Residue-by-residue listing for refined_5 Page 1 ---------------------------------------- This listing highlights the residues in the structure which may need investigation. The ideal values and standard deviations against which the structure has been compared are shown in the following table: <------------------------------- I D E A L V A L U E S -------------------------------> Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha ------------------------------------------------------------------------------------------ Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9 Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5 ------------------------------------------------------------------------------------------ In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above. Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*. The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing. Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments. Full print-out. ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - - - -62.1 177.5 - - - - - - 177.1 - 33.1 - 2 ALA 2 B - - - - - - - - - - 187.1 - 34.0 - * * 3 ASP 3 S l - - -64.7 - - - - - - - 180.5 - 30.5 - 4 THR 4 A - - -55.5 - - - - - - - 179.6 - 35.3 - 5 GLY 5 S - - - - - - - - - - - 179.0 - - - 6 GLU 6 l - 187.9 - 177.1 - - - - - - 179.5 - 33.0 - 7 VAL 7 E B - - -62.0 - - - - - - - 187.9 -2.2 33.0 - * * 8 GLN 8 E B 57.8 - - 181.5 - - - - - - 174.6 - 35.8 - 9 PHE 9 E B - 185.9 - - - - - - - - 181.4 -1.4 35.0 - 10 MET 10 E B 64.5 - - 171.9 - - - - - - 168.8 - 35.2 - +* +* 11 LYS 11 E B 73.5 - - - - - - - - - 172.8 -1.5 32.8 - * * 12 PRO 12 E - - - - - -74.8 - - - - - 181.9 - 38.1 - * * 13 PHE 13 e B 52.9 - - - - - - - - - 185.0 -.7 33.6 - +* +* 14 ILE 14 t B - - -57.6 177.0 - - - - - - 186.9 - 35.1 - * * 15 SER 15 T A - 185.2 - - - - - - - - 180.9 -.6 33.3 - +* +* 16 GLU 16 T A - - -60.9 185.4 - - - - - - 181.6 - 33.0 - 17 LYS 17 T A - 182.4 - 179.0 - - - - - - 182.7 -.9 34.3 - * * 18 SER 18 T A - - -58.1 - - - - - - - 171.1 -3.6 32.7 - +* ** ** Residue-by-residue listing for refined_5 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 19 SER 19 T A - - -64.5 - - - - - - - 182.8 - 34.2 - 20 LYS 20 T a 57.2 - - 180.1 - - - - - - 184.6 -1.7 34.2 - 21 SER 21 t B 55.8 - - - - - - - - - 179.2 -2.7 34.5 - 22 LEU 22 E B - 183.7 - - - - - - - - 182.5 -3.5 33.6 - ** ** 23 GLU 23 E B 63.4 - - 176.7 - - - - - - 177.3 - 32.3 - 24 ILE 24 E B - - -61.2 - - - - - - - 183.8 -2.0 34.8 - 25 PRO 25 h - - - - - -55.0 - - - - - 179.8 - 38.7 - * * 26 LEU 26 H A - 181.1 - - - -65.5 -33.5 - - - 176.4 - 33.2 - 27 GLY 27 H - - - - - - -63.7 -36.3 - - - 177.8 - - - 28 PHE 28 H A - - -79.7 - - -77.8 -25.7 - - - 174.3 - 30.2 - * * * * 29 ASN 29 H A - 177.4 - - - -59.2 -46.3 - - - 178.6 -1.7 35.1 - 30 GLU 30 H A - 178.9 - 186.8 - -74.2 -32.0 - - - 185.3 -1.8 36.8 - 31 TYR 31 H A - 187.8 - - - -68.8 -28.6 - - - 176.6 -1.4 35.2 - 32 PHE 32 h b 66.5 - - - - - - - - - 168.0 -1.7 29.6 - ** * ** 33 PRO 33 - - - - - -83.6 - - - - - 184.1 - 38.6 - +* * +* 34 ALA 34 B - - - - - - - - - - 172.5 - 35.4 - * * 35 PRO 35 - - - - - -57.2 - - - - - 188.3 - 38.9 - * * * 36 PHE 36 B 57.5 - - - - - - - - - 179.4 - 32.7 - 37 PRO 37 - - - - - -80.5 - - - - - 180.9 - 38.8 - * * * 38 ILE 38 S A - - -58.2 - - - - - - - 173.8 - 32.3 - * * 39 THR 39 B 53.0 - - - - - - - - - 181.1 - 33.2 - 40 VAL 40 E B - 170.3 - - - - - - - - 181.3 -2.7 35.8 - 41 ASP 41 E B - - -62.4 - - - - - - - 178.1 -2.3 32.8 - 42 LEU 42 E B - - -59.6 180.4 - - - - - - 183.7 -3.0 35.2 - * * 43 LEU 43 E B - - -59.1 - - - - - - - 182.1 -2.9 34.0 - * * 44 ASP 44 E B - 165.9 - - - - - - - - 181.6 -3.0 34.2 - * * * 45 TYR 45 e A 52.2 - - - - - - - - - 183.9 -.7 34.2 - +* +* 46 SER 46 T A - 184.2 - - - - - - - - 177.4 - 33.4 - 47 GLY 47 t - - - - - - - - - - - 181.7 -1.7 - - 48 ARG 48 e B - - -58.3 180.1 - - - - - - 177.8 - 33.8 - 49 SER 49 E B 53.2 - - - - - - - - - 180.5 - 34.0 - 50 TRP 50 E B - - -63.3 - - - - - - - 174.8 -2.2 34.3 - 51 THR 51 E B - - -57.0 - - - - - - - 184.0 - 33.9 - 52 VAL 52 E B - - -60.4 - - - - - - - 177.9 -3.2 33.9 - +* +* 53 ARG 53 e B - 175.0 - 174.2 - - - - - - 182.1 -3.1 33.8 - * * 54 MET 54 E B - 178.2 - 181.2 - - - - - - 181.9 -.7 35.6 - +* +* 55 LYS 55 E B - 183.2 - - - - - - - - 171.5 -2.5 35.9 - * * 56 LYS 56 E B - - -60.7 - - - - - - - 186.7 - 36.5 - * * Residue-by-residue listing for refined_5 Page 3 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 57 ARG 57 E b - 181.6 - 180.4 - - - - - - 173.9 -2.3 34.0 - * * 58 GLY 58 T - - - - - - - - - - - 188.1 - - - * * 59 GLU 59 T A - - -54.7 177.3 - - - - - - 189.6 -.9 36.9 - +* +* +* 60 LYS 60 E B - 188.3 - 177.8 - - - - - - 177.5 -2.3 34.7 - 61 VAL 61 E B - 182.7 - - - - - - - - 181.8 -.6 34.2 - +* +* 62 PHE 62 E B - - -56.5 - - - - - - - 172.8 -2.8 35.7 - * * * 63 LEU 63 E B - 185.6 - 171.2 - - - - - - 189.0 -2.7 34.9 - +* +* 64 THR 64 e ~a 56.0 - - - - - - - - - 185.5 -2.0 31.3 - ** ** 65 VAL 65 T B - - -63.2 - - - - - - - 183.1 - 31.2 - 66 GLY 66 h - - - - - - - - - - - 175.8 - - - 67 TRP 67 H A - 173.6 - - - -61.2 -24.9 - - - 180.5 -1.3 34.9 - * * * 68 GLU 68 H A 57.4 - - 181.8 - -65.6 -30.2 - - - 178.2 - 33.9 - 69 ASN 69 H A - - -63.7 - - -74.7 -29.4 - - - 181.5 -1.4 34.0 - 70 PHE 70 H A - 186.2 - - - -73.3 -52.3 - - - 182.2 -.9 36.5 - * * * 71 VAL 71 H A 70.2 - - - - -61.1 -45.3 - - - 179.3 -3.2 33.3 - * * 72 LYS 72 H A - - -59.0 - - -71.9 -34.0 - - - 185.1 -2.0 32.2 - 73 ASP 73 H A - 191.9 - - - -74.2 -39.5 - - - 178.2 -1.6 32.3 - 74 ASN 74 H A - - -72.0 - - -90.2 -18.8 - - - 187.3 -2.3 33.9 - ** +* * ** 75 ASN 75 h l - 183.3 - - - - - - - - 184.9 -1.2 31.2 - * * 76 LEU 76 t B 46.2 - - - - - - - - - 185.3 -1.2 29.6 - * * * * 77 GLU 77 t B 52.2 - - 181.8 - - - - - - 181.3 - 34.0 - 78 ASP 78 T B 61.0 - - - - - - - - - 185.5 - 32.1 - 79 GLY 79 T - - - - - - - - - - - 176.6 - - - 80 LYS 80 e B - - -54.9 181.7 - - - - - - 186.5 -1.0 34.7 - * * * 81 TYR 81 E B - - -50.0 - - - - - - - 176.8 -2.4 35.6 - * * 82 LEU 82 E B 52.4 - - - - - - - - - 177.1 -1.9 30.9 - 83 GLN 83 E B - 182.0 - 184.1 - - - - - - 177.1 -2.3 35.7 - 84 PHE 84 E B - - -67.4 - - - - - - - 175.4 -2.2 33.8 - 85 ILE 85 E B - - -55.7 178.1 - - - - - - 182.6 -2.9 34.9 - * * 86 TYR 86 E B - - -53.0 - - - - - - - 175.7 -3.8 37.2 - ** ** 87 ASP 87 e A 72.8 - - - - - - - - - 185.6 -.5 33.0 - +* +* 88 ARG 88 S l - - -55.3 - - - - - - - 183.5 - 31.3 - 89 ASP 89 S ~b - 186.3 - - - - - - - - 180.7 - 35.5 - ** ** 90 ARG 90 e A 64.5 - - 169.8 - - - - - - 179.6 - 34.1 - 91 THR 91 E B 45.1 - - - - - - - - - 183.8 - 33.3 - * * 92 PHE 92 E B - - -54.4 - - - - - - - 178.7 -2.4 33.7 - 93 TYR 93 E B - - -63.6 - - - - - - - 184.7 -1.6 33.4 - Residue-by-residue listing for refined_5 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 94 VAL 94 E B 61.7 - - - - - - - - - 173.5 -2.6 33.1 - * * 95 ILE 95 E B - - -60.1 178.9 - - - - - - 185.6 -2.6 34.0 - 96 ILE 96 E B - - -54.5 175.7 - - - - - - 175.7 - 34.7 - 97 TYR 97 E B - - -54.8 - - - - - - - 189.3 -3.3 35.2 - +* +* +* 98 GLY 98 S - - - - - - - - - - - 186.9 -.6 - - * +* +* 99 HIS 99 B 61.6 - - - - - - - - - 176.6 - 33.6 - 100 ASN 100 B - 178.2 - - - - - - - - 181.3 - 35.1 - 101 MET 101 b - 183.8 - 180.9 - - - - - - 179.1 - 32.6 - 102 CYS 102 - - - -63.1 - - - - - - - - -1.9 34.0 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * * * +* ** +* ** ** * ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.7 181.9 -60.0 178.8 -70.2 -70.1 -34.1 - - - 180.5 -2.0 34.1 Standard deviations: 7.5 5.8 5.5 4.0 13.3 8.3 9.2 - - - 4.7 .9 1.9 Numbers of values: 24 27 37 27 5 14 14 0 0 0 101 58 95 0 KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_5 Page 5 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - 1.237 1.523 1.542 1.471 - 116.81 120.17 110.39 111.24 111.69 123.03 2 ALA 2 1.346 1.246 1.517 1.519 1.455 121.97 115.40 120.23 110.91 109.23 110.42 124.36 * * 3 ASP 3 1.321 1.245 1.517 1.555 1.460 124.11 114.86 121.93 111.43 109.86 114.99 123.06 * * +** +** 4 THR 4 1.311 1.239 1.525 1.546 1.440 122.69 115.15 121.77 109.89 109.41 109.88 123.08 * * 5 GLY 5 1.294 1.237 1.486 - 1.416 121.77 116.16 119.61 - 109.83 - 124.24 +** +* ** +** 6 GLU 6 1.328 1.232 1.547 1.543 1.459 123.56 115.34 122.10 