Residue-by-residue listing for refined_11 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 - - - -62.5 178.9 - - - - - - 179.6 - 34.9 - 2 ALA 2 ~l - - - - - - - - - - 179.4 - 32.1 - ** ** 3 ASP 3 B - 187.4 - - - - - - - - 183.9 - 34.1 - 4 THR 4 A - - -52.3 - - - - - - - 182.5 - 34.8 - 5 GLY 5 S - - - - - - - - - - - 180.1 - - - 6 GLU 6 l - 177.6 - 183.5 - - - - - - 172.3 - 32.4 - * * 7 VAL 7 E B - - -60.4 - - - - - - - 187.5 -2.9 31.5 - * * * 8 GLN 8 E B - 185.6 - 179.2 - - - - - - 180.3 - 35.4 - 9 PHE 9 E B - 182.8 - - - - - - - - 177.6 -2.4 35.3 - 10 MET 10 E B 60.1 - - 166.6 - - - - - - 180.4 - 34.1 - 11 LYS 11 E B - 195.4 - - - - - - - - 180.3 -2.1 35.3 - 12 PRO 12 E - - - - - -62.4 - - - - - 184.1 - 39.0 - * * 13 PHE 13 e B - 187.8 - - - - - - - - 176.3 -1.1 34.5 - * * 14 ILE 14 t B - 178.6 - 179.1 - - - - - - 182.2 - 33.9 - 15 SER 15 T A - - -55.7 - - - - - - - 182.1 - 35.2 - 16 GLU 16 T A - 194.2 - - - - - - - - 187.3 - 35.2 - * * 17 LYS 17 T A - 191.4 - - - - - - - - 183.3 - 32.8 - 18 SER 18 T A - - -57.0 - - - - - - - 175.8 -2.2 33.2 - 19 SER 19 T A 51.7 - - - - - - - - - 181.1 - 34.1 - 20 LYS 20 T a - - -67.5 177.2 - - - - - - 180.4 -.8 33.3 - +* +* 21 SER 21 t B 57.5 - - - - - - - - - 179.8 -1.6 33.9 - Residue-by-residue listing for refined_11 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 ----------------------------------------------------------------------------------------------------------------------------------- 22 LEU 22 E B - 206.2 - 185.5 - - - - - - 179.8 -2.8 34.5 - * * * 23 GLU 23 E B 65.6 - - 184.1 - - - - - - 180.7 -.5 34.5 - +* +* 24 ILE 24 E B - - -50.1 - - - - - - - 186.2 -.9 33.2 - * * * * 25 PRO 25 h - - - - - -61.1 - - - - - 181.9 - 39.3 - +* +* 26 LEU 26 H A - - -72.5 - - -64.0 -33.4 - - - 176.2 - 30.1 - * * 27 GLY 27 H - - - - - - -64.8 -24.9 - - - 176.8 - - - * * 28 PHE 28 H A - 180.4 - - - -88.4 -36.2 - - - 179.4 -1.0 34.0 - +* * +* 29 ASN 29 H A - - -61.6 - - -62.0 -32.8 - - - 177.9 -2.5 35.1 - 30 GLU 30 H A - 182.1 - 183.6 - -67.5 -44.6 - - - 181.7 -2.1 35.5 - 31 TYR 31 H A - 173.3 - - - -75.7 -27.3 - - - 182.4 -.7 34.8 - * +* +* 32 PHE 32 h b - 171.4 - - - - - - - - 174.4 -2.3 33.0 - 33 PRO 33 - - - - - -89.5 - - - - - 180.2 - 39.2 - ** +* ** 34 ALA 34 B - - - - - - - - - - 168.7 - 35.2 - +* +* 35 PRO 35 - - - - - -67.8 - - - - - 183.6 - 39.6 - +* +* 36 PHE 36 B 71.9 - - - - - - - - - 177.6 - 32.4 - 37 PRO 37 - - - - - -85.0 - - - - - 178.4 - 39.1 - +* * +* 38 ILE 38 S A - - -58.0 - - - - - - - 179.9 - 33.3 - 39 THR 39 B 55.3 - - - - - - - - - 176.3 - 34.7 - 40 VAL 40 E B - 174.6 - - - - - - - - 181.6 -2.5 34.8 - 41 ASP 41 E B - 184.6 - - - - - - - - 