Residue-by-residue listing for refined_12 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 - 65.9 - - - - - - - - - 178.3 - 34.3 - 2 ALA 2 B - - - - - - - - - - 181.7 - 34.0 - 3 ASP 3 B - - -64.2 - - - - - - - 165.9 -.8 35.4 - ** +* ** 4 THR 4 A - - -56.9 - - - - - - - 177.1 -.5 34.9 - ** ** 5 GLY 5 - - - - - - - - - - - 177.1 - - - 6 GLU 6 B 53.3 - - 186.7 - - - - - - 183.2 - 32.6 - 7 VAL 7 E B - - -63.8 - - - - - - - 182.2 -1.0 32.6 - * * 8 GLN 8 E B 58.5 - - 182.6 - - - - - - 175.3 - 34.7 - 9 PHE 9 E B 58.9 - - - - - - - - - 182.2 -2.1 32.3 - 10 MET 10 E B - 179.0 - 181.3 - - - - - - 179.4 - 35.0 - 11 LYS 11 E B - - -70.5 182.2 - - - - - - 164.3 -3.1 36.3 - +** * +** 12 PRO 12 E - - - - - -80.2 - - - - - 182.6 - 39.2 - * +* +* 13 PHE 13 e B 58.0 - - - - - - - - - 182.5 -.8 33.1 - +* +* 14 ILE 14 h B - - -69.6 - - - - - - - 186.3 - 33.5 - * * 15 SER 15 H A - 186.7 - - - -58.8 -29.5 - - - 178.1 -.7 33.0 - +* +* 16 GLU 16 H A - 179.0 - 182.9 - -60.2 -28.8 - - - 182.6 - 36.0 - 17 LYS 17 H a - 184.1 - 176.4 - -111.1 -36.5 - - - 182.3 -2.2 34.0 - +*** +*** 18 SER 18 H A - - -58.0 - - -83.3 6.1 - - - 170.0 -3.8 32.6 - +* **** +* ** **** Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 19 SER 19 h A - - -66.3 - - - - - - - 177.0 -1.0 31.8 - * * 20 LYS 20 T A - - -87.0 - - - - - - - 184.3 -1.0 33.0 - * * * 21 SER 21 t B 56.1 - - - - - - - - - 177.1 -1.9 35.0 - 22 LEU 22 E B - 185.2 - - - - - - - - 182.2 -2.0 34.6 - 23 GLU 23 E B 77.1 - - - - - - - - - 182.1 -.5 32.5 - ** ** 24 ILE 24 E B - - -56.8 178.3 - - - - - - 181.7 -2.8 34.9 - 25 PRO 25 h - - - - - -46.1 - - - - - 186.9 - 37.7 - +* * * +* 26 LEU 26 H A - - -56.2 178.6 - -57.6 -29.2 - - - 181.8 - 34.9 - 27 GLY 27 H - - - - - - -72.2 -29.8 - - - 181.4 - - - 28 PHE 28 H A - - -66.6 - - -74.2 -20.7 - - - 180.2 -1.4 31.8 - +* +* 29 ASN 29 H A - 178.7 - - - -56.0 -47.3 - - - 179.2 -.7 34.7 - +* +* 30 GLU 30 h A - - -59.8 176.1 - - - - - - 188.2 -.6 34.9 - * +* +* 31 TYR 31 T A - 187.1 - - - - - - - - 179.0 - 34.3 - 32 PHE 32 t B - - -68.8 - - - - - - - 183.1 -2.0 30.7 - 33 PRO 33 S - - - - - -55.5 - - - - - 177.0 - 39.3 - +* +* 34 ALA 34 S B - - - - - - - - - - 178.5 - 34.2 - 35 PRO 35 S - - - - - -52.4 - - - - - 174.3 - 38.7 - * * * 36 PHE 36 S B - 183.9 - - - - - - - - 178.2 - 33.8 - 37 PRO 37 - - - - - -75.7 - - - - - 178.0 - 38.8 - * * 38 ILE 38 e a - - -56.1 - - - - - - - 180.9 - 33.1 - 39 THR 39 E B 47.3 - - - - - - - - - 177.3 - 33.8 - * * 40 VAL 40 E B - - -66.0 - - - - - - - 181.7 -3.1 33.6 - * * 41 ASP 41 E B - 188.1 - - - - - - - - 186.7 -2.7 32.7 - * * 42 LEU 42 E B - 197.6 - 172.5 - - - - - - 184.8 -3.1 35.0 - * * 43 LEU 43 e B - - -66.8 - - - - - - - 190.7 -3.6 32.2 - +* ** ** 44 ASP 44 B - 169.0 - - - - - - - - 178.6 - 36.0 - 45 TYR 45 S A - - -65.2 - - - - - - - 184.3 - 36.2 - 46 SER 46 S A - - -54.6 - - - - - - - 179.7 - 34.5 - 47 GLY 47 S - - - - - - - - - - - 176.9 - - - 48 ARG 48 B - 184.6 - - - - - - - - 180.9 - 34.9 - 49 SER 49 B 51.7 - - - - - - - - - 179.7 - 33.2 - 50 TRP 50 E B - - -50.6 - - - - - - - 172.7 -1.6 37.5 - * * * * 51 THR 51 E B - - -54.4 - - - - - - - 187.8 - 34.0 - * * 52 VAL 52 E B - - -61.2 - - - - - - - 179.9 -2.5 33.9 - 53 ARG 53 E B - 181.1 - 175.0 - - - - - - 177.7 -2.2 33.9 - 54 MET 54 E B - - -65.2 176.5 - - - - - - 182.8 -1.4 35.9 - 55 LYS 55 E B - 189.1 - 172.6 - - - - - - 175.2 -2.8 34.8 - * * 56 LYS 56 E B - - -56.7 - - - - - - - 177.9 - 37.0 - 57 ARG 57 E B - 178.3 - 178.9 - - - - - - 177.4 -2.5 32.5 - Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 58 GLY 58 T - - - - - - - - - - - 180.6 - - - 59 GLU 59 T A - - -53.2 177.2 - - - - - - 191.4 -.8 37.3 - +* +* +* 60 LYS 60 E B - 181.9 - 178.5 - - - - - - 175.1 -1.4 35.5 - 61 VAL 61 E B - 187.2 - - - - - - - - 176.1 -1.0 36.2 - * * 62 PHE 62 E B 51.1 - - - - - - - - - 183.8 -2.3 29.7 - * * 63 LEU 63 E B - 188.0 - 169.7 - - - - - - 189.2 -2.8 35.1 - +* * +* 64 THR 64 e a 53.5 - - - - - - - - - 185.7 -1.7 33.5 - 65 VAL 65 T B 61.5 - - - - - - - - - 183.9 - 32.0 - 66 GLY 66 h - - - - - - - - - - - 178.6 - - - 67 TRP 67 H A - 177.2 - - - -62.1 -33.9 - - - 183.4 -.9 35.8 - +* +* 68 GLU 68 H A - - -60.8 170.5 - -68.1 -25.8 - - - 177.0 -.6 31.9 - * +* +* 69 ASN 69 H A - - -63.3 - - -77.1 -35.5 - - - 181.6 -.7 35.2 - +* +* 70 PHE 70 H A - 171.2 - - - -73.8 -50.8 - - - 184.9 -1.5 34.4 - * * 71 VAL 71 H A 70.2 - - - - -60.0 -49.2 - - - 181.3 -3.7 32.8 - ** ** 72 LYS 72 H A - - -56.7 - - -72.2 -33.7 - - - 185.6 -1.4 31.1 - 73 ASP 73 H A - 185.3 - - - -70.7 -39.3 - - - 185.2 -1.5 31.8 - 74 ASN 74 h A - - -70.5 - - - - - - - 180.0 -2.1 30.9 - 75 ASN 75 t XX - 177.2 - - - - - - - - 177.0 -.6 31.0 - **** +* **** 76 LEU 76 l - - -69.6 - - - - - - - 181.2 -1.5 28.2 - +* +* 77 GLU 77 t B - 199.7 - - - - - - - - 182.2 - 33.9 - 78 ASP 78 T B - 176.4 - - - - - - - - 181.8 - 34.3 - 79 GLY 79 T - - - - - - - - - - - 179.0 - - - 80 LYS 80 e B - - -45.6 - - - - - - - 177.7 -1.5 35.2 - * * 81 TYR 81 E B - - -56.4 - - - - - - - 187.2 -1.3 33.6 - * * 82 LEU 82 E B - 191.0 - - - - - - - - 179.2 -2.9 35.8 - * * 83 GLN 83 E B - 184.5 - 180.4 - - - - - - 179.9 -2.7 34.1 - 84 PHE 84 E B - - -63.9 - - - - - - - 176.7 -2.9 35.4 - * * 85 ILE 85 E B - - -59.6 - - - - - - - 179.9 -3.0 33.2 - * * 86 TYR 86 E B - 183.0 - - - - - - - - 186.7 -3.5 36.7 - * +* +* 87 ASP 87 e A 72.0 - - - - - - - - - 179.1 -1.5 33.6 - 88 ARG 88 S l - 177.6 - 170.6 - - - - - - 175.8 - 30.6 - 89 ASP 89 S b - 191.7 - - - - - - - - 185.4 - 34.4 - 90 ARG 90 e A - 186.9 - - - - - - - - 182.5 - 34.7 - 91 THR 91 E B 49.0 - - - - - - - - - 175.5 - 31.8 - 92 PHE 92 E B - - -74.9 - - - - - - - 174.4 -2.6 35.2 - 93 TYR 93 E B - - -62.8 - - - - - - - 184.9 -3.0 34.4 - * * 94 VAL 94 E B 74.5 - - - - - - - - - 174.3 - 32.6 - 95 ILE 95 E B - - -63.9 180.0 - - - - - - 182.1 -2.5 33.6 - 96 