ID code: '5DER' 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' --------------------------------------------------------------------------------- 9 C1' C A 101 beta 4 10 7 29 C1' G A 102 beta 24 30 27 52 C1' A A 103 beta 47 53 50 74 C1' A A 104 beta 69 75 72 93 C1' U5R A 105 beta 94 92 95 117 C1' U A 106 beta 112 118 115 137 C1' C A 107 beta 132 138 135 157 C1' G A 108 beta 152 158 155 178 C1' C B 209 beta 173 179 176 198 C1' G B 210 beta 193 199 196 221 C1' A B 211 beta 216 222 219 243 C1' A B 212 beta 238 244 241 262 C1' U5R B 213 beta 263 261 264 286 C1' U B 214 beta 281 287 284 306 C1' C B 215 beta 301 307 304 326 C1' G B 216 beta 321 327 324 347 C1' C C 101 beta 342 348 345 367 C1' G C 102 beta 362 368 365 390 C1' A C 103 beta 385 391 388 412 C1' A C 104 beta 407 413 410 431 C1' U5R C 105 beta 432 430 433 455 C1' U C 106 beta 450 456 453 475 C1' C C 107 beta 470 476 473 495 C1' G C 108 beta 490 496 493 516 C1' C D 209 beta 511 517 514 536 C1' G D 210 beta 531 537 534 559 C1' A D 211 beta 554 560 557 581 C1' A D 212 beta 576 582 579 600 C1' U5R D 213 beta 601 599 602 624 C1' U D 214 beta 619 625 622 644 C1' C D 215 beta 639 645 642 664 C1' G D 216 beta 659 665 662 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 101 OK 9 5 8 27 C2' G A 102 OK 29 25 28 50 C2' A A 103 OK 52 48 51 72 C2' A A 104 OK 74 70 73 95 C2' U5R A 105 93 97 115 C2' U A 106 OK 117 113 116 135 C2' C A 107 OK 137 133 136 155 C2' G A 108 OK 157 153 156 176 C2' C B 209 OK 178 174 177 196 C2' G B 210 OK 198 194 197 219 C2' A B 211 OK 221 217 220 241 C2' A B 212 OK 243 239 242 264 C2' U5R B 213 262 266 284 C2' U B 214 OK 286 282 285 304 C2' C B 215 OK 306 302 305 324 C2' G B 216 OK 326 322 325 345 C2' C C 101 OK 347 343 346 365 C2' G C 102 OK 367 363 366 388 C2' A C 103 OK 390 386 389 410 C2' A C 104 OK 412 408 411 433 C2' U5R C 105 431 435 453 C2' U C 106 OK 455 451 454 473 C2' C C 107 OK 475 471 474 493 C2' G C 108 OK 495 491 494 514 C2' C D 209 OK 516 512 515 534 C2' G D 210 OK 536 532 535 557 C2' A D 211 OK 559 555 558 579 C2' A D 212 OK 581 577 580 602 C2' U5R D 213 600 604 622 C2' U D 214 OK 624 620 623 642 C2' C D 215 OK 644 640 643 662 C2' G D 216 OK 664 660 663 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 101 OK 3 6 7 25 C3' G A 102 OK 23 26 27 48 C3' A A 103 OK 46 49 50 70 C3' A A 104 OK 68 71 72 97 C3' U5R A 105 OK 99 98 95 113 C3' U A 106 OK 111 114 115 133 C3' C A 107 OK 131 134 135 153 C3' G A 108 OK 151 154 155 174 C3' C B 209 OK 172 175 176 194 C3' G B 210 OK 192 195 196 217 C3' A B 211 OK 215 218 219 239 C3' A B 212 OK 237 240 241 266 C3' U5R B 213 OK 268 267 264 282 C3' U B 214 OK 280 283 284 302 C3' C B 215 OK 300 303 304 322 C3' G B 216 OK 320 323 324 343 C3' C C 101 OK 341 344 345 363 C3' G C 102 OK 361 364 365 386 C3' A C 103 OK 384 387 388 408 C3' A C 104 OK 406 409 410 435 C3' U5R C 105 OK 437 436 433 451 C3' U C 106 OK 449 452 453 471 C3' C C 107 OK 469 472 473 491 C3' G C 108 OK 489 492 493 512 C3' C D 209 OK 510 513 514 532 C3' G D 210 OK 530 533 534 555 C3' A D 211 OK 553 556 557 577 C3' A D 212 OK 575 578 579 604 C3' U5R D 213 OK 606 605 602 620 C3' U D 214 OK 618 621 622 640 C3' C D 215 OK 638 641 642 660 C3' G D 216 OK 658 661 662 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 101 OK 5 2 4 