Residue-by-residue listing for refined_9 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 - - 177.5 - 180.6 - - - - - - 174.1 - 34.8 - * * 2 ALA 2 B - - - - - - - - - - 184.8 - 34.2 - 3 GLU 3 B - - -54.9 184.1 - - - - - - 184.1 -1.1 33.5 - * * 4 VAL 4 S b 54.9 - - - - - - - - - 175.8 - 30.2 - * * 5 HIS 5 S ~a - - -66.2 - - - - - - - 173.9 -.5 32.8 - ** * ** ** 6 ASN 6 S b - 184.8 - - - - - - - - 173.9 - 31.0 - * * 7 GLN 7 b - - -59.4 181.2 - - - - - - 179.3 - 34.5 - 8 LEU 8 E B - - -66.6 174.8 - - - - - - 179.4 -2.6 32.9 - 9 GLU 9 E B - - -65.2 - - - - - - - 178.7 - 32.6 - 10 ILE 10 E B - - -59.2 178.0 - - - - - - 175.2 -2.9 34.7 - * * 11 LYS 11 E B 63.5 - - 180.6 - - - - - - 185.0 -2.8 31.3 - 12 PHE 12 E B - - -53.8 - - - - - - - 182.2 - 35.9 - 13 ARG 13 E B - 184.8 - 167.2 - - - - - - 184.7 -3.1 32.2 - * * 14 LEU 14 E B - - -48.9 181.8 - - - - - - 175.3 -3.1 37.1 - * * * 15 THR 15 e A 45.3 - - - - - - - - - 176.7 -1.5 34.4 - * * 16 ASP 16 T A - - -63.4 - - - - - - - 176.2 - 33.5 - 17 GLY 17 t - - - - - - - - - - - 179.9 -1.8 - - 18 SER 18 B - - -54.5 - - - - - - - 176.0 - 36.5 - Residue-by-residue listing for refined_9 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 ASP 19 B B 52.3 - - - - - - - - - 181.5 - 28.1 - +* +* 20 ILE 20 B - - -58.6 177.4 - - - - - - 179.8 -2.2 36.4 - 21 GLY 21 - - - - - - - - - - - 184.5 - - - 22 PRO 22 - - - - - -69.4 - - - - - 181.3 - 37.3 - 23 LYS 23 E B - 181.0 - 181.1 - - - - - - 183.0 -2.1 36.8 - 24 ALA 24 E B - - - - - - - - - - 177.9 - 32.9 - 25 PHE 25 E B - - -51.6 - - - - - - - 170.5 -3.5 37.4 - * +* +* +* 26 PRO 26 t - - - - - -77.9 - - - - - 178.7 - 40.1 - * +* +* 27 ASP 27 T A - - -64.2 - - - - - - - 180.5 - 33.1 - 28 ALA 28 T A - - - - - - - - - - 176.7 - 33.7 - 29 THR 29 t B - 196.0 - - - - - - - - 180.9 -2.0 32.1 - 30 THR 30 h B 59.3 - - - - - - - - - 178.5 - 33.7 - 31 VAL 31 H A - 178.6 - - - -62.9 -26.4 - - - 176.0 -3.3 33.5 - * +* +* 32 SER 32 H A - 181.4 - - - -56.3 -49.4 - - - 180.9 -1.7 34.0 - 33 ALA 33 H A - - - - - -69.8 -25.9 - - - 176.7 - 33.5 - * * 34 LEU 34 H A - 173.8 - - - -67.8 -46.5 - - - 178.1 -1.2 36.4 - * * 35 LYS 35 H A - - -62.6 176.2 - -73.1 -32.3 - - - 172.1 -2.9 31.2 - * * * 36 GLU 36 H A - - -64.9 - - -57.5 -39.8 - - - 175.5 -2.5 35.2 - 37 THR 37 H A - - -68.0 - - -59.3 -43.1 - - - 177.5 -1.5 34.1 - 38 VAL 38 H A - 182.2 - - - -60.2 -50.5 - - - 180.0 -1.2 34.5 - * * 39 ILE 39 H A - - -58.2 177.5 - -56.8 -42.4 - - - 182.1 -2.7 35.3 - 40 SER 40 H A - 179.2 - - - -75.6 -39.4 - - - 184.0 -2.7 34.2 - 41 GLU 41 H A - - -79.3 - - -91.5 -4.3 - - - 177.9 -3.0 32.5 - ** *** * *** 42 TRP 42 h B - 190.0 - - - - - - - - 175.1 -1.5 36.1 - 43 PRO 43 t - - - - - -59.5 - - - - - 182.7 - 37.9 - * * 44 ARG 44 T A 57.4 - - 184.8 - - - - - - 181.8 -.6 34.9 - +* +* 45 GLU 45 T A - - -57.7 178.1 - - - - - - 180.3 - 33.3 - 46 LYS 46 t B - 196.7 - - - - - - - - 