Residue-by-residue listing for refined_6 Page 1 ---------------------------------------- This listing highlights the residues in the structure which may need investigation. The ideal values and standard deviations against which the structure has been compared are shown in the following table: <------------------------------- I D E A L V A L U E S -------------------------------> Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha ------------------------------------------------------------------------------------------ Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9 Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5 ------------------------------------------------------------------------------------------ In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above. Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*. The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing. Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments. Full print-out. ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - - 180.8 - 181.2 - - - - - - 179.8 - 34.8 - 2 ALA 2 B - - - - - - - - - - 177.2 - 34.8 - 3 ASP 3 B - 183.0 - - - - - - - - 185.1 - 33.7 - 4 THR 4 A - - -49.3 - - - - - - - 184.9 - 35.4 - * * 5 GLY 5 S - - - - - - - - - - - 174.4 - - - 6 GLU 6 S B - 177.1 - - - - - - - - 180.9 -1.0 33.7 - * * 7 VAL 7 E B - - -63.6 - - - - - - - 178.5 -3.2 34.4 - +* +* 8 GLN 8 E B - - -59.8 176.9 - - - - - - 179.5 - 35.5 - 9 PHE 9 E B - 180.3 - - - - - - - - 181.4 -2.2 35.2 - 10 MET 10 E B - 184.0 - 182.4 - - - - - - 178.4 - 35.1 - 11 LYS 11 E B 49.8 - - - - - - - - - 179.8 -1.4 30.6 - 12 PRO 12 - - - - - -71.6 - - - - - 181.5 - 38.5 - * * 13 PHE 13 B - - -74.2 - - - - - - - 172.7 - 34.1 - * * 14 ILE 14 t B - - -64.4 - - - - - - - 189.7 - 33.8 - +* +* 15 SER 15 T A - 183.8 - - - - - - - - 178.7 -.6 32.5 - +* +* 16 GLU 16 T A - - -58.8 186.9 - - - - - - 184.1 - 34.8 - 17 LYS 17 T A - 185.4 - - - - - - - - 181.3 -1.4 34.7 - 18 SER 18 T A 59.9 - - - - - - - - - 177.8 -3.1 33.3 - * * 19 SER 19 T A - 181.7 - - - - - - - - 181.7 - 34.2 - Residue-by-residue listing for refined_6 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 20 LYS 20 T A - - -70.0 - - - - - - - 187.9 -.9 34.5 - * +* +* 21 SER 21 t B 55.4 - - - - - - - - - 177.0 -1.5 36.5 - 22 LEU 22 E B - 189.9 - 173.0 - - - - - - 179.9 -2.5 33.4 - 23 GLU 23 E B 34.9 - - - - - - - - - 182.3 - 29.7 - +* * +* 24 ILE 24 e B - - -54.1 - - - - - - - 181.0 -1.2 34.7 - * * 25 PRO 25 h - - - - - -50.9 - - - - - 182.6 - 38.5 - * * * 26 LEU 26 H A - 189.0 - 169.8 - -60.2 -38.6 - - - 179.7 - 33.6 - 27 GLY 27 H - - - - - - -65.3 -35.8 - - - 179.4 - - - 28 PHE 28 H A - 183.9 - - - -72.1 -38.5 - - - 175.2 - 34.3 - 29 ASN 29 H A - 169.1 - - - -66.1 -40.6 - - - 178.8 -2.4 34.6 - 30 GLU 30 H A - 179.9 - 187.2 - -63.4 -30.0 - - - 184.1 -2.8 36.2 - * * 