Residue-by-residue listing for refined_2 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 - - 182.6 - 177.1 - - - - - - 179.4 - 34.9 - 2 ALA 2 ~l - - - - - - - - - - 179.4 - 31.8 - ** ** 3 GLU 3 b - - -63.7 182.5 - - - - - - 175.6 - 31.6 - 4 VAL 4 t B - 185.9 - - - - - - - - 186.0 -2.0 35.0 - * * 5 HIS 5 T b - - -56.0 - - - - - - - 173.8 -.7 31.5 - * +* +* 6 ASN 6 T A - 187.5 - - - - - - - - 172.8 -1.7 35.7 - * * 7 GLN 7 t B - - -58.9 - - - - - - - 176.8 -.6 36.1 - +* +* 8 LEU 8 E B - - -73.6 - - - - - - - 188.5 -1.2 30.5 - * * * 9 GLU 9 E B - - -56.2 - - - - - - - 177.1 - 33.2 - 10 ILE 10 E B - - -59.5 177.8 - - - - - - 174.7 -2.6 35.2 - 11 LYS 11 E B 57.1 - - 182.2 - - - - - - 184.0 -3.1 31.4 - * * 12 PHE 12 E B - - -61.4 - - - - - - - 180.1 -.6 34.5 - +* +* 13 ARG 13 E B - 191.8 - 179.9 - - - - - - 178.6 -2.9 34.0 - * * 14 LEU 14 E B - - -67.3 - - - - - - - 178.5 -3.5 35.5 - +* +* 15 THR 15 e A - 188.3 - - - - - - - - 179.4 -.8 34.6 - +* +* 16 ASP 16 T A - - -54.8 - - - - - - - 178.6 - 35.0 - 17 GLY 17 t - - - - - - - - - - - 176.6 -2.1 - - Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 18 SER 18 e B - - -55.8 - - - - - - - 181.2 - 35.7 - 19 ASP 19 E B 61.0 - - - - - - - - - 184.0 - 32.3 - 20 ILE 20 E B - 195.7 - 175.3 - - - - - - 182.1 -3.4 33.9 - +* +* 21 GLY 21 E - - - - - - - - - - - 184.0 - - - 22 PRO 22 E - - - - - -66.5 - - - - - 177.5 - 38.5 - * * 23 LYS 23 E B - - -63.4 176.6 - - - - - - 182.2 -1.9 33.0 - 24 ALA 24 E B - - - - - - - - - - 181.5 - 34.1 - 25 PHE 25 E B - - -54.7 - - - - - - - 177.4 -3.0 36.1 - * * 26 PRO 26 t - - - - - -69.0 - - - - - 180.8 - 39.3 - +* +* 27 ASP 27 T A - - -57.9 - - - - - - - 182.2 - 34.6 - 28 ALA 28 T A - - - - - - - - - - 176.3 - 33.4 - 29 THR 29 t B - - -58.6 - - - - - - - 184.9 -1.5 32.5 - 30 THR 30 h B - - -52.2 - - - - - - - 180.6 - 36.2 - 31 VAL 31 H A - 176.9 - - - -59.4 -30.5 - - - 176.4 -3.0 32.8 - * * 32 SER 32 H A - 183.9 - - - -58.0 -49.4 - - - 180.0 -.9 34.2 - +* +* 33 ALA 33 H A - - - - - -72.9 -24.0 - - - 178.0 - 33.9 - * * 34 LEU 34 H A - 172.0 - - - -61.7 -52.6 - - - 179.2 -1.6 35.5 - * * 35 LYS 35 H A 58.5 - - 190.8 - -68.7 -29.1 - - - 172.5 -2.3 29.7 - * * * 36 GLU 36 H A - - -66.4 - - -55.4 -44.9 - - - 175.8 -1.4 34.8 - 37 THR 37 H A - - -61.6 - - -67.4 -40.6 - - - 179.9 -1.8 34.0 - 38 VAL 38 H A - 173.4 - - - -54.7 -54.4 - - - 182.7 -2.1 34.9 - * * 39 ILE 39 H A - - -55.4 171.3 - -64.8 -32.5 - - - 178.4 -3.2 33.8 - +* +* 40 SER 40 H A - - -57.3 - - -69.8 -25.3 - - - 177.2 -1.4 33.5 - * * 41 GLU 41 H A - - -62.0 - - -93.2 -36.3 - - - 183.5 -1.3 36.8 - ** * ** 42 TRP 42 h B - 187.3 - - - - - - - - 174.8 -3.0 36.3 - * * 43 PRO 43 t - - - - - -63.8 - - - - - 183.4 - 38.7 - * * 44 ARG 44 T A - - -53.5 180.0 - - - - - - 178.0 -.6 34.1 - +* +* 45 GLU 45 T A - - -72.2 - - - - - - - 182.3 - 32.5 - 46 LYS 46 t B - 195.8 - - - - - - - - 181.4 -1.5 34.4 - 47 GLU 47 T B 59.4 - - 182.2 - - - - - - 183.0 -.5 32.2 - ** ** 48 ASN 48 T l - - -67.2 - - - - - - - 180.7 - 32.3 - 49 GLY 49 t - - - - - - - - - - - 179.7 -.9 - - +* +* 50 PRO 50 - - - - - -66.6 - - - - - 175.6 - 39.8 - +* +* 51 LYS 51 a - 184.6 - 179.8 - - - - - - 181.6 - 35.8 - 52 THR 52 g B 59.2 - - - - - - - - - 183.9 - 33.9 - 53 VAL 53 G A - 184.5 - - - - - - - - 186.2 - 34.7 - * * Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 54 LYS 54 G A - 190.8 - - - - - - - - 185.9 - 34.8 - * * 55 GLU 55 e A - - -55.1 170.9 - - - - - - 183.7 -1.8 36.1 - 56 VAL 56 E B - 181.7 - - - - - - - - 176.8 -1.7 34.2 - 57 LYS 57 E B - 183.6 - 179.4 - - - - - - 181.1 -2.0 34.8 - 58 LEU 58 E B - - -61.2 - - - - - - - 175.4 - 34.0 - 59 ILE 59 E B - - -62.6 180.7 - - - - - - 180.4 -2.2 33.4 - 60 SER 60 E B 56.6 - - - - - - - - - 178.2 -2.4 34.5 - 61 ALA 61 e XX - - - - - - - - - - 179.5 -.6 31.1 - **** +* **** 62 GLY 62 T - - - - - - - - - - - 180.1 -3.0 - - * * 63 LYS 63 E B - 182.1 - 181.6 - - - - - - 180.3 -1.4 34.9 - 64 VAL 64 E B - 181.8 - - - - - - - - 178.1 - 34.7 - 65 LEU 65 e B - - -70.6 - - - - - - - 178.1 -3.2 32.8 - +* +* 66 GLU 66 t B - 184.1 - - - - - - - - 186.4 -.9 32.8 - * +* +* 67 ASN 67 T A - 185.5 - - - - - - - - 182.3 - 35.4 - 68 SER 68 T A - - -54.8 - - - - - - - 179.1 - 34.2 - 69 LYS 69 t B - - -64.2 - - - - - - - 179.5 -1.8 34.8 - 70 THR 70 B B - - -42.8 - - - - - - - 182.7 - 35.9 - +* +* 71 VAL 71 G A - 177.7 - - - - - - - - 178.0 -3.4 32.3 - +* +* 72 LYS 72 G A - 176.3 - 181.4 - - - - - - 180.6 -2.0 36.9 - 73 ASP 73 G A - 180.1 - - - - - - - - 186.3 -.9 35.2 - * * * 74 TYR 74 G A - - -51.9 - - - - - - - 180.9 -1.6 35.6 - 75 ARG 75 g b - - -58.6 - - - - - - - 177.2 -.9 35.6 - +* +* 76 SER 76 B - - -52.5 - - - - - - - 177.6 - 37.0 - 77 PRO 77 t - - - - - -50.2 - - - - - 183.1 - 38.5 - * * * 78 VAL 78 T A - 181.4 - - - - - - - - 179.6 - 33.3 - 79 SER 79 T a - 186.1 - - - - - - - - 179.2 - 34.4 - 80 ASN 80 t B - 176.0 - - - - - - - - 179.5 -.9 34.5 - * * 81 LEU 81 B - - -53.4 184.4 - - - - - - 183.6 - 36.0 - 82 ALA 82 b - - - - - - - - - - 173.1 - 34.8 - * * 83 GLY 83 - - - - - - - - - - - 183.3 - - - 84 ALA 84 B - - - - - - - - - - 180.3 - 33.9 - 85 VAL 85 B - 183.0 - - - - - - - - 183.2 - 34.8 - 86 THR 86 E B - - -54.0 - - - - - - - 177.8 -1.9 35.0 - 87 THR 87 E B - - -56.8 - - - - - - - 178.7 - 34.8 - 88 MET 88 E B - - -64.5 179.1 - - - - - - 181.6 -2.4 32.6 - 89 HIS 89 E B - - -56.9 - - - - - - - 177.2 -3.6 35.1 - ** ** 90 VAL 90 E B - 180.9 - - - - - - - - 181.2 -3.0 33.7 - * * 91 ILE 91 E B - - -62.1 - - - - - - - 185.1 -3.1 34.8 - * * 92 ILE 92 E B - - -50.3 - - - - - - - 176.9 - 36.3 - * * 93 GLN 93 e B - - -63.6 - - - - - - - 172.1 -2.5 34.3 - * * Residue-by-residue listing for refined_2 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 - - - - - - - - - - 181.6 -.8 34.4 - +* +* 95 PRO 95 - - - - - -67.1 - - - - - 179.2 - 38.4 - * * 