ID code: '4NGF' 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' --------------------------------------------------------------------------------- 8290 C1' U E 1 beta 8285 8291 8288 8310 C1' C E 2 beta 8305 8311 8308 8330 C1' G E 3 beta 8325 8331 8328 8353 C1' A E 4 beta 8348 8354 8351 8375 C1' A E 5 beta 8370 8376 8373 8397 C1' G E 6 beta 8392 8398 8395 8420 C1' G E 7 beta 8415 8421 8418 8443 C1' U E 8 beta 8438 8444 8441 8463 C1' C E 9 beta 8458 8464 8461 8483 C1' C E 10 beta 8478 8484 8481 8503 C1' U E 11 beta 8498 8504 8501 8523 C1' U E 12 beta 8518 8524 8521 8543 C1' C E 13 beta 8538 8544 8541 8563 C1' G E 14 beta 8558 8564 8561 8586 C1' U E 15 beta 8581 8587 8584 8606 C1' U E 16 beta 8601 8607 8604 8626 C1' U E 17 beta 8621 8627 8624 8648 C1' U F 1 beta 8643 8649 8646 8668 C1' C F 2 beta 8663 8669 8666 8688 C1' G F 3 beta 8683 8689 8686 8711 C1' A F 4 beta 8706 8712 8709 8733 C1' A F 5 beta 8728 8734 8731 8755 C1' G F 6 beta 8750 8756 8753 8778 C1' G F 7 beta 8773 8779 8776 8801 C1' U F 8 beta 8796 8802 8799 8821 C1' C F 9 beta 8816 8822 8819 8841 C1' C F 10 beta 8836 8842 8839 8861 C1' U F 11 beta 8856 8862 8859 8881 C1' U F 12 beta 8876 8882 8879 8901 C1' C F 13 beta 8896 8902 8899 8921 C1' G F 14 beta 8916 8922 8919 8944 C1' U F 15 beta 8939 8945 8942 8964 C1' U F 16 beta 8959 8965 8962 8984 C1' U F 17 beta 8979 8985 8982 9006 C1' U G 1 beta 9001 9007 9004 9026 C1' C G 2 beta 9021 9027 9024 9046 C1' G G 3 beta 9041 9047 9044 9069 C1' A G 4 beta 9064 9070 9067 9091 C1' A G 5 beta 9086 9092 9089 9113 C1' G G 6 beta 9108 9114 9111 9136 C1' G G 7 beta 9131 9137 9134 9159 C1' U G 8 beta 9154 9160 9157 9179 C1' C G 9 beta 9174 9180 9177 9199 C1' C G 10 beta 9194 9200 9197 9219 C1' U G 11 beta 9214 9220 9217 9239 C1' U G 12 beta 9234 9240 9237 9259 C1' C G 13 beta 9254 9260 9257 9279 C1' G G 14 beta 9274 9280 9277 9302 C1' U G 15 beta 9297 9303 9300 9322 C1' U G 16 beta 9317 9323 9320 9342 C1' U G 17 beta 9337 9343 9340 9364 C1' U H 1 beta 9359 9365 9362 9384 C1' C H 2 beta 9379 9385 9382 9404 C1' G H 3 beta 9399 9405 9402 9427 C1' A H 4 beta 9422 9428 9425 9449 C1' A H 5 beta 9444 9450 9447 9471 C1' G H 6 beta 9466 9472 9469 9494 C1' G H 7 beta 9489 9495 9492 9517 C1' U H 8 beta 9512 9518 9515 9537 C1' C H 9 beta 9532 9538 9535 9557 C1' C H 10 beta 9552 9558 9555 9577 C1' U H 11 beta 9572 9578 9575 9597 C1' U H 12 beta 9592 9598 9595 9617 C1' C H 13 beta 9612 9618 9615 9637 C1' G H 14 beta 9632 9638 9635 9660 C1' U H 15 beta 9655 9661 9658 9680 C1' U H 16 