Residue-by-residue listing for refined_3 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 - - - -65.0 - - - - - - - 180.6 - 33.2 - 2 ALA 2 B - - - - - - - - - - 183.8 - 35.3 - 3 GLU 3 S A 67.0 - - - - - - - - - 177.8 - 30.0 - * * 4 VAL 4 b - 182.5 - - - - - - - - 178.4 - 33.4 - 5 HIS 5 B - - -67.1 - - - - - - - 177.6 -1.0 34.1 - * * 6 ASN 6 S A - - -62.4 - - - - - - - 181.0 - 33.8 - 7 GLN 7 e b - - -58.3 175.5 - - - - - - 178.1 - 35.8 - 8 LEU 8 E B - - -62.9 - - - - - - - 180.1 -2.5 34.0 - 9 GLU 9 E B - - -57.5 183.2 - - - - - - 179.4 -1.9 34.3 - 10 ILE 10 E B - - -57.5 178.4 - - - - - - 176.1 -2.9 34.2 - * * 11 LYS 11 E B 69.2 - - 172.8 - - - - - - 182.8 -2.8 32.4 - * * 12 PHE 12 E B - - -53.6 - - - - - - - 180.7 -.5 35.5 - ** ** 13 ARG 13 E B - 190.5 - 178.6 - - - - - - 180.7 -3.2 33.3 - +* +* 14 LEU 14 E b - - -68.9 - - - - - - - 181.3 -1.9 35.1 - 15 THR 15 e A - 188.4 - - - - - - - - 178.8 -.8 33.5 - +* +* 16 ASP 16 T A - - -63.2 - - - - - - - 176.4 - 32.5 - 17 GLY 17 t - - - - - - - - - - - 177.3 -1.9 - - 18 SER 18 e B - - -52.6 - - - - - - - 180.4 - 36.1 - 19 ASP 19 E B 62.5 - - - - - - - - - 181.6 - 32.8 - 20 ILE 20 E B - - -58.0 176.3 - - - - - - 182.9 -3.2 36.5 - +* +* Residue-by-residue listing for refined_3 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 E - - - - - - - - - - - 182.4 - - - 22 PRO 22 E - - - - - -58.2 - - - - - 178.6 - 38.3 - * * 23 LYS 23 E B - 186.4 - 181.7 - - - - - - 182.4 -2.6 36.2 - 24 ALA 24 E B - - - - - - - - - - 179.2 - 33.4 - 25 PHE 25 E B - - -51.8 - - - - - - - 169.9 -3.7 37.5 - +* ** * ** 26 PRO 26 t - - - - - -61.8 - - - - - 178.3 - 40.2 - +* +* 27 ASP 27 T A 71.5 - - - - - - - - - 177.7 - 33.5 - 28 ALA 28 T A - - - - - - - - - - 177.9 - 34.1 - 29 THR 29 t B - - -53.0 - - - - - - - 180.4 -2.2 34.8 - 30 THR 30 h B 51.2 - - - - - - - - - 177.6 - 34.9 - 31 VAL 31 H A - 180.8 - - - -67.0 -25.7 - - - 175.6 -3.2 32.9 - * +* +* 32 SER 32 H A 50.5 - - - - -63.6 -39.2 - - - 177.1 -1.1 33.7 - * * 33 ALA 33 H A - - - - - -74.8 -31.0 - - - 174.9 - 33.6 - 34 LEU 34 H A - 172.1 - - - -63.5 -45.5 - - - 177.6 -1.7 36.9 - 35 LYS 35 H A - 184.3 - - - -60.7 -47.5 - - - 176.9 -3.0 35.9 - * * 36 GLU 36 H A - - -69.4 - - -60.0 -37.3 - - - 177.2 -2.4 34.5 - 37 THR 37 H A - - -57.2 - - -62.1 -38.0 - - - 175.1 -2.1 33.7 - 38 VAL 38 H A - 178.0 - - - -60.8 -53.7 - - - 184.2 -1.6 35.6 - * * 39 ILE 39 H A - - -48.0 - - -59.3 -37.4 - - - 181.9 -2.4 35.0 - * * 40 SER 40 H A - 180.6 - - - -74.4 -39.1 - - - 183.8 -2.5 34.4 - 41 GLU 41 H A - 201.4 - - - -79.6 -45.7 - - - 184.6 -2.1 35.9 - * * * 42 TRP 42 h B - 188.2 - - - - - - - - 180.4 -3.1 34.5 - * * 43 PRO 43 t - - - - - -56.9 - - - - - 177.6 - 38.7 - * * 44 ARG 44 T A - 185.0 - 176.2 - - - - - - 180.7 - 33.8 - 45 GLU 45 T A - 182.9 - 182.7 - - - - - - 185.2 - 35.4 - 46 LYS 46 t B - 204.5 - - - - - - - - 177.3 -.8 36.1 - * +* +* 47 GLU 47 S B 54.2 - - - - - - - - - 185.5 - 30.6 - 48 ASN 48 