180.0 -.8 35.3 - +* +* 47 GLU 47 S B 56.5 - - - - - - - - - 181.6 - 30.2 - * * 48 ASN 48 S l - - -62.1 - - - - - - - 177.6 - 31.2 - 49 GLY 49 S - - - - - - - - - - - 176.9 - - - 50 PRO 50 - - - - - -57.0 - - - - - 178.7 - 39.2 - +* +* 51 LYS 51 a - 181.1 - 180.7 - - - - - - 180.7 - 34.6 - 52 THR 52 t B 56.0 - - - - - - - - - 187.3 - 33.0 - * * 53 VAL 53 T A 56.9 - - - - - - - - - 182.8 - 32.9 - 54 LYS 54 T A 61.8 - - 179.0 - - - - - - 188.4 - 33.4 - * * 55 GLU 55 e A - - -60.2 - - - - - - - 179.7 -.5 32.5 - ** ** 56 VAL 56 E B 59.9 - - - - - - - - - 183.6 -.9 32.0 - +* +* 57 LYS 57 E B - - -53.3 - - - - - - - 178.5 -1.6 34.8 - Residue-by-residue listing for refined_9 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 LEU 58 E B - - -75.5 - - - - - - - 177.2 -.6 34.2 - +* +* 59 ILE 59 E B - - -60.5 180.5 - - - - - - 180.5 -2.7 33.5 - 60 SER 60 E B - 180.1 - - - - - - - - 177.9 -2.2 34.5 - 61 ALA 61 T l - - - - - - - - - - 178.6 - 33.1 - 62 GLY 62 T - - - - - - - - - - - 181.1 - - - 63 LYS 63 E B - - -78.0 - - - - - - - 175.8 -1.6 35.5 - 64 VAL 64 E B - 185.3 - - - - - - - - 189.2 - 34.3 - +* +* 65 LEU 65 e B - - -53.3 184.2 - - - - - - 178.3 -2.9 34.2 - * * 66 GLU 66 t B - - -57.4 180.8 - - - - - - 183.8 - 35.0 - 67 ASN 67 T A - - -58.4 - - - - - - - 182.6 - 34.0 - 68 SER 68 T A 53.2 - - - - - - - - - 178.8 - 33.3 - 69 LYS 69 t B - - -68.6 - - - - - - - 178.1 -2.1 34.0 - 70 THR 70 B B 58.3 - - - - - - - - - 176.0 - 35.1 - 71 VAL 71 g A - 180.5 - - - - - - - - 179.0 -2.5 34.5 - 72 LYS 72 G A - 181.4 - 179.2 - - - - - - 179.1 -2.9 34.4 - * * 73 ASP 73 G A - - -76.5 - - - - - - - 181.6 - 34.3 - 74 TYR 74 G A - - -59.5 - - - - - - - 175.7 -1.5 33.2 - 75 ARG 75 g b - - -66.4 - - - - - - - 173.9 -1.7 36.8 - * * 76 SER 76 t B - 181.0 - - - - - - - - 183.0 - 35.2 - 77 PRO 77 T - - - - - -58.2 - - - - - 184.5 - 39.9 - +* +* 78 VAL 78 T A 65.3 - - - - - - - - - 185.0 - 34.8 - 79 SER 79 t b - 182.8 - - - - - - - - 177.4 -1.3 34.8 - 80 ASN 80 b 65.7 - - - - - - - - - 181.7 - 32.3 - 81 LEU 81 B - - -62.4 179.2 - - - - - - 181.2 - 35.9 - 82 ALA 82 S b - - - - - - - - - - 179.4 - 34.1 - 83 GLY 83 S - - - - - - - - - - - 179.1 -.6 - - +* +* 84 ALA 84 B - - - - - - - - - - 178.7 - 34.2 - 85 VAL 85 B - 181.4 - - - - - - - - 180.2 - 34.5 - 86 THR 86 E B - - -57.8 - - - - - - - 176.7 -3.1 34.4 - * * 87 THR 87 E B - - -60.8 - - - - - - - 178.7 -.6 34.3 - +* +* 88 MET 88 E B - - -65.9 179.1 - - - - - - 181.7 -2.2 32.9 - 89 HIS 89 E B - - -66.4 - - - - - - - 180.1 -2.1 32.9 - 90 VAL 90 E B - 183.8 - - - - - - - - 180.0 -2.9 34.5 - * * 91 ILE 91 E B - - -73.1 - - - - - - - 186.5 -2.6 34.2 - * * 92 ILE 92 E B - - -60.6 - - - - - - - 171.1 -.6 32.7 - +* +* +* 93 GLN 93 e B - - -70.9 177.4 - - - - - - 182.3 -1.1 32.7 - * * 94 ALA 94 B - - - - - - - - - - 179.7 -.6 34.2 - +* +* 95 PRO 95 - - - - - -57.4 - - - - - 179.5 - 38.6 - * * 96 VAL 96 b 57.4 - - - - - - - - - 185.1 - 31.1 - 97 THR 97 B - - -53.8 - - - - - - - 178.6 -.9 34.2 - +* +* Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 98 GLU 98 S A - 188.6 - - - - - - - - 172.5 -1.0 34.6 - * * * 99 LYS 99 b - 177.5 - - - - - - - - 185.6 - 32.9 - 100 GLU 100 a - - -53.1 173.3 - - - - - - 182.9 -1.1 37.4 - * * 101 LYS 101 - - 184.4 - 178.4 - - - - - - - - 35.2 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * * * ** *** +* ** +* *** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.7 183.1 -62.2 179.0 -63.2 -66.4 -36.4 - - - 179.6 -1.9 34.2 Standard deviations: 5.1 5.4 7.4 3.7 8.6 10.7 13.5 - - - 3.7 .9 2.0 Numbers of values: 16 24 42 25 6 11 11 0 0 0 100 53 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_9 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 - 1.241 1.517 1.537 1.454 - 116.16 120.48 110.04 109.92 110.17 123.32 2 ALA 2 1.318 1.245 1.512 1.515 1.438 122.37 115.40 121.15 110.75 108.39 110.64 123.40 * * * 3 GLU 3 1.301 1.235 1.503 1.512 1.424 122.34 115.65 120.62 111.42 110.90 110.24 123.73 +* * +* +* 4 VAL 4 1.312 1.237 1.518 1.550 1.438 122.10 113.43 122.44 112.27 113.69 112.94 124.10 * * * * * 5 HIS 5 1.290 1.232 1.495 1.547 1.450 124.62 116.38 120.15 110.71 107.29 113.46 123.37 +** * +* * +* +** 6 ASN 6 1.321 1.235 1.515 1.556 1.449 122.01 115.39 121.63 111.90 110.69 113.56 122.72 * +* +* 7 GLN 7 1.309 1.244 1.514 1.534 1.429 122.24 118.96 119.14 111.83 106.47 109.85 121.89 * +* * +* +* 8 LEU 8 1.294 1.218 1.483 1.511 1.443 119.34 115.88 120.85 110.83 112.17 111.25 123.25 ** ** * ** 9 GLU 9 1.296 1.232 1.497 1.540 1.431 120.17 115.22 121.37 108.92 110.02 114.55 123.39 ** * * ** ** 10 ILE 10 1.286 1.237 1.507 1.563 1.427 122.60 116.27 120.41 109.69 108.81 111.58 123.27 *** +* *** 11 LYS 11 1.304 1.247 1.517 1.543 1.422 121.06 116.08 120.78 112.45 109.01 113.35 123.12 +* +* * +* +* Residue-by-residue listing for refined_9 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 1.298 1.217 1.501 1.526 1.448 122.00 117.43 119.84 109.24 109.46 109.44 122.72 ** * ** 13 ARG 13 1.309 1.239 1.505 1.520 1.439 120.35 114.48 121.57 112.76 110.94 110.69 123.95 * * * 14 LEU 14 1.305 1.236 1.511 1.533 1.441 123.94 115.86 120.79 107.45 110.28 109.37 123.33 +* * * +* 15 THR 15 1.306 1.228 1.540 1.529 1.441 123.39 115.75 121.18 110.96 111.25 109.30 123.06 +* * +* 16 ASP 16 1.333 1.234 1.533 1.541 1.458 122.54 116.44 120.89 110.14 110.96 111.57 122.65 17 GLY 17 1.335 1.228 1.516 - 1.458 121.35 116.62 120.63 - 113.68 - 122.75 18 SER 18 1.301 1.229 1.516 1.524 1.444 121.73 117.82 119.82 108.99 109.20 108.86 122.36 ** ** 19 ASP 19 1.311 1.241 1.506 1.554 1.428 119.78 114.39 121.70 112.61 113.45 115.31 123.87 * * +* * * +** +** 20 ILE 20 1.295 1.232 1.506 1.566 1.436 124.28 116.62 118.97 109.01 107.44 109.97 124.38 ** * * * * ** 21 GLY 21 1.337 1.246 1.520 - 1.457 122.34 