Residue-by-residue listing for refined_5 Page 1 ---------------------------------------- This listing highlights the residues in the structure which may need investigation. The ideal values and standard deviations against which the structure has been compared are shown in the following table: <------------------------------- I D E A L V A L U E S -------------------------------> Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha ------------------------------------------------------------------------------------------ Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9 Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5 ------------------------------------------------------------------------------------------ In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above. Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*. The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing. Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments. Full print-out. ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - - 181.0 - 178.5 - - - - - - 177.2 - 33.3 - 2 ALA 2 b - - - - - - - - - - 186.0 - 33.6 - * * 3 ASP 3 S l - 178.2 - - - - - - - - 177.2 -1.4 31.3 - 4 THR 4 A - - -49.2 - - - - - - - 179.9 - 35.9 - * * 5 GLY 5 - - - - - - - - - - - 183.5 - - - 6 GLU 6 l - 175.2 - - - - - - - - 171.7 - 30.5 - * * 7 VAL 7 E B - - -62.4 - - - - - - - 183.9 -2.7 32.8 - 8 GLN 8 E B - - -62.7 180.9 - - - - - - 177.6 - 33.8 - 9 PHE 9 E B - 176.0 - - - - - - - - 178.6 -2.0 35.0 - 10 MET 10 E B - 179.1 - 182.4 - - - - - - 176.8 - 35.8 - 11 LYS 11 E B - 186.9 - 185.4 - - - - - - 171.4 -.8 35.5 - * +* +* 12 PRO 12 - - - - - -54.5 - - - - - 183.7 - 39.0 - * * 13 PHE 13 B - 192.6 - - - - - - - - 176.7 - 35.6 - 14 ILE 14 h B - - -56.1 176.7 - - - - - - 185.2 -.6 34.6 - +* +* 15 SER 15 H A - - -53.2 - - -64.8 -25.5 - - - 180.1 -.5 33.2 - * +* +* 16 GLU 16 H A - - -57.9 180.9 - -66.3 -31.8 - - - 183.9 - 34.3 - 17 LYS 17 H a - - -66.3 176.2 - -113.9 -41.9 - - - 186.0 -1.2 32.7 - **** * * **** 18 SER 18 H A - - -57.9 - - -80.3 -2.3 - - - 175.5 -3.4 32.4 - * *** +* *** Residue-by-residue listing for refined_5 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 19 SER 19 h A - - -62.7 - - - - - - - 177.0 -.7 30.6 - +* +* 20 LYS 20 T A - - -72.1 179.4 - - - - - - 180.3 -1.2 30.8 - * * 21 SER 21 t B 52.9 - - - - - - - - - 175.5 -1.9 34.8 - 22 LEU 22 E B - 189.1 - - - - - - - - 182.6 -2.6 33.8 - 23 GLU 23 E B 73.8 - - 175.1 - - - - - - 179.8 -.8 33.3 - +* +* 24 ILE 24 E B - - -63.5 178.4 - - - - - - 186.2 -3.5 33.4 - * +* +* 25 PRO 25 h - - - - - -60.2 - - - - - 179.8 - 38.1 - * * 26 LEU 26 H A - - -74.0 - - -52.8 -43.8 - - - 180.4 - 34.2 - * * 27 GLY 27 H - - - - - - -60.8 -30.7 - - - 181.0 - - - 28 PHE 28 H A - 197.6 - - - -88.1 -19.7 - - - 176.7 -1.0 33.2 - +* +* * +* 29 ASN 29 H A - 180.1 - - - -62.4 -44.9 - - - 176.0 -1.3 33.5 - 30 GLU 30 h A - - -72.8 - - - - - - - 179.3 -1.6 30.8 - 31 TYR 31 T A - 195.0 - - - - - - - - 175.4 -.7 34.0 - +* +* 32 PHE 32 t B - - -65.4 - - - - - - - 178.1 -1.7 34.3 - 33 PRO 33 - - - - - -67.4 - - - - - 178.9 - 39.0 - * * 34 ALA 34 S A - - - - - - - - - - 175.4 - 31.7 - 35 PRO 35 S - - - - - -55.7 - - - - - 183.6 - 38.8 - * * 36 PHE 36 B - 175.1 - - - - - - - - 176.5 - 33.5 - 37 PRO 37 - - - - - -74.9 - - - - - 181.2 - 38.7 - * * 38 ILE 38 e a - - -54.3 - - - - - - - 180.0 - 34.3 - 39 THR 39 E B 51.8 - - - - - - - - - 176.6 - 34.1 - 40 VAL 40 E B - - -64.5 - - - - - - - 181.5 -3.0 33.1 - * * 41 ASP 41 E B - - -70.4 - - - - - - - 179.4 -1.6 32.5 - 42 LEU 42 E B - - -59.1 180.9 - - - - - - 173.4 -2.5 35.2 - * * 43 LEU 43 E B - - -70.5 - - - - - - - 188.7 -2.5 32.1 - +* +* 44 ASP 44 B - 174.4 - - - - - - - - 177.2 - 35.8 - 45 TYR 45 S A - 187.8 - - - - - - - - 177.4 - 35.9 - 46 SER 46 S a - 178.5 - - - - - - - - 181.6 - 34.3 - 47 GLY 47 S - - - - - - - - - - - 174.0 - - - * * 48 ARG 48 B - - -56.7 179.8 - - - - - - 181.9 - 34.7 - 49 SER 49 B 59.0 - - - - - - - - - 177.3 - 32.9 - 50 TRP 50 E B - - -55.0 - - - - - - - 174.2 -1.0 37.5 - * * * 51 THR 51 E B - - -57.5 - - - - - - - 188.0 - 34.2 - * * 52 VAL 52 E B - - -58.5 - - - - - - - 179.5 -2.5 33.2 - 53 ARG 53 E B - 183.9 - 177.5 - - - - - - 186.5 -3.3 34.4 - * +* +* 54 MET 54 E B - 182.1 - 176.5 - - - - - - 182.3 -2.7 34.6 - 55 LYS 55 E B - - -65.9 - - - - - - - 172.7 -3.0 35.0 - * * * 56 LYS 56 E B - - -56.3 - - - - - - - 183.0 - 35.7 - Residue-by-residue listing for refined_5 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 ----------------------------------------------------------------------------------------------------------------------------------- 57 ARG 57 E b - 184.8 - 174.0 - - - - - - 187.4 -2.3 33.6 - * * 58 GLY 58 T - - - - - - - - - - - 176.2 - - - 59 GLU 59 T A - - -61.6 183.0 - - - - - - 182.6 - 33.8 - 60 LYS 60 E B - 180.7 - 177.5 - - - - - - 181.1 -.9 34.1 - +* +* 61 VAL 61 E B - 180.2 - - - - - - - - 178.4 -2.7 34.8 - 62 PHE 62 E B - - -65.5 - - - - - - - 175.0 -2.7 33.7 - 63 LEU 63 E B - 189.2 - 171.7 - - - - - - 190.1 -2.4 34.7 - +* +* 64 THR 64 e a 53.3 - - - - - - - - - 185.5 -1.3 33.6 - 65 VAL 65 T B - 182.6 - - - - - - - - 182.4 - 33.1 - 66 GLY 66 h - - - - - - - - - - - 177.9 - - - 67 TRP 67 H A - 177.7 - - - -61.5 -29.4 - - - 181.5 -.6 35.7 - +* +* 68 GLU 68 H A - 186.6 - 163.2 - -68.8 -26.0 - - - 174.0 -.7 27.6 - * * +* +* +* 69 ASN 69 H A - - -59.0 - - -71.1 -38.1 - - - 183.2 -1.2 34.3 - * * 70 PHE 70 H A - 176.4 - - - -73.4 -45.3 - - - 181.6 -1.3 33.4 - 71 VAL 71 H A 71.0 - - - - -66.6 -35.3 - - - 177.6 -3.5 33.9 - +* +* 72 LYS 72 H A - 185.6 - - - -70.8 -43.5 - - - 185.2 -1.4 34.6 - 73 ASP 73 H A - 185.3 - - - -72.8 -39.1 - - - 184.0 -2.3 32.1 - 74 ASN 