S l - - -65.4 - - - - - - - 180.9 - 29.9 - * * 49 GLY 49 S - - - - - - - - - - - 179.6 - - - 50 PRO 50 - - - - - -80.2 - - - - - 175.6 - 39.3 - * +* +* 51 LYS 51 a - - -64.4 - - - - - - - 182.9 - 33.8 - 52 THR 52 g B 56.2 - - - - - - - - - 184.2 - 33.5 - 53 VAL 53 G A 60.8 - - - - - - - - - 182.4 - 32.4 - 54 LYS 54 G A - - -59.0 174.1 - - - - - - 187.4 - 35.3 - * * 55 GLU 55 e A - - -55.6 177.0 - - - - - - 182.9 -1.1 34.7 - * * 56 VAL 56 E B - 182.7 - - - - - - - - 170.6 -.8 35.4 - +* +* +* 57 LYS 57 E B - - -75.6 - - - - - - - 175.7 -2.1 32.3 - 58 LEU 58 E B - - -69.5 - - - - - - - 178.9 -.7 33.9 - +* +* Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 59 ILE 59 E B - - -65.4 182.6 - - - - - - 181.1 -2.8 32.8 - * * 60 SER 60 E B - 186.2 - - - - - - - - 178.4 -2.7 34.6 - 61 ALA 61 T l - - - - - - - - - - 180.4 - 33.3 - 62 GLY 62 T - - - - - - - - - - - 178.3 - - - 63 LYS 63 E B - 175.3 - - - - - - - - 175.5 -1.0 34.9 - * * 64 VAL 64 E B 58.0 - - - - - - - - - 186.0 - 31.5 - * * 65 LEU 65 E B - 171.6 - - - - - - - - 177.8 -3.2 35.5 - +* +* 66 GLU 66 t B - - -62.2 183.4 - - - - - - 178.2 -.6 34.2 - +* +* 67 ASN 67 T A 55.0 - - - - - - - - - 179.6 - 29.0 - * * 68 SER 68 T A - - -52.0 - - - - - - - 181.1 - 35.0 - 69 LYS 69 t B - - -67.6 175.4 - - - - - - 172.2 -1.9 34.7 - * * 70 THR 70 h B - - -54.0 - - - - - - - 181.5 - 35.9 - 71 VAL 71 H A - 178.1 - - - -64.1 -38.7 - - - 178.4 -2.8 32.9 - * * 72 LYS 72 H A - 185.3 - 185.7 - -57.5 -35.0 - - - 180.1 -2.1 35.5 - 73 ASP 73 H A - - -67.0 - - -68.9 -28.3 - - - 183.2 - 35.2 - 74 TYR 74 H A - 199.5 - - - -88.0 -18.3 - - - 179.6 -.9 35.2 - +* +* +* +* 75 ARG 75 h B - - -93.3 - - - - - - - 175.2 -1.1 35.1 - +* * +* 76 SER 76 B B - 187.3 - - - - - - - - 182.4 -.5 35.7 - ** ** 77 PRO 77 T - - - - - -46.0 - - - - - 178.9 - 38.0 - +* * +* 78 VAL 78 T l - 179.4 - - - - - - - - 182.7 - 32.6 - 79 SER 79 B B - - -53.6 - - - - - - - 178.4 -2.3 34.2 - 80 ASN 80 b 56.8 - - - - - - - - - 182.7 -1.0 32.8 - * * 81 LEU 81 B - - -65.6 178.6 - - - - - - 180.2 - 35.7 - 82 ALA 82 S B - - - - - - - - - - 181.2 - 33.8 - 83 GLY 83 S - - - - - - - - - - - 180.6 -2.5 - - 84 ALA 84 E B - - - - - - - - - - 179.8 -.6 34.3 - +* +* 85 VAL 85 E B - 181.7 - - - - - - - - 178.0 -.5 33.7 - ** ** 86 THR 86 E B - - -57.6 - - - - - - - 179.1 -3.8 35.5 - ** ** 87 THR 87 E B - - -55.2 - - - - - - - 177.1 -.6 35.1 - +* +* 88 MET 88 E B - - -64.1 182.4 - - - - - - 185.0 -2.5 32.3 - 89 HIS 89 E B - 194.1 - - - - - - - - 181.8 -3.3 34.7 - +* +* 90 VAL 90 E B - 181.1 - - - - - - - - 180.1 -3.4 34.0 - +* +* 91 ILE 91 E B - - -67.6 - - - - - - - 179.8 -3.3 33.9 - +* +* 92 ILE 92 E B - - -68.7 - - - - - - - 178.0 -.7 34.3 - +* +* 93 GLN 93 e B - - -67.1 179.4 - - - - - - 178.8 -2.7 33.5 - Residue-by-residue listing for refined_3 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 94 ALA 94 B - - - - - - - - - - 181.1 -.6 34.5 - +* +* 95 PRO 95 - - - - - -66.4 - - - - - 