beta 9675 9681 9678 9700 C1' U H 17 beta 9695 9701 9698 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8288 C2' U E 1 OK 8290 8286 8289 8308 C2' C E 2 OK 8310 8306 8309 8328 C2' G E 3 OK 8330 8326 8329 8351 C2' A E 4 OK 8353 8349 8352 8373 C2' A E 5 OK 8375 8371 8374 8395 C2' G E 6 OK 8397 8393 8396 8418 C2' G E 7 OK 8420 8416 8419 8441 C2' U E 8 OK 8443 8439 8442 8461 C2' C E 9 OK 8463 8459 8462 8481 C2' C E 10 OK 8483 8479 8482 8501 C2' U E 11 OK 8503 8499 8502 8521 C2' U E 12 OK 8523 8519 8522 8541 C2' C E 13 OK 8543 8539 8542 8561 C2' G E 14 OK 8563 8559 8562 8584 C2' U E 15 OK 8586 8582 8585 8604 C2' U E 16 OK 8606 8602 8605 8624 C2' U E 17 OK 8626 8622 8625 8646 C2' U F 1 OK 8648 8644 8647 8666 C2' C F 2 OK 8668 8664 8667 8686 C2' G F 3 OK 8688 8684 8687 8709 C2' A F 4 OK 8711 8707 8710 8731 C2' A F 5 OK 8733 8729 8732 8753 C2' G F 6 OK 8755 8751 8754 8776 C2' G F 7 OK 8778 8774 8777 8799 C2' U F 8 OK 8801 8797 8800 8819 C2' C F 9 OK 8821 8817 8820 8839 C2' C F 10 OK 8841 8837 8840 8859 C2' U F 11 OK 8861 8857 8860 8879 C2' U F 12 OK 8881 8877 8880 8899 C2' C F 13 OK 8901 8897 8900 8919 C2' G F 14 OK 8921 8917 8920 8942 C2' U F 15 OK 8944 8940 8943 8962 C2' U F 16 OK 8964 8960 8963 8982 C2' U F 17 OK 8984 8980 8983 9004 C2' U G 1 OK 9006 9002 9005 9024 C2' C G 2 OK 9026 9022 9025 9044 C2' G G 3 OK 9046 9042 9045 9067 C2' A G 4 OK 9069 9065 9068 9089 C2' A G 5 OK 9091 9087 9090 9111 C2' G G 6 OK 9113 9109 9112 9134 C2' G G 7 OK 9136 9132 9135 9157 C2' U G 8 OK 9159 9155 9158 9177 C2' C G 9 OK 9179 9175 9178 9197 C2' C G 10 OK 9199 9195 9198 9217 C2' U G 11 OK 9219 9215 9218 9237 C2' U G 12 OK 9239 9235 9238 9257 C2' C G 13 OK 9259 9255 9258 9277 C2' G G 14 OK 9279 9275 9278 9300 C2' U G 15 OK 9302 9298 9301 9320 C2' U G 16 OK 9322 9318 9321 9340 C2' U G 17 OK 9342 9338 9341 9362 C2' U H 1 OK 9364 9360 9363 9382 C2' C H 2 OK 9384 9380 9383 9402 C2' G H 3 OK 9404 9400 9403 9425 C2' A H 4 OK 9427 9423 9426 9447 C2' A H 5 OK 9449 9445 9448 9469 C2' G H 6 OK 9471 9467 9470 9492 C2' G H 7 OK 9494 9490 9493 9515 C2' U H 8 OK 9517 9513 9516 9535 C2' C H 9 OK 9537 9533 9536 9555 C2' C H 10 OK 9557 9553 9556 9575 C2' U H 11 OK 9577 9573 9576 9595 C2' U H 12 OK 9597 9593 9596 9615 C2' C H 13 OK 9617 9613 9616 9635 C2' G H 14 OK 9637 9633 9636 9658 C2' U H 15 OK 9660 9656 9659 9678 C2' U H 16 OK 9680 9676 9679 9698 C2' U H 17 OK 9700 9696 9699 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8286 C3' U E 1 OK 8284 8287 8288 8306 C3' C E 2 OK 8304 8307 8308 8326 