74 h A - 188.1 - - - - - - - - 179.9 -3.0 34.2 - * * 75 ASN 75 t XX - 191.1 - - - - - - - - 171.6 -.6 31.2 - **** * +* **** 76 LEU 76 l - - -65.8 182.4 - - - - - - 175.7 -2.5 22.5 - *** *** 77 GLU 77 t B - 180.7 - 182.8 - - - - - - 179.6 - 34.6 - 78 ASP 78 T B 63.0 - - - - - - - - - 183.9 - 32.8 - 79 GLY 79 T - - - - - - - - - - - 174.0 - - - * * 80 LYS 80 t B - - -65.3 - - - - - - - 179.7 -1.7 34.8 - 81 TYR 81 E B - - -62.1 - - - - - - - 185.2 -1.1 32.5 - * * 82 LEU 82 E B 45.4 - - - - - - - - - 174.2 -.6 31.6 - * +* +* 83 GLN 83 E B - - -67.3 - - - - - - - 173.9 -2.1 36.1 - * * 84 PHE 84 E B - - -67.3 - - - - - - - 180.0 -2.9 33.8 - * * 85 ILE 85 E B - - -53.5 177.5 - - - - - - 183.1 -3.6 35.0 - ** ** 86 TYR 86 E B - 172.5 - - - - - - - - 174.6 -3.3 34.6 - +* +* 87 ASP 87 a - 179.8 - - - - - - - - 174.0 - 33.2 - * * 88 ARG 88 S ~a - 198.2 - - - - - - - - 184.6 - 34.5 - ** ** 89 ASP 89 S b - 193.2 - - - - - - - - 181.3 - 37.0 - 90 ARG 90 e A - 191.6 - - - - - - - - 181.7 - 35.6 - 91 THR 91 E B - 186.2 - - - - - - - - 180.2 - 33.0 - 92 PHE 92 E B - - -60.0 - - - - - - - 176.6 -2.9 35.8 - * * 93 TYR 93 E B - - -52.0 - - - - - - - 181.1 -2.3 36.4 - Residue-by-residue listing for refined_5 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 94 VAL 94 E B 65.8 - - - - - - - - - 175.8 -.9 31.5 - * * 95 ILE 95 E B - 183.5 - - - - - - - - 184.4 -2.3 31.4 - 96 ILE 96 E B - - -55.8 - - - - - - - 175.2 -.5 36.4 - ** ** 97 TYR 97 E B - - -65.4 - - - - - - - 179.0 -3.5 33.9 - +* +* 98 GLY 98 S - - - - - - - - - - - 179.5 -.7 - - +* +* 99 HIS 99 b 61.1 - - - - - - - - - 180.2 - 29.0 - * * 100 ASN 100 B - 178.3 - - - - - - - - 181.5 -1.3 32.8 - * * 101 MET 101 a - - -61.1 174.3 - - - - - - 180.7 - 35.2 - 102 CYS 102 - - - -57.9 - - - - - - - - - 34.4 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * **** *** +* ** *** **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.7 183.8 -61.6 178.0 -62.6 -71.6 -33.2 - - - 179.7 -1.9 33.9 Standard deviations: 9.0 6.6 6.0 4.7 8.6 14.4 11.7 - - - 4.1 1.0 2.3 Numbers of values: 10 38 40 23 5 15 15 0 0 0 101 59 95 0 KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_5 Page 5 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - 1.225 1.518 1.533 1.462 - 116.83 120.53 111.05 110.01 111.12 122.63 2 ALA 2 1.325 1.240 1.505 1.520 1.442 121.32 114.85 120.69 111.17 108.11 111.29 124.40 * * 3 ASP 3 1.319 1.229 1.514 1.542 1.459 124.15 115.06 121.57 111.63 110.07 113.52 123.15 * +* +* 4 THR 4 1.297 1.242 1.532 1.544 1.434 122.62 114.96 121.61 109.01 107.71 110.26 123.41 ** * * ** 5 GLY 5 1.329 1.230 1.505 - 1.429 121.66 116.33 120.19 - 112.22 - 123.45 * * 6 GLU 6 1.325 1.238 1.524 1.563 1.455 122.62 114.68 122.31 113.64 110.70 112.55 122.63 +* +* * +* 7 VAL 7 1.303 1.237 1.507 1.560 1.425 121.73 117.08 120.62 111.37 107.29 113.03 122.26 +* +* * * +* 