112.92 110.07 109.69 122.47 * * * * 7 VAL 7 1.314 1.224 1.504 1.561 1.429 121.49 116.75 120.68 111.20 107.67 112.85 122.57 * * +* * +* 8 GLN 8 1.271 1.238 1.508 1.512 1.418 120.63 115.23 121.06 110.02 112.21 108.04 123.70 **** ** * **** 9 PHE 9 1.306 1.245 1.517 1.532 1.442 122.64 117.03 119.92 110.37 107.71 110.11 123.06 +* * +* 10 MET 10 1.313 1.232 1.524 1.547 1.451 121.16 116.28 120.61 108.07 111.39 111.22 123.05 * * * 11 LYS 11 1.313 1.245 1.516 1.556 1.444 122.23 119.35 119.18 109.38 107.64 114.70 121.44 * * +* * ** ** Residue-by-residue listing for refined_5 Page 6 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 12 PRO 12 1.334 1.240 1.533 1.544 1.438 120.98 115.58 121.18 110.89 109.70 104.59 123.24 +* * +* 13 PHE 13 1.295 1.217 1.513 1.536 1.451 123.55 117.23 120.09 111.85 110.20 109.98 122.68 ** * ** 14 ILE 14 1.315 1.223 1.500 1.550 1.439 121.05 116.77 119.53 109.98 108.03 110.69 123.68 * * * * 15 SER 15 1.325 1.212 1.534 1.543 1.453 122.72 117.33 120.03 111.27 111.86 110.41 122.57 16 GLU 16 1.326 1.227 1.525 1.525 1.454 121.89 117.30 120.54 110.26 112.05 111.57 122.11 17 LYS 17 1.321 1.247 1.510 1.534 1.448 119.77 114.41 121.82 110.62 108.92 110.60 123.68 * * 18 SER 18 1.308 1.206 1.533 1.521 1.424 123.55 117.64 120.09 112.78 113.03 109.17 122.27 * * +* * * +* 19 SER 19 1.330 1.234 1.532 1.536 1.460 120.31 116.45 120.84 109.07 110.23 111.68 122.72 20 LYS 20 1.323 1.214 1.524 1.534 1.445 121.15 117.41 119.95 110.40 112.62 109.81 122.63 21 SER 21 1.322 1.230 1.538 1.538 1.454 120.62 116.33 121.00 110.73 112.14 109.10 122.67 22 LEU 22 1.309 1.237 1.525 1.564 1.433 122.65 116.35 120.91 113.33 108.26 109.54 122.73 * +* * +* * +* 23 GLU 23 1.312 1.250 1.528 1.532 1.438 120.93 115.17 121.40 111.37 111.91 111.58 123.38 * * * 24 ILE 24 1.303 1.237 1.538 1.558 1.442 123.09 118.10 119.63 110.66 108.01 110.29 122.25 +* * +* 25 PRO 25 1.359 1.241 1.526 1.530 1.472 122.93 115.94 120.99 109.24 112.98 104.39 123.06 * * * 26 LEU 26 1.321 1.238 1.526 1.533 1.451 121.99 115.87 120.83 111.76 110.35 110.52 123.25 27 GLY 27 1.326 1.226 1.510 - 1.442 121.05 116.13 120.45 - 111.09 - 123.38 28 PHE 28 1.337 1.226 1.511 1.528 1.455 122.00 116.54 120.48 111.98 112.77 113.33 122.98 +* +* 29 ASN 29 1.320 1.233 1.523 1.538 1.464 121.36 114.44 121.41 109.43 108.86 110.51 124.11 30 GLU 30 1.317 1.237 1.530 1.529 1.448 123.84 115.47 121.26 109.00 110.23 108.04 123.27 * * * 31 TYR 31 1.320 1.231 1.523 1.525 1.452 122.77 117.33 120.17 110.36 111.37 108.61 122.50 * * 32 PHE 32 1.325 1.247 1.540 1.571 1.441 119.52 117.03 121.90 112.67 113.47 113.39 120.88 ** * * +* * ** 33 PRO 33 1.331 1.246 1.514 1.525 1.429 122.32 115.31 121.46 110.11 108.76 104.65 123.23 ** * * +* ** 34 ALA 34 1.264 1.242 1.498 1.534 1.434 