181.2 - 38.4 - * * 96 VAL 96 S b 58.6 - - - - - - - - - 178.7 - 29.6 - * * 97 THR 97 S b - 180.3 - - - - - - - - 178.3 -2.1 31.9 - 98 GLU 98 S XX - - -61.3 177.2 - - - - - - 180.3 - 31.6 - **** **** 99 LYS 99 B - 184.9 - 179.6 - - - - - - 179.9 - 34.8 - 100 GLU 100 a - 186.5 - - - - - - - - 175.1 -.6 34.5 - +* +* 101 LYS 101 - - - -64.4 181.5 - - - - - - - - 33.7 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +* +* +* +* +* ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.3 184.8 -62.1 179.2 -61.6 -67.0 -37.4 - - - 179.6 -2.0 34.4 Standard deviations: 6.6 7.7 8.1 3.5 11.4 8.7 9.0 - - - 3.1 1.0 1.9 Numbers of values: 13 29 40 21 6 15 15 0 0 0 100 57 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_3 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 - 1.234 1.513 1.554 1.461 - 115.93 120.81 110.39 109.79 112.28 123.24 * * * 2 ALA 2 1.305 1.217 1.506 1.526 1.442 123.28 118.42 119.36 110.37 107.41 109.78 122.22 +* * * +* 3 GLU 3 1.312 1.234 1.513 1.548 1.451 119.87 115.25 121.60 112.34 112.31 113.66 123.12 * * * +* +* 4 VAL 4 1.283 1.235 1.501 1.528 1.443 121.42 114.07 121.78 108.82 108.93 113.66 124.03 *** * * * *** 5 HIS 5 1.269 1.232 1.505 1.553 1.459 124.77 116.68 120.08 109.23 108.78 112.55 123.23 **** * +* * **** 6 ASN 6 1.305 1.224 1.508 1.541 1.458 121.64 115.73 120.89 109.43 109.89 112.29 123.37 +* * +* 7 GLN 7 1.315 1.242 1.532 1.522 1.452 122.51 117.02 120.46 109.70 110.01 108.74 122.52 * * 8 LEU 8 1.319 1.220 1.508 1.552 1.455 121.04 117.12 120.54 108.66 109.08 113.11 122.34 * +* +* 9 GLU 9 1.293 1.205 1.494 1.513 1.437 120.26 116.77 120.57 108.99 109.21 112.02 122.66 +** * * * +** 10 ILE 10 1.275 1.240 1.508 1.560 1.433 121.30 116.47 120.45 109.89 108.84 111.87 123.03 +*** * +*** 11 LYS 11 1.304 1.245 1.501 1.534 1.425 120.57 115.88 120.75 110.64 109.19 113.40 123.36 +* * +* +* +* Residue-by-residue listing for refined_3 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 1.291 1.227 1.503 1.529 1.428 121.49 116.98 120.42 110.18 108.78 109.45 122.60 +** * +* +** 13 ARG 13 1.294 1.226 1.515 1.526 1.426 120.25 115.18 120.99 111.41 109.70 111.00 123.82 ** +* ** 14 LEU 14 1.304 1.241 1.522 1.551 1.447 124.58 115.87 120.95 108.84 110.83 110.76 123.14 +* * +* +* 15 THR 15 1.313 1.227 1.533 1.560 1.446 122.42 115.72 121.22 111.16 110.26 110.98 123.04 * * 16 ASP 16 1.327 1.230 1.534 1.542 1.466 122.04 117.11 120.60 110.30 112.23 112.26 122.29 * * 17 GLY 17 1.326 1.239 1.516 - 1.456 120.59 116.19 120.66 - 113.39 - 123.15 18 SER 18 1.301 1.209 1.524 1.523 1.448 122.50 119.16 119.17 110.27 107.35 108.45 121.65 +* * * * * +* 19 ASP 19 1.309 1.237 1.508 1.532 1.439 120.16 114.71 121.23 110.71 112.12 111.56 124.04 * * 20 ILE 20 1.304 1.229 1.514 1.566 1.441 124.14 116.28 119.71 108.71 107.40 110.08 123.99 +* * * +* 21 GLY 21 1.325 1.241 1.514 - 1.451 122.37 116.79 120.18 - 114.17 - 123.02 * * 22 PRO 22 1.347 1.241 1.525 1.540 1.466 123.80 115.13 