179.5 -.9 34.7 - * * 42 LEU 42 E B - - -56.7 182.7 - - - - - - 179.4 -2.8 35.9 - * * 43 LEU 43 E B - - -65.2 - - - - - - - 173.8 -3.3 34.2 - * +* +* 44 ASP 44 E B - 140.9 - - - - - - - - 186.0 -2.5 33.5 - +** * +** 45 TYR 45 e A - 187.4 - - - - - - - - 180.0 -.9 33.9 - +* +* 46 SER 46 T A - - -46.6 - - - - - - - 176.8 - 35.2 - * * 47 GLY 47 t - - - - - - - - - - - 180.8 -.5 - - ** ** 48 ARG 48 e B - 186.1 - - - - - - - - 174.5 - 35.1 - 49 SER 49 E B 50.1 - - - - - - - - - 179.4 - 32.8 - 50 TRP 50 E B - - -69.4 - - - - - - - 175.1 -2.3 33.6 - 51 THR 51 E B - - -54.9 - - - - - - - 185.4 - 34.4 - 52 VAL 52 E B - - -60.6 - - - - - - - 185.9 -2.8 31.8 - * * * 53 ARG 53 E B - 201.8 - - - - - - - - 181.0 -.6 37.3 - * +* +* 54 MET 54 E B - 171.1 - 185.0 - - - - - - 173.7 -.6 36.2 - * +* +* 55 LYS 55 E B - 189.8 - 167.9 - - - - - - 183.2 -1.8 32.5 - Residue-by-residue listing for refined_11 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 ----------------------------------------------------------------------------------------------------------------------------------- 56 LYS 56 E B - 213.8 - - - - - - - - 184.2 - 36.4 - +* +* 57 ARG 57 E b - - -66.1 176.3 - - - - - - 178.9 -3.0 34.1 - * * 58 GLY 58 T - - - - - - - - - - - 179.8 - - - 59 GLU 59 T A - - -75.5 - - - - - - - 179.3 - 32.7 - 60 LYS 60 E B 60.9 - - 177.4 - - - - - - 176.8 -2.9 33.0 - * * 61 VAL 61 E B - 179.7 - - - - - - - - 175.2 -.6 35.0 - +* +* 62 PHE 62 E B - 187.2 - - - - - - - - 177.1 -2.1 37.0 - 63 LEU 63 E B - 190.0 - 168.5 - - - - - - 190.1 -2.2 33.8 - +* +* 64 THR 64 E b - 183.3 - - - - - - - - 188.5 -1.6 33.0 - * * 65 VAL 65 T B - - -62.5 - - - - - - - 186.6 - 32.8 - * * 66 GLY 66 T - - - - - - - - - - - 173.1 - - - * * 67 TRP 67 h A - 156.0 - - - - - - - - 184.8 -1.5 35.8 - +* +* 68 GLU 68 H A 58.0 - - 185.7 - -57.3 -26.1 - - - 178.5 -.7 32.0 - * +* +* 69 ASN 69 H A - - -65.3 - - -58.1 -35.4 - - - 180.1 -1.7 33.3 - 70 PHE 70 H A - 176.7 - - - -74.0 -52.8 - - - 183.3 -2.1 35.2 - * * 71 VAL 71 H A - 168.4 - - - -65.2 -39.5 - - - 175.1 -1.3 29.2 - * * * 72 LYS 72 H A 68.5 - - 182.9 - -72.2 -28.9 - - - 182.2 -3.5 30.6 - +* +* 73 ASP 73 H A - 181.8 - - - -77.4 -41.6 - - - 180.5 -1.1 33.1 - * * * 74 ASN 74 H A - - -61.5 - - -89.1 -15.6 - - - 184.3 -3.0 33.8 - ** ** * ** 75 ASN 75 h l - 181.7 - - - - - - - - 180.6 -1.2 31.1 - * * 76 LEU 76 t B 58.2 - - 168.6 - - - - - - 183.0 -.9 31.0 - +* +* 77 GLU 77 t B 58.3 - - 178.4 - - - - - - 178.7 - 34.4 - 78 ASP 78 T B - 180.4 - - - - - - - - 182.8 - 35.6 - 79 GLY 79 T - - - - - - - - - - - 175.9 - - - 80 LYS 80 e B - - -59.8 - - - - - - - 182.1 -2.2 35.4 - 81 TYR 81 E B - - -61.5 - - - - - - - 178.3 -2.3 33.5 - 82 LEU 82 E B 47.8 - - - - - - - - - 183.3 -1.0 29.6 - * * * * 83 GLN 83 E B - 179.8 - 179.4 - - - - - - 182.4 -3.0 35.9 - * * 84 PHE 84 E B - - -57.6 - - - - - - - 173.1 -3.3 35.1 - * +* +* 85 ILE 85 E B - - -66.3 - - - - - - - 181.4 -2.5 32.9 - 86 TYR 86 E B - - -54.5 - - - - - - - 172.9 -3.4 36.4 - * +* +* 87 ASP 87 e a - 175.7 - - - - - - - - 179.0 -.6 34.1 - +* +* 88 ARG 88 S ~a - 190.2 - - - - - - - - 189.1 - 36.0 - ** +* ** 89 ASP 89 S b - 184.1 - - - - - - - - 183.5 - 36.0 - Residue-by-residue listing for refined_11 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 ----------------------------------------------------------------------------------------------------------------------------------- 90 ARG 90 e A - 185.2 - 196.2 - - - - - - 182.1 - 38.6 - * * * 91 THR 91 E B - - -54.4 - - - - - - - 182.4 - 35.9 - 92 PHE 92 E B - - -64.9 - - - - - - - 173.6 -1.8 36.3 - * * 93 TYR 93 E B - - -66.2 - - - - - - - 185.5 -2.3 34.1 - 94 VAL 94 E B - 184.7 - - - - - - - - 173.6 -3.1 34.4 - * * * 95 ILE 95 E B - - -61.2 - - - - - - - 182.5 -3.1 34.8 - * * 96 ILE 96 E B - 179.9 - 179.1 - - - - - - 175.0 - 34.1 - 97 TYR 97 E B 61.8 - - - - - - - - - 188.0 -2.4 28.2 - * +* +* 98 GLY 98 S - - - - - - - - - - - 175.7 - - - 99 HIS 99 S b - - -76.3 - - - - - - - 176.5 - 29.0 - * * 100 ASN 100 S b - 182.4 - - - - - - - - 181.6 - 34.2 - 101 MET 101 l - 184.0 - - - - - - - - 183.7 - 33.9 - 102 CYS 102 - - - -53.6 - - - - - - - - - 35.7 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * +** * * ** ** ** +* ** +* +** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.0 182.7 -61.2 179.4 -73.2 -70.4 -33.8 - - - 180.2 -1.9 34.3 Standard deviations: 6.7 11.9 6.9 7.0 13.2 10.3 9.7 - - - 4.2 .9 2.1 Numbers of values: 14 42 32 22 5 13 13 0 0 0 101 56 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_11 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 - 1.231 1.497 1.541 1.463 - 115.92 119.59 109.05 108.78 111.45 124.48 * * 2 ALA 2 1.342 1.241 1.519 1.527 1.468 124.53 116.29 121.37 111.22 111.88 111.90 122.34 +* +* 3 ASP 3 1.304 1.229 1.512 1.525 1.436 120.26 116.41 120.59 110.56 107.92 111.26 122.98 +* * * +* 4 THR 4 1.302 1.237 1.546 1.543 1.454 122.57 116.42 121.20 110.64 111.79 108.94 122.35 +* +* +* 5 GLY 5 1.306 1.236 1.491 - 1.428 120.94 116.75 119.21 - 109.92 - 124.04 +* * * +* 6 GLU 6 1.321 1.243 1.535 1.551 1.457 123.26 116.71 121.31 110.85 112.47 111.78 121.89 * * 7 VAL 7 1.294 1.231 1.499 1.567 1.425 119.23 117.38 120.30 112.39 106.45 114.35 122.30 ** * +* * * +* +* ** 8 GLN 8 1.278 1.241 1.507 1.531 1.422 119.63 115.75 120.77 111.43 110.23 107.96 123.48 +*** +* * * +*** 9 PHE 9 1.303 