31 TYR 31 H A - 183.3 - - - -68.8 -28.3 - - - 178.4 -1.2 34.4 - * * 32 PHE 32 h b 65.2 - - - - - - - - - 172.3 -.7 32.4 - * +* +* 33 PRO 33 - - - - - -79.8 - - - - - 181.9 - 38.8 - * * * 34 ALA 34 B - - - - - - - - - - 171.3 - 35.3 - +* +* 35 PRO 35 - - - - - -63.6 - - - - - 183.0 - 38.7 - * * 36 PHE 36 B 55.5 - - - - - - - - - 176.7 - 31.5 - 37 PRO 37 - - - - - -81.9 - - - - - 185.1 - 38.7 - * * * 38 ILE 38 e A - - -56.5 - - - - - - - 181.7 - 33.9 - 39 THR 39 E B - - -44.3 - - - - - - - 182.1 - 36.2 - * * 40 VAL 40 E B - 174.0 - - - - - - - - 179.4 -2.3 35.5 - 41 ASP 41 E B - - -60.7 - - - - - - - 177.4 -.8 33.9 - +* +* 42 LEU 42 E B - - -59.8 180.8 - - - - - - 181.7 -3.5 34.7 - +* +* 43 LEU 43 E B - - -66.5 - - - - - - - 178.8 -3.2 33.9 - +* +* 44 ASP 44 E B - 159.0 - - - - - - - - 183.7 -2.5 34.7 - * * 45 TYR 45 e A - 184.6 - - - - - - - - 180.9 -.8 34.2 - +* +* 46 SER 46 S A - 182.9 - - - - - - - - 177.9 - 33.5 - 47 GLY 47 S - - - - - - - - - - - 178.2 - - - 48 ARG 48 e B - 180.6 - - - - - - - - 177.2 - 35.2 - 49 SER 49 E B 52.3 - - - - - - - - - 181.3 - 31.5 - 50 TRP 50 E B - - -55.0 - - - - - - - 177.3 -2.9 36.1 - * * 51 THR 51 E B - - -60.3 - - - - - - - 186.2 - 33.7 - * * 52 VAL 52 E B - - -60.3 - - - - - - - 180.5 -2.7 32.7 - 53 ARG 53 E B - 190.2 - 175.7 - - - - - - 184.7 -.5 36.3 - ** ** 54 MET 54 E B - 183.4 - 179.1 - - - - - - 178.6 -.9 35.2 - +* +* 55 LYS 55 E B - 189.4 - 177.8 - - - - - - 177.6 -2.2 34.1 - Residue-by-residue listing for refined_6 Page 3 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 56 LYS 56 E B - 179.1 - - - - - - - - 182.2 - 36.0 - 57 ARG 57 E b 55.5 - - 176.8 - - - - - - 176.8 -1.7 32.0 - 58 GLY 58 T - - - - - - - - - - - 184.4 - - - 59 GLU 59 T A 56.0 - - - - - - - - - 174.9 - 31.5 - 60 LYS 60 E B 72.2 - - - - - - - - - 170.8 -.9 34.4 - +* * +* 61 VAL 61 E B - 180.9 - - - - - - - - 178.6 - 35.0 - 62 PHE 62 E B - 189.8 - - - - - - - - 179.0 -3.4 35.4 - +* +* 63 LEU 63 E B - 197.4 - - - - - - - - 189.1 -2.5 34.6 - +* +* 64 THR 64 E b - 180.2 - - - - - - - - 188.6 -.9 32.2 - * * * 65 VAL 65 T B 57.1 - - - - - - - - - 186.7 - 31.2 - * * 66 GLY 66 T - - - - - - - - - - - 173.2 - - - * * 67 TRP 67 h A - 164.6 - - - - - - - - 181.9 -1.8 34.8 - * * 68 GLU 68 H A - 176.4 - 176.5 - -54.9 -34.1 - - - 179.6 - 33.6 - 69 ASN 69 H A - - -61.8 - - -61.0 -35.7 - - - 183.0 -1.4 33.5 - 70 PHE 70 H A - 188.9 - - - -73.7 -47.4 - - - 183.9 -1.3 35.6 - * * 71 VAL 71 H A 74.2 - - - - -65.0 -46.1 - - - 179.6 -1.8 32.3 - 72 LYS 72 H A 65.2 - - 182.3 - -72.1 -33.8 - - - 181.7 -3.0 29.4 - * * * 73 ASP 73 H A - 174.1 - - - -66.7 -39.7 - - - 179.9 -2.0 32.6 - 74 ASN 74 H A - - -63.0 - - -93.9 -17.7 - - - 186.1 -2.1 34.8 - ** +* * ** 75 ASN 75 h l - 187.5 - - - - - - - - 185.6 -1.3 30.7 - 76 LEU 76 t B 55.2 - - - - - - - - - 180.6 -1.1 31.9 - * * 77 GLU 77 t B 55.2 - - - - - - - - - 181.5 - 32.2 - 78 ASP 78 T B 62.2 - - - - - - - - - 182.2 - 33.2 - 79 GLY 79 T - - - - - - - - - - - 177.2 - - - 80 LYS 80 t B - - -64.3 172.4 - - - - - - 185.1 -1.2 34.4 - * * 81 TYR 81 E B - - -59.7 - - - - - - - 180.5 -1.7 34.0 - 82 LEU 82 E B - - -66.3 - - - - - - - 179.7 -.9 33.2 - +* +* 83 GLN 83 E B - 186.9 - 185.0 - - - - - - 178.9 -2.8 36.2 - * * 84 PHE 84 E B - - -62.5 - - - - - - - 177.7 -3.2 34.5 - * * 85 ILE 85 E B - - -58.1 176.3 - - - - - - 185.5 -2.5 35.3 - 86 TYR 86 E B - 174.7 - - - - - - - - 171.8 -3.3 34.7 - * +* +* 87 ASP 87 e B - 183.6 - - - - - - - - 182.9 -.8 34.6 - +* +* 88 ARG 88 S b - - -64.2 - - - - - - - 180.3 - 31.8 - 89 ASP 89 S ~b - 192.0 - - - - - - - - 176.4 -1.9 36.1 - ** ** 90 ARG 90 e a - - -74.1 - - - - - - - 180.1 - 33.3 - 91 THR 91 E B - - -55.9 - - - - - - - 182.8 - 35.5 - 92 PHE 92 E B - - -61.9 - - - - - - - 174.9 -1.8 35.2 - 93 TYR 93 E B - - -56.3 - - - - - - - 187.1 -1.5 34.2 - * * Residue-by-residue listing for refined_6 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 94 VAL 94 E B - 185.7 - - - - - - - - 173.5 -3.5 34.9 - * ** ** 95 ILE 95 E B - 184.4 - - - - - - - - 184.1 -1.9 33.2 - 96 ILE 96 E B - - -50.4 176.9 - - - - - - 176.5 - 35.7 - * * 97 TYR 97 E B - - -58.0 - - - - - - - 180.4 -3.8 34.2 - ** ** 98 GLY 98 - - - - - - - - - - - 176.5 -.8 - - +* +* 99 HIS 99 a 53.1 - - - - - - - - - 182.8 - 30.5 - 100 ASN 100 ~l - 181.0 - - - - - - - - 178.9 - 31.6 - ** ** 101 MET 101 b - 184.5 - 175.4 - - - - - - 180.1 - 32.4 - 102 CYS 102 - - 183.6 - - - - - - - - - -1.3 34.8 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** +* * * * ** +* +* ** * ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.6 182.2 -60.5 178.5 -69.6 -67.9 -35.9 - - - 180.3 -1.9 34.2 Standard deviations: 9.0 7.2 6.5 4.8 12.7 9.4 7.7 - - - 3.9 .9 1.9 Numbers of values: 17 41 30 19 5 13 13 0 0 0 101 56 95 0 KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_6 Page 5 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - 1.233 1.504 1.528 1.459 - 116.33 120.53 110.25 109.62 109.99 123.14 2 ALA 2 1.314 1.237 1.504 1.514 1.437 122.13 116.47 120.32 109.86 109.41 110.38 123.20 * * * * 3 ASP 3 1.303 1.241 1.520 1.533 1.444 121.57 116.90 120.27 111.14 108.25 111.12 122.83 +* * +* 4 THR 4 1.305 1.251 1.549 1.540 1.443 121.83 116.56 121.00 110.07 111.45 108.75 122.40 +* * +* +* 5 GLY 5 1.320 1.232 1.484 - 1.440 120.52 114.29 120.98 - 110.05 - 124.74 +* * * +* 6 GLU 6 1.285 1.247 1.535 1.559 1.446 124.29 115.26 121.09 114.00 109.10 108.32 123.57 *** * * ** * *** 7 VAL 7 1.314 1.230 1.516 1.565 1.449 123.98 116.62 120.77 108.71 110.08 112.35 122.61 * * * 8 GLN 8 1.300 1.232 1.522 1.530 1.427 121.59 117.11 120.35 110.75 108.57 108.93 122.53 ** +* ** 9 PHE 9 1.303 1.213 1.517 1.542 1.445 121.51 117.25 120.11 110.96 109.20 109.03 122.63 +* +* 10 MET 10 