C3' G E 3 OK 8324 8327 8328 8349 C3' A E 4 OK 8347 8350 8351 8371 C3' A E 5 OK 8369 8372 8373 8393 C3' G E 6 OK 8391 8394 8395 8416 C3' G E 7 OK 8414 8417 8418 8439 C3' U E 8 OK 8437 8440 8441 8459 C3' C E 9 OK 8457 8460 8461 8479 C3' C E 10 OK 8477 8480 8481 8499 C3' U E 11 OK 8497 8500 8501 8519 C3' U E 12 OK 8517 8520 8521 8539 C3' C E 13 OK 8537 8540 8541 8559 C3' G E 14 OK 8557 8560 8561 8582 C3' U E 15 OK 8580 8583 8584 8602 C3' U E 16 OK 8600 8603 8604 8622 C3' U E 17 OK 8620 8623 8624 8644 C3' U F 1 OK 8642 8645 8646 8664 C3' C F 2 OK 8662 8665 8666 8684 C3' G F 3 OK 8682 8685 8686 8707 C3' A F 4 OK 8705 8708 8709 8729 C3' A F 5 OK 8727 8730 8731 8751 C3' G F 6 OK 8749 8752 8753 8774 C3' G F 7 OK 8772 8775 8776 8797 C3' U F 8 OK 8795 8798 8799 8817 C3' C F 9 OK 8815 8818 8819 8837 C3' C F 10 OK 8835 8838 8839 8857 C3' U F 11 OK 8855 8858 8859 8877 C3' U F 12 OK 8875 8878 8879 8897 C3' C F 13 OK 8895 8898 8899 8917 C3' G F 14 OK 8915 8918 8919 8940 C3' U F 15 OK 8938 8941 8942 8960 C3' U F 16 OK 8958 8961 8962 8980 C3' U F 17 OK 8978 8981 8982 9002 C3' U G 1 OK 9000 9003 9004 9022 C3' C G 2 OK 9020 9023 9024 9042 C3' G G 3 OK 9040 9043 9044 9065 C3' A G 4 OK 9063 9066 9067 9087 C3' A G 5 OK 9085 9088 9089 9109 C3' G G 6 OK 9107 9110 9111 9132 C3' G G 7 OK 9130 9133 9134 9155 C3' U G 8 OK 9153 9156 9157 9175 C3' C G 9 OK 9173 9176 9177 9195 C3' C G 10 OK 9193 9196 9197 9215 C3' U G 11 OK 9213 9216 9217 9235 C3' U G 12 OK 9233 9236 9237 9255 C3' C G 13 OK 9253 9256 9257 9275 C3' G G 14 OK 9273 9276 9277 9298 C3' U G 15 OK 9296 9299 9300 9318 C3' U G 16 OK 9316 9319 9320 9338 C3' U G 17 OK 9336 9339 9340 9360 C3' U H 1 OK 9358 9361 9362 9380 C3' C H 2 OK 9378 9381 9382 9400 C3' G H 3 OK 9398 9401 9402 9423 C3' A H 4 OK 9421 9424 9425 9445 C3' A H 5 OK 9443 9446 9447 9467 C3' G H 6 OK 9465 9468 9469 9490 C3' G H 7 OK 9488 9491 9492 9513 C3' U H 8 OK 9511 9514 9515 9533 C3' C H 9 OK 9531 9534 9535 9553 C3' C H 10 OK 9551 9554 9555 9573 C3' U H 11 OK 9571 9574 9575 9593 C3' U H 12 OK 9591 9594 9595 9613 C3' C H 13 OK 9611 9614 9615 9633 C3' G H 14 OK 9631 9634 9635 9656 C3' U H 15 OK 9654 9657 9658 9676 C3' U H 16 OK 9674 9677 9678 9696 C3' U H 17 OK 9694 9697 9698 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8284 C4' U E 1 OK 8286 8283 8285 8304 C4' C E 2 OK 8306 8303 8305 8324 C4' G E 3 OK 8326 8323 8325 8347 C4' A E 4 OK 8349 8346 8348 8369 C4' A E 5 OK 8371 8368 8370 8391 C4' G E 6 OK 8393 8390 8392 8414 C4' G E 7 OK 8416 8413 8415 8437 C4' U E 8 OK 8439 