8 GLN 8 1.290 1.237 1.495 1.526 1.419 120.47 115.48 120.97 110.99 111.37 110.39 123.53 +** * ** +** 9 PHE 9 1.295 1.236 1.517 1.546 1.428 122.27 115.88 120.44 110.94 109.17 109.49 123.67 ** +* ** 10 MET 10 1.306 1.231 1.498 1.537 1.439 123.11 117.10 120.09 108.74 108.03 110.72 122.80 +* * * +* 11 LYS 11 1.296 1.237 1.501 1.533 1.429 121.00 117.94 119.42 108.75 108.70 111.01 122.59 ** * +* ** Residue-by-residue listing for refined_5 Page 6 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 12 PRO 12 1.344 1.249 1.524 1.531 1.453 122.15 116.82 120.96 110.30 108.92 103.62 122.20 * * 13 PHE 13 1.284 1.224 1.513 1.534 1.425 120.42 117.89 119.73 110.38 108.50 109.22 122.36 *** +* *** 14 ILE 14 1.323 1.226 1.506 1.552 1.442 119.58 117.19 119.79 109.49 107.31 111.98 123.02 * * * 15 SER 15 1.306 1.213 1.512 1.519 1.456 122.16 116.72 120.58 110.82 112.54 110.63 122.67 +* +* 16 GLU 16 1.283 1.229 1.525 1.515 1.430 120.92 116.66 120.92 110.52 110.50 110.00 122.41 *** * *** 17 LYS 17 1.322 1.236 1.492 1.508 1.462 119.79 115.42 121.20 110.61 113.45 111.13 123.32 +* * * +* 18 SER 18 1.301 1.218 1.523 1.535 1.419 121.29 117.60 120.02 112.29 111.82 110.82 122.39 ** ** * ** 19 SER 19 1.338 1.222 1.520 1.523 1.448 118.88 117.24 120.63 111.43 111.62 113.79 122.11 +* +* +* 20 LYS 20 1.323 1.228 1.505 1.527 1.452 119.39 117.28 120.05 111.82 113.45 112.52 122.65 * * * 21 SER 21 1.312 1.221 1.504 1.523 1.436 120.25 116.37 120.85 110.34 111.71 109.30 122.78 * * * * 22 LEU 22 1.291 1.239 1.510 1.557 1.431 120.61 116.05 120.55 112.58 105.88 110.74 123.32 +** * * * +* +** 23 GLU 23 1.311 1.235 1.539 1.549 1.432 120.94 116.35 120.99 111.74 109.78 110.83 122.60 * * * 24 ILE 24 1.297 1.234 1.541 1.544 1.442 122.32 116.99 120.74 111.52 109.76 110.70 122.27 ** * ** 25 PRO 25 1.348 1.240 1.539 1.536 1.474 124.02 114.53 121.63 110.24 115.42 103.57 123.82 +* * * +* 26 LEU 26 1.338 1.225 1.519 1.552 1.472 124.56 116.17 120.64 109.20 111.94 111.27 123.18 * +* +* 27 GLY 27 1.323 1.232 1.518 - 1.449 121.21 116.58 120.62 - 112.94 - 122.80 28 PHE 28 1.317 1.221 1.544 1.543 1.441 121.23 116.77 120.88 112.07 109.18 110.72 122.35 * * 29 ASN 29 1.342 1.235 1.521 1.538 1.480 121.55 115.67 121.18 109.36 109.82 112.46 123.12 * * * 30 GLU 30 1.325 1.230 1.532 1.545 1.462 122.33 116.34 121.12 111.18 112.03 113.73 122.51 +* +* 31 TYR 31 1.310 1.245 1.550 1.536 1.446 121.82 115.91 121.38 111.89 108.98 109.56 122.70 * * * 32 PHE 32 1.332 1.237 1.518 1.541 1.452 121.71 118.10 119.87 108.40 109.22 112.67 122.03 * * 33 PRO 33 1.339 1.241 1.532 1.538 1.462 122.52 115.79 120.82 109.87 111.85 103.64 123.38 34 ALA 34 1.325 1.247 1.551 1.531 1.459 122.52 119.75 119.13 111.72 112.70 111.50 121.10 * +* * +* 35 PRO 35 1.390 1.235 1.525 1.532 1.469 121.73 116.30 120.57 109.95 110.58 103.95 123.13 *** *** 36 PHE 36 1.308 1.239 1.534 