96 VAL 96 S A 60.6 - - - - - - - - - 171.1 - 31.8 - +* +* 97 THR 97 S B - 179.0 - - - - - - - - 181.6 - 32.3 - 98 GLU 98 b 53.3 - - - - - - - - - 179.6 -.5 32.5 - ** ** 99 LYS 99 B - 189.7 - - - - - - - - 179.6 - 31.7 - 100 GLU 100 B - 184.1 - 182.4 - - - - - - 177.2 - 35.6 - 101 LYS 101 - - 184.2 - 182.4 - - - - - - - - 33.9 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** +* * ** * +* ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.2 183.6 -59.2 179.9 -63.9 -66.0 -38.1 - - - 179.8 -1.9 34.4 Standard deviations: 2.5 5.6 6.3 4.3 6.9 10.9 10.9 - - - 3.4 .9 1.9 Numbers of values: 8 33 41 21 6 11 11 0 0 0 100 56 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_2 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 - 1.231 1.523 1.539 1.456 - 116.41 119.71 110.96 108.81 109.35 123.86 2 ALA 2 1.341 1.244 1.530 1.533 1.474 124.39 116.33 121.65 111.39 112.40 111.92 122.02 * * * 3 GLU 3 1.311 1.242 1.515 1.520 1.430 121.25 115.25 121.42 110.68 111.95 113.23 123.21 * * +* +* 4 VAL 4 1.304 1.249 1.499 1.538 1.433 121.84 116.26 120.93 108.70 106.11 112.38 122.81 +* * * +* +* 5 HIS 5 1.275 1.230 1.503 1.539 1.436 120.59 114.78 121.54 111.68 111.59 112.74 123.44 +*** * * * +*** 6 ASN 6 1.306 1.232 1.500 1.533 1.451 122.55 113.64 122.37 109.60 105.15 110.57 124.00 +* * * ** ** 7 GLN 7 1.310 1.237 1.512 1.544 1.418 123.58 117.26 119.71 108.06 105.98 111.48 123.01 * ** * * +* ** 8 LEU 8 1.289 1.238 1.525 1.536 1.447 121.08 116.68 120.90 112.36 111.15 113.37 122.40 +** * +* +** 9 GLU 9 1.309 1.241 1.516 1.550 1.449 121.40 114.73 121.64 108.26 111.91 113.58 123.51 * +* +* 10 ILE 10 1.307 1.240 1.516 1.562 1.443 123.45 116.30 120.32 108.70 108.69 111.60 123.35 +* +* 11 LYS 11 1.303 1.241 1.504 1.539 1.428 121.79 115.71 121.22 112.66 109.36 112.85 123.04 +* +* * * +* Residue-by-residue listing for refined_2 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 1.290 1.220 1.484 1.521 1.431 121.72 116.23 120.68 110.37 110.25 110.31 123.09 +** +* * +** 13 ARG 13 1.284 1.226 1.510 1.532 1.415 120.60 115.80 120.63 111.04 108.86 110.83 123.56 *** ** *** 14 LEU 14 1.301 1.240 1.512 1.559 1.441 123.49 116.28 120.64 108.41 109.14 111.38 123.07 +* * +* 15 THR 15 1.306 1.225 1.553 1.555 1.456 122.65 115.40 121.80 110.87 110.17 109.52 122.79 +* * * +* 16 ASP 16 1.320 1.227 1.531 1.529 1.464 123.21 116.42 120.91 109.03 111.08 110.30 122.65 17 GLY 17 1.321 1.236 1.518 - 1.457 121.52 116.22 121.03 - 112.89 - 122.75 18 SER 18 1.303 1.211 1.518 1.526 1.443 121.92 118.58 119.43 110.47 107.69 108.90 121.98 +* * * * +* 19 ASP 19 1.296 1.232 1.506 1.534 1.443 120.63 115.49 120.95 111.43 111.23 111.87 123.55 ** ** 20 ILE 20 1.302 1.246 1.537 1.577 1.440 123.48 116.38 119.71 111.20 108.87 111.08 123.80 +* * +* 21 GLY 21 1.341 1.244 1.527 - 1.466 122.49 116.81 120.39 - 113.87 - 122.79 * * 22 PRO 22 1.347 1.240 1.526 1.539 1.465 123.79 115.70 121.18 109.70 113.48 