8436 8438 8457 C4' C E 9 OK 8459 8456 8458 8477 C4' C E 10 OK 8479 8476 8478 8497 C4' U E 11 OK 8499 8496 8498 8517 C4' U E 12 OK 8519 8516 8518 8537 C4' C E 13 OK 8539 8536 8538 8557 C4' G E 14 OK 8559 8556 8558 8580 C4' U E 15 OK 8582 8579 8581 8600 C4' U E 16 OK 8602 8599 8601 8620 C4' U E 17 OK 8622 8619 8621 8642 C4' U F 1 OK 8644 8641 8643 8662 C4' C F 2 OK 8664 8661 8663 8682 C4' G F 3 OK 8684 8681 8683 8705 C4' A F 4 OK 8707 8704 8706 8727 C4' A F 5 OK 8729 8726 8728 8749 C4' G F 6 OK 8751 8748 8750 8772 C4' G F 7 OK 8774 8771 8773 8795 C4' U F 8 OK 8797 8794 8796 8815 C4' C F 9 OK 8817 8814 8816 8835 C4' C F 10 OK 8837 8834 8836 8855 C4' U F 11 OK 8857 8854 8856 8875 C4' U F 12 OK 8877 8874 8876 8895 C4' C F 13 OK 8897 8894 8896 8915 C4' G F 14 OK 8917 8914 8916 8938 C4' U F 15 OK 8940 8937 8939 8958 C4' U F 16 OK 8960 8957 8959 8978 C4' U F 17 OK 8980 8977 8979 9000 C4' U G 1 OK 9002 8999 9001 9020 C4' C G 2 OK 9022 9019 9021 9040 C4' G G 3 OK 9042 9039 9041 9063 C4' A G 4 OK 9065 9062 9064 9085 C4' A G 5 OK 9087 9084 9086 9107 C4' G G 6 OK 9109 9106 9108 9130 C4' G G 7 OK 9132 9129 9131 9153 C4' U G 8 OK 9155 9152 9154 9173 C4' C G 9 OK 9175 9172 9174 9193 C4' C G 10 OK 9195 9192 9194 9213 C4' U G 11 OK 9215 9212 9214 9233 C4' U G 12 OK 9235 9232 9234 9253 C4' C G 13 OK 9255 9252 9254 9273 C4' G G 14 OK 9275 9272 9274 9296 C4' U G 15 OK 9298 9295 9297 9316 C4' U G 16 OK 9318 9315 9317 9336 C4' U G 17 OK 9338 9335 9337 9358 C4' U H 1 OK 9360 9357 9359 9378 C4' C H 2 OK 9380 9377 9379 9398 C4' G H 3 OK 9400 9397 9399 9421 C4' A H 4 OK 9423 9420 9422 9443 C4' A H 5 OK 9445 9442 9444 9465 C4' G H 6 OK 9467 9464 9466 9488 C4' G H 7 OK 9490 9487 9489 9511 C4' U H 8 OK 9513 9510 9512 9531 C4' C H 9 OK 9533 9530 9532 9551 C4' C H 10 OK 9553 9550 9552 9571 C4' U H 11 OK 9573 9570 9572 9591 C4' U H 12 OK 9593 9590 9592 9611 C4' C H 13 OK 9613 9610 9612 9631 C4' G H 14 OK 9633 9630 9632 9654 C4' U H 15 OK 9656 9653 9655 9674 C4' U H 16 OK 9676 9673 9675 9694 C4' U H 17 OK 9696 9693 9695 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8283 C5' U E 1 8282 8284 8303 C5' C E 2 8302 8304 8323 C5' G E 3 8322 8324 8346 C5' A E 4 8345 8347 8368 C5' A E 5 8367 8369 8390 C5' G E 6 8389 8391 8413 C5' G E 7 8412 8414 8436 C5' U E 8 8435 8437 8456 C5' C E 9 8455 8457 8476 C5' C E 10 8475 8477 8496 C5' U E 11 8495 8497 8516 C5' U E 12 8515 8517 8536 C5' C E 13 8535 8537 8556 C5' G E 14 8555 8557 8579 C5' U E 15 8578 8580 8599 C5' U E 16 8598 8600 8619 C5' U E 17 8618 8620 