1.309 1.235 1.520 1.543 1.449 121.77 116.68 120.34 110.08 109.23 110.00 122.96 * * 11 LYS 11 1.315 1.225 1.534 1.574 1.459 121.94 118.04 119.80 113.95 111.48 111.74 122.10 * ** ** ** 12 PRO 12 1.354 1.234 1.527 1.536 1.475 123.37 116.03 120.80 109.94 112.42 104.09 123.16 Residue-by-residue listing for refined_6 Page 6 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 13 PHE 13 1.310 1.226 1.501 1.526 1.453 123.02 115.88 120.74 109.05 112.33 111.32 123.34 * * * 14 ILE 14 1.317 1.224 1.514 1.579 1.440 121.99 117.19 119.48 109.88 105.65 113.68 123.33 * +* * +* 15 SER 15 1.328 1.225 1.533 1.533 1.470 122.72 117.59 119.82 110.72 113.97 111.05 122.59 16 GLU 16 1.315 1.229 1.513 1.516 1.446 121.03 115.61 121.35 108.48 110.00 111.39 123.00 17 LYS 17 1.311 1.235 1.514 1.536 1.432 121.65 115.48 120.95 111.56 109.16 109.15 123.48 * * * 18 SER 18 1.322 1.216 1.538 1.536 1.438 122.40 116.89 120.57 111.66 111.89 109.94 122.53 * * 19 SER 19 1.322 1.237 1.543 1.539 1.453 121.56 116.63 121.07 110.48 111.13 110.14 122.30 20 LYS 20 1.322 1.231 1.515 1.540 1.465 121.07 116.49 120.52 109.24 112.35 110.53 122.97 21 SER 21 1.304 1.212 1.507 1.516 1.433 121.32 117.45 119.88 109.82 110.16 107.72 122.67 +* * +* +* 22 LEU 22 1.300 1.245 1.510 1.559 1.431 120.48 115.84 120.77 112.74 107.23 110.77 123.36 ** * * * * ** 23 GLU 23 1.300 1.235 1.525 1.544 1.423 121.96 114.84 122.28 114.34 112.39 112.07 122.86 ** +* ** ** 24 ILE 24 1.298 1.244 1.527 1.562 1.437 121.96 117.33 120.07 109.71 108.26 111.47 122.56 ** * * ** 25 PRO 25 1.351 1.246 1.528 1.524 1.468 123.28 115.49 120.97 110.74 112.99 102.99 123.54 * * 26 LEU 26 1.326 1.217 1.526 1.565 1.457 122.98 116.43 120.46 112.71 109.91 109.48 123.05 +* * +* 27 GLY 27 1.323 1.233 1.516 - 1.450 121.59 115.99 120.68 - 112.17 - 123.31 28 PHE 28 1.324 1.223 1.531 1.543 1.462 122.44 115.51 121.23 111.71 108.98 109.42 123.24 29 ASN 29 1.321 1.235 1.527 1.538 1.469 122.74 115.18 121.60 110.18 110.53 109.93 123.22 30 GLU 30 1.316 1.236 1.525 1.524 1.450 123.68 115.14 121.22 109.02 110.16 108.82 123.63 * * 31 TYR 31 1.316 1.247 1.534 1.543 1.441 123.22 116.98 120.43 112.07 111.05 108.36 122.51 * * * 32 PHE 32 1.332 1.226 1.541 1.567 1.450 120.84 118.01 121.05 111.30 112.11 111.68 120.88 +* * +* 33 PRO 33 1.336 1.247 1.518 1.531 1.443 121.91 116.30 120.75 109.77 109.59 104.60 122.94 +* * +* 34 ALA 34 1.291 1.248 1.515 1.532 1.443 122.02 118.60 119.51 110.24 109.40 109.43 121.84 +** * +** 35 PRO 35 1.349 1.238 1.517 1.532 1.455 121.61 117.86 119.75 110.19 108.34 104.38 122.38 * * * 36 PHE 36 1.301 1.233 1.518 1.535 1.405 119.99 117.23 120.93 112.84 111.98 111.48 121.80 +* +** * +** 37 PRO 37 1.330 1.224 1.511 1.530 1.432 121.62 116.63 120.64 111.14 108.73 103.59 122.72 ** * ** 38 ILE 38 1.297 1.235 1.518 1.556 1.446 120.59 115.80 121.56 110.23 110.20 111.43 122.61 ** ** 39 THR 