122.86 119.10 118.61 110.48 107.80 109.65 122.28 *4.6* * * * * * *4.6* 35 PRO 35 1.351 1.245 1.513 1.528 1.452 121.19 116.74 119.84 110.07 107.32 104.36 123.42 +* * * +* 36 PHE 36 1.304 1.234 1.521 1.543 1.410 121.93 116.57 121.32 112.67 111.97 110.08 122.05 +* +** * +** 37 PRO 37 1.334 1.222 1.510 1.534 1.432 121.98 116.72 120.75 110.77 110.05 103.60 122.53 ** ** 38 ILE 38 1.296 1.231 1.517 1.556 1.435 120.21 116.08 121.28 112.33 109.30 111.97 122.62 ** * * ** 39 THR 39 1.314 1.237 1.528 1.553 1.423 120.34 114.91 121.48 110.82 110.13 111.94 123.62 * +* +* 40 VAL 40 1.293 1.224 1.499 1.577 1.443 125.68 117.64 119.84 109.66 106.62 110.58 122.50 +** * * ** +* +** 41 ASP 41 1.287 1.242 1.495 1.535 1.428 120.07 115.41 121.04 111.10 110.70 111.97 123.55 *** * +* *** 42 LEU 42 1.297 1.240 1.492 1.537 1.431 122.09 116.16 120.52 109.44 107.01 111.28 123.31 ** +* * * ** 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 ----------------------------------------------------------------------------------------------------------------------------------- 43 LEU 43 1.298 1.244 1.509 1.555 1.429 120.83 115.27 120.95 110.16 110.00 111.59 123.77 ** * +* ** 44 ASP 44 1.297 1.242 1.518 1.527 1.446 123.37 114.20 121.61 110.81 112.26 109.46 124.19 ** * ** 45 TYR 45 1.312 1.234 1.539 1.544 1.463 125.39 117.58 120.26 110.33 113.68 109.45 122.12 * ** ** 46 SER 46 1.321 1.239 1.531 1.547 1.443 121.22 116.39 120.69 111.47 110.48 110.63 122.93 47 GLY 47 1.323 1.228 1.506 - 1.445 120.78 116.34 120.61 - 112.63 - 123.04 48 ARG 48 1.310 1.235 1.528 1.529 1.453 121.69 116.52 120.78 110.76 110.56 110.44 122.64 * * 49 SER 49 1.304 1.231 1.520 1.542 1.446 121.91 116.69 120.70 111.08 110.25 110.29 122.61 +* +* 50 TRP 50 1.300 1.235 1.506 1.541 1.456 121.05 115.97 120.66 108.59 110.93 112.12 123.36 ** ** 51 THR 51 1.300 1.240 1.530 1.534 1.422 121.80 115.06 121.61 111.02 108.75 110.88 123.32 ** +* ** 52 VAL 52 1.292 1.224 1.515 1.553 1.433 123.70 116.54 120.50 110.00 110.37 111.61 122.92 +** * * +** 53 ARG 53 1.295 1.236 1.515 1.532 1.438 121.68 115.11 121.35 111.17 109.74 110.51 123.53 ** * ** 54 MET 54 1.299 1.222 1.503 1.523 1.438 123.07 116.80 120.79 110.45 108.55 108.95 122.39 ** * * ** 55 LYS 55 1.285 1.233 1.517 1.528 1.411 120.40 115.58 121.12 110.23 111.15 108.29 123.29 *** ** * *** 56 LYS 56 1.304 1.233 1.503 1.529 1.435 122.32 116.64 120.28 108.52 103.19 110.66 123.00 +* * * +** +** 57 ARG 57 1.272 1.237 1.513 1.538 1.437 120.82 114.55 120.95 110.74 112.07 110.04 124.47 **** * **** 58 GLY 58 1.315 1.228 1.504 - 1.445 124.10 115.62 121.04 - 116.61 - 123.33 ** * ** 59 GLU 59 1.297 1.221 1.510 1.523 1.434 122.35 117.38 120.06 107.51 111.58 109.23 122.52 ** * * ** 60 LYS 60 1.311 1.233 1.536 1.560 1.464 119.70 