ID code: '5M0J' 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' --------------------------------------------------------------------------------- 8235 C1' G E 1 beta 8230 8236 8233 8258 C1' A E 2 beta 8253 8259 8256 8280 C1' U E 3 beta 8275 8281 8278 8300 C1' A E 4 beta 8295 8301 8298 8322 C1' A E 5 beta 8317 8323 8320 8344 C1' C E 6 beta 8339 8345 8342 8364 C1' U E 7 beta 8359 8365 8362 8384 C1' G E 8 beta 8379 8385 8382 8407 C1' A E 9 beta 8402 8408 8405 8429 C1' A E 10 beta 8424 8430 8427 8451 C1' U E 11 beta 8446 8452 8449 8471 C1' C E 12 beta 8466 8472 8469 8491 C1' G E 13 beta 8486 8492 8489 8514 C1' A E 14 beta 8509 8515 8512 8536 C1' A E 15 beta 8531 8537 8534 8558 C1' A E 16 beta 8553 8559 8556 8580 C1' G E 17 beta 8575 8581 8578 8603 C1' A E 18 beta 8598 8604 8601 8625 C1' C E 19 beta 8620 8626 8623 8645 C1' A E 20 beta 8640 8646 8643 8667 C1' U E 21 beta 8662 8668 8665 8687 C1' U E 22 beta 8682 8688 8685 8707 C1' A E 23 beta 8702 8708 8705 8729 C1' U E 24 beta 8724 8730 8727 8749 C1' C E 25 beta 8744 8750 8747 8769 C1' A E 26 beta 8764 8770 8767 8791 C1' C E 27 beta 8786 8792 8789 8811 C1' G E 28 beta 8806 8812 8809 8832 C1' G F 1 beta 8827 8833 8830 8855 C1' A F 2 beta 8850 8856 8853 8877 C1' U F 3 beta 8872 8878 8875 8897 C1' A F 4 beta 8892 8898 8895 8919 C1' A F 5 beta 8914 8920 8917 8941 C1' C F 6 beta 8936 8942 8939 8961 C1' U F 7 beta 8956 8962 8959 8981 C1' G F 8 beta 8976 8982 8979 9004 C1' A F 9 beta 8999 9005 9002 9026 C1' A F 10 beta 9021 9027 9024 9048 C1' U F 11 beta 9043 9049 9046 9068 C1' C F 12 beta 9063 9069 9066 9088 C1' G F 13 beta 9083 9089 9086 9111 C1' A F 14 beta 9106 9112 9109 9133 C1' A F 15 beta 9128 9134 9131 9155 C1' A F 16 beta 9150 9156 9153 9177 C1' G F 17 beta 9172 9178 9175 9200 C1' A F 18 beta 9195 9201 9198 9222 C1' C F 19 beta 9217 9223 9220 9242 C1' A F 20 beta 9237 9243 9240 9264 C1' U F 21 beta 9259 9265 9262 9284 C1' U F 22 beta 9279 9285 9282 9304 C1' A F 23 beta 9299 9305 9302 9326 C1' U F 24 beta 9321 9327 9324 9346 C1' C F 25 beta 9341 9347 9344 9366 C1' A F 26 beta 9361 9367 9364 9388 C1' C F 27 beta 9383 9389 9386 9408 C1' G F 28 beta 9403 9409 9406 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8233 C2' G E 1 OK 8235 8231 8234 8256 C2' A E 2 OK 8258 8254 8257 8278 C2' U E 3 OK 8280 8276 8279 8298 C2' A E 4 OK 8300 8296 8299 8320 C2' A E 5 OK 8322 8318 8321 8342 C2' C E 6 OK 8344 8340 8343 8362 C2' U E 7 OK 8364 8360 8363 8382 C2' G E 8 OK 8384 8380 8383 8405 C2' A E 9 OK 8407 8403 8406 8427 C2' A E 10 OK 8429 8425 8428 8449 C2' U E 11 OK 8451 8447 8450 8469 C2' C E 12 OK 8471 8467 8470 8489 C2' G E 13 OK 8491 8487 8490 8512 C2' A E 14 OK 8514 8510 8513 8534 C2' A E 15 OK 8536 8532 8535 8556 C2' A E 16 OK 8558 8554 8557 8578 C2' G E 17 OK 8580 8576 8579 8601 C2' A E 18 OK 8603 8599 8602 8623 C2' C E 19 OK 8625 8621 8624 8643 C2' A E 20 OK 8645 8641 8644 8665 C2' U E 21 OK 8667 8663 8666 8685 C2' U E 22 OK 8687 8683 8686 8705 C2' A E 23 OK 8707 8703 8706 8727 C2' U E 24 OK 8729 8725 8728 8747 C2' C E 25 OK 8749 8745 8748 8767 C2' A E 26 OK 8769 8765 8768 8789 C2' C E 27 OK 8791 8787 8790 8809 C2' G