104.15 123.11 * * 23 LYS 23 1.318 1.228 1.479 1.535 1.454 122.67 115.42 120.48 110.12 109.51 112.97 124.09 ** * ** 24 ALA 24 1.277 1.239 1.525 1.521 1.452 121.83 116.46 120.74 110.86 110.55 109.94 122.80 +*** +*** 25 PHE 25 1.319 1.230 1.502 1.528 1.450 122.02 117.71 119.90 106.96 109.08 111.51 122.39 * +* +* 26 PRO 26 1.317 1.241 1.529 1.528 1.457 122.59 115.73 120.94 109.20 111.56 103.73 123.32 * * 27 ASP 27 1.310 1.225 1.530 1.538 1.465 123.16 116.58 121.05 109.56 110.98 110.47 122.32 * * 28 ALA 28 1.322 1.241 1.532 1.519 1.461 121.75 116.83 120.85 110.46 112.29 110.63 122.32 29 THR 29 1.306 1.213 1.508 1.541 1.434 121.34 114.74 121.48 112.71 108.96 111.28 123.71 +* * +* +* 30 THR 30 1.280 1.233 1.561 1.535 1.419 123.96 116.95 120.34 111.07 111.12 106.78 122.71 +*** +* ** * +** +*** 31 VAL 31 1.349 1.241 1.536 1.562 1.479 122.85 116.59 120.65 110.48 111.75 111.89 122.75 * * * 32 SER 32 1.321 1.228 1.541 1.543 1.446 121.15 116.07 120.74 110.91 109.34 110.27 123.04 33 ALA 33 1.333 1.232 1.524 1.511 1.455 122.49 116.18 120.71 110.24 111.41 110.41 123.10 34 LEU 34 1.320 1.230 1.527 1.527 1.418 123.29 116.13 120.83 111.78 109.55 107.65 122.98 ** +* ** 35 LYS 35 1.323 1.216 1.504 1.506 1.452 121.41 115.78 120.68 113.79 112.16 112.28 123.53 * +* * +* 36 GLU 36 1.300 1.238 1.538 1.526 1.465 121.95 116.51 120.79 109.23 109.67 110.67 122.69 ** ** 37 THR 37 1.328 1.231 1.538 1.547 1.449 121.33 115.71 120.72 109.87 110.00 111.50 123.53 38 VAL 38 1.332 1.208 1.521 1.565 1.464 123.46 115.72 120.59 109.64 110.60 110.48 123.61 * * 39 ILE 39 1.308 1.226 1.532 1.546 1.474 123.74 116.46 121.04 111.34 111.29 109.80 122.50 +* * * * +* 40 SER 40 1.317 1.228 1.552 1.527 1.449 121.41 116.74 120.71 111.41 111.30 109.96 122.55 * * 41 GLU 41 1.331 1.240 1.537 1.519 1.449 122.59 114.61 121.61 107.78 110.13 109.02 123.78 * * Residue-by-residue listing for refined_2 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 42 TRP 42 1.311 1.229 1.527 1.543 1.452 125.04 117.85 120.28 110.05 110.95 107.77 121.84 * +* +* +* 43 PRO 43 1.341 1.222 1.525 1.536 1.457 122.03 116.30 121.04 110.29 110.05 103.99 122.65 44 ARG 44 1.297 1.222 1.525 1.515 1.450 122.02 116.42 120.87 110.82 111.20 109.69 122.71 ** ** 45 GLU 45 1.316 1.234 1.533 1.543 1.461 122.28 116.84 120.00 110.35 112.27 112.24 123.16 * * 46 LYS 46 1.331 1.232 1.544 1.561 1.463 122.25 116.49 120.73 111.59 109.79 109.23 122.77 +* +* 47 GLU 47 1.327 1.246 1.519 1.529 1.444 121.96 115.65 120.69 111.43 111.54 111.85 123.64 48 ASN 48 1.332 1.234 1.514 1.559 1.478 123.99 115.06 121.44 110.74 109.51 113.32 123.47 * * * +* +* 49 GLY 49 1.314 1.234 1.514 - 1.422 121.86 117.60 119.94 - 111.38 - 122.46 * +* +* 50 PRO 50 1.331 1.241 1.522 1.533 1.463 123.65 115.10 121.49 108.68 113.17 103.34 123.40 * * * 51 LYS 51 1.304 1.239 1.524 1.520 1.433 122.80 115.13 121.78 109.69 108.69 109.17 123.09 +* * +* 52 THR 52 1.317 1.238 