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 GLU 1 - - - -58.0 - - - - - - - 174.4 - 34.8 - 2 ALA 2 b - - - - - - - - - - 182.5 - 32.9 - 3 GLU 3 b - 190.1 - - - - - - - - 179.4 - 32.8 - 4 VAL 4 B - 183.1 - - - - - - - - 182.8 -1.3 35.2 - 5 HIS 5 b 51.3 - - - - - - - - - 174.4 - 29.3 - * * 6 ASN 6 S a - - -61.1 - - - - - - - 179.6 - 34.4 - 7 GLN 7 S b - - -65.4 - - - - - - - 185.2 - 34.4 - 8 LEU 8 E B - - -64.3 - - - - - - - 183.0 -1.6 32.0 - 9 GLU 9 E B - - -59.6 173.0 - - - - - - 182.2 -.5 33.1 - ** ** 10 ILE 10 E B - - -56.8 176.9 - - - - - - 171.7 -2.6 35.4 - * * 11 LYS 11 E B 68.9 - - 170.4 - - - - - - 182.2 -2.5 32.3 - 12 PHE 12 E B - - -61.4 - - - - - - - 177.1 - 34.4 - 13 ARG 13 E B - 177.3 - 177.0 - - - - - - 180.8 -2.5 32.9 - 14 LEU 14 t B - - -66.9 - - - - - - - 181.0 -3.5 34.1 - +* +* 15 THR 15 T A 47.4 - - - - - - - - - 180.6 - 34.5 - * * 16 ASP 16 T A - - -65.6 - - - - - - - 178.4 - 33.0 - 17 GLY 17 t - - - - - - - - - - - 178.2 -1.2 - - * * 18 SER 18 B 46.4 - - - - - - - - - 179.6 - 35.3 - * * 19 ASP 19 B B 59.0 - - - - - - - - - 181.0 - 32.1 - 20 ILE 20 B - - -57.5 178.1 - - - - - - 181.7 -2.8 35.3 - * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 21 GLY 21 - - - - - - - - - - - 182.8 - - - 22 PRO 22 - - - - - -65.8 - - - - - 179.0 - 38.0 - * * 23 LYS 23 E B - - -69.7 178.8 - - - - - - 180.4 -2.4 34.5 - 24 ALA 24 E B - - - - - - - - - - 177.9 - 33.2 - 25 PHE 25 E B - - -57.8 - - - - - - - 173.3 -3.7 36.6 - * ** ** 26 PRO 26 t - - - - - -62.0 - - - - - 181.1 - 39.2 - +* +* 27 ASP 27 T A 60.2 - - - - - - - - - 183.1 - 32.9 - 28 ALA 28 T A - - - - - - - - - - 177.7 - 33.6 - 29 THR 29 t B - - -54.9 - - - - - - - 179.2 -1.4 35.3 - 30 THR 30 h B 56.8 - - - - - - - - - 177.6 - 34.5 - 31 VAL 31 H A - 176.2 - - - -65.2 -27.4 - - - 175.9 -3.2 32.7 - * +* +* 32 SER 32 H A - 186.8 - - - -65.3 -45.1 - - - 178.2 -1.5 34.1 - 33 ALA 33 H A - - - - - -71.0 -27.3 - - - 175.9 - 33.7 - * * 34 LEU 34 H A - 173.6 - - - -63.0 -44.5 - - - 176.7 -2.0 35.7 - 35 LYS 35 H A - - -67.2 180.4 - -68.0 -37.1 - - - 173.3 -2.2 32.5 - * * 36 GLU 36 H A - - -69.5 - - -59.2 -36.1 - - - 176.3 -1.9 33.9 - 37 THR 37 H A - - -59.7 - - -66.6 -39.1 - - - 177.6 -2.0 33.8 - 38 VAL 38 H A - 180.6 - - - -61.6 -44.9 - - - 178.6 -1.8 33.5 - 39 ILE 39 H A - - -56.1 179.4 - -56.7 -35.3 - - - 181.3 -2.6 35.2 - 40 SER 40 H A - 184.5 - - - -72.4 -37.6 - - - 183.5 -1.4 33.8 - 41 GLU 41 H A - - -56.3 - - -87.8 -34.9 - - - 184.9 -1.9 35.8 - +* +* 42 TRP 42 h B - 193.7 - - - - - - - - 173.5 -3.7 36.1 - * ** ** 43 PRO 43 t - - - - - -62.0 - - - - - 185.3 - 38.0 - * * 44 ARG 44 T A - - -52.5 174.0 - - - - - - 178.1 -.8 34.3 - +* +* 45 GLU 45 T A - 180.7 - 178.7 - - - - - - 182.6 - 35.2 - 46 LYS 46 t B - 195.0 - 183.1 - - - - - - 176.0 -1.3 35.2 - * * 47 GLU 47 B 63.3 - - - - - - - - - 178.4 - 33.7 - 48 ASN 48 S l - - -66.9 - - - - - - - 180.6 - 32.6 - 49 GLY 49 S - - - - - - - - - - - 177.0 - - - 50 PRO 50 - - - - - -50.0 - - - - - 176.3 - 41.1 - * ** ** 51 LYS 51 ~a - 182.2 - 188.5 - - - - - - 184.8 - 35.3 - ** ** 52 THR 52 t B 57.8 - - - - - - - - - 185.4 - 33.0 - 53 VAL 53 T A 53.0 - - - - - - - - - 182.7 - 34.2 - 54 LYS 54 T A - 182.6 - - - - - - - - 187.7 - 34.5 - * * 55 GLU 55 e A - - -54.7 - - - - - - - 181.7 -1.1 33.7 - * * 56 VAL 56 E B - 178.0 - - - - - - - - 176.1 -.8 35.6 - +* +* 57 LYS 57 E B - - -67.4 - - - - - - - 180.6 -1.6 32.9 - 58 LEU 58 E B - - -66.3 - - - - - - - 180.4 - 33.2 - 59 ILE 59 E B - - -71.3 - - - - - - - 173.7 -3.4 34.8 - * +* +* 60 SER 60 E B - 183.7 - - - - - - - - 181.7 -2.4 34.6 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 61 ALA 61 T l - - - - - - - - - - 181.6 - 33.1 - 62 GLY 62 T - - - - - - - - - - - 181.9 - - - 63 LYS 63 E B - 180.0 - - - - - - - - 175.6 -1.9 34.8 - 64 VAL 64 E B - 183.3 - - - - - - - - 180.4 - 35.6 - 65 LEU 65 e B - - -72.9 - - - - - - - 180.1 -2.6 32.9 - 66 GLU 66 t B - 184.1 - - - - - - - - 185.6 - 33.3 - 67 ASN 67 T A - - -58.9 - - - - - - - 183.7 - 35.6 - 68 SER 68 T A - - -56.4 - - - - - - - 183.6 - 34.0 - 69 LYS 69 t B - - -65.5 191.6 - - - - - - 179.3 -1.8 31.8 - 70 THR 70 h B 51.2 - - - - - - - - - 176.8 - 35.5 - 71 VAL 71 H A - 181.3 - - - -65.5 -30.4 - - - 179.6 -2.9 34.9 - * * 72 LYS 72 H A - 188.6 - 181.6 - -57.1 -33.9 - - - 183.0 -2.3 36.8 - 73 ASP 73 H A - 184.8 - - - -66.3 -30.3 - - - 180.7 -.8 34.0 - +* +* 74 TYR 74 H A - - -64.6 - - -92.6 -14.1 - - - 178.5 -1.1 34.3 - ** ** * ** 75 ARG 75 h b - - -91.0 - - - - - - - 175.1 -.9 36.3 - +* +* +* 76 SER 76 B - 180.0 - - - - - - - - 176.3 - 36.4 - 77 PRO 77 - - - - - -61.8 - - - - - 182.3 - 38.7 - * * 78 VAL 78 S A - 184.9 - - - - - - - - 175.6 - 32.6 - 79 SER 79 S B - 185.0 - - - - - - - - 186.7 - 34.2 - * * 80 ASN 80 S l - 182.3 - - - - - - - - 182.6 -.9 30.9 - * * 81 LEU 81 B - 180.2 - - - - - - - - 179.8 - 35.4 - 82 ALA 82 b - - - - - - - - - - 180.1 - 33.3 - 83 GLY 83 - - - - - - - - - - - 180.4 - - - 84 ALA 84 B - - - - - - - - - - 180.6 -1.2 34.5 - * * 85 VAL 85 B - 182.8 - - - - - - - - 190.6 - 34.5 - +* +* 86 THR 86 E B - - -52.3 - - - - - - - 175.5 -3.0 37.2 - * * 87 THR 87 E B - 182.4 - - - - - - - - 178.9 - 31.2 - 88 MET 88 E B - - -59.8 187.8 - - - - - - 181.5 -1.7 33.0 - 89 HIS 89 E B - - -65.8 - - - - - - - 181.8 -1.5 32.9 - 90 VAL 90 E B - 184.5 - - - - - - - - 177.9 -3.0 35.2 - * * 91 ILE 91 E B - - -71.4 182.5 - - - - - - 181.5 -3.2 33.5 - * * 92 ILE 92 E B - - -75.7 - - - - - - - 172.2 -.7 33.0 - * +* +* 93 GLN 93 e B - - -63.8 182.5 - - - - - - 185.4 -1.1 33.3 - * * 94 ALA 94 B - - - - - - - - - - 173.2 -.6 34.6 - * +* +* 95 PRO 95 - - - - - -70.4 - - - - - 174.7 - 40.3 - +* +* 96 VAL 96 S A - 177.9 - - - - - - - - 172.3 - 32.5 - * * 97 THR 97 b - 179.5 - - - - - - - - 178.3 - 31.2 - 98 GLU 98 b - 186.3 - - - - - - - - 192.7 -1.5 35.1 - ** ** 99 LYS 99 B - 185.4 - 182.2 - - - - - - 183.4 - 35.3 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 100 GLU 100 A 59.2 - - 185.6 - - - - - - 180.8 - 33.7 - 101 LYS 101 - - 179.4 - - - - - - - - - - 33.3 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * +* * ** ** ** ** ** ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.2 183.0 -63.5 180.6 -62.0 -67.9 -34.5 - - - 179.8 -1.9 34.3 Standard deviations: 6.6 4.5 7.6 5.4 6.8 10.1 8.1 - - - 3.9 .9 1.9 Numbers of values: 12 34 36 19 6 15 15 0 0 0 100 49 96 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 GLU 1 - 1.240 1.504 1.557 1.464 - 116.14 120.63 107.79 109.25 112.75 123.23 * * * * 2 ALA 2 1.300 1.231 1.504 1.525 1.428 122.13 115.34 121.20 111.56 108.00 112.03 123.27 ** +* * * ** 3 GLU 3 1.308 1.239 1.523 1.555 1.416 122.19 114.71 121.72 114.39 108.92 109.45 123.32 * * ** ** ** 4 VAL 4 1.306 1.235 1.506 1.554 1.432 122.70 116.49 120.72 109.32 107.81 111.26 122.79 +* * * +* 5 HIS 5 1.292 1.227 1.513 1.554 1.436 120.92 114.57 121.79 113.45 113.45 113.04 123.51 +** * * +* * +** 6 ASN 6 1.318 1.223 1.504 1.537 1.466 122.87 115.26 121.58 108.75 108.68 112.36 123.16 * * * 7 GLN 7 1.316 1.244 1.511 1.522 1.430 123.41 118.05 119.56 111.25 108.23 110.05 122.36 * * * 8 LEU 8 1.310 1.212 1.498 1.521 1.448 118.65 115.59 121.14 110.39 111.68 113.04 123.27 * * +* * +* 9 GLU 9 1.295 1.238 1.499 1.502 1.431 121.56 114.64 121.69 111.05 111.41 110.89 123.67 ** * * * ** 10 ILE 10 1.285 1.232 1.518 1.571 1.432 122.93 116.74 120.29 108.80 109.47 111.16 122.91 *** * * *** 11 LYS 11 1.308 1.250 1.520 1.534 1.434 120.63 116.81 120.42 110.51 108.86 113.69 122.77 * * +* +* 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 PHE 12 1.303 1.226 1.510 1.530 1.448 121.16 116.59 120.27 109.50 110.86 111.02 123.14 +* +* 13 ARG 13 1.313 1.227 1.516 1.531 1.444 121.10 115.64 120.91 110.60 110.58 112.02 123.45 * * 14 LEU 14 1.302 1.245 1.526 1.556 1.440 123.10 115.89 121.18 109.86 110.45 111.42 122.92 +* * +* 15 THR 15 1.307 1.228 1.532 1.533 1.442 123.01 116.11 121.31 110.67 111.93 109.31 122.57 +* * +* 16 ASP 16 1.317 1.234 1.524 1.534 1.462 121.97 116.72 120.51 110.45 112.27 111.41 122.77 17 GLY 17 1.321 1.238 1.511 - 1.456 120.74 115.65 121.02 - 112.38 - 123.32 18 SER 18 1.298 1.229 1.523 1.527 1.426 122.91 117.59 120.11 111.92 109.29 107.74 122.25 ** +* +* ** 19 ASP 19 1.306 1.233 1.513 1.539 1.422 121.11 115.33 121.23 111.82 111.38 111.86 123.43 +* +* +* 20 ILE 20 1.301 1.222 1.517 1.564 1.449 123.36 116.59 119.25 109.40 107.92 110.92 124.13 +* * +* 21 GLY 21 1.335 1.236 1.530 - 1.459 122.79 117.18 120.59 - 114.44 - 122.23 * * 22 PRO 22 1.344 1.242 1.525 1.523 1.465 123.32 115.13 121.54 110.22 113.96 104.01 123.33 * * 23 LYS 23 1.304 1.217 1.465 1.512 1.449 123.34 115.81 120.22 108.27 109.59 