1.224 1.520 1.545 1.433 122.38 116.86 120.33 111.00 108.89 108.96 122.81 +* * +* 10 MET 10 1.306 1.230 1.503 1.529 1.457 121.79 116.78 120.21 108.57 109.58 112.63 123.00 +* * * +* 11 LYS 11 1.306 1.230 1.542 1.567 1.440 121.03 118.70 119.80 112.86 107.44 107.59 121.48 +* +* * * * +* +* Residue-by-residue listing for refined_11 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 1.358 1.225 1.524 1.538 1.483 122.38 117.30 120.63 109.88 111.17 103.60 122.06 * * * 13 PHE 13 1.305 1.225 1.522 1.535 1.445 120.73 116.81 120.14 110.57 109.90 110.04 123.01 +* +* 14 ILE 14 1.324 1.233 1.533 1.568 1.434 121.71 117.03 120.23 111.35 108.43 110.94 122.74 * * * * 15 SER 15 1.316 1.230 1.538 1.540 1.467 122.61 115.74 121.30 109.46 110.74 109.80 122.96 16 GLU 16 1.315 1.218 1.519 1.553 1.436 122.12 118.08 119.92 110.56 109.59 109.39 121.92 * * * 17 LYS 17 1.338 1.217 1.513 1.531 1.459 118.02 116.91 120.63 110.45 112.67 111.50 122.43 ** ** 18 SER 18 1.309 1.218 1.526 1.530 1.446 120.81 116.31 120.79 111.51 111.18 110.48 122.91 * * 19 SER 19 1.313 1.241 1.551 1.518 1.438 121.73 116.54 120.78 111.52 111.86 108.80 122.69 * * * * * 20 LYS 20 1.338 1.234 1.518 1.531 1.467 121.61 117.23 120.11 109.48 112.91 111.65 122.66 21 SER 21 1.311 1.229 1.517 1.541 1.438 121.01 117.57 120.36 111.20 109.67 110.55 122.07 * * * 22 LEU 22 1.304 1.245 1.509 1.548 1.426 119.83 115.86 120.71 110.97 105.99 111.10 123.32 +* +* * +* +* 23 GLU 23 1.296 1.240 1.528 1.550 1.434 121.85 116.68 121.21 111.75 108.12 109.66 122.04 ** * * ** 24 ILE 24 1.286 1.247 1.534 1.551 1.425 119.54 117.27 120.34 111.53 107.89 111.95 122.36 *** +* * * * *** 25 PRO 25 1.345 1.224 1.517 1.533 1.478 123.52 116.76 120.26 109.46 113.06 103.31 122.93 26 LEU 26 1.329 1.236 1.520 1.548 1.463 121.88 116.63 120.29 112.17 112.56 113.44 123.04 * +* +* 27 GLY 27 1.328 1.232 1.523 - 1.454 120.81 115.99 121.33 - 111.24 - 122.68 28 PHE 28 1.317 1.208 1.531 1.541 1.442 122.01 116.14 120.63 111.30 109.36 110.34 123.20 * * 29 ASN 29 1.329 1.229 1.509 1.533 1.485 123.35 115.48 121.04 108.01 111.10 111.19 123.45 * * * 30 GLU 30 1.311 1.225 1.529 1.528 1.440 122.73 115.20 121.13 110.29 109.33 108.91 123.64 * * 31 TYR 31 1.321 1.236 1.535 1.547 1.462 123.76 116.07 121.09 110.96 111.73 108.71 122.83 * * * 32 PHE 32 1.300 1.238 1.545 1.551 1.439 122.83 117.35 121.46 113.15 112.25 108.95 121.00 ** * +* * ** 33 PRO 33 1.348 1.248 1.513 1.523 1.434 122.42 114.74 121.81 109.13 111.74 104.22 123.45 ** * * * ** 34 ALA 34 1.280 1.230 1.514 1.530 1.438 123.11 118.91 119.03 110.05 109.01 109.80 121.99 +*** * * * +*** 35 PRO 35 1.339 1.245 1.529 1.541 1.468 121.74 118.90 119.12 109.74 107.40 103.41 