ID code: '1DP7' 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' C D 1 beta 4 9 7 27 C1' G D 2 beta 23 28 26 49 C1' +U D 3 beta 45 50 48 68 C1' T D 4 beta 64 69 67 88 C1' A D 5 beta 84 89 87 109 C1' C D 6 beta 105 110 108 128 C1' C D 7 beta 124 129 127 147 C1' A D 8 beta 143 148 146 168 C1' +U D 9 beta 164 169 167 187 C1' G D 10 beta 183 188 186 209 C1' G D 11 beta 205 210 208 231 C1' T D 12 beta 227 232 230 251 C1' A D 13 beta 247 252 250 272 C1' A D 14 beta 268 273 271 293 C1' C D 15 beta 289 294 292 312 C1' G D 16 beta 308 313 311 332 C1' C E 1 beta 328 333 331 351 C1' G E 2 beta 347 352 350 373 C1' +U E 3 beta 369 374 372 392 C1' T E 4 beta 388 393 391 412 C1' A E 5 beta 408 413 411 433 C1' C E 6 beta 429 434 432 452 C1' C E 7 beta 448 453 451 471 C1' A E 8 beta 467 472 470 492 C1' +U E 9 beta 488 493 491 511 C1' G E 10 beta 507 512 510 533 C1' G E 11 beta 529 534 532 555 C1' T E 12 beta 551 556 554 575 C1' A E 13 beta 571 576 574 596 C1' A E 14 beta 592 597 595 617 C1' C E 15 beta 613 618 616 636 C1' G E 16 beta 632 637 635 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C D 1 8 5 26 C2' G D 2 27 24 48 C2' +U D 3 49 46 67 C2' T D 4 68 65 87 C2' A D 5 88 85 108 C2' C D 6 109 106 127 C2' C D 7 128 125 146 C2' A D 8 147 144 167 C2' +U D 9 168 165 186 C2' G D 10 187 184 208 C2' G D 11 209 206 230 C2' T D 12 231 228 250 C2' A D 13 251 248 271 C2' A D 14 272 269 292 C2' C D 15 293 290 311 C2' G D 16 312 309 331 C2' C E 1 332 329 350 C2' G E 2 351 348 372 C2' +U E 3 373 370 391 C2' T E 4 392 389 411 C2' A E 5 412 409 432 C2' C E 6 433 430 451 C2' C E 7 452 449 470 C2' A E 8 471 468 491 C2' +U E 9 492 489 510 C2' G E 10 511 508 532 C2' G E 11 533 530 554 C2' T E 12 555 552 574 C2' A E 13 575 572 595 C2' A E 14 596 593 616 C2' C E 15 617 614 635 C2' G E 16 636 633 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C D 1 OK 3 6 7 24 C3' G D 2 OK 22 25 26 46 C3' +U D 3 OK 44 47 48 65 C3' T D 4 OK 63 66 67 85 C3' A D 5 OK 83 86 87 106 C3' C D 6 OK 104 107 108 125 C3' C D 7 OK 123 126 127 144 C3' A D 8 OK 142 145 146 165 C3' +U D 9 OK 163 166 167 184 C3' G D 10 OK 182 185 186 206 C3' G D 11 OK 204 207 208 228 C3' T D 12 OK 226 229 230 248 C3' A D 13 OK 246 249 250 269 C3' A D 14 OK 267 270 271 290 C3' C D 15 OK 288 291 292 309 C3' G D 16 OK 307 310 311 329 C3' C E 1 OK 327 330 331 348 C3' G E 2 OK 346 349 350 370 C3' +U E 3 OK 368 371 372 389 C3' T E 4 OK 387 390 391 409 C3' A E 5 OK 407 410 411 430 C3' C E 6 OK 428 431 432 449 C3' C E 7 OK 447 450 451 468 C3' A E 8 OK 466 469 470 489 C3' +U E 9 OK 487 490 491 508 C3' G E 10 OK 506 509 510 530 C3' G E 11 OK 528 531 532 552 C3' T E 12 OK 550 553 554 572 C3' A E 13 OK 570 573 574 593 C3' A E 14 OK 591 594 595 614 C3' C E 15 OK 612 615 616 633 C3' G E 16 OK 631 634 635 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C D 1 OK 5 2 4 22 C4' G D 2 OK 24 21 23 44 C4' +U D 3 OK 46 43 45 63 C4' T D 4 OK 65 62 64 83 C4' A D 5 OK 85 82 84 104 C4' C D 6 OK 106 103 105 123 C4' C D 7 OK 125 122 124 142 C4' A D 8 OK 144 141 143 