Residue-by-residue listing for refined_8 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 - - 180.3 - 182.4 - - - - - - 175.9 - 35.7 - 2 ALA 2 B - - - - - - - - - - 178.7 - 34.2 - 3 ASP 3 B - 168.9 - - - - - - - - 180.7 -.9 32.6 - +* +* 4 THR 4 S a - - -55.0 - - - - - - - 184.1 - 34.5 - 5 GLY 5 S - - - - - - - - - - - 186.7 - - - * * 6 GLU 6 B - 180.5 - 186.9 - - - - - - 172.5 - 35.6 - * * 7 VAL 7 E B - - -66.7 - - - - - - - 179.9 -2.7 33.0 - 8 GLN 8 E B 68.0 - - - - - - - - - 176.9 - 33.9 - 9 PHE 9 E B 57.7 - - - - - - - - - 179.6 -2.2 32.3 - 10 MET 10 E B 56.6 - - 181.8 - - - - - - 178.6 - 34.0 - 11 LYS 11 E B 54.3 - - 175.4 - - - - - - 175.6 -1.0 33.8 - * * 12 PRO 12 E - - - - - -77.1 - - - - - 179.1 - 38.9 - * * * 13 PHE 13 e B - - -71.7 - - - - - - - 180.9 -.6 31.6 - +* +* 14 ILE 14 h B - - -60.1 176.4 - - - - - - 185.0 - 35.0 - 15 SER 15 H A 52.7 - - - - -58.8 -31.4 - - - 177.0 - 31.7 - 16 GLU 16 H A - 181.3 - 186.9 - -60.6 -31.9 - - - 183.1 - 35.5 - 17 LYS 17 H A - - -70.4 - - -98.2 -40.8 - - - 181.0 -1.5 33.1 - +** +** 18 SER 18 H A - 180.7 - - - -61.7 -23.2 - - - 178.5 -3.5 33.2 - * ** ** 19 SER 19 h A - - -63.5 - - - - - - - 182.8 -1.7 33.1 - 20 LYS 20 T a 55.4 - - 183.8 - - - - - - 182.6 -1.9 31.3 - Residue-by-residue listing for refined_8 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 ----------------------------------------------------------------------------------------------------------------------------------- 21 SER 21 t B 55.8 - - - - - - - - - 176.0 -3.0 34.9 - * * 22 LEU 22 E B - 187.6 - 170.5 - - - - - - 181.6 -1.4 34.0 - 23 GLU 23 E B 51.7 - - 170.6 - - - - - - 178.1 -.6 33.7 - +* +* 24 ILE 24 E B - - -62.5 178.4 - - - - - - 181.0 -1.6 34.0 - 25 PRO 25 h - - - - - -63.5 - - - - - 182.9 - 38.1 - * * 26 LEU 26 H A - - -66.4 - - -57.0 -44.0 - - - 181.6 - 34.4 - 27 GLY 27 H - - - - - - -60.5 -33.8 - - - 180.6 - - - 28 PHE 28 H A - - -61.1 - - -87.8 -26.0 - - - 176.8 -.6 32.2 - +* * +* +* 29 ASN 29 H A - 176.6 - - - -60.9 -30.1 - - - 181.5 -2.1 35.0 - 30 GLU 30 h A - - -57.0 180.2 - - - - - - 179.2 -1.4 33.4 - 31 TYR 31 T A - - -65.9 - - - - - - - 179.3 -1.6 32.7 - 32 PHE 32 t b 50.2 - - - - - - - - - 179.8 -1.5 29.8 - * * 33 PRO 33 - - - - - -79.2 - - - - - 180.4 - 38.5 - * * * 34 ALA 34 b - - - - - - - - - - 179.9 - 34.8 - 35 PRO 35 S - - - - - -62.1 - - - - - 173.5 - 38.0 - * * * 36 PHE 36 S B - 183.2 - - - - - - - - 181.6 - 32.9 - 37 PRO 37 - - - - - -74.7 - - - - - 178.0 - 38.8 - * * 38 ILE 38 e a - - -60.9 - - - - - - - 182.4 - 32.0 - 39 THR 39 E B 46.2 - - - - - - - - - 178.3 - 32.0 - * * 40 VAL 40 E B 59.7 - - - - - - - - - 182.5 -2.9 34.5 - * * 41 ASP 41 E B - - -68.7 - - - - - - - 179.5 -2.6 32.5 - 42 LEU 42 E B - - -69.1 - - - - - - - 179.3 -1.6 33.8 - 43 LEU 43 E B - - -86.1 - - - - - - - 177.0 -3.3 33.7 - * +* +* 44 ASP 44 E B - 178.4 - - - - - - - - 181.2 -1.8 35.8 - 45 TYR 45 e A - 187.3 - - - - - - - - 181.1 -.8 34.5 - +* +* 46 SER 46 T A - 183.8 - - - - - - - - 179.8 - 34.5 - 47 GLY 