117.70 120.20 - 112.49 - 122.10 * * 22 PRO 22 1.337 1.234 1.520 1.535 1.443 122.46 115.00 121.42 110.96 112.72 104.89 123.57 +* * +* * +* 23 LYS 23 1.293 1.222 1.518 1.528 1.440 123.75 118.63 118.89 110.95 106.86 106.89 122.48 +** * * * +* ** +** 24 ALA 24 1.314 1.238 1.515 1.531 1.455 120.15 115.33 121.36 110.88 111.20 111.56 123.27 * * 25 PHE 25 1.306 1.238 1.510 1.536 1.432 123.23 118.30 120.18 105.80 107.48 111.22 121.48 +* * * ** * ** 26 PRO 26 1.309 1.221 1.531 1.539 1.448 121.48 118.40 119.56 109.03 108.71 103.35 122.04 +* * * +* 27 ASP 27 1.319 1.230 1.523 1.541 1.483 120.71 116.11 121.18 109.02 110.87 113.05 122.69 * +* +* 28 ALA 28 1.321 1.233 1.534 1.521 1.446 121.88 117.72 120.33 110.49 111.84 110.42 121.95 29 THR 29 1.327 1.249 1.536 1.567 1.446 119.77 116.53 120.73 110.74 108.96 113.89 122.67 * * * 30 THR 30 1.306 1.247 1.530 1.550 1.433 121.13 115.44 121.22 109.72 111.29 111.81 123.34 +* * +* 31 VAL 31 1.319 1.223 1.528 1.554 1.451 123.27 116.59 120.69 110.79 110.32 111.20 122.71 32 SER 32 1.321 1.211 1.542 1.539 1.441 121.47 117.27 120.05 111.08 109.92 110.31 122.53 33 ALA 33 1.343 1.247 1.530 1.519 1.477 121.63 115.23 121.57 110.69 110.96 110.67 123.20 * * 34 LEU 34 1.313 1.228 1.537 1.533 1.414 124.00 115.43 121.57 111.88 108.62 106.45 122.98 * ** * ** ** 35 LYS 35 1.314 1.227 1.525 1.515 1.444 122.66 116.95 120.02 113.75 112.33 110.34 123.03 * +* +* 36 GLU 36 1.337 1.230 1.518 1.526 1.468 122.09 114.97 121.34 108.54 108.99 111.13 123.69 37 THR 37 1.322 1.221 1.527 1.539 1.433 123.12 116.62 120.47 111.08 110.70 110.02 122.88 * * 38 VAL 38 1.324 1.205 1.523 1.552 1.455 121.33 115.68 120.65 108.91 108.97 112.18 123.60 * * 39 ILE 39 1.324 1.229 1.546 1.561 1.470 123.45 116.02 121.13 109.29 111.18 109.84 122.85 40 SER 40 1.314 1.237 1.545 1.538 1.447 122.73 116.94 120.56 110.85 112.73 109.27 122.51 * * 41 GLU 41 1.318 1.234 1.547 1.539 1.446 122.43 117.18 120.60 111.68 113.86 110.28 122.23 * * 42 TRP 42 1.310 1.238 1.527 1.546 1.462 122.14 119.32 119.20 109.91 107.59 108.98 121.37 * +* * * +* Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 43 PRO 43 1.346 1.225 1.539 1.534 1.459 121.84 115.69 121.35 110.97 111.13 104.12 122.95 * * 44 ARG 44 1.307 1.227 1.527 1.526 1.457 123.11 116.23 121.20 110.37 111.53 108.97 122.56 +* +* 45 GLU 45 1.310 1.238 1.525 1.528 1.444 122.25 115.92 120.92 111.85 110.60 110.18 123.16 * * 46 LYS 46 1.329 1.235 1.523 1.559 1.451 122.29 116.64 120.56 110.40 107.47 109.97 122.80 * * * 47 GLU 47 1.306 1.244 1.512 1.552 1.419 121.18 114.46 121.11 112.43 111.50 113.85 124.42 +* * ** * +* ** 48 ASN 48 1.311 1.228 1.514 1.550 1.468 124.55 115.60 121.48 110.67 111.52 113.94 122.78 * +* ** ** 49 GLY 49 1.294 1.238 1.489 - 1.421 121.78 118.68 118.83 - 108.86 - 122.47 +** * +* * * +** 50 PRO 50 1.335 1.230 1.531 1.533 1.469 122.59 116.54 120.69 109.95 111.33 103.17 122.74 51 