E 28 OK 8811 8807 8810 8830 C2' G F 1 OK 8832 8828 8831 8853 C2' A F 2 OK 8855 8851 8854 8875 C2' U F 3 OK 8877 8873 8876 8895 C2' A F 4 OK 8897 8893 8896 8917 C2' A F 5 OK 8919 8915 8918 8939 C2' C F 6 OK 8941 8937 8940 8959 C2' U F 7 OK 8961 8957 8960 8979 C2' G F 8 OK 8981 8977 8980 9002 C2' A F 9 OK 9004 9000 9003 9024 C2' A F 10 OK 9026 9022 9025 9046 C2' U F 11 OK 9048 9044 9047 9066 C2' C F 12 OK 9068 9064 9067 9086 C2' G F 13 OK 9088 9084 9087 9109 C2' A F 14 OK 9111 9107 9110 9131 C2' A F 15 OK 9133 9129 9132 9153 C2' A F 16 OK 9155 9151 9154 9175 C2' G F 17 OK 9177 9173 9176 9198 C2' A F 18 OK 9200 9196 9199 9220 C2' C F 19 OK 9222 9218 9221 9240 C2' A F 20 OK 9242 9238 9241 9262 C2' U F 21 OK 9264 9260 9263 9282 C2' U F 22 OK 9284 9280 9283 9302 C2' A F 23 OK 9304 9300 9303 9324 C2' U F 24 OK 9326 9322 9325 9344 C2' C F 25 OK 9346 9342 9345 9364 C2' A F 26 OK 9366 9362 9365 9386 C2' C F 27 OK 9388 9384 9387 9406 C2' G F 28 OK 9408 9404 9407 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8231 C3' G E 1 OK 8229 8232 8233 8254 C3' A E 2 OK 8252 8255 8256 8276 C3' U E 3 OK 8274 8277 8278 8296 C3' A E 4 OK 8294 8297 8298 8318 C3' A E 5 OK 8316 8319 8320 8340 C3' C E 6 OK 8338 8341 8342 8360 C3' U E 7 OK 8358 8361 8362 8380 C3' G E 8 OK 8378 8381 8382 8403 C3' A E 9 OK 8401 8404 8405 8425 C3' A E 10 OK 8423 8426 8427 8447 C3' U E 11 OK 8445 8448 8449 8467 C3' C E 12 OK 8465 8468 8469 8487 C3' G E 13 OK 8485 8488 8489 8510 C3' A E 14 OK 8508 8511 8512 8532 C3' A E 15 OK 8530 8533 8534 8554 C3' A E 16 OK 8552 8555 8556 8576 C3' G E 17 OK 8574 8577 8578 8599 C3' A E 18 OK 8597 8600 8601 8621 C3' C E 19 OK 8619 8622 8623 8641 C3' A E 20 OK 8639 8642 8643 8663 C3' U E 21 OK 8661 8664 8665 8683 C3' U E 22 OK 8681 8684 8685 8703 C3' A E 23 OK 8701 8704 8705 8725 C3' U E 24 OK 8723 8726 8727 8745 C3' C E 25 OK 8743 8746 8747 8765 C3' A E 26 OK 8763 8766 8767 8787 C3' C E 27 OK 8785 8788 8789 8807 C3' G E 28 OK 8805 8808 8809 8828 C3' G F 1 OK 8826 8829 8830 8851 C3' A F 2 OK 8849 8852 8853 8873 C3' U F 3 OK 8871 8874 8875 8893 C3' A F 4 OK 8891 8894 8895 8915 C3' A F 5 OK 8913 8916 8917 8937 C3' C F 6 OK 8935 8938 8939 8957 C3' U F 7 OK 8955 8958 8959 8977 C3' G F 8 OK 8975 8978 8979 9000 C3' A F 9 OK 8998 9001 9002 9022 C3' A F 10 OK 9020 9023 9024 9044 C3' U F 11 OK 9042 9045 9046 9064 C3' C F 12 OK 9062 9065 9066 9084 C3' G F 13 OK 9082 9085 9086 9107 C3' A F 14 OK 9105 9108 9109 9129 C3' A F 15 OK 9127 9130 9131 9151 C3' A F 16 OK 9149 9152 9153 9173 C3' G F 17 OK 9171 9174 9175 9196 C3' A F 18 OK 9194 9197 9198 9218 C3' C F 19 OK 9216 9219 9220 9238 C3' A F 20 OK 9236 9239 9240 9260 C3' U F 21 OK 9258 9261 9262 9280 C3' U F 22 OK 9278 9281 9282 9300 C3' A F 23 OK 9298 9301 9302 9322 C3' U F 24 OK 9320 9323 9324 9342 C3' C F 25 OK 9340 9343 9344 9362 C3' A F 26 OK 9360 9363 9364 9384 C3' C F 27 OK 9382 9385 9386 9404 C3' G F 28 OK 9402 9405 9406 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8229 C4' G E 1 OK 8231 8228 8230 8252 C4' A E 2 OK 8254 8251 8253 8274 C4' U E 3 OK 8276 8273 8275 8294 C4' A E 4 OK 8296 8293 8295 8316 C4' A E 5 OK 8318 8315 8317 