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 GLU 1 - 58.7 - - 180.1 - - - - - - 181.9 - 33.5 - 2 ALA 2 B - - - - - - - - - - 176.5 - 34.8 - 3 GLU 3 b - 198.8 - - - - - - - - 188.8 - 34.5 - +* +* 4 VAL 4 B 60.0 - - - - - - - - - 175.0 - 30.8 - 5 HIS 5 B - - -65.5 - - - - - - - 181.2 - 34.7 - 6 ASN 6 b - 183.8 - - - - - - - - 178.2 - 32.8 - 7 GLN 7 B - - -60.0 174.5 - - - - - - 179.7 -1.6 36.2 - 8 LEU 8 E B - - -68.3 - - - - - - - 183.5 -2.8 33.7 - * * 9 GLU 9 E B - - -56.6 173.0 - - - - - - 182.2 -.6 32.7 - +* +* 10 ILE 10 E B - - -57.6 177.6 - - - - - - 172.5 -2.2 36.1 - * * 11 LYS 11 E B 68.7 - - 173.9 - - - - - - 184.1 -2.8 31.5 - * * 12 PHE 12 E B - - -54.1 - - - - - - - 179.1 - 35.8 - 13 ARG 13 E B - 188.1 - 177.7 - - - - - - 179.5 -3.2 33.4 - +* +* 14 LEU 14 E B - - -62.9 179.5 - - - - - - 181.1 -3.4 35.6 - +* +* 15 THR 15 e A - 195.4 - - - - - - - - 177.3 -1.1 33.3 - * * 16 ASP 16 T A - - -57.2 - - - - - - - 179.9 - 36.0 - 17 GLY 17 t - - - - - - - - - - - 180.5 -1.9 - - 18 SER 18 B - - -50.5 - - - - - - - 183.8 - 36.2 - * * 19 ASP 19 B B 65.2 - - - - - - - - - 176.7 - 33.3 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 20 ILE 20 B - - -56.7 177.9 - - - - - - 182.0 -2.6 35.9 - 21 GLY 21 - - - - - - - - - - - 183.2 - - - 22 PRO 22 - - - - - -69.2 - - - - - 178.7 - 38.2 - * * 23 LYS 23 E B - - -61.9 - - - - - - - 180.2 -2.8 34.8 - 24 ALA 24 E B - - - - - - - - - - 180.5 - 33.7 - 25 PHE 25 E B - - -56.0 - - - - - - - 173.5 -3.3 35.8 - * +* +* 26 PRO 26 t - - - - - -64.2 - - - - - 177.3 - 40.0 - +* +* 27 ASP 27 T A - - -60.0 - - - - - - - 182.6 - 35.2 - 28 ALA 28 T A - - - - - - - - - - 175.8 - 33.6 - 29 THR 29 t B - - -62.1 - - - - - - - 182.7 -2.1 32.4 - 30 THR 30 h B 59.3 - - - - - - - - - 175.2 - 34.7 - 31 VAL 31 H A - 177.2 - - - -67.8 -26.2 - - - 176.1 -2.6 33.0 - * * 32 SER 32 H A - 183.7 - - - -60.3 -49.7 - - - 179.8 -1.8 35.0 - 33 ALA 33 H A - - - - - -71.3 -27.3 - - - 177.1 - 33.6 - * * 34 LEU 34 H A - 175.1 - - - -64.3 -46.5 - - - 175.4 -1.7 35.3 - 35 LYS 35 H A - - -73.1 177.9 - -67.3 -38.3 - - - 177.0 -2.7 31.4 - 36 GLU 36 H A - - -65.6 - - -56.6 -33.4 - - - 178.2 -2.2 34.5 - 37 THR 37 H A - - -57.1 - - -72.4 -46.4 - - - 182.8 -1.6 33.8 - 38 VAL 38 H A 69.0 - - - - -63.6 -40.2 - - - 179.5 -1.9 32.5 - 39 ILE 39 H A - - -53.4 172.6 - -64.0 -34.8 - - - 178.5 -2.6 34.4 - 40 SER 40 H A - - -58.2 - - -75.8 -33.8 - - - 179.4 -1.1 34.0 - * * 41 GLU 41 H A - - -66.6 - - -72.9 -26.0 - - - 178.2 -2.1 34.6 - * * 42 TRP 42 h B - 194.7 - - - - - - - - 180.1 -1.6 35.6 - 43 PRO 43 t - - - - - -61.6 - - - - - 175.1 - 39.1 - * * 44 ARG 44 T A 64.5 - - - - - - - - - 175.8 - 31.3 - 45 GLU 45 T A - - -61.0 - - - - - - - 179.0 - 35.8 - 46 LYS 46 t b - 194.5 - - - - - - - - 174.9 -1.6 36.2 - 47 GLU 47 b - - -62.3 183.1 - - - - - - 180.5 - 34.1 - 48 ASN 48 S a - - -72.1 - - - - - - - 175.7 - 32.3 - 49 GLY 49 S - - - - - - - - - - - 173.2 -1.9 - - * * 50 PRO 50 S - - - - - -61.7 - - - - - 179.0 - 39.5 - +* +* 51 LYS 51 a 49.7 - - 195.8 - - - - - - 177.2 - 32.7 - 52 THR 52 t B 59.3 - - - - - - - - - 179.5 - 33.8 - 53 VAL 53 T A 59.0 - - - - - - - - - 180.4 - 33.9 - 54 LYS 54 T A - 180.7 - 190.5 - - - - - - 191.0 - 38.0 - +* * +* 55 GLU 55 e A - - -52.9 168.4 - - - - - - 185.0 -.8 36.0 - +* +* 56 VAL 56 E B - 181.3 - - - - - - - - 174.6 -1.0 34.9 - * * 57 LYS 57 E B - - -67.9 182.7 - - - - - - 179.1 -2.6 35.2 - 58 LEU 58 E B - 191.8 - - - - - - - - 188.5 - 35.1 - * * 59 ILE 59 E B - - -60.8 178.6 - - - - - - 176.3 -1.3 35.1 - * * 60 SER 60 E B 57.8 - - - - - - - - - 177.1 -2.6 35.0 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 61 ALA 61 T l - - - - - - - - - - 180.2 -.5 32.8 - +* +* 62 GLY 62 T - - - - - - - - - - - 178.5 - - - 63 LYS 63 E B - - -61.6 180.3 - - - - - - 180.7 -1.2 36.4 - * * 64 VAL 64 E B - 183.1 - - - - - - - - 182.2 - 34.7 - 65 LEU 65 e B - - -56.8 - - - - - - - 180.3 -2.4 35.2 - 66 GLU 66 t B - 185.2 - - - - - - - - 185.1 - 33.1 - 67 ASN 67 T A - - -65.9 - - - - - - - 187.5 - 35.2 - * * 68 SER 68 T A 54.0 - - - - - - - - - 183.0 - 32.5 - 69 LYS 69 t B - - -61.5 178.9 - - - - - - 185.1 -1.1 33.0 - * * 70 THR 70 h B - - -31.7 - - - - - - - 176.9 - 37.0 - ** ** 71 VAL 71 H A - 176.2 - - - -59.7 -38.6 - - - 174.5 -2.9 33.7 - * * 72 LYS 72 H A - 162.6 - - - -51.8 -36.3 - - - 184.1 -2.7 33.2 - * * * 73 ASP 73 H A - - -62.4 - - -75.6 -23.9 - - - 181.2 -.8 33.2 - * +* +* 74 TYR 74 H A - - -57.7 - - -108.5 -.8 - - - 188.5 -1.1 36.9 - +*** *** * * +*** 75 ARG 75 h B 79.2 - - 184.6 - - - - - - 176.2 -1.0 33.9 - * * 76 SER 76 t B - - -56.0 - - - - - - - 183.2 - 35.8 - 77 PRO 77 T - - - - - -85.9 - - - - - 177.0 - 39.6 - +* +* +* 78 VAL 78 T l 59.8 - - - - - - - - - 173.4 - 26.2 - * ** ** 79 SER 79 T l - - -58.8 - - - - - - - 180.5 - 33.0 - 80 ASN 80 T a - 183.2 - - - - - - - - 182.8 - 33.7 - 81 LEU 81 t b - - -62.5 181.0 - - - - - - 179.2 -.8 36.9 - +* +* 82 ALA 82 S l - - - - - - - - - - 181.6 - 31.4 - 83 GLY 83 S - - - - - - - - - - - 176.9 - - - 84 ALA 84 S B - - - - - - - - - - 181.3 - 34.8 - 85 VAL 85 B - 180.9 - - - - - - - - 181.6 - 34.5 - 86 THR 86 E B - - -51.0 - - - - - - - 183.3 -3.2 35.3 - * +* +* 87 THR 87 E B - - -54.0 - - - - - - - 177.5 -.6 35.3 - +* +* 88 MET 88 E B - - -90.3 - - - - - - - 181.8 -2.7 34.1 - +* +* 89 HIS 89 E B - 190.6 - - - - - - - - 183.8 -2.4 34.8 - 90 VAL 90 E B - 179.5 - - - - - - - - 177.8 -3.4 33.6 - +* +* 91 ILE 91 E B - - -68.9 181.2 - - - - - - 186.1 -.9 33.7 - * * * 92 ILE 92 E B - - -58.1 - - - - - - - 169.9 - 35.8 - +* +* 93 GLN 93 e B - - -64.4 182.4 - - - - - - 178.8 -2.9 34.9 - * * 94 ALA 94 B - - - - - - - - - - 176.6 -.6 34.2 - +* +* 95 PRO 95 - - - - - -59.5 - - - - - 180.2 - 38.5 - * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 96 VAL 96 S A - 179.3 - - - - - - - - 179.8 - 33.8 - 97 THR 97 S b - 179.5 - - - - - - - - 177.1 - 31.2 - 98 GLU 98 S b - 185.7 - 173.8 - - - - - - 182.9 - 32.7 - 99 LYS 99 l - 185.6 - 180.6 - - - - - - 178.0 - 31.6 - 100 GLU 100 A 44.5 - - - - - - - - - 177.4 - 29.9 - * * * 101 LYS 101 - 58.6 - - 180.7 - - - - - - - - 31.8 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * * ** +* +*** *** +* +* ** +*** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 60.5 184.0 -60.5 179.5 -67.0 -68.8 -33.5 - - - 179.7 -1.9 34.4 Standard deviations: 8.0 7.9 8.4 5.7 9.8 13.0 12.0 - - - 3.8 .9 2.1 Numbers of values: 16 24 42 25 6 15 15 0 0 0 100 49 96 0 KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_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 GLU 1 - 1.242 1.519 1.526 1.452 - 117.25 119.97 111.44 109.65 110.61 122.78 2 ALA 2 1.320 1.236 1.516 1.520 1.442 121.26 115.41 120.85 109.96 111.07 109.77 123.74 3 GLU 3 1.306 1.234 1.526 1.553 1.422 124.21 116.54 120.33 112.30 104.16 110.38 123.07 +* * +* * * +** +** 4 VAL 4 1.315 1.234 1.513 1.556 1.449 121.21 114.07 122.28 111.14 114.35 113.00 123.65 * * * 5 HIS 5 1.291 1.235 1.502 1.545 1.450 123.78 117.83 119.48 109.45 106.56 111.99 122.70 +** * * +* +** 6 ASN 6 1.304 1.238 1.529 1.531 1.451 120.31 115.24 121.55 111.27 110.61 111.45 123.07 +* +* 7 GLN 7 1.315 1.233 1.509 1.519 1.427 122.74 116.92 120.46 109.18 108.28 109.43 122.62 +* * +* 8 LEU 8 1.285 1.216 1.497 1.529 1.442 120.91 116.43 120.93 110.14 109.09 112.03 122.63 *** * *** 9 GLU 9 1.280 1.241 1.500 1.507 1.427 120.48 114.47 121.56 111.21 111.00 111.48 123.97 *** * * +* *** 10 ILE 10 1.294 1.240 1.515 1.571 1.438 123.40 116.58 120.30 108.26 108.86 110.81 123.08 ** * * ** 11 LYS 11 1.305 1.244 1.508 1.535 1.433 120.72 116.07 120.64 110.94 109.08 114.32 123.30 +* * ** ** 12 PHE 12 1.296 1.233 1.511 1.533 1.440 121.74 117.28 120.01 109.58 109.32 109.38 122.69 ** ** 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 ----------------------------------------------------------------------------------------------------------------------------------- 13 ARG 13 1.313 1.226 1.513 1.531 1.439 120.60 115.65 120.67 110.78 110.29 111.40 123.68 * * * 14 LEU 14 1.314 1.238 1.519 1.533 1.455 123.62 116.31 120.81 108.75 110.59 109.95 122.82 * * * 15 THR 15 1.320 1.224 1.526 1.557 1.451 121.69 114.47 122.07 111.21 109.45 111.47 123.43 16 ASP 16 1.312 1.228 1.525 1.534 1.454 123.05 116.03 121.12 108.36 109.64 110.07 122.84 * * 17 GLY 17 1.321 1.222 1.520 - 1.444 121.76 116.72 120.41 - 112.84 - 122.84 18 SER 18 1.311 1.229 1.533 1.516 1.456 122.00 117.98 119.86 109.99 109.08 107.92 122.16 * +* +* 19 ASP 19 1.316 1.241 1.516 1.531 1.436 120.67 113.99 121.85 110.12 113.23 111.14 124.13 * * * 20 ILE 20 1.307 1.226 1.525 1.564 1.446 124.88 