23 C4' G A 102 OK 25 22 24 46 C4' A A 103 OK 48 45 47 68 C4' A A 104 OK 70 67 69 99 C4' U5R A 105 OK 97 100 94 111 C4' U A 106 OK 113 110 112 131 C4' C A 107 OK 133 130 132 151 C4' G A 108 OK 153 150 152 172 C4' C B 209 OK 174 171 173 192 C4' G B 210 OK 194 191 193 215 C4' A B 211 OK 217 214 216 237 C4' A B 212 OK 239 236 238 268 C4' U5R B 213 OK 266 269 263 280 C4' U B 214 OK 282 279 281 300 C4' C B 215 OK 302 299 301 320 C4' G B 216 OK 322 319 321 341 C4' C C 101 OK 343 340 342 361 C4' G C 102 OK 363 360 362 384 C4' A C 103 OK 386 383 385 406 C4' A C 104 OK 408 405 407 437 C4' U5R C 105 OK 435 438 432 449 C4' U C 106 OK 451 448 450 469 C4' C C 107 OK 471 468 470 489 C4' G C 108 OK 491 488 490 510 C4' C D 209 OK 512 509 511 530 C4' G D 210 OK 532 529 531 553 C4' A D 211 OK 555 552 554 575 C4' A D 212 OK 577 574 576 606 C4' U5R D 213 OK 604 607 601 618 C4' U D 214 OK 620 617 619 638 C4' C D 215 OK 640 637 639 658 C4' G D 216 OK 660 657 659 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 101 1 3 22 C5' G A 102 21 23 45 C5' A A 103 44 46 67 C5' A A 104 66 68 100 C5' U5R A 105 102 99 110 C5' U A 106 109 111 130 C5' C A 107 129 131 150 C5' G A 108 149 151 171 C5' C B 209 170 172 191 C5' G B 210 190 192 214 C5' A B 211 213 215 236 C5' A B 212 235 237 269 C5' U5R B 213 271 268 279 C5' U B 214 278 280 299 C5' C B 215 298 300 319 C5' G B 216 318 320 340 C5' C C 101 339 341 360 C5' G C 102 359 361 383 C5' A C 103 382 384 405 C5' A C 104 404 406 438 C5' U5R C 105 440 437 448 C5' U C 106 447 449 468 C5' C C 107 467 469 488 C5' G C 108 487 489 509 C5' C D 209 508 510 529 C5' G D 210 528 530 552 C5' A D 211 551 553 574 C5' A D 212 573 575 607 C5' U5R D 213 609 606 617 C5' U D 214 616 618 637 C5' C D 215 636 638 657 C5' G D 216 656 658 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G A 102 distorted distorted 6 19 20 21 41 P A A 103 distorted distorted 26 42 43 44 63 P A A 104 distorted distorted 49 64 65 66 103 P U5R A 105 distorted distorted 71 104 105 102 106 P U A 106 distorted distorted 98 107 108 109 126 P C A 107 distorted distorted 114 127 128 129 146 P G A 108 distorted distorted 134 147 148 149 187 P G B 210 distorted distorted 175 188 189 190 210 P A B 211 distorted distorted 195 211 212 213 232 P A B 212 distorted distorted 218 233 234 235 272 P U5R B 213 distorted distorted 240 273 274 271 275 P U B 214 distorted distorted 267 276 277 278 295 P C B 215 distorted distorted 283 296 297 298 315 P G B 216 distorted distorted 303 316 317 318 356 P G C 102 distorted distorted 344 357 358 359 379 P A C 103 distorted distorted 364 380 381 382 401 P A C 104 distorted distorted 387 402 403 404 441 P U5R C 105 distorted distorted 409 442 443 440 444 P U C 106 distorted distorted 436 445 446 447 464 P C C 107 distorted distorted 452 465 466 467 484 P G C 108 distorted distorted 472 485 486 487 525 P G D 210 distorted distorted 513 526 527 528 548 P A D 211 distorted distorted 533 549 550 551 570 P A D 212 distorted distorted 556 571 572 573 610 P U5R D 213 distorted distorted 578 611 612 609 613 P U D 214 distorted distorted 605 614 615 616 633 P C D 215 distorted distorted 621 634 635 636 653 P G D 216 distorted distorted 641 654 655 656 ---------------------------------------------------------------------------------