116.80 120.51 111.90 110.94 108.30 122.60 * +* * * +* 61 VAL 61 1.318 1.239 1.515 1.548 1.444 121.85 116.20 120.75 109.33 108.66 112.24 123.04 62 PHE 62 1.298 1.222 1.504 1.539 1.430 121.61 116.25 120.61 108.85 109.41 110.47 123.10 ** * * ** 63 LEU 63 1.286 1.220 1.516 1.560 1.429 122.21 117.18 120.22 113.44 103.90 108.69 122.47 *** +* * +* +** * *** 64 THR 64 1.306 1.233 1.537 1.553 1.439 120.09 115.83 121.11 111.30 115.07 111.79 122.99 +* * * +* 65 VAL 65 1.310 1.232 1.507 1.549 1.448 122.61 115.36 121.42 111.30 112.09 113.25 123.18 * * * * 66 GLY 66 1.301 1.230 1.483 - 1.428 120.76 115.29 120.94 - 110.25 - 123.73 ** +* * ** 67 TRP 67 1.333 1.227 1.515 1.537 1.454 122.52 114.71 122.04 109.79 109.16 110.52 123.21 68 GLU 68 1.292 1.213 1.548 1.514 1.438 122.06 116.59 121.03 111.58 110.39 109.43 122.34 +** * * +** 69 ASN 69 1.325 1.202 1.505 1.547 1.462 121.91 114.85 121.52 109.79 108.93 111.99 123.61 * * 70 PHE 70 1.304 1.243 1.525 1.547 1.447 124.71 115.09 121.07 110.38 108.51 107.74 123.82 +* +* +* +* 71 VAL 71 1.335 1.224 1.521 1.586 1.450 122.64 115.82 120.92 110.77 110.45 111.94 123.26 +* +* 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 1.312 1.233 1.530 1.540 1.452 122.02 118.00 120.01 110.48 113.08 112.15 121.99 * * 73 ASP 73 1.338 1.234 1.517 1.523 1.482 119.41 116.63 120.68 110.17 112.38 112.38 122.69 * * * * 74 ASN 74 1.309 1.233 1.501 1.543 1.464 120.86 115.36 120.35 109.18 110.91 112.07 124.25 * * * 75 ASN 75 1.326 1.243 1.521 1.542 1.470 124.15 115.61 121.65 111.62 109.69 113.65 122.66 * +* +* 76 LEU 76 1.298 1.234 1.528 1.549 1.427 120.96 115.03 121.47 114.96 113.73 110.92 123.48 ** +* +** +** 77 GLU 77 1.314 1.236 1.523 1.513 1.453 123.85 116.25 120.04 110.87 111.14 109.73 123.71 * * * 78 ASP 78 1.335 1.234 1.507 1.543 1.470 122.73 115.06 121.21 110.65 111.43 112.79 123.73 * * 79 GLY 79 1.302 1.230 1.500 - 1.438 121.67 114.43 122.06 - 108.78 - 123.51 +* * +* 80 LYS 80 1.309 1.241 1.525 1.530 1.430 123.10 117.71 119.82 111.60 107.26 109.55 122.47 * * * * 81 TYR 81 1.308 1.230 1.495 1.545 1.446 120.69 116.74 120.35 108.52 109.11 111.02 122.92 +* * +* 82 LEU 82 1.289 1.236 1.501 1.554 1.425 120.43 115.90 120.81 113.16 111.01 112.48 123.24 +** * * +* +* * +** 83 GLN 83 1.288 1.234 1.500 1.528 1.420 121.73 116.53 120.19 109.65 108.02 109.92 123.28 +** * +* * +** 84 PHE 84 1.296 1.235 1.484 1.532 1.432 121.09 115.60 120.52 108.92 109.48 113.15 123.86 ** +* * +* ** 85 ILE 85 1.285 1.235 1.519 1.550 1.418 121.85 116.00 120.40 110.17 106.76 111.08 123.52 *** ** +* *** 86 TYR 86 1.307 1.237 1.537 1.553 1.447 122.55 118.91 119.99 106.88 109.34 110.01 121.10 +* * * +* * +* 87 ASP 87 1.326 1.228 1.511 1.537 1.480 118.58 114.22 121.54 110.34 109.30 112.56 124.05 * +* * +* 88 