1.534 1.444 122.00 117.21 120.65 111.37 112.32 109.89 122.14 * * 37 PRO 37 1.343 1.231 1.528 1.532 1.458 122.56 116.74 120.60 110.48 110.64 103.60 122.66 38 ILE 38 1.306 1.239 1.525 1.558 1.449 120.89 116.09 121.16 109.26 109.63 111.88 122.74 +* +* 39 THR 39 1.314 1.240 1.517 1.551 1.431 121.46 115.47 121.16 109.71 111.23 111.36 123.36 * * * 40 VAL 40 1.297 1.235 1.517 1.584 1.437 123.76 117.58 120.27 110.66 107.60 113.37 122.13 ** +* * * * * ** Residue-by-residue listing for refined_5 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 ----------------------------------------------------------------------------------------------------------------------------------- 41 ASP 41 1.289 1.230 1.491 1.532 1.454 120.16 116.08 120.73 110.65 111.58 112.26 123.18 +** +* * +** 42 LEU 42 1.304 1.240 1.513 1.541 1.439 121.83 115.99 120.42 108.59 110.21 111.10 123.58 +* * +* 43 LEU 43 1.307 1.220 1.501 1.553 1.444 121.95 116.06 120.43 110.55 108.75 114.15 123.49 +* * * ** ** 44 ASP 44 1.283 1.243 1.510 1.533 1.445 122.88 114.92 120.87 110.60 111.62 107.75 124.21 *** +* *** 45 TYR 45 1.323 1.230 1.538 1.537 1.441 124.23 116.17 120.95 110.53 109.07 108.17 122.87 * * * 46 SER 46 1.319 1.237 1.527 1.538 1.430 122.13 116.58 120.52 110.95 109.09 110.32 122.84 * * 47 GLY 47 1.325 1.228 1.520 - 1.452 119.93 116.60 120.70 - 113.84 - 122.68 48 ARG 48 1.311 1.227 1.526 1.528 1.457 122.22 119.14 119.67 110.36 107.27 110.46 121.16 * * * * * 49 SER 49 1.300 1.238 1.529 1.532 1.448 117.62 114.66 121.77 111.45 113.52 110.07 123.55 ** ** ** 50 TRP 50 1.312 1.247 1.530 1.531 1.414 124.83 116.93 120.33 109.39 108.78 107.18 122.67 * ** +* +* ** 51 THR 51 1.306 1.242 1.521 1.541 1.443 121.59 116.37 120.67 110.69 107.48 111.24 122.94 +* * +* 52 VAL 52 1.304 1.228 1.525 1.553 1.436 121.37 115.59 121.20 110.56 112.28 111.37 123.20 +* * +* 53 ARG 53 1.303 1.244 1.529 1.531 1.440 123.08 116.41 120.59 111.48 108.53 109.59 122.99 +* +* 54 MET 54 1.306 1.232 1.531 1.536 1.448 122.08 116.81 120.32 111.79 110.16 108.50 122.84 +* * +* 55 LYS 55 1.332 1.240 1.518 1.546 1.453 121.94 115.57 120.97 106.45 111.65 112.91 123.44 +* * +* 56 LYS 56 1.321 1.235 1.509 1.533 1.427 122.55 117.00 120.34 108.03 105.26 112.10 122.63 +* * ** ** 57 ARG 57 1.274 1.236 1.512 1.531 1.439 120.82 115.07 121.65 112.90 109.19 109.27 123.27 +*** * +*** 58 GLY 58 1.304 1.233 1.502 - 1.427 120.99 117.46 119.88 - 108.55 - 122.65 +* +* * +* 59 GLU 59 1.301 1.237 1.524 1.522 1.451 120.69 115.42 121.44 109.95 109.95 111.51 123.12 +* +* 60 LYS 60 1.311 1.235 1.526 1.560 1.435 122.23 116.20 121.07 111.77 109.20 110.05 122.70 * * * * 61 VAL 61 1.296 1.227 1.511 1.550 1.436 121.99 117.05 120.48 110.09 108.92 110.69 122.42 ** * ** 62 PHE 62 1.301 1.242 1.497 1.537 1.431 120.55 115.11 121.25 109.82 110.54 111.95 123.64 ** * * ** 63 LEU 63 1.289 1.234 1.526 