39 1.301 1.251 1.533 1.523 1.417 120.63 114.93 121.07 109.55 109.55 108.75 123.99 +* * ** +* ** 40 VAL 40 1.304 1.235 1.530 1.583 1.458 125.61 117.76 119.83 109.50 107.38 110.77 122.40 +* +* ** * ** 41 ASP 41 1.313 1.241 1.495 1.537 1.450 121.14 115.42 120.98 108.99 110.26 112.50 123.60 * * * * 42 LEU 42 1.295 1.239 1.504 1.532 1.428 122.42 116.21 120.68 110.02 107.96 111.04 123.10 ** * +* * ** 43 LEU 43 1.293 1.229 1.506 1.553 1.434 121.51 114.94 121.28 109.48 110.56 112.12 123.78 +** * * +** Residue-by-residue listing for refined_6 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 44 ASP 44 1.288 1.235 1.513 1.524 1.441 123.88 114.76 121.31 110.73 111.00 109.28 123.93 +** * +** 45 TYR 45 1.311 1.226 1.545 1.541 1.448 124.20 117.38 120.40 111.35 112.27 108.89 122.20 * * * 46 SER 46 1.318 1.234 1.543 1.541 1.447 121.11 117.10 120.48 111.19 110.93 110.42 122.42 47 GLY 47 1.321 1.235 1.518 - 1.458 120.25 116.60 120.93 - 113.26 - 122.46 48 ARG 48 1.300 1.228 1.540 1.545 1.455 122.17 117.75 120.31 112.24 108.53 107.71 121.85 ** * +* ** 49 SER 49 1.301 1.234 1.521 1.543 1.446 120.74 115.72 120.83 112.77 111.80 111.42 123.42 +* * +* 50 TRP 50 1.319 1.225 1.520 1.535 1.461 122.56 116.76 120.48 107.53 109.62 110.76 122.76 * * 51 THR 51 1.297 1.243 1.549 1.538 1.443 121.83 116.06 121.19 111.72 109.93 109.97 122.75 ** * * ** 52 VAL 52 1.317 1.237 1.529 1.555 1.456 122.89 115.71 120.95 110.27 112.18 112.24 123.32 53 ARG 53 1.314 1.238 1.534 1.524 1.451 122.85 117.19 120.21 109.70 107.92 108.43 122.60 * * * * 54 MET 54 1.311 1.219 1.518 1.540 1.463 121.80 117.55 120.20 110.74 110.04 108.76 122.22 * * * 55 LYS 55 1.324 1.227 1.540 1.525 1.452 119.48 116.11 121.25 110.64 112.09 109.64 122.65 * * 56 LYS 56 1.317 1.227 1.481 1.505 1.459 122.91 115.09 120.92 108.77 107.54 109.97 123.97 ** * * ** 57 ARG 57 1.262 1.237 1.524 1.529 1.427 121.72 115.90 121.44 111.68 112.90 111.39 122.66 *4.8* +* *4.8* 58 GLY 58 1.300 1.236 1.500 - 1.430 120.74 115.58 120.84 - 112.55 - 123.52 ** * ** 59 GLU 59 1.305 1.231 1.521 1.556 1.449 122.88 117.02 120.51 111.64 112.66 112.31 122.47 +* * * +* 60 LYS 60 1.321 1.243 1.517 1.539 1.411 120.63 115.76 121.02 108.36 109.50 112.83 123.21 ** * ** 61 VAL 61 1.298 1.231 1.513 1.560 1.424 121.49 117.71 120.02 108.98 105.56 112.53 122.25 ** +* ** ** 62 PHE 62 1.279 1.237 1.497 1.531 1.413 120.01 116.57 120.74 111.56 107.05 108.89 122.67 +*** * ** * +*** 63 LEU 63 1.289 1.231 1.508 1.523 1.414 119.82 115.79 120.68 111.40 105.38 110.58 123.49 +** ** * ** +** 64 THR 64 1.293 1.253 1.557 1.581 1.432 121.97 116.14 120.73 113.96 111.81 109.62 123.12 +** * +* +* * ** * +** 65 VAL 65 1.321 1.217 1.520 1.559 1.436 123.71 114.22 122.09 112.99 111.70 111.82 123.68 * * +* +* 66 GLY 66 1.289 1.232 1.483 - 1.424 122.53 114.30 121.55 - 107.77 - 124.11 +** +* +* * * +* +** 67 TRP 67 1.334 