112.54 123.96 +* +** * +** 24 ALA 24 1.284 1.232 1.510 1.525 1.446 120.93 115.49 121.11 110.60 110.48 111.63 123.40 *** *** 25 PHE 25 1.293 1.242 1.493 1.533 1.427 123.27 118.21 120.05 107.26 107.42 111.17 121.64 +** +* +* * * * +** 26 PRO 26 1.311 1.241 1.524 1.529 1.444 121.08 116.38 120.38 109.82 110.13 103.74 123.23 +* * +* 27 ASP 27 1.309 1.224 1.525 1.548 1.455 121.97 116.60 120.89 111.17 111.34 111.26 122.35 * * 28 ALA 28 1.315 1.234 1.534 1.514 1.456 121.50 116.76 120.55 110.58 112.52 110.14 122.69 * * 29 THR 29 1.318 1.234 1.535 1.539 1.449 121.84 116.98 120.20 109.70 109.74 109.70 122.81 * * 30 THR 30 1.316 1.234 1.524 1.543 1.440 121.36 116.71 120.60 109.59 110.39 111.06 122.69 31 VAL 31 1.318 1.234 1.539 1.552 1.453 121.98 116.35 121.09 111.63 110.40 111.41 122.52 * * 32 SER 32 1.321 1.233 1.549 1.538 1.442 121.28 116.32 121.01 111.46 108.84 109.94 122.58 * * 33 ALA 33 1.342 1.236 1.530 1.519 1.466 122.06 115.80 121.24 110.73 110.36 110.54 122.96 34 LEU 34 1.324 1.226 1.527 1.524 1.417 123.53 115.96 120.96 111.39 108.83 107.77 123.05 ** * +* ** 35 LYS 35 1.325 1.223 1.518 1.506 1.443 121.73 117.04 120.05 111.26 111.40 111.46 122.91 * * 36 GLU 36 1.337 1.235 1.535 1.531 1.460 121.45 115.88 121.29 110.20 109.74 111.09 122.83 37 THR 37 1.322 1.231 1.531 1.549 1.443 122.26 116.38 120.57 110.74 109.93 111.02 123.01 38 VAL 38 1.330 1.203 1.520 1.555 1.450 121.42 116.51 120.03 109.49 109.26 112.96 123.38 * * 39 ILE 39 1.337 1.239 1.540 1.563 1.483 122.56 115.43 121.61 108.16 110.25 111.31 122.95 * * 40 SER 40 1.314 1.235 1.536 1.538 1.429 122.03 117.05 120.19 110.82 111.27 110.39 122.76 * +* +* 41 GLU 41 1.324 1.228 1.541 1.520 1.433 122.18 116.05 120.66 108.98 112.16 109.00 123.29 * * 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 TRP 42 1.316 1.247 1.526 1.543 1.459 123.97 117.71 120.22 109.55 110.41 108.54 121.99 * * * 43 PRO 43 1.347 1.224 1.524 1.530 1.446 122.07 115.31 121.44 110.86 110.04 104.49 123.24 * * * * 44 ARG 44 1.303 1.229 1.524 1.527 1.454 123.32 115.08 121.73 112.28 110.22 108.43 123.19 +* * * +* 45 GLU 45 1.307 1.229 1.550 1.534 1.444 123.05 116.70 120.83 111.18 110.39 108.15 122.44 +* * * +* 46 LYS 46 1.336 1.244 1.526 1.523 1.460 121.54 116.11 120.81 107.64 111.05 111.38 123.08 * * 47 GLU 47 1.299 1.249 1.519 1.548 1.417 122.58 116.52 119.98 110.15 108.41 112.45 123.49 ** ** * ** 48 ASN 48 1.329 1.233 1.519 1.539 1.483 123.28 116.10 121.05 109.96 112.39 112.36 122.84 * * * 49 GLY 49 1.300 1.237 1.491 - 1.402 121.51 117.18 119.50 - 110.36 - 123.25 ** * *** *** 50 PRO 50 1.331 1.239 1.538 1.518 1.476 124.74 113.50 122.60 107.83 115.99 101.61 123.90 ** * * +* * * ** 51 LYS 51 1.311 1.217 1.508 1.536 1.441 124.66 115.22 121.55 108.08 107.61 112.12 123.22 * +* * * +* 52 THR 52 1.324 1.237 1.549 1.538 1.430 121.65 114.45 121.48 110.95 113.57 110.47 124.04 * * * 53 VAL 