LYS 51 1.310 1.228 1.517 1.539 1.455 121.41 115.82 121.34 109.92 110.23 110.52 122.84 * * 52 THR 52 1.307 1.242 1.536 1.536 1.424 122.38 115.71 120.99 111.06 111.25 111.38 123.29 +* +* +* 53 VAL 53 1.316 1.233 1.529 1.574 1.457 123.96 116.98 120.19 111.30 112.84 110.90 122.79 * * * * 54 LYS 54 1.326 1.236 1.533 1.544 1.460 121.42 117.05 120.29 109.68 112.59 111.54 122.60 55 GLU 55 1.324 1.232 1.525 1.524 1.469 120.48 117.31 120.75 110.96 113.64 110.92 121.92 56 VAL 56 1.303 1.238 1.530 1.564 1.441 119.63 116.49 121.06 111.90 109.62 112.71 122.39 +* * * +* 57 LYS 57 1.315 1.229 1.523 1.536 1.443 121.14 116.07 120.49 110.24 110.61 109.85 123.43 58 LEU 58 1.317 1.231 1.519 1.563 1.457 122.75 116.92 120.31 109.44 109.83 111.90 122.75 +* +* 59 ILE 59 1.312 1.246 1.526 1.571 1.451 121.84 115.61 121.22 110.61 109.87 111.76 123.16 * * * 60 SER 60 1.308 1.240 1.512 1.546 1.442 123.06 116.04 119.99 110.54 108.39 110.67 123.85 * * * 61 ALA 61 1.337 1.241 1.532 1.529 1.472 123.50 115.75 120.94 111.38 111.55 110.43 123.29 62 GLY 62 1.328 1.240 1.511 - 1.446 121.28 116.22 120.64 - 112.87 - 123.15 63 LYS 63 1.310 1.238 1.496 1.518 1.417 123.03 116.06 120.43 109.61 110.67 109.48 123.51 * * ** ** 64 VAL 64 1.312 1.239 1.516 1.553 1.438 121.25 115.73 120.64 110.01 106.54 112.20 123.63 * * +* +* 65 LEU 65 1.303 1.240 1.518 1.525 1.444 122.58 115.76 120.84 110.26 112.13 109.95 123.39 +* +* 66 GLU 66 1.313 1.230 1.506 1.520 1.444 122.35 116.24 120.17 109.17 108.88 110.89 123.57 * * 67 ASN 67 1.315 1.240 1.531 1.547 1.479 123.13 116.30 120.65 109.21 112.24 111.19 123.04 * * 68 SER 68 1.320 1.231 1.545 1.524 1.442 122.16 117.49 120.36 111.65 113.23 109.30 122.15 69 LYS 69 1.320 1.226 1.510 1.531 1.456 121.62 116.97 120.26 109.48 110.27 111.64 122.77 70 THR 70 1.309 1.236 1.519 1.551 1.423 121.80 117.23 119.90 109.36 109.01 110.98 122.88 * +* +* 71 VAL 71 1.323 1.236 1.533 1.560 1.463 121.46 114.62 121.60 109.66 108.65 111.44 123.73 72 LYS 72 1.325 1.225 1.531 1.525 1.451 124.43 116.96 120.27 110.63 111.62 109.42 122.75 +* +* 73 ASP 73 1.333 1.233 1.513 1.529 1.462 122.47 116.09 121.16 108.97 112.08 111.17 122.75 74 TYR 74 1.307 1.234 1.522 1.512 1.422 121.81 115.64 121.12 112.69 111.14 109.30 123.23 +* +* * +* Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 75 ARG 75 1.317 1.237 1.518 1.523 1.427 123.25 116.16 120.58 107.87 109.00 109.56 123.26 +* * +* 76 SER 76 1.305 1.216 1.536 1.540 1.430 121.73 118.22 120.09 110.99 107.50 109.33 121.69 +* * * * +* 77 PRO 77 1.340 1.237 1.523 1.524 1.487 123.49 114.96 121.71 108.92 113.96 102.63 123.33 * * * 78 VAL 78 1.279 1.228 1.545 1.555 1.453 122.64 116.79 121.07 110.48 111.74 109.24 122.11 +*** * +*** 79 SER 79 1.303 1.234 1.533 1.545 1.450 120.84 116.00 120.63 111.29 110.68 108.65 123.35 +* * +* 80 ASN 80 1.319 1.239 1.514 1.558 1.455 123.97 116.49 120.47 110.65 109.02 113.65 123.02 * * +* +* 81 LEU 81 1.300 1.244 1.513 1.490 1.397 122.71 115.43 121.08 109.80 111.06 108.26 123.47 ** ** *** * *** 82 ALA 82 1.303 1.231 1.513 1.518 1.432 123.04 116.11 120.67 110.56 109.62 110.67 123.18 +* * +* 83 GLY 83 1.315 1.238 1.512 - 1.450 120.81 115.76 121.02 - 112.36 - 123.20 * * 84 ALA 84 1.306 1.237 1.511 1.520 1.434 122.00 116.18 120.68 110.55 109.78 110.55 123.14 +* * +* 85 VAL 85 1.300 1.236 1.512 1.551 1.438 121.46 116.25 120.99 109.44 108.71 111.87 122.74 ** * ** 86 THR 86 1.289 1.221 1.521 1.539 1.426 121.62 116.24 120.91 110.37 110.14 110.51 122.81 +** +* +** 87 THR 87 1.284 1.235 1.516 1.542 1.419 121.80 116.32 120.92 110.39 108.88 111.13 122.73 *** ** *** 88 MET 88 1.294 1.239 1.498 1.528 1.438 121.41 116.32 120.33 111.65 109.64 111.49 123.32 ** * * ** 89 HIS 89 1.312 1.237 1.498 1.541 1.444 121.13 115.43 120.71 110.54 110.05 112.53 123.84 * * * * 90 VAL 90 1.301 1.230 1.494 1.548 1.437 122.58 114.60 121.37 109.25 109.22 111.98 124.02 ** * * ** 91 ILE 91 1.275 1.244 1.499 1.560 1.419 123.15 115.40 121.12 111.29 107.63 111.05 123.46 +*** * ** * +*** 92 ILE 92 1.302 1.238 1.512 1.550 1.420 120.86 115.03 121.68 110.40 112.98 111.96 123.28 +* +* +* 93 GLN 93 1.294 1.224 1.503 1.533 1.423 122.21 115.73 121.16 112.28 107.94 111.89 123.02 +** * +* * * +** 94 ALA 94 1.302 1.237 1.507 1.518 1.437 121.32 117.48 120.08 110.47 109.91 110.51 122.43 +* * +* 95 PRO 95 1.336 1.250 1.513 1.536 1.457 122.66 116.04 120.73 110.03 111.29 104.27 123.22 * * 96 VAL 96 1.312 1.229 1.533 1.564 1.441 121.24 115.25 122.19 112.75 110.34 112.70 122.51 * +* +* 97 THR 97 1.296 1.234 1.518 1.540 1.414 121.53 115.13 121.45 111.21 110.42 110.05 123.35 ** ** ** 98 GLU 98 1.303 1.228 1.528 1.545 1.432 122.75 115.55 121.18 113.53 106.55 108.05 123.25 +* * +* +* * +* 99 LYS 99 1.327 1.240 1.520 1.538 1.423 122.43 114.94 121.34 111.76 108.11 111.90 123.69 +* * +* 100 GLU 100 1.290 1.231 1.509 1.521 1.441 123.91 114.65 121.52 108.49 109.20 108.02 123.83 +** * * +** 101 LYS 101 1.305 - 1.508 1.541 1.430 123.11 - - 110.60 107.67 109.87 - +* * * +* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 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_9 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 1.343 1.310 .013 +*** * * C-N (Pro) 1.341 .016 6 1.309 1.346 1.334 .012 +* C-O C-O 1.231 .020 100 1.205 1.250 1.234 .008 * CA-C CH1E-C (except Gly) 1.525 .021 96 1.483 1.547 1.520 .013 ** * CH2G*-C (Gly) 1.516 .018 5 1.489 1.520 1.510 .011 * CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.515 1.531 1.521 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.529 1.574 1.553 .011 * CH1E-CH2E (the rest) 1.530 .020 62 1.490 1.563 1.534 .013 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.397 1.483 1.442 .016 *** * NH1-CH2G* (Gly) 1.451 .016 5 1.421 1.458 1.447 .014 +* N-CH1E (Pro) 1.466 .015 6 1.443 1.487 1.460 .014 +* * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 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 89 113.43 119.32 116.17 1.02 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.76 118.68 117.00 1.06 * CH1E-C-N (Pro) 116.9 1.5 6 114.96 118.40 116.10 1.16 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.37 124.42 123.02 .59 * O-C-N (Pro) 122.0 1.4 6 122.04 123.57 122.98 .50 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.34 124.62 122.17 1.15 * +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.81 122.34 121.51 .52 * C-N-CH1E (Pro) 122.6 5.0 6 121.48 123.49 122.42 .64 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 118.89 122.44 120.77 .65 * CH2G*-C-O (Gly) 120.8 2.1 5 118.83 121.02 120.26 .76 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 110.47 111.38 110.72 .28 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.91 112.75 110.46 .99 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 105.80 113.75 110.49 1.46 ** +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 106.47 113.86 110.11 1.77 +* NH1-CH2G*-C (Gly) 112.5 2.9 5 108.86 113.68 112.05 1.66 * N-CH1E-C (Pro) 111.8 2.5 6 108.71 113.96 111.52 1.61 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 110.42 111.56 110.68 .34 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 109.24 113.89 111.33 1.13 * * N-CH1E-CH2E (Pro) 103.0 1.1 6 102.63 104.89 103.74 .76 +* NH1-CH1E-CH2E (the rest) 110.5 1.7 56 106.45 115.31 110.67 1.85 ** +** ------------------------------------------------------------------------------------------------------------- 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_9 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] 74 84.1% Residues in additional allowed regions [a,b,l,p] 13 14.8% 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 84.1 83.8 10.0 .0 Inside b. Omega angle st dev 100 3.7 6.0 3.0 -.8 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 96 2.0 3.1 1.6 -.7 Inside e. H-bond energy st dev 53 .9 .8 .2 .5 Inside f. Overall G-factor 101 .0 -.4 .3 1.3 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 16 5.1 18.1 6.5 -2.0 BETTER b. Chi-1 trans st dev 24 5.4 19.0 5.3 -2.6 BETTER c. Chi-1 gauche plus st dev 42 7.4 17.5 4.9 -2.1 BETTER d. Chi-1 pooled st dev 82 7.7 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 25 3.7 20.4 5.0 -3.3 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% 84.1 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.7 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .92 3 Residue-by-residue listing for refined_9 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.45 Chi1-chi2 distribution .07 Chi1 only -.06 Chi3 & chi4 .33 Omega -.09 ------ -.11 ===== Main-chain covalent forces:- Main-chain bond lengths .01 Main-chain bond angles .40 ------ .24 ===== OVERALL AVERAGE .01 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.