1.554 1.424 122.56 116.14 120.65 113.73 104.62 108.39 123.12 +** * +* +* ** * +** 64 THR 64 1.314 1.235 1.539 1.552 1.444 121.48 116.66 121.11 110.43 114.58 110.04 122.23 * * * 65 VAL 65 1.305 1.222 1.514 1.552 1.453 121.60 115.60 121.02 111.23 110.74 111.36 123.34 +* +* 66 GLY 66 1.306 1.226 1.484 - 1.424 121.54 114.25 121.48 - 110.24 - 124.24 +* +* +* * +* 67 TRP 67 1.314 1.221 1.485 1.535 1.426 124.37 116.27 120.67 109.46 108.89 110.02 123.01 * +* +* * +* 68 GLU 68 1.322 1.224 1.546 1.535 1.426 118.56 116.59 120.88 115.61 111.53 113.71 122.46 +* +* +** +* +** Residue-by-residue listing for refined_5 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 69 ASN 69 1.339 1.217 1.505 1.547 1.469 121.52 115.37 121.35 108.74 108.95 112.51 123.21 * * 70 PHE 70 1.315 1.238 1.526 1.545 1.451 122.57 116.05 121.01 111.46 111.42 110.26 122.93 * * 71 VAL 71 1.312 1.219 1.516 1.550 1.448 121.84 115.37 121.44 110.48 109.73 111.25 123.19 * * 72 LYS 72 1.305 1.235 1.521 1.532 1.426 121.69 116.46 120.75 110.46 109.70 110.18 122.75 +* +* +* 73 ASP 73 1.331 1.228 1.530 1.525 1.464 120.12 117.78 120.29 110.48 113.68 111.93 121.90 74 ASN 74 1.318 1.240 1.544 1.541 1.457 120.60 114.80 121.89 111.83 110.09 109.08 123.31 75 ASN 75 1.337 1.231 1.510 1.527 1.491 126.18 115.12 120.64 111.45 111.46 112.93 124.23 +* ** * ** 76 LEU 76 1.305 1.220 1.517 1.511 1.463 123.69 116.76 120.53 114.07 119.31 115.75 122.18 +* * ** +** *** *** 77 GLU 77 1.278 1.248 1.529 1.527 1.449 120.61 115.46 120.58 110.10 108.84 110.52 123.95 +*** +*** 78 ASP 78 1.323 1.230 1.517 1.561 1.468 123.17 116.09 120.95 110.46 109.82 112.84 122.91 +* * +* 79 GLY 79 1.298 1.231 1.495 - 1.440 121.13 114.92 121.44 - 109.20 - 123.64 ** * * ** 80 LYS 80 1.314 1.237 1.508 1.536 1.439 122.02 116.87 120.28 109.65 108.21 111.19 122.85 * * * 81 TYR 81 1.299 1.231 1.494 1.533 1.440 120.86 116.51 120.32 112.09 109.41 111.70 123.16 ** * * ** 82 LEU 82 1.295 1.235 1.518 1.553 1.428 121.15 114.84 121.28 112.80 113.79 110.61 123.83 ** * +* * ** 83 GLN 83 1.306 1.236 1.495 1.526 1.442 123.49 116.42 120.27 107.37 108.61 111.22 123.30 +* * * +* 84 PHE 84 1.288 1.232 1.492 1.535 1.430 121.00 115.93 120.49 109.86 108.13 112.60 123.56 +** +* * * * +** 85 ILE 85 1.295 1.243 1.503 1.552 1.426 121.74 115.25 121.10 109.60 107.10 111.58 123.61 ** * +* * ** 86 TYR 86 1.287 1.233 1.510 1.541 1.417 122.52 115.68 121.08 111.59 110.65 108.97 123.18 *** ** *** 87 ASP 87 1.306 1.222 1.516 1.540 1.437 121.01 116.09 120.65 111.53 108.26 111.71 123.19 +* * * +* 88 ARG 88 1.308 1.236 1.523 1.543 1.447 122.89 113.49 122.60 111.62 105.97 110.19 123.83 +* * * +* +* 89 ASP 89 1.328 1.233 1.536 1.566 1.430 124.44 116.99 120.55 110.90 106.34 107.25 122.45 +* * +* +* +* +* 90 ARG 90 1.276 1.230 1.545 1.544 1.440 123.01 115.56 122.05 110.86 108.00 108.70 122.38 +*** * * +*** 91 