53 1.326 1.234 1.535 1.582 1.470 126.60 116.71 120.90 110.76 113.47 109.46 122.39 +* +** * +** 54 LYS 54 1.304 1.236 1.538 1.538 1.448 121.65 116.74 120.69 110.60 111.83 109.35 122.52 +* +* 55 GLU 55 1.320 1.235 1.541 1.527 1.466 120.16 116.83 120.71 110.23 113.19 110.13 122.46 56 VAL 56 1.311 1.227 1.525 1.554 1.464 121.76 117.02 120.31 108.25 110.13 110.79 122.63 * * 57 LYS 57 1.321 1.224 1.525 1.540 1.442 121.79 116.91 120.28 110.65 110.48 112.12 122.81 58 LEU 58 1.316 1.230 1.521 1.561 1.462 121.92 115.93 120.54 109.95 110.62 112.46 123.53 +* * +* 59 ILE 59 1.311 1.237 1.518 1.559 1.453 124.01 115.14 121.34 109.21 111.73 110.66 123.52 * * * 60 SER 60 1.302 1.230 1.511 1.536 1.422 122.89 116.81 119.50 110.97 106.50 110.74 123.61 +* +* +* +* 61 ALA 61 1.337 1.235 1.535 1.536 1.477 123.26 115.69 121.37 111.29 110.65 110.90 122.88 62 GLY 62 1.325 1.226 1.516 - 1.453 121.55 116.23 121.06 - 112.06 - 122.71 63 LYS 63 1.311 1.236 1.515 1.537 1.435 122.19 115.93 120.48 110.18 110.48 110.03 123.57 * * * 64 VAL 64 1.321 1.245 1.531 1.561 1.451 122.03 116.65 120.06 108.01 108.11 111.70 123.28 * * 65 LEU 65 1.315 1.242 1.520 1.540 1.447 122.50 115.98 120.81 110.37 111.73 111.99 123.21 66 GLU 66 1.312 1.230 1.517 1.526 1.440 122.10 114.96 120.82 111.02 110.39 111.17 124.15 * * 67 ASN 67 1.322 1.237 1.520 1.533 1.473 124.90 115.63 120.80 108.35 112.38 109.81 123.56 +* +* 68 SER 68 1.319 1.235 1.520 1.517 1.446 122.63 116.66 120.88 110.48 113.24 109.63 122.45 69 LYS 69 1.281 1.233 1.505 1.509 1.414 120.96 115.05 121.28 111.66 112.63 111.73 123.62 *** * ** *** 70 THR 70 1.299 1.242 1.520 1.533 1.408 123.44 116.08 120.81 109.88 110.99 109.23 123.11 ** +** * +** 71 VAL 71 1.325 1.234 1.536 1.564 1.454 122.00 114.10 121.89 110.10 108.21 110.68 123.96 * * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 72 LYS 72 1.320 1.224 1.528 1.523 1.454 125.71 116.39 120.65 109.09 111.33 107.61 122.95 ** +* ** 73 ASP 73 1.327 1.229 1.523 1.540 1.469 122.22 115.98 121.04 110.15 111.24 110.73 122.98 74 TYR 74 1.316 1.227 1.526 1.533 1.447 122.34 115.72 121.01 110.94 110.89 109.55 123.26 75 ARG 75 1.308 1.240 1.520 1.524 1.433 123.99 114.81 121.42 108.89 111.39 108.74 123.78 * * * * * 76 SER 76 1.302 1.238 1.523 1.548 1.425 123.85 118.48 119.45 110.18 107.07 108.64 122.04 +* +* * * * * +* 77 PRO 77 1.346 1.242 1.543 1.536 1.469 122.66 116.78 120.72 110.33 111.64 103.53 122.49 78 VAL 78 1.328 1.240 1.523 1.544 1.463 121.25 114.83 121.75 111.00 110.13 112.25 123.42 79 SER 79 1.295 1.241 1.528 1.541 1.432 122.41 115.26 120.77 111.45 107.40 110.48 123.95 ** * * ** 80 ASN 80 1.328 1.236 1.515 1.556 1.464 124.26 114.94 121.71 112.30 109.14 113.91 123.19 * * * ** ** 81 LEU 81 1.308 1.236 1.508 1.527 1.418 122.56 115.29 120.99 110.74 109.85 108.83 123.72 +* ** ** 82 ALA 82 1.281 1.234 1.514 1.525 1.411 123.63 115.96 120.87 111.37 