8338 C4' C E 6 OK 8340 8337 8339 8358 C4' U E 7 OK 8360 8357 8359 8378 C4' G E 8 OK 8380 8377 8379 8401 C4' A E 9 OK 8403 8400 8402 8423 C4' A E 10 OK 8425 8422 8424 8445 C4' U E 11 OK 8447 8444 8446 8465 C4' C E 12 OK 8467 8464 8466 8485 C4' G E 13 OK 8487 8484 8486 8508 C4' A E 14 OK 8510 8507 8509 8530 C4' A E 15 OK 8532 8529 8531 8552 C4' A E 16 OK 8554 8551 8553 8574 C4' G E 17 OK 8576 8573 8575 8597 C4' A E 18 OK 8599 8596 8598 8619 C4' C E 19 OK 8621 8618 8620 8639 C4' A E 20 OK 8641 8638 8640 8661 C4' U E 21 OK 8663 8660 8662 8681 C4' U E 22 OK 8683 8680 8682 8701 C4' A E 23 OK 8703 8700 8702 8723 C4' U E 24 OK 8725 8722 8724 8743 C4' C E 25 OK 8745 8742 8744 8763 C4' A E 26 OK 8765 8762 8764 8785 C4' C E 27 OK 8787 8784 8786 8805 C4' G E 28 OK 8807 8804 8806 8826 C4' G F 1 OK 8828 8825 8827 8849 C4' A F 2 OK 8851 8848 8850 8871 C4' U F 3 OK 8873 8870 8872 8891 C4' A F 4 OK 8893 8890 8892 8913 C4' A F 5 OK 8915 8912 8914 8935 C4' C F 6 OK 8937 8934 8936 8955 C4' U F 7 OK 8957 8954 8956 8975 C4' G F 8 OK 8977 8974 8976 8998 C4' A F 9 OK 9000 8997 8999 9020 C4' A F 10 OK 9022 9019 9021 9042 C4' U F 11 OK 9044 9041 9043 9062 C4' C F 12 OK 9064 9061 9063 9082 C4' G F 13 OK 9084 9081 9083 9105 C4' A F 14 OK 9107 9104 9106 9127 C4' A F 15 OK 9129 9126 9128 9149 C4' A F 16 OK 9151 9148 9150 9171 C4' G F 17 OK 9173 9170 9172 9194 C4' A F 18 OK 9196 9193 9195 9216 C4' C F 19 OK 9218 9215 9217 9236 C4' A F 20 OK 9238 9235 9237 9258 C4' U F 21 OK 9260 9257 9259 9278 C4' U F 22 OK 9280 9277 9279 9298 C4' A F 23 OK 9300 9297 9299 9320 C4' U F 24 OK 9322 9319 9321 9340 C4' C F 25 OK 9342 9339 9341 9360 C4' A F 26 OK 9362 9359 9361 9382 C4' C F 27 OK 9384 9381 9383 9402 C4' G F 28 OK 9404 9401 9403 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8228 C5' G E 1 8227 8229 8251 C5' A E 2 8250 8252 8273 C5' U E 3 8272 8274 8293 C5' A E 4 8292 8294 8315 C5' A E 5 8314 8316 8337 C5' C E 6 8336 8338 8357 C5' U E 7 8356 8358 8377 C5' G E 8 8376 8378 8400 C5' A E 9 8399 8401 8422 C5' A E 10 8421 8423 8444 C5' U E 11 8443 8445 8464 C5' C E 12 8463 8465 8484 C5' G E 13 8483 8485 8507 C5' A E 14 8506 8508 8529 C5' A E 15 8528 8530 8551 C5' A E 16 8550 8552 8573 C5' G E 17 8572 8574 8596 C5' A E 18 8595 8597 8618 C5' C E 19 8617 8619 8638 C5' A E 20 8637 8639 8660 C5' U E 21 8659 8661 8680 C5' U E 22 8679 8681 8700 C5' A E 23 8699 8701 8722 C5' U E 24 8721 8723 8742 C5' C E 25 8741 8743 8762 C5' A E 26 8761 8763 8784 C5' C E 27 8783 8785 8804 C5' G E 28 8803 8805 8825 C5' G F 1 8824 8826 8848 C5' A F 2 8847 8849 8870 C5' U F 3 8869 8871 8890 C5' A F 4 8889 8891 8912 C5' A F 5 8911 8913 8934 C5' C F 6 8933 8935 8954 C5' U F 7 8953 8955 8974 C5' G F 8 8973 8975 8997 C5' A F 9 8996 8998 9019 C5' A F 10 9018 9020 9041 C5' U F 11 9040 9042 9061 C5' C F 12 9060 9062 9081 C5' G F 13 9080 9082 9104 C5' A F 14 9103 9105 9126 C5' A F 15 9125 9127 9148 C5' A F 16 9147 9149 9170 C5' G F 17 9169 9171 9193 C5' A F 18 9192 9194 9215 C5' C F 19 9214 9216 9235 C5' A F 20 9234 9236 9257 C5' U F 21 9256 9258 9277 C5' U F 22 9276 9278 9297 C5' A F 23 9296 9298 9319 C5' U F 24 9318 9320 9339 C5' C F 