121.49 110.07 113.79 103.98 123.38 * * 23 LYS 23 1.299 1.214 1.516 1.536 1.440 123.55 118.44 119.21 110.42 106.13 108.70 122.33 ** * * +* * ** 24 ALA 24 1.299 1.238 1.519 1.518 1.448 120.14 115.68 120.93 111.09 111.21 110.51 123.38 ** ** 25 PHE 25 1.314 1.234 1.522 1.544 1.444 123.21 118.49 120.14 105.45 108.16 111.16 121.34 * * ** * * ** 26 PRO 26 1.323 1.240 1.528 1.526 1.461 122.06 117.53 119.94 108.29 109.53 103.53 122.52 * * 27 ASP 27 1.318 1.222 1.537 1.538 1.475 121.22 115.71 121.60 109.89 110.03 111.88 122.66 28 ALA 28 1.317 1.233 1.536 1.516 1.451 122.76 116.84 120.69 110.19 111.29 110.20 122.47 29 THR 29 1.316 1.232 1.516 1.536 1.447 121.32 116.26 120.78 109.62 109.11 110.89 122.94 30 THR 30 1.289 1.243 1.527 1.533 1.423 121.87 116.42 120.75 110.33 110.77 109.58 122.82 +** +* * +** 31 VAL 31 1.321 1.209 1.526 1.561 1.448 122.02 115.93 121.34 111.28 108.61 112.33 122.73 * * 32 SER 32 1.311 1.219 1.538 1.519 1.434 122.46 117.20 120.53 112.06 111.08 109.09 122.26 * * * * 33 ALA 33 1.330 1.229 1.521 1.518 1.464 121.52 115.75 121.09 110.84 109.59 110.92 123.16 34 LEU 34 1.322 1.229 1.531 1.531 1.424 123.73 114.28 121.64 111.49 107.92 106.17 124.02 +* * * +** +** 35 LYS 35 1.313 1.220 1.527 1.524 1.440 124.96 115.99 120.76 110.56 110.32 107.75 123.25 * +* +* +* 36 GLU 36 1.317 1.229 1.522 1.516 1.460 122.92 116.31 120.78 110.36 111.18 109.61 122.90 37 THR 37 1.323 1.235 1.547 1.552 1.447 121.62 115.71 121.04 111.25 109.48 110.66 123.22 * * 38 VAL 38 1.331 1.221 1.526 1.561 1.459 122.88 115.58 120.62 107.91 109.66 111.35 123.76 39 ILE 39 1.334 1.229 1.541 1.576 1.476 123.31 115.75 121.38 108.66 110.41 111.19 122.86 * * 40 SER 40 1.312 1.244 1.547 1.536 1.445 122.48 116.99 120.41 110.62 112.51 109.21 122.60 * * * 41 GLU 41 1.329 1.232 1.534 1.546 1.454 121.65 115.52 121.09 110.20 109.17 108.53 123.37 * * 42 TRP 42 1.318 1.245 1.530 1.534 1.444 122.93 116.62 120.71 110.89 110.84 109.44 122.67 43 PRO 43 1.341 1.226 1.527 1.530 1.462 123.48 115.57 121.46 110.07 113.02 103.54 122.95 Residue-by-residue listing for refined_3 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 44 ARG 44 1.306 1.227 1.536 1.524 1.449 122.92 115.53 121.85 111.47 110.08 109.88 122.62 +* +* 45 GLU 45 1.310 1.248 1.557 1.535 1.454 122.67 115.72 121.21 110.89 110.58 107.99 123.03 * +* * +* 46 LYS 46 1.318 1.236 1.551 1.556 1.458 123.51 117.23 120.37 110.31 110.01 108.03 122.40 * * * * * 47 GLU 47 1.332 1.238 1.515 1.543 1.446 121.06 115.19 120.99 110.74 111.70 114.66 123.78 ** ** 48 ASN 48 1.322 1.243 1.509 1.543 1.459 123.52 114.11 122.18 112.33 111.15 114.32 123.58 * * * ** ** 49 GLY 49 1.297 1.233 1.497 - 1.410 122.60 118.58 119.15 - 108.90 - 122.25 ** * +** * * * +** 50 PRO 50 1.314 1.225 1.532 1.512 1.453 122.73 116.03 121.17 110.16 113.53 102.23 122.75 +* +* 51 LYS 51 1.313 1.232 1.518 1.559 1.456 122.12 115.84 121.21 109.05 109.74 112.89 122.95 * * * * 52 THR 52 1.317 1.245 1.548 