THR 91 1.311 1.243 1.542 1.568 1.431 121.61 116.10 120.74 111.68 110.29 111.33 123.09 * * * * * 92 PHE 92 1.321 1.234 1.515 1.538 1.451 122.79 116.43 120.63 107.88 109.39 110.98 122.94 * * 93 TYR 93 1.297 1.228 1.514 1.534 1.448 121.81 119.17 119.10 108.57 106.45 110.09 121.72 ** * * +* ** 94 VAL 94 1.312 1.235 1.525 1.572 1.451 118.15 115.75 121.19 111.31 111.70 113.22 122.99 * * +* * * +* 95 ILE 95 1.306 1.241 1.537 1.606 1.436 122.12 115.24 121.39 114.75 107.71 111.92 123.28 +* ** * +** * +** 96 ILE 96 1.313 1.233 1.523 1.563 1.454 123.25 116.27 120.55 108.13 110.33 109.88 123.18 * * Residue-by-residue listing for refined_5 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 ----------------------------------------------------------------------------------------------------------------------------------- 97 TYR 97 1.310 1.239 1.510 1.522 1.439 121.90 115.28 120.77 109.28 109.79 112.21 123.95 * * * * 98 GLY 98 1.296 1.238 1.487 - 1.426 123.03 118.20 119.19 - 108.01 - 122.61 ** +* +* * +* ** 99 HIS 99 1.308 1.233 1.522 1.564 1.440 119.35 115.28 121.86 113.76 111.25 114.15 122.79 +* +* * +* ** ** 100 ASN 100 1.306 1.231 1.512 1.538 1.446 121.87 115.41 121.11 111.42 110.68 111.45 123.47 +* +* 101 MET 101 1.300 1.233 1.514 1.527 1.442 122.65 116.05 121.02 110.18 109.86 109.45 122.92 ** ** 102 CYS 102 1.311 - 1.518 1.530 1.437 121.71 - - 110.69 109.49 110.30 - * * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** +* ** ** ** +* * +** +** *** * +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 10 ---------------------------------------- A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S +------------------+ | BOND LENGTHS | +------------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Bond X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- C-N C-NH1 (except Pro) 1.329 .014 96 1.274 1.342 1.309 .015 +*** * C-N (Pro) 1.341 .016 5 1.339 1.390 1.353 .019 *** C-O C-O 1.231 .020 101 1.213 1.249 1.233 .007 CA-C CH1E-C (except Gly) 1.525 .021 95 1.485 1.551 1.519 .014 +* * CH2G*-C (Gly) 1.516 .018 7 1.484 1.520 1.501 .013 +* CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.520 1.531 1.526 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.541 1.606 1.558 .015 ** CH1E-CH2E (the rest) 1.530 .020 75 1.508 1.566 1.537 .012 * +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.414 1.491 1.443 .014 ** +* NH1-CH2G* (Gly) 1.451 .016 7 1.424 1.452 1.435 .011 +* N-CH1E (Pro) 1.466 .015 5 1.453 1.474 1.463 .008 ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 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 89 113.49 119.75 116.24 1.03 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 7 114.25 118.20 116.33 1.27 * CH1E-C-N (Pro) 116.9 1.5 5 114.53 116.82 116.04 .84 +* O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 121.10 124.40 122.95 .60 * O-C-N (Pro) 122.0 1.4 5 122.20 123.82 123.04 .57 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 117.62 126.18 121.78 1.45 ** ** C-NH1-CH2G* (Gly) 120.6 1.7 7 119.93 123.03 121.35 .86 * C-N-CH1E (Pro) 122.6 5.0 5 121.73 124.02 122.60 .77 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 119.10 122.60 120.80 .60 * * CH2G*-C-O (Gly) 120.8 2.1 7 119.19 121.48 120.50 .76 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 111.17 111.72 111.45 .27 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.13 114.75 110.55 1.38 +** CH2E-CH1E-C (the rest) 110.1 1.9 75 106.45 115.61 110.74 1.56 +* +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.62 119.31 109.89 2.22 ** +** NH1-CH2G*-C (Gly) 112.5 2.9 7 108.01 113.84 110.71 2.12 +* N-CH1E-C (Pro) 111.8 2.5 5 108.92 115.42 111.48 2.18 * * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 111.29 111.50 111.39 .10 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.88 113.37 111.47 .98 * N-CH1E-CH2E (Pro) 103.0 1.1 5 103.57 103.95 103.68 .14 NH1-CH1E-CH2E (the rest) 110.5 1.7 70 107.18 115.75 110.95 1.71 +* *** ------------------------------------------------------------------------------------------------------------- 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_5 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] 73 83.0% 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] 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 7 Number of proline residues 5 ---- Total number of residues 102 Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good quality model would be expected to have over 90% in the most favoured regions [E,H,L]. S T E R E O C H E M I S T R Y O F M A I N - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. %-tage residues in A, B, L 88 83.0 83.8 10.0 -.1 Inside b. Omega angle st dev 101 4.1 6.0 3.0 -.6 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 2.3 3.1 1.6 -.5 Inside e. H-bond energy st dev 59 1.0 .8 .2 .8 Inside f. Overall G-factor 102 -.1 -.4 .3 1.0 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 10 9.0 18.1 6.5 -1.4 BETTER b. Chi-1 trans st dev 38 6.6 19.0 5.3 -2.3 BETTER c. Chi-1 gauche plus st dev 40 6.0 17.5 4.9 -2.3 BETTER d. Chi-1 pooled st dev 88 7.6 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 23 4.7 20.4 5.0 -3.1 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 83.0 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 7.9 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .98 3 Residue-by-residue listing for refined_5 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.46 Chi1-chi2 distribution -.21 Chi1 only -.09 Chi3 & chi4 .43 Omega -.27 ------ -.22 ===== Main-chain covalent forces:- Main-chain bond lengths -.07 Main-chain bond angles .33 ------ .17 ===== OVERALL AVERAGE -.09 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.