117.39 119.05 109.11 106.98 110.53 123.54 +* +* * +* +* 21 GLY 21 1.338 1.234 1.535 - 1.471 122.23 117.50 120.32 - 114.23 - 122.18 * * * 22 PRO 22 1.349 1.232 1.526 1.525 1.469 123.64 115.46 121.44 109.96 114.39 103.92 123.09 * * 23 LYS 23 1.309 1.219 1.479 1.541 1.457 123.02 117.01 119.56 106.73 107.20 114.39 123.41 * ** +* * ** ** 24 ALA 24 1.286 1.236 1.518 1.523 1.437 120.56 116.14 120.86 111.23 109.51 110.57 123.00 *** * *** 25 PHE 25 1.308 1.228 1.511 1.532 1.435 122.32 117.70 120.54 108.10 109.36 110.82 121.69 +* * * +* 26 PRO 26 1.312 1.239 1.530 1.531 1.457 122.20 116.84 120.14 108.67 110.80 103.43 123.02 +* +* 27 ASP 27 1.332 1.226 1.522 1.546 1.479 121.82 115.50 121.30 107.29 109.55 112.30 123.18 * * * * 28 ALA 28 1.327 1.228 1.536 1.514 1.452 122.68 117.38 120.51 110.62 112.50 110.10 122.11 29 THR 29 1.310 1.231 1.538 1.546 1.442 120.96 116.75 120.69 112.85 110.17 110.77 122.50 * +* +* 30 THR 30 1.312 1.239 1.519 1.534 1.441 121.43 115.98 120.94 108.71 111.90 111.03 123.08 * * 31 VAL 31 1.330 1.235 1.531 1.554 1.453 121.61 115.31 121.59 111.34 109.07 111.87 123.08 * * 32 SER 32 1.321 1.235 1.538 1.539 1.434 122.35 116.50 120.48 110.80 109.20 109.34 122.93 * * 33 ALA 33 1.336 1.238 1.530 1.520 1.463 122.12 115.69 121.16 110.94 110.73 110.44 123.14 34 LEU 34 1.321 1.237 1.537 1.526 1.418 123.50 116.38 120.93 112.40 108.95 107.30 122.65 ** * * +* ** 35 LYS 35 1.329 1.214 1.517 1.520 1.444 121.26 117.29 120.12 111.37 111.87 112.76 122.56 * * 36 GLU 36 1.324 1.238 1.531 1.524 1.464 121.37 115.39 121.42 109.87 110.41 110.33 123.17 37 THR 37 1.313 1.221 1.547 1.548 1.427 122.24 117.67 119.96 111.04 111.06 110.38 122.31 * * +* +* 38 VAL 38 1.342 1.227 1.532 1.572 1.478 121.24 115.45 120.95 110.48 111.17 112.64 123.56 * * * 39 ILE 39 1.317 1.226 1.537 1.563 1.473 122.74 116.10 121.00 110.06 109.71 110.84 122.89 40 SER 40 1.325 1.236 1.538 1.527 1.454 122.02 116.36 121.05 110.50 111.11 110.21 122.59 41 GLU 41 1.329 1.233 1.507 1.510 1.434 122.61 116.17 120.67 109.86 111.63 109.91 123.15 * * * 42 TRP 42 1.297 1.235 1.514 1.522 1.421 121.21 118.09 119.98 109.99 107.17 109.83 121.89 ** +* * ** 43 PRO 43 1.332 1.219 1.516 1.537 1.449 121.96 116.57 120.80 109.54 111.40 104.02 122.63 * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 44 ARG 44 1.312 1.227 1.526 1.558 1.454 121.30 114.20 121.73 113.84 108.58 111.96 124.02 * * +* +* 45 GLU 45 1.339 1.229 1.545 1.546 1.453 124.94 116.62 120.60 107.90 110.79 110.56 122.77 +* * +* 46 LYS 46 1.332 1.236 1.549 1.563 1.464 122.80 118.28 119.86 110.65 107.03 108.22 121.85 * +* * * * +* 47 GLU 47 1.321 1.246 1.525 1.524 1.445 120.87 116.34 120.70 109.30 110.34 111.66 122.96 48 ASN 48 1.321 1.234 1.531 1.539 1.464 123.51 116.30 120.78 110.45 113.84 111.71 122.87 * * 49 GLY 49 1.312 1.228 1.507 - 1.429 121.87 118.06 119.91 - 109.64 - 122.03 * * * 50 PRO 50 1.330 1.239 1.527 1.530 1.464 122.60 115.98 120.90 109.70 110.90 103.13 123.04 51 LYS 51 1.298 1.242 1.528 1.537 1.441 122.50 116.56 120.82 113.25 111.87 109.30 122.61 ** +* ** 52 THR 52 1.322 1.241 1.551 1.530 1.439 121.88 115.32 121.38 108.74 112.02 112.03 123.30 * * * 53 VAL 53 1.332 1.236 1.538 1.571 1.474 124.44 115.30 121.20 110.69 111.42 110.51 123.48 * +* +* 54 LYS 54 1.320 1.234 1.528 1.533 1.461 124.40 114.98 121.73 107.40 110.98 107.61 123.28 * * +* +* 55 GLU 55 1.292 1.236 1.525 1.503 1.444 122.73 116.59 120.68 110.85 112.92 106.34 122.68 +** * ** +** 56 VAL 56 1.301 1.232 1.536 1.559 1.452 121.60 116.87 120.53 109.10 111.90 110.52 122.60 ** ** 57 LYS 57 1.323 1.235 1.504 1.537 1.453 121.31 116.48 120.34 107.60 108.75 112.43 123.18 * * * 58 LEU 58 1.306 1.241 1.522 1.561 1.421 120.96 116.59 120.40 113.61 104.75 108.02 123.01 +* +* +* +* ** * ** 59 ILE 59 1.316 1.231 1.524 1.568 1.452 121.76 115.49 121.34 109.88 111.92 109.68 123.16 * * * 60 SER 60 1.309 1.238 1.527 1.540 1.429 122.73 116.64 119.86 110.52 108.98 109.77 123.39 * +* +* 61 ALA 61 1.330 1.237 1.544 1.527 1.486 123.82 116.82 120.79 110.79 113.62 110.54 122.33 * * * 62 GLY 62 1.307 1.236 1.521 - 1.458 120.60 116.66 120.88 - 112.91 - 122.45 +* +* 63 LYS 63 1.312 1.229 1.510 1.511 1.411 122.60 117.06 119.73 109.63 108.64 108.49 123.21 * ** * ** 64 VAL 64 1.312 1.243 1.523 1.554 1.453 121.82 116.68 120.69 109.38 109.07 111.34 122.61 * * 65 LEU 65 1.309 1.234 1.513 1.520 1.422 121.47 116.34 120.37 109.45 110.43 110.09 123.30 * +* +* 66 GLU 66 1.314 1.242 1.532 1.538 1.449 121.28 115.41 120.59 111.39 110.11 111.18 124.00 * * 67 ASN 67 1.326 1.239 1.522 1.542 1.476 125.27 116.40 120.23 107.72 114.05 110.55 123.37 +* * * +* 68 SER 68 1.315 1.239 1.524 1.524 1.457 122.74 116.95 120.69 111.48 114.72 109.96 122.36 * * 69 LYS 69 1.282 1.249 1.523 1.507 1.420 121.26 115.77 121.16 111.98 111.17 110.15 123.07 *** * +* *** 70 THR 70 1.296 1.238 1.533 1.533 1.429 121.80 117.80 119.44 108.77 109.06 108.45 122.76 ** +* +* ** 71 VAL 71 1.350 1.224 1.523 1.568 1.477 121.06 114.24 121.57 110.18 108.01 112.41 124.12 * * * * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 72 LYS 72 1.318 1.231 1.535 1.550 1.441 124.44 117.16 120.55 112.51 113.41 108.81 122.27 +* * +* 73 ASP 73 1.312 1.228 1.520 1.530 1.430 121.16 117.07 120.35 110.72 111.83 111.22 122.58 * * * 74 TYR 74 1.322 1.232 1.532 1.521 1.446 121.57 117.30 120.03 106.26 111.37 110.16 122.67 ** ** 75 ARG 75 1.323 1.241 1.540 1.530 1.430 122.09 115.34 121.37 110.91 112.47 109.66 123.26 * * 76 SER 76 1.310 1.231 1.535 1.519 1.421 122.93 117.95 120.24 110.62 108.23 108.45 121.79 * +* * * +* 77 PRO 77 1.331 1.247 1.536 1.525 1.455 122.86 114.10 121.20 110.01 113.87 102.11 124.70 +* +* +* 78 VAL 78 1.342 1.229 1.527 1.566 1.467 126.36 113.63 122.05 113.37 116.52 