1.536 1.434 121.83 115.61 120.90 110.32 112.26 110.88 123.49 * * * 53 VAL 53 1.335 1.239 1.561 1.576 1.473 124.85 117.93 120.02 110.87 114.51 111.04 122.04 +* * +* * +* 54 LYS 54 1.326 1.224 1.525 1.535 1.479 121.87 116.51 120.92 108.03 111.73 110.63 122.55 * * * 55 GLU 55 1.305 1.237 1.532 1.515 1.454 121.52 116.67 120.94 110.43 112.48 108.76 122.39 +* * +* 56 VAL 56 1.313 1.231 1.522 1.556 1.450 120.97 116.71 120.67 107.58 111.04 111.66 122.59 * * 57 LYS 57 1.298 1.232 1.523 1.542 1.443 121.38 116.61 120.28 110.12 110.39 113.55 123.10 ** +* ** 58 LEU 58 1.321 1.218 1.513 1.577 1.459 121.94 117.04 120.33 109.34 107.94 113.13 122.58 ** * +* ** 59 ILE 59 1.296 1.233 1.515 1.567 1.444 121.61 116.00 121.04 111.32 110.17 112.10 122.94 ** * ** 60 SER 60 1.298 1.226 1.522 1.537 1.418 121.59 116.10 120.31 111.30 109.01 109.60 123.51 ** ** ** 61 ALA 61 1.339 1.237 1.539 1.530 1.473 123.76 116.33 121.02 111.26 111.68 110.18 122.61 * * 62 GLY 62 1.322 1.236 1.517 - 1.451 121.01 115.87 121.03 - 112.08 - 123.08 63 LYS 63 1.308 1.236 1.516 1.541 1.442 122.73 116.35 120.24 110.16 109.60 110.10 123.38 * * 64 VAL 64 1.323 1.242 1.531 1.574 1.444 121.34 114.90 121.70 112.43 109.41 113.03 123.38 * +* +* 65 LEU 65 1.291 1.248 1.516 1.525 1.396 123.80 115.24 121.21 111.62 111.07 107.57 123.55 +** *** * +* *** 66 GLU 66 1.313 1.240 1.506 1.526 1.430 121.58 115.39 121.04 109.19 110.20 111.90 123.56 * * * 67 ASN 67 1.313 1.214 1.527 1.561 1.459 122.90 115.72 121.27 113.82 112.84 113.21 123.00 * +* +* +* +* 68 SER 68 1.316 1.233 1.559 1.519 1.450 123.34 116.99 120.78 110.52 112.59 108.19 122.23 +* * +* 69 LYS 69 1.317 1.224 1.529 1.528 1.463 122.29 116.06 121.08 109.26 112.03 110.18 122.83 70 THR 70 1.309 1.245 1.544 1.553 1.441 122.54 118.31 119.45 110.11 105.59 109.71 122.24 * * ** * ** 71 VAL 71 1.319 1.232 1.533 1.565 1.469 120.85 115.26 121.10 110.79 109.85 112.31 123.60 72 LYS 72 1.319 1.229 1.541 1.540 1.462 124.18 116.87 120.68 109.75 110.82 109.04 122.45 * * Residue-by-residue listing for refined_3 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 73 ASP 73 1.334 1.227 1.500 1.524 1.456 122.50 116.01 120.91 108.07 111.16 111.07 123.07 * * * 74 TYR 74 1.307 1.229 1.532 1.530 1.441 121.51 114.98 121.53 110.76 109.11 109.03 123.49 +* +* 75 ARG 75 1.312 1.244 1.514 1.538 1.440 123.87 115.32 121.21 109.79 111.48 109.62 123.45 * * * 76 SER 76 1.298 1.238 1.533 1.545 1.428 122.51 118.59 119.14 111.03 106.13 109.04 122.24 ** +* * +* ** 77 PRO 77 1.356 1.247 1.526 1.541 1.469 123.44 115.20 120.93 110.40 113.13 104.19 123.84 * * * * 78 VAL 78 1.334 1.235 1.578 1.552 1.459 125.07 117.01 121.66 113.03 112.76 109.10 121.24 +** +* +* * * +** 79 SER 79 1.316 1.236 1.529 1.524 1.435 121.20 115.40 121.12 110.86 110.84 109.86 123.43 * * 80 ASN 80 1.310 1.238 1.508 1.552 1.457 123.89 116.33 120.79 110.90 108.97 112.67 122.85 * * * * * 81 LEU 81 1.301 1.240 1.519 1.498 1.398 122.87 115.60 121.25 