8641 C5' U F 1 8640 8642 8661 C5' C F 2 8660 8662 8681 C5' G F 3 8680 8682 8704 C5' A F 4 8703 8705 8726 C5' A F 5 8725 8727 8748 C5' G F 6 8747 8749 8771 C5' G F 7 8770 8772 8794 C5' U F 8 8793 8795 8814 C5' C F 9 8813 8815 8834 C5' C F 10 8833 8835 8854 C5' U F 11 8853 8855 8874 C5' U F 12 8873 8875 8894 C5' C F 13 8893 8895 8914 C5' G F 14 8913 8915 8937 C5' U F 15 8936 8938 8957 C5' U F 16 8956 8958 8977 C5' U F 17 8976 8978 8999 C5' U G 1 8998 9000 9019 C5' C G 2 9018 9020 9039 C5' G G 3 9038 9040 9062 C5' A G 4 9061 9063 9084 C5' A G 5 9083 9085 9106 C5' G G 6 9105 9107 9129 C5' G G 7 9128 9130 9152 C5' U G 8 9151 9153 9172 C5' C G 9 9171 9173 9192 C5' C G 10 9191 9193 9212 C5' U G 11 9211 9213 9232 C5' U G 12 9231 9233 9252 C5' C G 13 9251 9253 9272 C5' G G 14 9271 9273 9295 C5' U G 15 9294 9296 9315 C5' U G 16 9314 9316 9335 C5' U G 17 9334 9336 9357 C5' U H 1 9356 9358 9377 C5' C H 2 9376 9378 9397 C5' G H 3 9396 9398 9420 C5' A H 4 9419 9421 9442 C5' A H 5 9441 9443 9464 C5' G H 6 9463 9465 9487 C5' G H 7 9486 9488 9510 C5' U H 8 9509 9511 9530 C5' C H 9 9529 9531 9550 C5' C H 10 9549 9551 9570 C5' U H 11 9569 9571 9590 C5' U H 12 9589 9591 9610 C5' C H 13 9609 9611 9630 C5' G H 14 9629 9631 9653 C5' U H 15 9652 9654 9673 C5' U H 16 9672 9674 9693 C5' U H 17 9692 9694 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8279 P U E 1 distorted distorted 8280 8281 8282 8299 P C E 2 distorted distorted 8287 8300 8301 8302 8319 P G E 3 distorted distorted 8307 8320 8321 8322 8342 P A E 4 distorted distorted 8327 8343 8344 8345 8364 P A E 5 distorted distorted 8350 8365 8366 8367 8386 P G E 6 distorted distorted 8372 8387 8388 8389 8409 P G E 7 distorted distorted 8394 8410 8411 8412 8432 P U E 8 distorted distorted 8417 8433 8434 8435 8452 P C E 9 distorted distorted 8440 8453 8454 8455 8472 P C E 10 distorted distorted 8460 8473 8474 8475 8492 P U E 11 distorted distorted 8480 8493 8494 8495 8512 P U E 12 distorted distorted 8500 8513 8514 8515 8532 P C E 13 distorted distorted 8520 8533 8534 8535 8552 P G E 14 distorted distorted 8540 8553 8554 8555 8575 P U E 15 distorted distorted 8560 8576 8577 8578 8595 P U E 16 distorted distorted 8583 8596 8597 8598 8615 P U E 17 distorted distorted 8603 8616 8617 8618 8637 P U F 1 OK OK 8638 8639 8640 8657 P C F 2 distorted distorted 8645 8658 8659 8660 8677 P G F 3 distorted distorted 8665 8678 8679 8680 8700 P A F 4 distorted distorted 8685 8701 8702 8703 8722 P A F 5 distorted distorted 8708 8723 8724 8725 8744 P G