 C5' G F 25 572 574 595 C5' C F 26 594 596 614 C5' A F 27 613 615 635 C5' G F 28 634 636 657 C5' C F 29 656 658 676 C5' T F 30 675 677 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P G E 2 distorted distorted 6 20 21 22 41 P C E 3 distorted distorted 27 42 43 44 60 P T E 4 distorted distorted 49 61 62 63 80 P G E 5 distorted distorted 68 81 82 83 102 P C E 6 distorted distorted 88 103 104 105 121 P C E 7 distorted distorted 110 122 123 124 140 P A E 8 distorted distorted 129 141 142 143 161 P C E 9 distorted distorted 148 162 163 164 180 P G E 10 distorted distorted 169 181 182 183 202 P C E 11 distorted distorted 188 203 204 205 221 P A E 12 distorted distorted 210 222 223 224 242 P C E 13 distorted distorted 229 243 244 245 261 P C E 14 distorted distorted 250 262 263 264 280 P A E 15 distorted distorted 269 281 282 283 301 P G E 16 distorted distorted 288 302 303 304 323 P T E 17 distorted distorted 309 324 325 326 362 P C F 15 distorted distorted 349 363 364 365 381 P T F 16 distorted distorted 370 382 383 384 401 P G F 17 distorted distorted 389 402 403 404 423 P G F 18 distorted distorted 409 424 425 426 445 P T F 19 distorted distorted 431 446 447 448 465 P G F 20 distorted distorted 453 466 467 468 487 P C F 21 distorted distorted 473 488 489 490 506 P A F 22 distorted distorted 495 507 508 509 527 P T F 23 distorted distorted 514 528 529 530 547 P G F 24 distorted distorted 535 548 549 550 569 P G F 25 distorted distorted 555 570 571 572 591 P C F 26 distorted distorted 577 592 593 594 610 P A F 27 distorted distorted 599 611 612 613 631 P G F 28 distorted distorted 618 632 633 634 653 P C F 29 distorted distorted 639 654 655 656 672 P T F 30 distorted distorted 661 673 674 675 ---------------------------------------------------------------------------------