1.543 1.523 1.430 122.69 115.29 120.81 109.52 111.99 111.09 123.89 * * 53 VAL 53 1.339 1.236 1.528 1.558 1.487 125.06 116.00 120.65 108.22 113.69 110.92 123.33 +* +* +* 54 LYS 54 1.312 1.233 1.549 1.543 1.462 122.96 116.46 120.96 110.41 112.11 108.90 122.56 * * * 55 GLU 55 1.310 1.239 1.541 1.513 1.451 122.06 117.23 120.46 109.68 112.07 107.60 122.31 * +* +* 56 VAL 56 1.322 1.234 1.531 1.556 1.468 121.19 116.30 120.64 109.05 111.54 111.51 123.05 57 LYS 57 1.315 1.235 1.533 1.525 1.452 122.24 117.24 120.00 110.58 109.20 109.52 122.76 * * 58 LEU 58 1.320 1.237 1.540 1.573 1.464 121.51 116.83 120.48 109.33 110.86 111.92 122.67 ** ** 59 ILE 59 1.334 1.230 1.538 1.567 1.479 122.70 116.88 120.73 109.43 110.31 112.63 122.39 * * * 60 SER 60 1.314 1.239 1.523 1.537 1.448 122.11 116.38 119.85 110.57 110.35 109.86 123.74 * * 61 ALA 61 1.345 1.238 1.510 1.531 1.487 125.10 113.94 122.04 111.81 112.63 112.28 124.03 * +* +* * * +* 62 GLY 62 1.248 1.230 1.497 - 1.426 123.71 115.74 120.82 - 110.17 - 123.42 *5.8* * +* +* *5.8* 63 LYS 63 1.319 1.238 1.510 1.526 1.439 122.62 116.45 120.23 109.99 108.84 110.42 123.32 * * 64 VAL 64 1.303 1.238 1.523 1.551 1.446 121.78 116.34 120.67 109.43 109.87 111.16 122.97 +* +* 65 LEU 65 1.314 1.233 1.499 1.536 1.432 121.38 115.73 120.95 109.94 110.82 113.04 123.30 * * * * * 66 GLU 66 1.305 1.237 1.535 1.536 1.427 121.15 115.24 121.01 112.41 109.81 110.72 123.76 +* +* * +* 67 ASN 67 1.313 1.239 1.540 1.535 1.465 124.64 116.21 121.20 109.83 112.40 108.54 122.58 * +* * +* 68 SER 68 1.317 1.241 1.549 1.528 1.457 121.92 116.69 120.91 110.87 112.15 109.22 122.39 * * 69 LYS 69 1.319 1.232 1.516 1.525 1.448 121.81 116.59 120.80 109.87 109.49 110.26 122.61 70 THR 70 1.293 1.231 1.543 1.529 1.434 121.54 118.03 119.61 110.02 107.68 108.94 122.35 +** * * +* +** Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 71 VAL 71 1.329 1.230 1.536 1.571 1.470 121.57 114.92 121.23 111.66 110.45 112.10 123.78 * * * 72 LYS 72 1.324 1.238 1.528 1.533 1.469 125.24 116.01 120.47 109.33 111.25 107.30 123.47 +* +* +* 73 ASP 73 1.326 1.240 1.536 1.551 1.471 123.33 116.05 121.41 109.49 111.38 109.63 122.49 * * 74 TYR 74 1.310 1.230 1.525 1.519 1.432 121.98 117.18 120.42 110.04 111.74 108.37 122.40 * * * * 75 ARG 75 1.322 1.248 1.524 1.523 1.420 121.28 114.75 121.43 108.26 110.74 110.56 123.82 +* +* 76 SER 76 1.300 1.244 1.540 1.529 1.426 124.13 118.58 119.28 110.09 108.25 107.24 122.12 ** +* * * * +* ** 77 PRO 77 1.355 1.233 1.536 1.546 1.470 122.94 116.05 120.91 110.30 111.83 103.86 123.03 78 VAL 78 1.322 1.232 1.527 1.545 1.459 122.66 115.74 121.51 110.71 111.09 111.16 122.68 79 SER 79 1.304 1.230 1.542 1.539 1.459 122.52 115.21 121.64 111.38 109.65 109.38 123.12 +* +* 80 ASN 80 1.295 1.235 1.508 1.550 1.443 124.08 117.34 120.03 111.18 108.01 110.25 122.57 ** * * * ** 81 LEU 81 1.310 1.237 1.496 1.483 1.394 121.41 116.21 120.50 108.90 109.07 109.62 