163 C4' +U D 9 OK 165 162 164 182 C4' G D 10 OK 184 181 183 204 C4' G D 11 OK 206 203 205 226 C4' T D 12 OK 228 225 227 246 C4' A D 13 OK 248 245 247 267 C4' A D 14 OK 269 266 268 288 C4' C D 15 OK 290 287 289 307 C4' G D 16 OK 309 306 308 327 C4' C E 1 OK 329 326 328 346 C4' G E 2 OK 348 345 347 368 C4' +U E 3 OK 370 367 369 387 C4' T E 4 OK 389 386 388 407 C4' A E 5 OK 409 406 408 428 C4' C E 6 OK 430 427 429 447 C4' C E 7 OK 449 446 448 466 C4' A E 8 OK 468 465 467 487 C4' +U E 9 OK 489 486 488 506 C4' G E 10 OK 508 505 507 528 C4' G E 11 OK 530 527 529 550 C4' T E 12 OK 552 549 551 570 C4' A E 13 OK 572 569 571 591 C4' A E 14 OK 593 590 592 612 C4' C E 15 OK 614 611 613 631 C4' G E 16 OK 633 630 632 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C D 1 1 3 21 C5' G D 2 20 22 43 C5' +U D 3 42 44 62 C5' T D 4 61 63 82 C5' A D 5 81 83 103 C5' C D 6 102 104 122 C5' C D 7 121 123 141 C5' A D 8 140 142 162 C5' +U D 9 161 163 181 C5' G D 10 180 182 203 C5' G D 11 202 204 225 C5' T D 12 224 226 245 C5' A D 13 244 246 266 C5' A D 14 265 267 287 C5' C D 15 286 288 306 C5' G D 16 305 307 326 C5' C E 1 325 327 345 C5' G E 2 344 346 367 C5' +U E 3 366 368 386 C5' T E 4 385 387 406 C5' A E 5 405 407 427 C5' C E 6 426 428 446 C5' C E 7 445 447 465 C5' A E 8 464 466 486 C5' +U E 9 485 487 505 C5' G E 10 504 506 527 C5' G E 11 526 528 549 C5' T E 12 548 550 569 C5' A E 13 568 570 590 C5' A E 14 589 591 611 C5' C E 15 610 612 630 C5' G E 16 629 631 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P G D 2 distorted distorted 6 18 19 20 39 P +U D 3 distorted distorted 25 40 41 42 58 P T D 4 distorted distorted 47 59 60 61 78 P A D 5 distorted distorted 66 79 80 81 99 P C D 6 distorted distorted 86 100 101 102 118 P C D 7 distorted distorted 107 119 120 121 137 P A D 8 distorted distorted 126 138 139 140 158 P +U D 9 distorted distorted 145 159 160 161 177 P G D 10 distorted distorted 166 178 179 180 199 P G D 11 distorted distorted 185 200 201 202 221 P T D 12 distorted distorted 207 222 223 224 241 P A D 13 distorted distorted 229 242 243 244 262 P A D 14 distorted distorted 249 263 264 265 283 P C D 15 distorted distorted 270 284 285 286 302 P G D 16 distorted distorted 291 303 304 305 341 P G E 2 distorted distorted 330 342 343 344 363 P +U E 3 distorted distorted 349 364 365 366 382 P T E 4 distorted distorted 371 383 384 385 402 P A E 5 distorted distorted 390 403 404 405 423 P C E 6 distorted distorted 410 424 425 426 442 P C E 7 distorted distorted 431 443 444 445 461 P A E 8 distorted distorted 450 462 463 464 482 P +U E 9 distorted distorted 469 483 484 485 501 P G E 10 distorted distorted 490 502 503 504 523 P G E 11 distorted distorted 509 524 525 526 545 P T E 12 distorted distorted 531 546 547 548 565 P A E 13 distorted distorted 553 566 567 568 586 P A E 14 distorted distorted 573 587 588 589 607 P C E 15 distorted distorted 594 608 609 610 626 P G E 16 distorted distorted 615 627 628 629 ---------------------------------------------------------------------------------