ILE 96 E B - - -55.7 177.1 - - - - - - 178.8 - 35.6 - Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 97 TYR 97 E B - - -64.0 - - - - - - - 177.9 -3.4 33.2 - +* +* 98 GLY 98 S - - - - - - - - - - - 178.5 -.8 - - +* +* 99 HIS 99 S a - 189.9 - - - - - - - - 174.6 - 33.1 - 100 ASN 100 S b - 180.7 - - - - - - - - 186.1 - 33.7 - * * 101 MET 101 XX - - -56.8 - - - - - - - 171.9 - 32.3 - **** * **** 102 CYS 102 - - - -58.2 - - - - - - - - -2.3 35.7 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * +* +*** **** +** ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.9 183.8 -61.9 177.5 -62.0 -70.5 -32.3 - - - 180.3 -1.9 34.1 Standard deviations: 9.4 6.7 7.4 4.4 15.1 13.9 13.7 - - - 4.6 1.0 2.0 Numbers of values: 16 32 40 22 5 15 15 0 0 0 101 59 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_12 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 - 1.235 1.509 1.551 1.462 - 116.76 120.10 109.97 108.84 111.47 123.11 * * 2 ALA 2 1.310 1.240 1.513 1.517 1.442 121.61 116.15 120.94 110.64 109.64 110.61 122.89 * * 3 ASP 3 1.307 1.231 1.492 1.546 1.448 121.24 116.38 120.73 106.25 111.68 112.73 122.89 +* +* ** * ** 4 THR 4 1.302 1.232 1.536 1.547 1.437 119.97 114.03 122.19 110.07 105.24 111.36 123.74 +* * * ** ** 5 GLY 5 1.336 1.238 1.487 - 1.424 122.36 115.43 120.92 - 111.96 - 123.65 +* +* * +* 6 GLU 6 1.288 1.244 1.517 1.546 1.413 122.21 115.63 121.63 113.65 108.34 110.61 122.64 +** ** +* * +** 7 VAL 7 1.297 1.228 1.499 1.559 1.424 120.64 115.76 121.28 111.41 110.04 112.43 122.95 ** * +* * ** 8 GLN 8 1.279 1.234 1.503 1.522 1.407 121.75 116.29 120.57 110.95 110.51 109.45 123.12 +*** * +** +*** 9 PHE 9 1.294 1.235 1.510 1.555 1.446 121.03 116.19 120.44 111.89 110.21 112.02 123.37 ** * ** 10 MET 10 1.307 1.234 1.507 1.535 1.444 122.33 116.24 120.65 110.05 109.92 110.01 123.11 +* +* 11 LYS 11 1.303 1.238 1.504 1.530 1.439 122.31 117.06 120.72 105.63 111.71 111.92 122.21 +* * ** ** Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 12 PRO 12 1.326 1.245 1.534 1.547 1.432 121.54 117.15 120.60 110.20 106.61 104.18 122.23 ** ** * ** 13 PHE 13 1.289 1.232 1.503 1.541 1.440 120.64 116.67 120.62 111.81 110.09 110.94 122.71 +** * +** 14 ILE 14 1.298 1.214 1.504 1.577 1.423 120.71 116.97 119.80 111.65 107.44 111.88 123.23 ** * +* * * ** 15 SER 15 1.328 1.219 1.521 1.525 1.464 122.55 115.59 121.06 111.10 111.59 110.89 123.25 16 GLU 16 1.301 1.229 1.530 1.526 1.446 123.53 116.35 121.00 109.75 110.17 108.40 122.62 ** * * ** 17 LYS 17 1.315 1.237 1.521 1.521 1.445 120.90 115.11 121.75 111.95 110.32 109.07 123.09 18 SER 18 1.299 1.204 1.532 1.522 1.419 122.53 118.56 119.90 112.43 112.96 109.75 121.54 ** * ** * * ** 19 SER 19 1.327 1.226 1.538 1.541 1.460 118.24 116.11 120.90 111.22 109.40 113.27 122.99 +* +* +* 20 LYS 20 1.338 1.233 1.526 1.560 1.462 121.93 117.09 120.31 108.92 111.86 113.29 122.61 * +* +* 21 SER 21 1.329 1.234 1.528 1.538 1.452 