ARG 88 1.327 1.235 1.515 1.566 1.466 124.99 115.43 120.92 109.63 108.60 116.23 123.57 +* +* *** *** 89 ASP 89 1.308 1.229 1.519 1.561 1.436 124.20 118.47 118.89 111.32 104.45 109.63 122.62 +* +* * * * * ** ** 90 ARG 90 1.291 1.240 1.531 1.542 1.449 121.55 116.50 121.11 109.77 109.73 111.51 122.38 +** +** 91 THR 91 1.309 1.228 1.505 1.554 1.428 121.23 116.71 120.78 111.72 109.06 111.38 122.48 * +* * +* 92 PHE 92 1.305 1.238 1.497 1.536 1.432 120.03 115.52 121.05 110.32 110.51 111.49 123.42 +* * * +* 93 TYR 93 1.294 1.234 1.510 1.538 1.444 121.79 116.70 120.38 112.03 108.71 110.72 122.89 +** * +** 94 VAL 94 1.309 1.237 1.535 1.568 1.443 120.92 115.07 121.59 110.55 112.50 111.47 123.29 * * * 95 ILE 95 1.308 1.237 1.518 1.557 1.442 123.42 116.90 120.23 110.54 106.77 111.99 122.84 +* +* +* 96 ILE 96 1.310 1.242 1.515 1.554 1.446 121.19 115.00 121.59 109.43 111.14 110.77 123.40 * * 97 TYR 97 1.294 1.226 1.506 1.523 1.429 122.98 116.90 120.07 110.71 105.84 110.00 123.03 ** +* +* ** 98 GLY 98 1.294 1.232 1.500 - 1.435 120.23 116.10 121.07 - 108.32 - 122.82 +** * * +** 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 ----------------------------------------------------------------------------------------------------------------------------------- 99 HIS 99 1.302 1.232 1.508 1.550 1.453 120.85 115.74 120.49 110.39 111.81 111.02 123.76 +* +* 100 ASN 100 1.314 1.244 1.511 1.538 1.447 122.58 116.50 120.57 109.74 108.95 110.35 122.91 * * 101 MET 101 1.305 1.235 1.526 1.534 1.438 121.18 115.03 121.48 111.51 110.61 111.60 123.37 +* * +* 102 CYS 102 1.303 - 1.512 1.542 1.440 123.93 - - 110.22 108.40 111.73 - +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *4.6* * +* ** +** ** +* * +** +** *** * *4.6* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 10 ---------------------------------------- A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S +------------------+ | BOND LENGTHS | +------------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Bond X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- C-N C-NH1 (except Pro) 1.329 .014 96 1.264 1.346 1.308 .015 *4.6* * * C-N (Pro) 1.341 .016 5 1.331 1.359 1.342 .011 * C-O C-O 1.231 .020 101 1.202 1.250 1.233 .009 * CA-C CH1E-C (except Gly) 1.525 .021 95 1.484 1.548 1.518 .013 +* * CH2G*-C (Gly) 1.516 .018 7 1.483 1.510 1.498 .009 +* CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.519 1.534 1.527 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.534 1.586 1.556 .011 +* CH1E-CH2E (the rest) 1.530 .020 75 1.512 1.571 1.538 .012 ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.410 1.482 1.444 .014 +** * NH1-CH2G* (Gly) 1.451 .016 7 1.416 1.445 1.436 .010 ** N-CH1E (Pro) 1.466 .015 5 1.429 1.472 1.445 .016 ** * ------------------------------------------------------------------------------------------------------------- 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 89 114.20 119.35 116.23 1.10 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 7 114.43 116.34 115.72 .63 CH1E-C-N (Pro) 116.9 1.5 5 115.31 116.74 116.05 .58 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.88 124.47 123.04 .65 * O-C-N (Pro) 122.0 1.4 5 122.53 123.42 123.10 .30 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.58 125.68 121.96 1.39 +* ** C-NH1-CH2G* (Gly) 120.6 1.7 7 120.23 124.10 121.48 1.18 ** C-N-CH1E (Pro) 122.6 5.0 5 120.98 122.93 121.88 .72 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 118.61 122.10 120.74 .68 * CH2G*-C-O (Gly) 120.8 2.1 7 119.61 122.06 120.82 .69 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.48 110.91 110.69 .22 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 109.33 112.33 110.59 .79 * CH2E-CH1E-C (the rest) 110.1 1.9 75 106.88 114.96 110.59 1.39 +* +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 103.19 115.07 109.94 2.14 +** * NH1-CH2G*-C (Gly) 112.5 2.9 7 108.32 116.61 111.07 2.62 * * N-CH1E-C (Pro) 111.8 2.5 5 107.32 112.98 109.76 1.86 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.65 110.42 110.03 .39 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.88 113.25 111.48 .85 * N-CH1E-CH2E (Pro) 103.0 1.1 5 103.60 104.65 104.32 .38 +* * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 107.74 116.23 110.82 1.66 +* *** ------------------------------------------------------------------------------------------------------------- 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] 78 88.6% Residues in additional allowed regions [a,b,l,p] 8 9.1% 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 88.6 83.8 10.0 .5 Inside b. Omega angle st dev 101 4.7 6.0 3.0 -.4 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 1.9 3.1 1.6 -.8 Inside e. H-bond energy st dev 58 .9 .8 .2 .2 Inside f. Overall G-factor 102 -.1 -.4 .3 .9 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 24 7.5 18.1 6.5 -1.6 BETTER b. Chi-1 trans st dev 27 5.8 19.0 5.3 -2.5 BETTER c. Chi-1 gauche plus st dev 37 5.5 17.5 4.9 -2.5 BETTER d. Chi-1 pooled st dev 88 8.1 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 27 4.0 20.4 5.0 -3.3 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 8.7 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .86 2 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 -.44 Chi1-chi2 distribution -.23 Chi1 only .04 Chi3 & chi4 .43 Omega -.38 ------ -.25 ===== Main-chain covalent forces:- Main-chain bond lengths -.11 Main-chain bond angles .35 ------ .16 ===== OVERALL AVERAGE -.11 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.