114.86 124.29 +** * +* +* +* +** 79 SER 79 1.311 1.231 1.541 1.526 1.482 125.36 116.81 120.80 111.08 114.83 109.51 122.27 * * ** * ** 80 ASN 80 1.293 1.238 1.512 1.554 1.457 120.66 115.27 121.40 110.94 109.47 111.15 123.29 +** * +** 81 LEU 81 1.296 1.242 1.524 1.497 1.384 123.82 115.55 120.33 110.12 110.62 106.79 124.12 ** +* +*** * ** +*** 82 ALA 82 1.338 1.232 1.530 1.526 1.468 124.31 115.36 121.53 111.96 112.33 111.90 123.11 * * * 83 GLY 83 1.304 1.240 1.500 - 1.440 122.21 114.51 121.55 - 109.23 - 123.92 +* * +* 84 ALA 84 1.306 1.242 1.514 1.521 1.436 123.34 116.73 120.29 110.22 108.79 110.21 122.97 +* * +* 85 VAL 85 1.308 1.237 1.512 1.552 1.436 121.08 115.37 121.52 109.31 108.88 111.97 123.10 +* * +* 86 THR 86 1.281 1.226 1.525 1.532 1.409 122.33 116.63 120.85 111.73 108.17 108.43 122.44 *** +** * * +* *** 87 THR 87 1.296 1.234 1.527 1.538 1.427 121.10 115.75 121.09 110.13 110.57 109.23 123.16 ** +* * ** 88 MET 88 1.305 1.238 1.491 1.530 1.443 122.41 115.61 120.72 110.35 109.51 111.18 123.66 +* +* +* 89 HIS 89 1.296 1.224 1.505 1.526 1.421 121.57 115.61 121.14 111.21 107.89 109.70 123.24 ** +* * ** 90 VAL 90 1.276 1.230 1.498 1.556 1.430 122.16 114.11 121.90 110.68 110.85 111.41 123.97 +*** * * * +*** 91 ILE 91 1.280 1.237 1.511 1.545 1.417 123.66 115.78 120.91 112.15 107.88 110.64 123.29 +*** ** * * * +*** 92 ILE 92 1.295 1.229 1.520 1.559 1.430 121.65 116.31 120.59 108.59 111.31 110.20 123.06 ** * ** 93 GLN 93 1.309 1.218 1.495 1.536 1.437 121.31 116.72 120.45 108.67 106.95 112.38 122.82 * * * +* * +* 94 ALA 94 1.291 1.247 1.503 1.527 1.431 120.91 118.13 119.81 110.60 109.10 110.87 122.03 +** * * +** 95 PRO 95 1.335 1.246 1.521 1.530 1.448 122.13 116.23 120.63 110.14 110.40 104.32 123.11 * * * 96 VAL 96 1.310 1.233 1.516 1.546 1.449 122.18 115.83 121.04 110.04 109.90 111.69 123.09 * * 97 THR 97 1.310 1.240 1.549 1.565 1.419 120.78 115.47 121.79 113.06 112.15 111.65 122.66 * * ** +* ** 98 GLU 98 1.323 1.232 1.518 1.544 1.453 123.00 115.00 120.69 111.55 108.80 112.09 124.25 99 LYS 99 1.329 1.233 1.534 1.544 1.465 124.77 115.79 121.63 111.26 111.23 112.90 122.54 +* * +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 100 GLU 100 1.308 1.242 1.519 1.552 1.444 121.86 115.70 121.27 113.76 112.36 112.45 123.01 * * +* * +* 101 LYS 101 1.306 - 1.523 1.546 1.432 121.66 - - 112.64 109.44 112.21 - +* * * * +* ----------------------------------------------------------------------------------------------------------------------------------- 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 94 1.276 1.350 1.312 .015 +*** * * C-N (Pro) 1.341 .016 6 1.312 1.349 1.332 .011 +* C-O C-O 1.231 .020 100 1.214 1.249 1.234 .007 CA-C CH1E-C (except Gly) 1.525 .021 96 1.479 1.551 1.523 .013 ** * CH2G*-C (Gly) 1.516 .018 5 1.500 1.535 1.517 .012 * CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.514 1.527 1.522 .004 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.530 1.572 1.554 .013 * CH1E-CH2E (the rest) 1.530 .020 62 1.497 1.563 1.532 .014 +* +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.384 1.486 1.444 .018 +*** * NH1-CH2G* (Gly) 1.451 .016 5 1.429 1.471 1.448 .015 * * N-CH1E (Pro) 1.466 .015 6 1.448 1.469 1.457 .