F 6 distorted distorted 8730 8745 8746 8747 8767 P G F 7 distorted distorted 8752 8768 8769 8770 8790 P U F 8 distorted distorted 8775 8791 8792 8793 8810 P C F 9 distorted distorted 8798 8811 8812 8813 8830 P C F 10 distorted distorted 8818 8831 8832 8833 8850 P U F 11 distorted distorted 8838 8851 8852 8853 8870 P U F 12 distorted distorted 8858 8871 8872 8873 8890 P C F 13 distorted distorted 8878 8891 8892 8893 8910 P G F 14 distorted distorted 8898 8911 8912 8913 8933 P U F 15 distorted distorted 8918 8934 8935 8936 8953 P U F 16 distorted distorted 8941 8954 8955 8956 8973 P U F 17 distorted distorted 8961 8974 8975 8976 8995 P U G 1 OK OK 8996 8997 8998 9015 P C G 2 distorted distorted 9003 9016 9017 9018 9035 P G G 3 distorted distorted 9023 9036 9037 9038 9058 P A G 4 distorted distorted 9043 9059 9060 9061 9080 P A G 5 distorted distorted 9066 9081 9082 9083 9102 P G G 6 distorted distorted 9088 9103 9104 9105 9125 P G G 7 distorted distorted 9110 9126 9127 9128 9148 P U G 8 distorted distorted 9133 9149 9150 9151 9168 P C G 9 distorted distorted 9156 9169 9170 9171 9188 P C G 10 distorted distorted 9176 9189 9190 9191 9208 P U G 11 distorted distorted 9196 9209 9210 9211 9228 P U G 12 distorted distorted 9216 9229 9230 9231 9248 P C G 13 distorted distorted 9236 9249 9250 9251 9268 P G G 14 distorted distorted 9256 9269 9270 9271 9291 P U G 15 distorted distorted 9276 9292 9293 9294 9311 P U G 16 distorted distorted 9299 9312 9313 9314 9331 P U G 17 distorted distorted 9319 9332 9333 9334 9353 P U H 1 distorted distorted 9354 9355 9356 9373 P C H 2 distorted distorted 9361 9374 9375 9376 9393 P G H 3 distorted distorted 9381 9394 9395 9396 9416 P A H 4 distorted distorted 9401 9417 9418 9419 9438 P A H 5 distorted distorted 9424 9439 9440 9441 9460 P G H 6 distorted distorted 9446 9461 9462 9463 9483 P G H 7 distorted distorted 9468 9484 9485 9486 9506 P U H 8 distorted distorted 9491 9507 9508 9509 9526 P C H 9 distorted distorted 9514 9527 9528 9529 9546 P C H 10 distorted distorted 9534 9547 9548 9549 9566 P U H 11 distorted distorted 9554 9567 9568 9569 9586 P U H 12 distorted distorted 9574 9587 9588 9589 9606 P C H 13 distorted distorted 9594 9607 9608 9609 9626 P G H 14 distorted distorted 9614 9627 9628 9629 9649 P U H 15 distorted distorted 9634 9650 9651 9652 9669 P U H 16 distorted distorted 9657 9670 9671 9672 9689 P U H 17 distorted distorted 9677 9690 9691 9692 ---------------------------------------------------------------------------------