110.42 111.56 107.98 123.14 ** +* *** * *** 82 ALA 82 1.301 1.233 1.503 1.523 1.410 122.61 115.56 120.91 111.38 108.78 110.81 123.48 +* * +** +** 83 GLY 83 1.299 1.234 1.509 - 1.444 121.04 115.85 121.06 - 111.40 - 123.09 ** ** 84 ALA 84 1.315 1.238 1.505 1.517 1.443 121.69 116.26 120.51 110.04 110.15 110.64 123.23 * * 85 VAL 85 1.306 1.232 1.520 1.552 1.439 121.56 115.05 121.35 109.74 110.27 112.21 123.59 +* +* 86 THR 86 1.286 1.236 1.529 1.543 1.421 123.95 116.40 120.82 109.44 108.90 110.17 122.76 *** +* * *** 87 THR 87 1.294 1.232 1.525 1.544 1.427 121.39 116.83 120.59 109.93 109.36 110.23 122.54 ** +* ** 88 MET 88 1.307 1.235 1.496 1.529 1.442 120.93 115.92 120.66 111.73 109.36 112.33 123.42 +* * * +* 89 HIS 89 1.298 1.229 1.503 1.533 1.429 121.69 115.43 120.99 111.22 109.09 109.60 123.58 ** * +* ** 90 VAL 90 1.287 1.238 1.489 1.552 1.430 122.02 113.84 121.99 110.13 109.19 111.95 124.16 *** +* * * *** 91 ILE 91 1.268 1.243 1.498 1.533 1.400 123.20 114.14 121.52 111.90 109.93 110.03 124.32 **** * *** * * **** 92 ILE 92 1.300 1.239 1.512 1.582 1.421 123.29 115.77 120.90 109.84 108.69 112.14 123.27 ** +* +* ** 93 GLN 93 1.300 1.227 1.498 1.523 1.429 121.74 115.69 120.79 110.48 109.92 111.66 123.50 ** * +* ** 94 ALA 94 1.297 1.244 1.513 1.521 1.431 121.85 117.74 120.20 110.63 108.40 110.40 122.00 ** * ** 95 PRO 95 1.335 1.240 1.517 1.534 1.457 122.38 116.42 120.69 110.26 110.94 104.35 122.89 * * 96 VAL 96 1.312 1.244 1.537 1.572 1.444 120.89 114.37 122.65 113.27 111.56 113.67 122.78 * * * +* * +* 97 THR 97 1.299 1.243 1.533 1.562 1.408 122.91 114.68 121.54 112.72 110.43 111.90 123.67 ** +** +* +** 98 GLU 98 1.331 1.242 1.520 1.529 1.461 124.74 115.47 121.72 111.81 112.24 111.90 122.80 +* +* 99 LYS 99 1.291 1.234 1.511 1.524 1.405 122.18 116.56 120.44 110.63 108.86 110.09 122.99 +** +** +** Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 100 GLU 100 1.306 1.228 1.527 1.526 1.439 120.96 115.49 121.07 111.01 108.83 109.88 123.43 +* * +* 101 LYS 101 1.310 - 1.504 1.538 1.441 123.91 - - 109.86 107.61 112.76 - * * * * * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +** ** *** +* * * ** ** +** * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 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 1.268 1.339 1.310 .014 **** * C-N (Pro) 1.341 .016 6 1.314 1.356 1.336 .014 +* C-O C-O 1.231 .020 100 1.205 1.248 1.233 .009 * CA-C CH1E-C (except Gly) 1.525 .021 96 1.489 1.578 1.523 .016 +* +** CH2G*-C (Gly) 1.516 .018 5 1.497 1.517 1.511 .007 * CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.516 1.530 1.521 .004 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.528 1.582 1.556 .015 +* CH1E-CH2E (the rest) 1.530 .020 62 1.498 1.577 1.535 .013 +* ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.396 1.479 1.444 .017 *** * NH1-CH2G* (Gly) 1.451 .016 5 1.410 1.456 1.442 .017 +** N-CH1E (Pro) 1.466 .015 6 1.453 1.469 1.461 .005 ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 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 89 113.84 119.16 116.12 1.05 * * CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.85 118.58 116.66 1.02 * CH1E-C-N (Pro) 116.9 1.5 6 115.13 117.53 115.98 .83 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.24 124.32 123.00 .59 * O-C-N (Pro) 122.0 1.4 6 122.52 123.84 123.06 .43 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.87 125.07 122.34 1.21 * +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.59 122.60 121.52 .81 * C-N-CH1E (Pro) 122.6 5.0 6 122.06 123.80 122.98 .63 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.14 122.65 120.86 .62 * CH2G*-C-O (Gly) 120.8 2.1 5 119.15 121.06 120.42 .71 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 110.04 111.38 110.72 .47 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 107.58 113.27 110.42 1.46 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 105.45 113.82 110.31 1.22 ** +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.59 114.51 110.02 1.60 ** * NH1-CH2G*-C (Gly) 112.5 2.9 5 108.90 114.17 111.99 1.82 * N-CH1E-C (Pro) 111.8 2.5 6 109.53 113.79 112.32 1.55 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 109.78 110.92 110.43 .35 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 109.10 113.67 111.34 1.18 * * N-CH1E-CH2E (Pro) 103.0 1.1 6 102.23 104.35 103.64 .70 * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 106.17 114.66 110.61 1.97 +** ** ------------------------------------------------------------------------------------------------------------- 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_3 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] 76 86.4% Residues in additional allowed regions [a,b,l,p] 11 12.5% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 1 1.1% ---- ------ 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 86.4 83.8 10.0 .3 Inside b. Omega angle st dev 100 3.1 6.0 3.0 -1.0 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 -.7 Inside e. H-bond energy st dev 57 1.0 .8 .2 1.0 Inside f. Overall G-factor 101 .0 -.4 .3 1.2 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 13 6.6 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 29 7.7 19.0 5.3 -2.1 BETTER c. Chi-1 gauche plus st dev 40 8.1 17.5 4.9 -1.9 BETTER d. Chi-1 pooled st dev 82 8.6 18.2 4.8 -2.0 BETTER e. Chi-2 trans st dev 21 3.5 20.4 5.0 -3.4 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% 86.4 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.4 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 1.01 3 Residue-by-residue listing for refined_3 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.46 Chi1-chi2 distribution -.24 Chi1 only -.03 Chi3 & chi4 .10 Omega .11 ------ -.14 ===== Main-chain covalent forces:- Main-chain bond lengths -.06 Main-chain bond angles .40 ------ .20 ===== OVERALL AVERAGE -.02 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.