121.97 * +* +* 36 PHE 36 1.321 1.239 1.535 1.535 1.411 120.14 116.88 121.13 112.06 111.76 110.98 121.93 ** * ** 37 PRO 37 1.334 1.230 1.518 1.526 1.441 122.59 117.11 120.52 110.59 110.30 103.08 122.34 +* +* 38 ILE 38 1.299 1.232 1.524 1.558 1.438 120.16 115.91 120.92 110.69 108.94 112.19 123.13 ** * ** 39 THR 39 1.317 1.230 1.527 1.552 1.442 122.14 115.95 120.50 109.09 110.60 111.24 123.54 40 VAL 40 1.319 1.235 1.517 1.557 1.459 124.27 117.02 119.82 109.93 108.27 110.95 123.15 * * * 41 ASP 41 1.312 1.248 1.516 1.526 1.444 121.70 115.96 120.67 110.55 109.51 109.85 123.33 * * Residue-by-residue listing for refined_11 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 LEU 42 1.303 1.231 1.497 1.533 1.442 121.98 116.60 120.16 107.65 108.68 111.31 123.24 +* * * +* 43 LEU 43 1.296 1.227 1.499 1.555 1.432 121.36 114.99 121.25 108.65 110.34 112.63 123.75 ** * * * * ** 44 ASP 44 1.285 1.241 1.493 1.535 1.440 123.35 114.93 120.87 111.48 108.99 111.09 124.19 *** +* *** 45 TYR 45 1.301 1.236 1.536 1.539 1.444 123.25 116.52 120.68 111.37 111.64 109.61 122.79 +* +* 46 SER 46 1.317 1.242 1.545 1.525 1.447 121.83 116.15 121.22 110.45 109.31 109.11 122.63 47 GLY 47 1.325 1.236 1.516 - 1.442 120.47 117.25 120.26 - 113.89 - 122.48 48 ARG 48 1.311 1.234 1.534 1.538 1.453 121.25 116.61 120.53 110.30 109.83 109.40 122.82 * * 49 SER 49 1.307 1.242 1.529 1.536 1.435 122.23 116.73 120.36 112.38 110.02 110.73 122.82 +* * * +* 50 TRP 50 1.314 1.228 1.510 1.541 1.463 122.04 115.98 120.70 108.99 111.74 112.37 123.31 * * * 51 THR 51 1.306 1.240 1.535 1.535 1.430 122.03 115.57 121.28 110.66 108.30 110.63 123.13 +* * * +* 52 VAL 52 1.299 1.235 1.526 1.537 1.448 123.49 116.75 120.41 111.29 111.97 112.32 122.84 ** ** 53 ARG 53 1.322 1.219 1.538 1.530 1.453 121.65 116.78 120.61 107.71 109.15 108.69 122.60 * * * 54 MET 54 1.305 1.222 1.503 1.532 1.466 122.75 117.06 120.09 108.90 109.85 109.20 122.84 +* * +* 55 LYS 55 1.315 1.243 1.508 1.507 1.424 120.74 115.09 121.28 112.56 109.48 110.92 123.60 * * +* * +* 56 LYS 56 1.300 1.231 1.487 1.511 1.441 123.10 115.02 121.06 109.81 106.21 108.88 123.91 ** +* +* ** 57 ARG 57 1.252 1.231 1.506 1.529 1.451 122.59 115.87 120.63 110.00 111.32 110.69 123.46 *5.5* *5.5* 58 GLY 58 1.313 1.233 1.502 - 1.441 121.69 116.08 120.75 - 112.23 - 123.14 * * 59 GLU 59 1.310 1.213 1.520 1.539 1.447 122.21 117.85 120.20 110.19 112.12 112.25 121.94 * * * 60 LYS 60 1.317 1.233 1.522 1.527 1.434 120.22 115.83 121.09 110.71 111.56 111.45 123.04 * * 61 VAL 61 1.304 1.232 1.507 1.559 1.443 122.71 116.21 120.41 107.95 108.74 112.63 123.37 +* +* 62 PHE 62 1.294 1.246 1.504 1.538 1.428 122.28 116.13 120.75 110.08 105.53 