109.20 111.38 123.15 *** ** * *** 83 GLY 83 1.314 1.237 1.512 - 1.456 121.89 115.14 121.43 - 111.63 - 123.42 * * 84 ALA 84 1.299 1.242 1.507 1.522 1.435 123.88 116.99 120.26 110.66 109.25 110.23 122.75 ** * * ** 85 VAL 85 1.306 1.237 1.503 1.540 1.431 120.01 114.18 121.98 109.61 106.75 112.17 123.85 +* * * * +* +* 86 THR 86 1.275 1.208 1.510 1.544 1.423 123.12 117.81 120.25 109.38 109.74 107.68 121.88 +*** * +* ** +*** 87 THR 87 1.289 1.240 1.517 1.548 1.411 119.49 115.28 121.63 112.53 110.76 112.81 123.05 +** ** * +* +** 88 MET 88 1.302 1.243 1.489 1.536 1.431 121.58 115.90 120.65 110.52 108.54 112.97 123.41 +* +* * * +* 89 HIS 89 1.291 1.218 1.498 1.534 1.437 121.14 116.17 120.76 111.73 109.48 111.48 123.03 +** * * +** 90 VAL 90 1.280 1.229 1.484 1.559 1.427 122.14 115.24 121.04 109.53 108.24 111.27 123.71 *** +* +* * *** 91 ILE 91 1.276 1.244 1.498 1.532 1.402 122.12 113.90 121.94 111.54 108.74 111.31 124.13 +*** * +** * * +*** 92 ILE 92 1.290 1.242 1.503 1.582 1.415 123.00 115.10 121.24 111.08 110.60 112.21 123.55 +** * +* ** +** 93 GLN 93 1.296 1.229 1.488 1.522 1.419 121.58 115.27 120.78 111.38 106.62 112.19 123.91 ** +* ** +* ** 94 ALA 94 1.291 1.242 1.521 1.518 1.433 122.38 116.92 120.38 110.30 112.04 109.45 122.69 +** * +** 95 PRO 95 1.349 1.235 1.517 1.548 1.470 123.66 116.02 121.15 108.95 110.22 102.96 122.83 96 VAL 96 1.308 1.236 1.537 1.549 1.458 121.30 116.44 120.86 111.24 109.65 112.37 122.69 * * 97 THR 97 1.335 1.228 1.546 1.583 1.438 120.86 114.16 122.26 112.37 109.40 113.59 123.37 * +* * * * * +* 98 GLU 98 1.296 1.235 1.503 1.556 1.434 125.46 116.21 120.36 112.67 102.98 109.39 123.38 ** * * * ** * +** +** 99 LYS 99 1.300 1.239 1.549 1.546 1.409 121.22 115.74 119.76 113.11 110.25 106.55 124.50 ** * +** +* ** +** 100 GLU 100 1.339 1.234 1.547 1.541 1.487 126.95 117.90 120.02 110.19 115.74 109.25 122.08 * +* +** +* +** 101 LYS 101 1.309 - 1.510 1.539 1.442 121.02 - - 111.17 109.78 111.35 - * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 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 94 1.275 1.342 1.311 .015 +*** * C-N (Pro) 1.341 .016 6 1.311 1.349 1.338 .013 +* C-O C-O 1.231 .020 100 1.203 1.250 1.233 .008 * CA-C CH1E-C (except Gly) 1.525 .021 96 1.465 1.550 1.520 .015 +** * CH2G*-C (Gly) 1.516 .018 5 1.491 1.530 1.512 .012 * CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.514 1.536 1.523 .006 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.532 1.583 1.554 .015 +* CH1E-CH2E (the rest) 1.530 .020 62 1.502 1.561 1.534 .013 * +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.402 1.487 1.442 .018 +** +* NH1-CH2G* (Gly) 1.451 .016 5 1.402 1.459 1.445 .022 *** N-CH1E (Pro) 1.466 .015 6 1.444 1.476 1.462 .012 * ------------------------------------------------------------------------------------------------------------- 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 