1.232 1.526 1.544 1.458 123.32 114.82 121.59 110.50 109.98 109.68 123.52 68 GLU 68 1.315 1.214 1.537 1.526 1.450 123.10 116.78 120.58 111.23 111.70 109.94 122.59 * * 69 ASN 69 1.324 1.192 1.501 1.537 1.467 121.97 116.03 120.64 109.67 110.82 112.02 123.20 +* * +* 70 PHE 70 1.302 1.249 1.515 1.548 1.437 122.92 115.59 120.83 109.90 108.55 109.72 123.57 +* * +* 71 VAL 71 1.337 1.222 1.515 1.580 1.443 121.44 116.37 120.43 110.98 110.34 113.09 123.20 * * 72 LYS 72 1.324 1.224 1.525 1.553 1.449 120.74 117.42 119.89 112.63 112.76 113.94 122.67 * * ** ** Residue-by-residue listing for refined_6 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 73 ASP 73 1.340 1.236 1.515 1.525 1.489 120.52 116.40 120.81 110.63 112.78 111.40 122.78 +* +* 74 ASN 74 1.303 1.228 1.501 1.537 1.459 120.93 114.77 120.72 108.84 110.23 111.25 124.49 +* * +* 75 ASN 75 1.328 1.238 1.531 1.545 1.471 124.51 115.45 121.77 113.00 110.29 112.76 122.66 +* +* * +* 76 LEU 76 1.313 1.234 1.507 1.560 1.437 121.30 115.18 120.90 112.67 112.34 111.12 123.92 * * * * * 77 GLU 77 1.298 1.241 1.523 1.548 1.435 123.84 115.84 120.20 111.10 110.71 112.72 123.95 ** * * * ** 78 ASP 78 1.334 1.242 1.518 1.540 1.472 123.66 115.68 121.21 109.97 111.75 111.73 123.08 * * 79 GLY 79 1.307 1.229 1.495 - 1.440 121.34 114.75 121.52 - 110.04 - 123.72 +* * +* 80 LYS 80 1.303 1.235 1.505 1.523 1.429 122.89 116.18 120.61 112.05 108.43 109.27 123.21 +* +* * +* 81 TYR 81 1.298 1.217 1.479 1.529 1.433 121.29 116.25 120.81 110.66 109.84 110.91 122.93 ** ** * ** 82 LEU 82 1.279 1.247 1.493 1.542 1.416 120.66 115.43 120.90 110.68 109.17 112.48 123.66 +*** +* ** * +*** 83 GLN 83 1.291 1.235 1.497 1.515 1.418 121.41 115.52 120.65 107.56 108.16 110.99 123.83 +** * ** * * +** 84 PHE 84 1.283 1.234 1.501 1.535 1.413 122.77 115.77 120.82 110.77 108.61 110.55 123.36 *** * ** *** 85 ILE 85 1.288 1.240 1.502 1.545 1.430 122.06 115.59 120.53 109.85 107.03 110.80 123.85 +** * * * +** 86 TYR 86 1.297 1.226 1.508 1.546 1.423 122.36 115.02 121.28 110.04 111.90 110.11 123.70 ** +* ** 87 ASP 87 1.292 1.232 1.520 1.544 1.441 122.84 119.41 118.41 111.82 104.58 110.28 122.17 +** +* * ** +** 88 ARG 88 1.319 1.230 1.530 1.534 1.470 120.61 115.03 121.16 111.22 112.38 112.04 123.76 89 ASP 89 1.320 1.224 1.533 1.565 1.436 125.69 117.83 119.73 110.31 103.68 109.80 122.44 +* * ** +** +** 90 ARG 90 1.287 1.218 1.513 1.545 1.458 123.11 115.32 121.59 110.09 108.98 112.59 123.05 *** * *** 91 THR 91 1.301 1.234 1.531 1.543 1.428 122.01 116.38 120.52 110.44 108.37 109.35 123.09 +* +* * * +* 92 PHE 92 1.323 1.232 1.511 1.536 1.452 121.54 116.09 120.80 108.30 110.92 111.02 123.11 93 TYR 93 1.304 1.232 1.517 1.540 1.452 121.79 117.43 119.91 111.25 106.94 110.77 122.63 +* +* +* 94 VAL 94 1.309 1.235 1.533 1.559 1.450 121.14 115.69 121.06 108.69 112.34 110.79 123.25 * * 95 ILE 95 1.319 1.240 