108.11 123.10 ** * +* ** * ** 63 LEU 63 1.277 1.214 1.513 1.544 1.415 121.37 116.73 119.95 114.79 105.14 108.67 123.31 +*** ** ** ** * +*** 64 THR 64 1.300 1.243 1.564 1.585 1.446 122.07 115.54 121.01 112.98 112.39 109.18 123.45 ** +* +* +* * ** 65 VAL 65 1.329 1.228 1.518 1.555 1.449 125.26 115.30 121.80 110.76 112.71 111.49 122.90 +* +* 66 GLY 66 1.296 1.228 1.480 - 1.431 120.86 114.40 121.57 - 109.01 - 124.02 ** ** * * ** 67 TRP 67 1.331 1.244 1.509 1.539 1.451 123.44 114.16 121.72 109.70 109.93 109.18 124.02 * * 68 GLU 68 1.309 1.211 1.522 1.522 1.445 122.91 116.57 120.22 112.36 111.93 110.85 123.18 * * * * 69 ASN 69 1.337 1.213 1.514 1.534 1.468 122.91 116.38 120.29 110.01 111.94 111.50 123.32 70 PHE 70 1.309 1.227 1.503 1.550 1.451 123.09 115.04 121.62 109.80 109.06 110.25 123.30 * * * * Residue-by-residue listing for refined_11 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 1.311 1.227 1.517 1.554 1.434 121.46 117.59 120.07 114.05 112.74 112.89 122.34 * * ** ** 72 LYS 72 1.320 1.227 1.534 1.552 1.438 119.50 117.69 120.08 112.00 111.05 113.80 122.22 * * * +* +* 73 ASP 73 1.352 1.234 1.513 1.531 1.486 119.26 116.84 120.48 109.19 112.78 112.19 122.64 +* * * +* 74 ASN 74 1.301 1.230 1.506 1.544 1.452 120.30 115.04 120.64 109.92 110.05 111.81 124.28 +* +* 75 ASN 75 1.330 1.237 1.530 1.541 1.479 124.71 116.28 121.30 111.45 112.50 112.81 122.39 * +* * +* 76 LEU 76 1.310 1.242 1.513 1.560 1.442 121.12 114.62 121.19 111.17 111.95 113.86 124.19 * +* +* +* 77 GLU 77 1.310 1.243 1.513 1.519 1.440 124.02 115.16 120.49 109.46 110.34 111.09 124.33 * * * 78 ASP 78 1.323 1.242 1.522 1.546 1.473 123.88 115.75 121.01 109.28 109.66 109.75 123.20 * * 79 GLY 79 1.304 1.229 1.492 - 1.431 121.29 115.18 121.00 - 110.06 - 123.82 +* * * +* 80 LYS 80 1.316 1.239 1.510 1.533 1.444 122.33 117.79 119.95 109.77 107.94 110.11 122.25 * * 81 TYR 81 1.305 1.234 1.485 1.529 1.425 119.07 115.26 120.88 110.52 110.79 111.56 123.85 +* +* +* * +* 82 LEU 82 1.296 1.247 1.509 1.562 1.413 121.70 114.59 121.69 115.02 110.92 112.52 123.61 ** +* ** +** * +** 83 GLN 83 1.284 1.230 1.512 1.523 1.417 123.29 116.56 120.42 111.29 108.69 107.75 123.01 *** ** +* *** 84 PHE 84 1.296 1.243 1.506 1.532 1.431 121.70 115.55 121.05 108.39 110.39 111.34 123.37 ** * ** 85 ILE 85 1.296 1.238 1.515 1.585 1.433 122.32 116.32 120.52 110.39 107.09 114.10 123.10 ** +* * * +* ** 86 TYR 86 1.297 1.239 1.503 1.533 1.436 121.59 115.98 120.73 107.14 109.03 111.01 123.29 ** * * +* ** 87 ASP 87 1.294 1.226 1.515 1.538 1.442 120.89 114.81 121.24 110.47 108.75 111.22 123.90 +** +** 88 ARG 88 1.316 1.236 1.528 1.552 1.453 124.65 114.16 122.62 110.72 104.60 109.02 