120.34 116.19 120.60 110.27 111.84 109.05 123.21 22 LEU 22 1.313 1.240 1.520 1.560 1.449 122.28 116.91 120.21 111.95 107.42 109.54 122.87 * +* * +* 23 GLU 23 1.316 1.244 1.541 1.567 1.439 120.82 116.56 120.61 114.42 108.74 109.70 122.70 +* * ** ** 24 ILE 24 1.313 1.220 1.541 1.563 1.455 122.23 118.05 119.54 109.98 109.52 110.29 122.41 * * 25 PRO 25 1.361 1.247 1.553 1.523 1.482 123.79 114.85 121.59 110.93 114.61 103.31 123.52 * * * * * * * 26 LEU 26 1.334 1.240 1.535 1.535 1.477 124.83 116.82 120.49 109.04 113.42 109.70 122.69 +* +* 27 GLY 27 1.318 1.232 1.504 - 1.447 120.95 116.57 120.69 - 112.75 - 122.72 28 PHE 28 1.322 1.226 1.513 1.529 1.445 120.69 116.87 120.11 110.66 112.14 112.89 123.00 * * 29 ASN 29 1.329 1.236 1.518 1.544 1.470 121.99 115.19 121.23 110.16 110.45 110.00 123.54 30 GLU 30 1.307 1.230 1.527 1.510 1.449 122.95 115.85 120.92 109.77 111.92 109.31 123.23 +* +* 31 TYR 31 1.306 1.232 1.534 1.536 1.457 122.17 117.65 120.00 110.60 112.43 109.38 122.34 +* +* 32 PHE 32 1.331 1.236 1.528 1.537 1.461 119.90 117.04 120.15 111.72 111.77 113.38 122.81 * +* +* 33 PRO 33 1.362 1.233 1.508 1.527 1.476 123.45 115.07 121.27 109.83 112.38 103.03 123.66 * * * * 34 ALA 34 1.302 1.253 1.530 1.524 1.438 122.07 117.21 120.22 110.51 109.91 110.50 122.54 +* * * +* 35 PRO 35 1.359 1.230 1.519 1.531 1.466 123.14 115.76 121.18 110.75 110.61 103.31 123.05 * * 36 PHE 36 1.305 1.235 1.516 1.533 1.427 122.04 117.52 120.26 110.95 108.18 111.39 122.11 +* +* * +* 37 PRO 37 1.334 1.242 1.516 1.544 1.448 122.12 116.64 120.69 109.92 110.35 104.36 122.66 * * * 38 ILE 38 1.295 1.227 1.517 1.560 1.425 120.29 116.71 120.72 110.82 108.65 112.63 122.46 ** +* ** 39 THR 39 1.306 1.234 1.515 1.545 1.429 121.08 115.42 121.23 110.07 111.47 111.37 123.35 +* +* +* 40 VAL 40 1.297 1.233 1.511 1.560 1.439 123.88 117.91 119.84 110.29 107.72 112.68 122.25 ** * * ** 41 ASP 41 1.292 1.239 1.513 1.525 1.444 119.75 116.08 120.68 112.41 109.45 110.83 123.23 +** * * +** Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 42 LEU 42 1.300 1.241 1.546 1.565 1.438 122.06 115.72 120.76 113.53 108.51 107.06 123.52 ** +* * +* ** ** 43 LEU 43 1.327 1.206 1.522 1.556 1.462 123.80 115.48 120.98 110.44 111.98 112.77 123.52 * * * * * 44 ASP 44 1.303 1.235 1.528 1.544 1.460 124.30 116.04 120.43 110.42 110.94 107.72 123.53 +* * +* +* 45 TYR 45 1.328 1.235 1.511 1.528 1.456 123.51 115.43 121.16 107.36 110.59 110.57 123.42 * * * 46 SER 46 1.308 1.235 1.526 1.521 1.431 122.16 116.50 120.65 111.38 110.61 108.87 122.81 * * * 47 GLY 47 1.317 1.229 1.505 - 1.434 119.82 117.77 120.07 - 114.08 - 122.15 * * 48 ARG 48 1.313 1.228 1.522 1.529 1.449 119.97 117.52 120.14 109.87 107.55 110.76 122.33 * * * 49 SER 49 1.294 1.242 1.518 1.525 1.434 119.98 115.53 121.28 112.22 111.39 109.82 123.14 ** * * ** 50 TRP 50 1.302 1.229 1.497 1.512 1.416 123.03 117.10 120.40 107.33 109.27 109.04 122.48 +* * ** * ** 51 