1.540 1.580 1.452 122.67 117.37 120.11 110.95 107.70 112.72 122.48 * * * 96 ILE 96 1.316 1.225 1.522 1.555 1.459 121.47 116.66 120.83 108.07 110.26 110.82 122.50 97 TYR 97 1.293 1.242 1.506 1.526 1.435 121.44 115.79 120.60 109.84 108.83 111.55 123.59 +** * +** 98 GLY 98 1.305 1.233 1.508 - 1.425 120.98 116.02 121.38 - 112.63 - 122.60 +* +* +* 99 HIS 99 1.300 1.217 1.505 1.558 1.450 121.55 116.21 119.67 112.01 111.83 113.68 124.04 ** * * +* ** 100 ASN 100 1.335 1.232 1.513 1.545 1.477 123.72 116.21 121.43 110.75 111.54 113.25 122.33 * +* +* 101 MET 101 1.295 1.238 1.514 1.525 1.424 120.09 114.66 121.69 112.31 109.26 111.59 123.48 ** +* * ** Residue-by-residue listing for refined_6 Page 9 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 102 CYS 102 1.294 - 1.515 1.543 1.425 123.31 - - 111.76 107.67 109.38 - +** +* * +** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *4.8* +* ** ** +** ** +* * ** +** ** * *4.8* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_6 Page 10 ---------------------------------------- A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S +------------------+ | BOND LENGTHS | +------------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Bond X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- C-N C-NH1 (except Pro) 1.329 .014 96 1.262 1.340 1.308 .015 *4.8* * C-N (Pro) 1.341 .016 5 1.330 1.354 1.344 .009 C-O C-O 1.231 .020 101 1.192 1.253 1.233 .010 +* * CA-C CH1E-C (except Gly) 1.525 .021 95 1.479 1.557 1.520 .014 ** +* CH2G*-C (Gly) 1.516 .018 7 1.483 1.518 1.500 .013 +* CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.514 1.532 1.523 .009 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.523 1.583 1.559 .017 +* CH1E-CH2E (the rest) 1.530 .020 75 1.505 1.574 1.538 .013 * ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.405 1.489 1.444 .016 +** +* NH1-CH2G* (Gly) 1.451 .016 7 1.424 1.458 1.438 .012 +* N-CH1E (Pro) 1.466 .015 5 1.432 1.475 1.454 .016 ** ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_6 Page 11 ---------------------------------------- +-----------------+ | BOND ANGLES | +-----------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Angle X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 89 114.22 119.41 116.28 .99 +* CH2G*-C-NH1 (Gly) 116.4 2.1 7 114.29 116.60 115.36 .85 * CH1E-C-N (Pro) 116.9 1.5 5 115.49 117.86 116.46 .79 O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.88 124.74 123.03 .64 * * O-C-N (Pro) 122.0 1.4 5 122.38 123.54 122.95 .39 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.48 125.69 122.08 1.23 * ** C-NH1-CH2G* (Gly) 120.6 1.7 7 120.25 122.53 121.14 .71 * C-N-CH1E (Pro) 122.6 5.0 5 121.61 123.37 122.36 .80 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 118.41 122.28 120.69 .60 * CH2G*-C-O (Gly) 120.8 2.1 7 120.68 121.55 121.13 .33 