123.14 * +* * * ** ** 89 ASP 89 1.323 1.221 1.540 1.560 1.425 123.07 115.92 120.40 111.68 108.22 107.49 123.59 +* +* * +* +* 90 ARG 90 1.294 1.232 1.550 1.536 1.453 126.56 115.64 122.23 108.54 108.08 106.16 122.13 +** * +** * +** +** 91 THR 91 1.294 1.239 1.533 1.537 1.433 121.71 116.22 120.55 109.86 109.00 109.06 123.21 +** * * +** 92 PHE 92 1.315 1.228 1.519 1.544 1.452 122.08 116.81 120.41 107.36 110.01 110.68 122.79 * * * 93 TYR 93 1.301 1.232 1.509 1.526 1.455 121.62 116.77 120.24 110.17 108.30 111.40 122.99 ** * ** 94 VAL 94 1.301 1.237 1.525 1.554 1.443 121.63 115.20 121.23 108.84 111.89 111.47 123.55 ** ** 95 ILE 95 1.311 1.230 1.528 1.568 1.447 123.88 117.23 120.22 109.59 106.80 111.84 122.53 * * * +* +* 96 ILE 96 1.301 1.238 1.519 1.574 1.454 121.40 116.65 120.55 110.49 110.30 111.04 122.73 +* * +* 97 TYR 97 1.312 1.251 1.515 1.544 1.431 120.07 115.21 121.02 113.96 111.63 114.71 123.77 * * * ** ** ** Residue-by-residue listing for refined_11 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 ----------------------------------------------------------------------------------------------------------------------------------- 98 GLY 98 1.304 1.232 1.502 - 1.431 122.76 118.25 119.44 - 107.37 - 122.30 +* * * +* +* 99 HIS 99 1.311 1.230 1.504 1.532 1.460 120.63 114.48 121.12 112.41 113.79 114.02 124.31 * * ** ** 100 ASN 100 1.318 1.237 1.508 1.535 1.464 124.85 116.14 120.07 108.89 108.07 112.62 123.64 +* * * +* 101 MET 101 1.333 1.234 1.548 1.556 1.482 123.40 115.22 122.18 111.77 109.18 109.75 122.54 * * * * 102 CYS 102 1.317 - 1.521 1.524 1.431 121.95 - - 110.13 109.16 108.98 - * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *5.5* * ** +* ** +** * * +** ** +** * *5.5* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_11 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 1.252 1.352 1.309 .015 *5.5* +* * C-N (Pro) 1.341 .016 5 1.334 1.358 1.345 .008 * C-O C-O 1.231 .020 101 1.208 1.251 1.233 .009 * * CA-C CH1E-C (except Gly) 1.525 .021 95 1.485 1.564 1.520 .015 +* +* CH2G*-C (Gly) 1.516 .018 7 1.480 1.523 1.501 .014 ** CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.527 1.530 1.528 .001 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.535 1.585 1.558 .014 +* CH1E-CH2E (the rest) 1.530 .020 75 1.507 1.567 1.537 .012 * +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.411 1.486 1.445 .016 ** * NH1-CH2G* (Gly) 1.451 .016 7 1.428 1.454 1.437 .009 * N-CH1E (Pro) 1.466 .015 5 1.434 1.483 1.461 .020 ** * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_11 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 89 114.16 118.91 116.23 .95 * * CH2G*-C-NH1 (Gly) 116.4 2.1 7 114.40 