ID code: '3DW5' 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' --------------------------------------------------------------------------------- 10 C1' U A2647 beta 4 11 8 121 C1' U A2650 beta 116 122 119 141 C1' C A2651 beta 136 142 139 161 C1' C A2652 beta 156 162 159 181 C1' U A2653 beta 176 182 179 201 C1' A A2654 beta 196 202 199 223 C1' G A2655 beta 218 224 221 243 C1' OMU A2656 beta 250 235 244 267 C1' A A2657 beta 262 268 265 289 C1' C A2658 beta 284 290 287 309 C1' G A2659 beta 304 310 307 332 C1' A A2660 beta 327 333 330 354 C1' G A2661 beta 349 355 352 377 C1' A A2662 beta 372 378 375 399 C1' G A2663 beta 394 400 397 422 C1' G A2664 beta 417 423 420 445 C1' A A2665 beta 440 446 443 467 C1' C A2666 beta 462 468 465 487 C1' C A2667 beta 482 488 485 507 C1' G A2668 beta 502 508 505 530 C1' G A2669 beta 525 531 528 553 C1' A A2670 beta 548 554 551 575 C1' G A2671 beta 570 576 573 598 C1' U A2672 beta 593 599 596 618 C1' G A2673 beta 613 619 616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8 C2' U A2647 OK 10 5 9 119 C2' U A2650 OK 121 117 120 139 C2' C A2651 OK 141 137 140 159 C2' C A2652 OK 161 157 160 179 C2' U A2653 OK 181 177 180 199 C2' A A2654 OK 201 197 200 221 C2' G A2655 OK 223 219 222 244 C2' OMU A2656 OK 243 247 245 265 C2' A A2657 OK 267 263 266 287 C2' C A2658 OK 289 285 288 307 C2' G A2659 OK 309 305 308 330 C2' A A2660 OK 332 328 331 352 C2' G A2661 OK 354 350 353 375 C2' A A2662 OK 377 373 376 397 C2' G A2663 OK 399 395 398 420 C2' G A2664 OK 422 418 421 443 C2' A A2665 OK 445 441 444 465 C2' C A2666 OK 467 463 466 485 C2' C A2667 OK 487 483 486 505 C2' G A2668 OK 507 503 506 528 C2' G A2669 OK 530 526 529 551 C2' A A2670 OK 553 549 552 573 C2' G A2671 OK 575 571 574 596 C2' U A2672 OK 598 594 597 616 C2' G A2673 OK 618 614 617 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A2647 3 8 117 C3' U A2650 OK 115 118 119 137 C3' C A2651 OK 135 138 139 157 C3' C A2652 OK 155 158 159 177 C3' U A2653 OK 175 178 179 197 C3' A A2654 OK 195 198 199 219 C3' G A2655 OK 217 220 221 247 C3' OMU A2656 OK 248 249 244 263 C3' A A2657 OK 261 264 265 285 C3' C A2658 OK 283 286 287 305 C3' G A2659 OK 303 306 307 328 C3' A A2660 OK 326 329 330 350 C3' G A2661 OK 348 351 352 373 C3' A A2662 OK 371 374 375 395 C3' G A2663 OK 393 396 397 418 C3' G A2664 OK 416 419 420 441 C3' A A2665 OK 439 442 443 463 C3' C A2666 OK 461 464 465 483 C3' C A2667 OK 481 484 485 503 C3' G A2668 OK 501 504 505 526 C3' G A2669 OK 524 527 528 549 C3' A A2670 OK 547 550 551 571 C3' G A2671 OK 569 572 573 594 C3' U A2672 OK 592 595 596 614 C3' G A2673 OK 612 615 616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A2647 OK 5 2 4 115 C4' U A2650 117 116 135 C4' C A2651 OK 137 134 136 155 C4' C A2652 OK 157 154 156 175 C4' U A2653 OK 177 174 176 195 C4' A A2654 OK 197 194 196 217 C4' G A2655 OK 219 216 218 248 C4' OMU A2656 OK 247 251 250 261 C4' A A2657 OK 263 260 262 283 C4' C A2658 OK 285 282 284 303 C4' G A2659 OK 305 302 304 326 C4' A A2660 OK 328 325 327 348 C4' G A2661 OK 350 347 349 371 C4' A A2662 OK 373 370 372 393 C4' G A2663 OK 395 392 394 416 C4' G A2664 OK 418 415 417 439 C4' A A2665 OK 441 438 440 461 C4' C A2666 OK 463 460 462 481 C4' C A2667 OK 483 480 482 501 C4' G A2668 OK 503 500 502 524 C4' G A2669 OK 526 523 525 547 C4' A A2670 OK 549 546 548 569 C4' G A2671 OK 571 568 570 592 C4' U A2672 OK 594 591 593 612 C4' G A2673 OK 614 611 613 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A2647 1 3 134 C5' C A2651 133 135 154 C5' C A2652 153 155 174 C5' U A2653 173 175 194 C5' A A2654 193 195 216 C5' G A2655 215 217 251 C5' OMU A2656 252 248 260 C5' A A2657 259 261 282 C5' C A2658 281 283 302 C5' G A2659 301 303 325 C5' A A2660 324 326 347 C5' G A2661 346 348 370 C5' A A2662 369 371 392 C5' G A2663 391 393 415 C5' G A2664 414 416 438 C5' A A2665 437 439 460 C5' C A2666 459 461 480 C5' C A2667 479 481 500 C5' G A2668 499 501 523 C5' G A2669 522 524 546 C5' A A2670 545 547 568 C5' G A2671 567 569 591 C5' U A2672 590 592 611 C5' G A2673 610 612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P G A2648 20 P G A2648 65 P C A2649 66 P C A2649 105 P U A2650 106 P U A2650 130 P C A2651 distorted distorted 118 131 132 133 150 P C A2652 distorted distorted 138 151 152 153 170 P U A2653 distorted distorted 158 171 172 173 190 P A A2654 distorted distorted 178 191 192 193 212 P G A2655 distorted distorted 198 213 214 215 253 P OMU A2656 distorted distorted 220 254 255 252 256 P A A2657 distorted distorted 249 257 258 259 278 P C A2658 distorted distorted 264 279 280 281 298 P G A2659 distorted distorted 286 299 300 301 321 P A A2660 distorted distorted 306 322 323 324 343 P G A2661 distorted distorted 329 344 345 346 366 P A A2662 distorted distorted 351 367 368 369 388 P G A2663 distorted distorted 374 389 390 391 411 P G A2664 distorted distorted 396 412 413 414 434 P A A2665 distorted distorted 419 435 436 437 456 P C A2666 distorted distorted 442 457 458 459 476 P C A2667 distorted distorted 464 477 478 479 496 P G A2668 distorted distorted 484 497 498 499 519 P G A2669 distorted distorted 504 520 521 522 542 P A A2670 distorted distorted 527 543 544 545 564 P G A2671 distorted distorted 550 565 566 567 587 P U A2672 distorted distorted 572 588 589 590 607 P G A2673 distorted distorted 595 608 609 610 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