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 109.86 110.24 110.05 .19 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.07 113.96 110.25 1.44 ** CH2E-CH1E-C (the rest) 110.1 1.9 75 107.53 114.34 110.82 1.41 * ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 103.68 113.97 109.91 2.03 +** NH1-CH2G*-C (Gly) 112.5 2.9 7 107.77 113.26 111.21 1.83 +* N-CH1E-C (Pro) 111.8 2.5 5 108.34 112.99 110.41 1.92 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.43 110.38 109.91 .48 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 108.75 113.68 111.16 1.43 +* * N-CH1E-CH2E (Pro) 103.0 1.1 5 102.99 104.60 103.93 .58 * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 107.71 113.94 110.66 1.42 +* ** ------------------------------------------------------------------------------------------------------------- The small molecule data used in the above analysis is from Engh & Huber (1991). The atom labelling follows that used in the X-PLOR dictionary, with some additional atoms (marked with an asterisk) as defined by Engh & Huber. Residue-by-residue listing for refined_6 Page 12 ---------------------------------------- R A M A C H A N D R A N P L O T S T A T I S T I C S Residues in most favoured regions [A,B,L] 78 88.6% Residues in additional allowed regions [a,b,l,p] 8 9.1% Residues in generously allowed regions [~a,~b,~l,~p] 2 2.3% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 88 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 7 Number of proline residues 5 ---- Total number of residues 102 Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good quality model would be expected to have over 90% in the most favoured regions [E,H,L]. S T E R E O C H E M I S T R Y O F M A I N - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. %-tage residues in A, B, L 88 88.6 83.8 10.0 .5 Inside b. Omega angle st dev 101 3.9 6.0 3.0 -.7 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 1.9 3.1 1.6 -.8 Inside e. H-bond energy st dev 56 .9 .8 .2 .5 Inside f. Overall G-factor 102 -.1 -.4 .3 1.0 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 17 9.0 18.1 6.5 -1.4 BETTER b. Chi-1 trans st dev 41 7.2 19.0 5.3 -2.2 BETTER c. Chi-1 gauche plus st dev 30 6.5 17.5 4.9 -2.2 BETTER d. Chi-1 pooled st dev 88 8.7 18.2 4.8 -2.0 BETTER e. Chi-2 trans st dev 19 4.8 20.4 5.0 -3.1 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 88.6 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.1 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .92 3 Residue-by-residue listing for refined_6 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.45 Chi1-chi2 distribution -.38 Chi1 only -.05 Chi3 & chi4 .34 Omega -.11 ------ -.21 ===== Main-chain covalent forces:- Main-chain bond lengths -.13 Main-chain bond angles .39 ------ .17 ===== OVERALL AVERAGE -.08 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.