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 89 113.63 118.28 116.19 1.02 * * CH2G*-C-NH1 (Gly) 116.4 2.1 5 114.51 118.06 116.69 1.21 CH1E-C-N (Pro) 116.9 1.5 6 114.10 116.84 115.86 .90 +* O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.69 124.29 122.99 .58 O-C-N (Pro) 122.0 1.4 6 122.63 124.70 123.27 .66 +* C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 120.31 126.36 122.29 1.31 +** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.60 122.23 121.73 .60 C-N-CH1E (Pro) 122.6 5.0 6 121.96 123.64 122.57 .57 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.05 122.28 120.78 .64 * CH2G*-C-O (Gly) 120.8 2.1 5 119.91 121.55 120.62 .56 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 109.96 111.96 110.79 .58 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.26 113.37 110.38 1.41 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 106.26 113.84 110.29 1.65 ** +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.16 116.52 110.26 2.14 +** +* NH1-CH2G*-C (Gly) 112.5 2.9 5 109.23 114.23 111.77 1.97 * N-CH1E-C (Pro) 111.8 2.5 6 110.40 114.39 111.96 1.57 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 109.77 111.90 110.55 .60 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 108.43 114.86 111.09 1.35 +* +* N-CH1E-CH2E (Pro) 103.0 1.1 6 102.11 104.32 103.49 .73 * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 106.34 114.39 110.45 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] 15 17.0% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% 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 83.0 83.8 10.0 -.1 Inside b. Omega angle st dev 100 3.8 6.0 3.0 -.7 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 96 2.1 3.1 1.6 -.6 Inside e. H-bond energy st dev 49 .9 .8 .2 .3 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 16 8.0 18.1 6.5 -1.6 BETTER b. Chi-1 trans st dev 24 7.9 19.0 5.3 -2.1 BETTER c. Chi-1 gauche plus st dev 42 8.4 17.5 4.9 -1.9 BETTER d. Chi-1 pooled st dev 82 9.4 18.2 4.8 -1.8 BETTER e. Chi-2 trans st dev 25 5.7 20.4 5.0 -2.9 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 10.4 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .88 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 -.58 Chi1-chi2 distribution -.17 Chi1 only -.05 Chi3 & chi4 .29 Omega -.03 ------ -.18 ===== Main-chain covalent forces:- Main-chain bond lengths .01 Main-chain bond angles .36 ------ .22 ===== OVERALL AVERAGE -.04 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.