123.28 * * ** *** *** 82 ALA 82 1.290 1.226 1.495 1.533 1.415 122.57 115.04 121.00 109.72 109.33 111.04 123.88 +** * ** +** 83 GLY 83 1.276 1.237 1.503 - 1.438 122.33 114.35 121.54 - 108.92 - 124.11 +*** * * +*** 84 ALA 84 1.324 1.244 1.512 1.522 1.446 123.93 115.30 121.16 110.46 111.83 110.27 123.53 * * 85 VAL 85 1.307 1.239 1.510 1.549 1.436 121.99 116.07 120.78 109.35 108.06 111.66 123.15 +* * * +* 86 THR 86 1.285 1.228 1.529 1.544 1.434 121.96 116.72 120.52 110.45 109.87 109.64 122.74 *** * * *** 87 THR 87 1.304 1.228 1.515 1.547 1.429 121.66 116.78 120.76 109.58 108.70 111.32 122.43 +* +* +* 88 MET 88 1.295 1.225 1.494 1.528 1.434 120.81 116.10 120.79 111.85 109.83 111.67 123.08 ** * * ** 89 HIS 89 1.294 1.239 1.495 1.540 1.435 121.52 116.41 120.16 109.04 108.64 111.41 123.42 +** * * +** 90 VAL 90 1.297 1.243 1.484 1.552 1.428 120.76 113.63 122.00 110.08 108.03 112.76 124.37 ** +* +* * * ** 91 ILE 91 1.266 1.240 1.497 1.538 1.395 123.26 115.35 121.16 111.58 107.98 109.80 123.48 *4.5* * *** * * *4.5* 92 ILE 92 1.288 1.229 1.505 1.553 1.419 121.67 116.93 120.22 108.60 108.47 110.25 122.78 +** ** +** 93 GLN 93 1.308 1.234 1.500 1.534 1.433 120.42 115.54 121.08 109.45 110.24 111.54 123.34 +* * * +* 94 ALA 94 1.290 1.232 1.502 1.522 1.418 121.56 117.84 120.12 110.96 106.28 111.04 121.98 +** * ** +* +** 95 PRO 95 1.320 1.243 1.527 1.540 1.452 122.37 116.59 120.32 111.02 111.29 103.55 123.08 * * 96 VAL 96 1.335 1.237 1.538 1.571 1.461 121.87 115.85 121.44 112.28 109.93 112.37 122.68 * * * 97 THR 97 1.309 1.235 1.528 1.567 1.423 121.59 116.24 121.17 111.98 107.68 113.05 122.51 * +* * * +* 98 GLU 98 1.291 1.239 1.508 1.555 1.438 122.30 118.06 119.62 113.31 109.72 110.56 122.31 +** * * +* +** Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 99 LYS 99 1.305 1.230 1.517 1.533 1.408 119.59 115.39 121.49 112.45 110.79 112.09 123.06 +* +** * * +** 100 GLU 100 1.293 1.236 1.518 1.535 1.430 122.82 116.71 120.35 110.12 108.61 109.45 122.92 +** * +** 101 LYS 101 1.303 - 1.513 1.536 1.427 121.31 - - 110.94 107.63 111.41 - +* +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *5.8* * ** ** *** +* * +* ** +** * *5.8* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_2 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 1.248 1.349 1.310 .018 *5.8* * * C-N (Pro) 1.341 .016 6 1.317 1.355 1.335 .014 * C-O C-O 1.231 .020 100 1.208 1.249 1.234 .008 * CA-C CH1E-C (except Gly) 1.525 .021 96 1.479 1.561 1.522 .017 ** +* CH2G*-C (Gly) 1.516 .018 5 1.497 1.527 1.512 .011 * CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.511 1.533 1.524 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.523 1.577 1.552 .013 * CH1E-CH2E (the rest) 1.530 .020 62 1.483 1.573 1.534 .014 ** ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.394 1.487 1.445 .019 *** +* NH1-CH2G* (Gly) 1.451 .016 5 1.422 1.466 1.442 .017 +* N-CH1E (Pro) 1.466 .015 6 1.452 1.470 