25 9338 9340 9359 C5' A F 26 9358 9360 9381 C5' C F 27 9380 9382 9401 C5' G F 28 9400 9402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8247 P A E 2 distorted distorted 8232 8248 8249 8250 8269 P U E 3 distorted distorted 8255 8270 8271 8272 8289 P A E 4 distorted distorted 8277 8290 8291 8292 8311 P A E 5 distorted distorted 8297 8312 8313 8314 8333 P C E 6 distorted distorted 8319 8334 8335 8336 8353 P U E 7 distorted distorted 8341 8354 8355 8356 8373 P G E 8 distorted distorted 8361 8374 8375 8376 8396 P A E 9 distorted distorted 8381 8397 8398 8399 8418 P A E 10 distorted distorted 8404 8419 8420 8421 8440 P U E 11 distorted distorted 8426 8441 8442 8443 8460 P C E 12 distorted distorted 8448 8461 8462 8463 8480 P G E 13 distorted distorted 8468 8481 8482 8483 8503 P A E 14 distorted distorted 8488 8504 8505 8506 8525 P A E 15 distorted distorted 8511 8526 8527 8528 8547 P A E 16 distorted distorted 8533 8548 8549 8550 8569 P G E 17 distorted distorted 8555 8570 8571 8572 8592 P A E 18 distorted distorted 8577 8593 8594 8595 8614 P C E 19 distorted distorted 8600 8615 8616 8617 8634 P A E 20 distorted distorted 8622 8635 8636 8637 8656 P U E 21 distorted distorted 8642 8657 8658 8659 8676 P U E 22 distorted distorted 8664 8677 8678 8679 8696 P A E 23 distorted distorted 8684 8697 8698 8699 8718 P U E 24 distorted distorted 8704 8719 8720 8721 8738 P C E 25 distorted distorted 8726 8739 8740 8741 8758 P A E 26 distorted distorted 8746 8759 8760 8761 8780 P C E 27 distorted distorted 8766 8781 8782 8783 8800 P G E 28 distorted distorted 8788 8801 8802 8803 8844 P A F 2 distorted distorted 8829 8845 8846 8847 8866 P U F 3 distorted distorted 8852 8867 8868 8869 8886 P A F 4 distorted distorted 8874 8887 8888 8889 8908 P A F 5 distorted distorted 8894 8909 8910 8911 8930 P C F 6 distorted distorted 8916 8931 8932 8933 8950 P U F 7 distorted distorted 8938 8951 8952 8953 8970 P G F 8 distorted distorted 8958 8971 8972 8973 8993 P A F 9 distorted distorted 8978 8994 8995 8996 9015 P A F 10 distorted distorted 9001 9016 9017 9018 9037 P U F 11 distorted distorted 9023 9038 9039 9040 9057 P C F 12 distorted distorted 9045 9058 9059 9060 9077 P G F 13 distorted distorted 9065 9078 9079 9080 9100 P A F 14 distorted distorted 9085 9101 9102 9103 9122 P A F 15 distorted distorted 9108 9123 9124 9125 9144 P A F 16 distorted distorted 9130 9145 9146 9147 9166 P G F 17 distorted distorted 9152 9167 9168 9169 9189 P A F 18 distorted distorted 9174 9190 9191 9192 9211 P C F 19 distorted distorted 9197 9212 9213 9214 9231 P A F 20 distorted distorted 9219 9232 9233 9234 9253 P U F 21 distorted distorted 9239 9254 9255 9256 9273 P U F 22 distorted distorted 9261 9274 9275 9276 9293 P A F 23 distorted distorted 9281 9294 9295 9296 9315 P U F 24 distorted distorted 9301 9316 9317 9318 9335 P C F 25 distorted distorted 9323 9336 9337 9338 9355 P A F 26 distorted distorted 9343 9356 9357 9358 9377 P C F 27 distorted distorted 9363 9378 9379 9380 9397 P G F 28 distorted distorted 9385 9398 9399 9400 ---------------------------------------------------------------------------------