89 113.90 118.48 116.04 .95 * * CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.14 117.18 116.28 .81 CH1E-C-N (Pro) 116.9 1.5 6 113.50 116.78 115.52 1.07 ** O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.64 124.50 123.10 .55 O-C-N (Pro) 122.0 1.4 6 122.49 123.90 123.17 .44 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.65 126.95 122.39 1.38 +* +** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.74 122.79 121.70 .66 * C-N-CH1E (Pro) 122.6 5.0 6 121.08 124.74 122.92 1.17 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.25 122.60 120.85 .64 * CH2G*-C-O (Gly) 120.8 2.1 5 119.50 121.43 120.72 .67 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 110.30 111.56 110.89 .43 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.01 112.53 110.11 1.20 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 107.26 114.39 110.46 1.39 * ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 102.98 115.74 110.13 1.89 +** +* NH1-CH2G*-C (Gly) 112.5 2.9 5 110.36 114.44 112.17 1.32 N-CH1E-C (Pro) 111.8 2.5 6 110.04 115.99 112.00 2.25 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 109.45 112.03 110.79 .81 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 107.68 113.59 111.11 1.28 ** * N-CH1E-CH2E (Pro) 103.0 1.1 6 101.61 104.49 103.39 .92 * * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 106.55 113.91 110.71 1.68 ** ** ------------------------------------------------------------------------------------------------------------- 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] 75 85.2% Residues in additional allowed regions [a,b,l,p] 12 13.6% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.1% 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 5 Number of proline residues 6 ---- Total number of residues 101 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 85.2 83.8 10.0 .1 Inside b. Omega angle st dev 100 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 96 1.9 3.1 1.6 -.8 Inside e. H-bond energy st dev 49 .9 .8 .2 .3 Inside f. Overall G-factor 101 -.1 -.4 .3 1.1 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 12 6.6 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 34 4.5 19.0 5.3 -2.7 BETTER c. Chi-1 gauche plus st dev 36 7.6 17.5 4.9 -2.0 BETTER d. Chi-1 pooled st dev 82 7.1 18.2 4.8 -2.3 BETTER e. Chi-2 trans st dev 19 5.4 20.4 5.0 -3.0 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% 85.2 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.3 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .89 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 -.55 Chi1-chi2 distribution -.24 Chi1 only .03 Chi3 & chi4 .38 Omega -.09 ------ -.18 ===== Main-chain covalent forces:- Main-chain bond lengths -.08 Main-chain bond angles .38 ------ .19 ===== OVERALL AVERAGE -.05 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.