118.25 116.27 1.19 CH1E-C-N (Pro) 116.9 1.5 5 114.74 118.90 116.96 1.33 * * O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 121.00 124.48 123.03 .67 * O-C-N (Pro) 122.0 1.4 5 121.97 123.45 122.55 .56 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.02 126.56 122.03 1.50 ** +** C-NH1-CH2G* (Gly) 120.6 1.7 7 120.47 122.76 121.26 .71 * C-N-CH1E (Pro) 122.6 5.0 5 121.74 123.52 122.53 .57 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 119.03 122.62 120.71 .61 * * CH2G*-C-O (Gly) 120.8 2.1 7 119.21 121.57 120.51 .84 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.05 111.22 110.63 .59 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 107.95 114.05 110.70 1.43 ** CH2E-CH1E-C (the rest) 110.1 1.9 75 107.14 115.02 110.50 1.55 +* +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.60 113.79 109.89 1.94 ** NH1-CH2G*-C (Gly) 112.5 2.9 7 107.37 113.89 110.53 1.98 +* N-CH1E-C (Pro) 111.8 2.5 5 107.40 113.06 110.73 1.89 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.80 111.90 110.85 1.05 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 108.94 114.35 111.51 1.47 +* +* N-CH1E-CH2E (Pro) 103.0 1.1 5 103.08 104.22 103.53 .38 * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 106.16 114.71 110.56 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_11 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] 75 85.2% Residues in additional allowed regions [a,b,l,p] 11 12.5% Residues in generously allowed regions [~a,~b,~l,~p] 2 2.3% 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 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 85.2 83.8 10.0 .1 Inside b. Omega angle st dev 101 4.2 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 2.1 3.1 1.6 -.6 Inside e. H-bond energy st dev 56 .9 .8 .2 .5 Inside f. Overall G-factor 102 -.1 -.4 .3 1.0 Inside 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 14 6.7 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 42 11.9 19.0 5.3 -1.3 BETTER c. Chi-1 gauche plus st dev 32 6.9 17.5 4.9 -2.2 BETTER d. Chi-1 pooled st dev 88 10.3 18.2 4.8 -1.6 BETTER e. Chi-2 trans st dev 22 7.0 20.4 5.0 -2.7 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% 85.2 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.9 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .92 3 Residue-by-residue listing for refined_11 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.50 Chi1-chi2 distribution -.45 Chi1 only .09 Chi3 & chi4 .53 Omega -.18 ------ -.23 ===== Main-chain covalent forces:- Main-chain bond lengths -.08 Main-chain bond angles .35 ------ .17 ===== OVERALL AVERAGE -.09 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.