THR 51 1.281 1.242 1.525 1.524 1.410 119.57 115.51 121.13 111.98 106.33 110.62 123.33 *** +** * * +* *** 52 VAL 52 1.298 1.233 1.514 1.555 1.431 122.30 115.96 121.01 110.01 111.50 111.28 123.02 ** * ** 53 ARG 53 1.301 1.235 1.516 1.528 1.438 121.55 115.67 120.78 110.69 110.93 110.47 123.55 ** * ** 54 MET 54 1.312 1.221 1.494 1.520 1.450 122.94 117.65 119.87 108.20 108.07 110.78 122.47 * * * * * 55 LYS 55 1.290 1.234 1.511 1.526 1.432 119.81 115.93 120.70 110.70 110.96 109.22 123.37 +** * * +** 56 LYS 56 1.316 1.235 1.508 1.534 1.437 121.68 117.18 120.22 105.90 105.51 112.04 122.54 * ** ** ** 57 ARG 57 1.271 1.237 1.509 1.538 1.447 120.63 115.45 121.24 111.05 111.46 111.89 123.30 **** **** 58 GLY 58 1.306 1.230 1.495 - 1.431 120.90 115.90 120.87 - 112.33 - 123.22 +* * * +* 59 GLU 59 1.300 1.228 1.513 1.525 1.446 121.96 116.02 120.93 106.91 109.41 109.58 123.05 ** +* ** 60 LYS 60 1.312 1.242 1.525 1.544 1.435 120.83 115.07 121.37 110.92 112.62 107.71 123.56 * * +* +* 61 VAL 61 1.314 1.233 1.505 1.547 1.429 122.83 117.05 120.24 107.11 106.89 112.10 122.69 * +* +* +* 62 PHE 62 1.278 1.238 1.503 1.546 1.422 120.40 114.97 121.23 114.22 110.85 113.05 123.74 +*** * +* ** * +*** 63 LEU 63 1.291 1.235 1.540 1.558 1.435 123.44 116.19 120.43 114.28 107.39 106.43 123.36 +** * * ** * ** +** 64 THR 64 1.335 1.232 1.542 1.550 1.460 122.55 115.96 121.24 109.27 115.67 110.77 122.80 +* +* 65 VAL 65 1.317 1.239 1.514 1.575 1.452 122.32 115.46 121.03 112.46 110.48 111.87 123.46 * +* +* 66 GLY 66 1.314 1.230 1.484 - 1.426 121.41 114.61 121.40 - 110.23 - 123.98 * +* +* +* 67 TRP 67 1.314 1.214 1.486 1.521 1.431 123.61 115.50 121.10 108.82 109.39 110.24 123.34 * +* * * +* 68 GLU 68 1.304 1.225 1.535 1.516 1.458 120.59 115.21 121.69 113.17 110.36 110.62 123.05 +* +* +* Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 69 ASN 69 1.314 1.211 1.512 1.544 1.454 123.06 115.25 121.45 108.88 108.90 111.08 123.30 * * * 70 PHE 70 1.309 1.244 1.492 1.546 1.446 123.35 114.79 120.76 110.13 110.71 110.67 124.44 * +* +* 71 VAL 71 1.323 1.212 1.513 1.587 1.430 122.65 116.31 120.84 111.67 109.77 112.11 122.80 +* * * +* 72 LYS 72 1.312 1.228 1.523 1.530 1.433 120.53 117.80 119.81 111.52 112.95 112.62 122.38 * * * * 73 ASP 73 1.343 1.232 1.536 1.539 1.485 118.77 117.27 120.49 110.31 113.68 112.41 122.23 * * +* * +* 74 ASN 74 1.320 1.233 1.500 1.531 1.461 121.61 116.24 119.56 111.94 113.06 112.46 124.18 * * * 75 ASN 75 1.345 1.226 1.503 1.563 1.486 124.13 115.83 120.16 112.97 111.11 112.26 124.01 * * +* * * +* * +* 76 LEU 76 1.307 1.238 1.529 1.529 1.492 123.03 117.61 120.45 111.15 115.52 115.08 121.82 +* +* +* +** +** 77 GLU 77 1.287 1.235 1.524 1.546 1.446 119.69 115.51 120.74 113.70 108.26 108.39 123.73 *** * +* * * *** 78 ASP 78 1.291 1.231 1.523 1.533 1.481 124.12 115.94 121.02 109.92 111.91 110.17 123.03 +** * * +** 79 GLY 79 1.307 1.239 1.503 - 1.438 121.35 115.47 121.25 - 110.70 - 123.28 +* +* 80 LYS 80 1.318 1.245 1.525 1.540 1.453 121.21 116.77 120.49 109.04 108.84 110.90 122.74 81 TYR 81 1.307 1.235 1.489 1.535 1.446 121.46 117.50 119.79 111.22 106.58 111.94 122.70 +* +* +* +* 82 LEU 82 1.291 1.236 1.515 1.516 1.411 119.68 116.23 120.65 111.08 110.50 107.53 123.11 +** ** * +* +** 83 GLN 83 1.307 1.239 1.518 1.530 1.435 121.72 115.87 120.74 110.72 109.82 110.49 123.38 +* * +* 84 PHE 84 1.309 1.235 1.494 1.527 1.448 122.62 116.67 120.04 108.22 109.70 111.13 123.28 * * * 85 ILE 85 1.304 1.230 1.516 1.581 1.432 121.13 116.23 120.68 109.40 108.33 114.17 123.09 +* +* * * +* +* 86 TYR 86 1.292 1.225 1.517 1.544 1.440 122.45 116.86 120.49 111.25 106.39 107.07 122.64 +** +* ** +** 87 ASP 87 1.319 1.245 1.513 1.542 1.471 121.42 114.92 121.14 110.58 110.79 111.01 123.92 88 ARG 88 1.333 1.230 1.541 1.560 1.461 124.14 115.41 122.03 115.12 111.00 110.55 122.50 * * +** +** 89 ASP 89 1.317 1.212 1.539 1.541 1.433 121.95 117.91 119.79 111.70 106.34 110.22 122.28 * +* +* 90 ARG 90 1.290 1.233 1.552 1.571 1.452 123.33 115.99 121.94 114.64 109.47 106.06 122.02 +** * ** ** +** +** 91 THR 91 1.323 1.232 1.550 1.545 1.448 121.21 115.40 121.42 111.22 114.78 111.24 123.14 * * * 92 PHE 92 1.330 1.216 1.514 1.537 1.464 123.43 117.05 120.28 107.12 110.72 112.10 122.67 +* +* 93 TYR 93 1.297 1.241 1.505 1.531 1.455 121.66 118.29 119.51 110.41 107.00 111.12 122.18 ** * +* ** 94 VAL 94 1.313 1.244 1.537 1.551 1.453 117.91 115.13 121.36 110.19 113.28 111.91 123.49 * ** ** 95 ILE 95 1.326 1.237 1.531 1.563 1.447 123.59 116.16 120.62 110.11 108.73 112.40 123.21 * * 96 ILE 96 1.317 1.239 1.515 1.559 1.454 122.96 116.14 120.85 108.46 108.83 111.13 123.00 97 TYR 97 1.301 1.241 1.509 1.515 1.433 121.44 114.28 121.26 110.30 110.99 111.68 124.44 ** * ** Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 98 GLY 98 1.298 1.245 1.496 - 1.427 123.81 118.44 119.38 - 107.68 - 122.17 ** * +* +* +* ** 99 HIS 99 1.300 1.225 1.521 1.533 1.447 118.99 115.49 121.12 111.98 107.71 111.37 123.35 ** +* * ** 100 ASN 100 1.312 1.242 1.499 1.541 1.471 123.50 116.06 119.91 109.56 107.86 112.91 123.95 * * * * * 101 MET 101 1.347 1.237 1.534 1.546 1.497 124.89 114.02 122.26 111.37 108.80 112.45 123.72 * ** +* * * ** 102 CYS 102 1.288 - 1.523 1.527 1.403 125.28 - - 110.26 105.98 109.88 - +** +** +* +* +** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +* ** +** ** * +** ** +** * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 1.271 1.347 1.309 .015 **** * * C-N (Pro) 1.341 .016 5 1.326 1.362 1.348 .015 * C-O C-O 1.231 .020 101 1.204 1.253 1.233 .009 * * CA-C CH1E-C (except Gly) 1.525 .021 95 1.486 1.553 1.519 .015 +* * CH2G*-C (Gly) 1.516 .018 7 1.484 1.505 1.497 .008 +* * CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.517 1.524 1.520 .003 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.524 1.587 1.558 .015 +* CH1E-CH2E (the rest) 1.530 .020 75 1.510 1.571 1.537 .013 ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.403 1.497 1.446 .018 +** ** NH1-CH2G* (Gly) 1.451 .016 7 1.424 1.447 1.432 .007 +* * N-CH1E (Pro) 1.466 .015 5 1.432 1.482 1.461 .019 ** * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 89 114.02 118.56 116.25 .94 * * CH2G*-C-NH1 (Gly) 116.4 2.1 7 114.61 118.44 116.31 1.27 CH1E-C-N (Pro) 116.9 1.5 5 114.85 117.15 115.90 .88 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 121.54 124.44 123.02 .56 O-C-N (Pro) 122.0 1.4 5 122.23 123.66 123.02 .53 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 117.91 125.28 121.84 1.52 ** +* C-NH1-CH2G* (Gly) 120.6 1.7 7 119.82 123.81 121.51 1.17 +* C-N-CH1E (Pro) 122.6 5.0 5 121.54 123.79 122.81 .84 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 119.51 122.26 120.73 .59 CH2G*-C-O (Gly) 120.8 2.1 7 119.38 121.40 120.65 .65 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.51 110.64 110.57 .07 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 107.11 112.46 110.34 1.27 +* CH2E-CH1E-C (the rest) 110.1 1.9 75 105.63 115.12 110.69 1.96 ** +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.24 115.67 110.02 2.15 ** +* NH1-CH2G*-C (Gly) 112.5 2.9 7 107.68 114.08 111.39 1.92 +* N-CH1E-C (Pro) 111.8 2.5 5 106.61 114.61 110.91 2.64 ** * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 110.50 110.61 110.55 .06 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 110.29 114.17 111.79 .89 +* N-CH1E-CH2E (Pro) 103.0 1.1 5 103.03 104.36 103.64 .53 * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 106.06 115.08 110.59 1.79 +** +** ------------------------------------------------------------------------------------------------------------- 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_12 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] 0 .0% Residues in disallowed regions [XX] 2 2.3% ---- ------ 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 4.6 6.0 3.0 -.5 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 2.0 3.1 1.6 -.7 Inside e. H-bond energy st dev 59 1.0 .8 .2 .8 Inside f. Overall G-factor 102 -.1 -.4 .3 .9 Inside 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 16 9.4 18.1 6.5 -1.3 BETTER b. Chi-1 trans st dev 32 6.7 19.0 5.3 -2.3 BETTER c. Chi-1 gauche plus st dev 40 7.4 17.5 4.9 -2.1 BETTER d. Chi-1 pooled st dev 88 8.3 18.2 4.8 -2.0 BETTER e. Chi-2 trans st dev 22 4.4 20.4 5.0 -3.2 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 8.8 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .97 3 Residue-by-residue listing for refined_12 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.53 Chi1-chi2 distribution -.17 Chi1 only -.04 Chi3 & chi4 .35 Omega -.25 ------ -.23 ===== Main-chain covalent forces:- Main-chain bond lengths -.13 Main-chain bond angles .32 ------ .13 ===== OVERALL AVERAGE -.11 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.