1.461 .006 ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_2 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 89 113.63 118.58 116.16 .96 * * CH2G*-C-NH1 (Gly) 116.4 2.1 5 114.35 117.60 116.14 1.09 CH1E-C-N (Pro) 116.9 1.5 6 115.10 116.59 115.91 .48 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.84 124.37 123.03 .56 O-C-N (Pro) 122.0 1.4 6 122.65 123.40 123.10 .24 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.59 125.24 122.32 1.15 * +* C-NH1-CH2G* (Gly) 120.6 1.7 5 121.52 123.71 122.38 .75 +* * C-N-CH1E (Pro) 122.6 5.0 6 122.03 123.79 122.90 .65 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.28 122.37 120.79 .60 CH2G*-C-O (Gly) 120.8 2.1 5 119.94 121.54 120.74 .55 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 109.72 111.81 110.74 .62 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.22 112.71 110.25 1.20 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 106.96 113.79 110.32 1.32 +* +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.15 113.69 110.03 1.64 ** NH1-CH2G*-C (Gly) 112.5 2.9 5 108.92 113.87 111.45 1.79 * N-CH1E-C (Pro) 111.8 2.5 6 110.05 113.48 111.90 1.16 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 109.94 112.28 110.94 .76 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 106.78 113.05 111.03 1.35 +** N-CH1E-CH2E (Pro) 103.0 1.1 6 103.34 104.15 103.77 .27 * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 107.24 113.58 110.52 1.64 +* +* ------------------------------------------------------------------------------------------------------------- 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_2 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] 78 88.6% Residues in additional allowed regions [a,b,l,p] 8 9.1% 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 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 88.6 83.8 10.0 .5 Inside b. Omega angle st dev 100 3.4 6.0 3.0 -.9 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 96 1.9 3.1 1.6 -.8 Inside e. H-bond energy st dev 56 .9 .8 .2 .6 Inside f. Overall G-factor 101 .0 -.4 .3 1.3 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 8 2.5 18.1 6.5 -2.4 BETTER b. Chi-1 trans st dev 33 5.6 19.0 5.3 -2.5 BETTER c. Chi-1 gauche plus st dev 41 6.3 17.5 4.9 -2.3 BETTER d. Chi-1 pooled st dev 82 7.9 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 21 4.3 20.4 5.0 -3.2 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% 88.6 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.9 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .95 3 Residue-by-residue listing for refined_2 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.47 Chi1-chi2 distribution -.11 Chi1 only .12 Chi3 & chi4 .36 Omega .03 ------ -.09 ===== Main-chain covalent forces:- Main-chain bond lengths -.14 Main-chain bond angles .42 ------ .18 ===== OVERALL AVERAGE .00 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.