47 t - - - - - - - - - - - 179.0 -1.6 - - 48 ARG 48 e B - 182.0 - - - - - - - - 183.1 - 35.6 - 49 SER 49 E B 57.5 - - - - - - - - - 177.9 - 34.0 - 50 TRP 50 E B - - -53.0 - - - - - - - 175.3 -1.7 37.6 - * * 51 THR 51 E B - - -54.0 - - - - - - - 185.3 - 35.6 - 52 VAL 52 E B - 182.5 - - - - - - - - 177.1 -2.1 33.8 - 53 ARG 53 E B - 181.6 - 175.2 - - - - - - 185.0 -3.3 33.8 - +* +* 54 MET 54 E B - 177.1 - 175.9 - - - - - - 179.8 -1.9 34.5 - 55 LYS 55 E B - - -64.8 175.8 - - - - - - 169.9 -2.3 36.6 - +* +* 56 LYS 56 E B - - -67.0 180.3 - - - - - - 178.3 - 34.4 - 57 ARG 57 E b - - -57.3 194.4 - - - - - - 182.6 -2.9 32.1 - * * 58 GLY 58 T - - - - - - - - - - - 183.3 -.7 - - +* +* 59 GLU 59 T A - - -60.4 178.0 - - - - - - 185.8 - 35.0 - 60 LYS 60 E B - 181.2 - 181.6 - - - - - - 175.3 -1.6 34.5 - Residue-by-residue listing for refined_8 Page 3 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 61 VAL 61 E B - - -64.0 - - - - - - - 177.0 -.7 32.9 - +* +* 62 PHE 62 E B - - -59.8 - - - - - - - 171.9 -2.3 35.9 - * * 63 LEU 63 E B - - -60.2 183.3 - - - - - - 186.6 -1.8 33.9 - * * 64 THR 64 e a 51.1 - - - - - - - - - 180.2 -1.9 32.4 - 65 VAL 65 T B 58.6 - - - - - - - - - 184.5 - 31.3 - 66 GLY 66 h - - - - - - - - - - - 175.1 - - - 67 TRP 67 H A - 168.0 - - - -68.5 -24.6 - - - 179.6 -.8 33.9 - * +* +* 68 GLU 68 H A - 188.5 - - - -69.8 -26.1 - - - 175.3 -.7 32.0 - * +* +* 69 ASN 69 H A - - -58.3 - - -73.3 -39.7 - - - 184.4 -.6 35.7 - +* +* 70 PHE 70 H A - 189.4 - - - -69.9 -51.0 - - - 183.5 -1.4 36.3 - * * 71 VAL 71 H A 69.1 - - - - -59.8 -45.1 - - - 179.6 -3.6 32.8 - ** ** 72 LYS 72 H A - - -58.6 - - -71.4 -34.3 - - - 186.2 -1.5 33.2 - * * 73 ASP 73 H A - 187.1 - - - -70.1 -41.8 - - - 175.8 -2.0 33.2 - 74 ASN 74 H A - - -73.3 - - -108.8 13.1 - - - 178.4 -2.3 30.1 - +*** *4.6* * *4.6* 75 ASN 75 h XX - 192.2 - - - - - - - - 174.4 -.5 31.3 - **** ** **** 76 LEU 76 l - - -74.1 - - - - - - - 181.8 -1.9 28.7 - * * 77 GLU 77 t B - 181.8 - 177.7 - - - - - - 183.7 - 34.7 - 78 ASP 78 T B 62.6 - - - - - - - - - 177.0 - 33.3 - 79 GLY 79 T - - - - - - - - - - - 181.1 - - - 80 LYS 80 e B - - -70.4 161.2 - - - - - - 185.5 -.7 33.7 - +* +* 81 TYR 81 E B - - -70.5 - - - - - - - 177.9 - 34.1 - 82 LEU 82 E B 51.2 - - 170.3 - - - - - - 181.7 -.6 31.0 - +* +* 83 GLN 83 E B - 180.5 - 182.3 - - - - - - 181.6 -2.6 35.8 - 84 PHE 84 E B - - -54.5 - - - - - - - 175.5 -3.4 36.5 - +* +* 85 ILE 85 E B - - -60.1 182.8 - - - - - - 184.0 -2.7 32.6 - 86 TYR 86 E B - 179.4 - - - - - - - - 176.1 -3.5 34.5 - +* +* 87 ASP 87 e B - 183.2 - - - - - - - - 179.1 -.7 35.8 - +* +* 88 ARG 88 S b - - -92.7 - - - - - - - 181.0 - 28.5 - +* +* +* 89 ASP 89 S b - 192.2 - - - - - - - - 176.3 -2.0 36.7 - 90 ARG 90 e a - - -61.9 - - - - - - - 181.3 - 33.3 - 91 THR 91 E B - - -54.0 - - - - - - - 176.8 - 36.0 - 92 PHE 92 E B - - -67.0 - - - - - - - 175.1 -3.0 35.5 - * * 93 TYR 93 E B - - -65.6 - - - - - - - 183.8 -2.3 33.5 - 94 VAL 94 E B - 185.1 - - - - - - - - 179.0 -3.6 34.5 - ** ** 95 ILE 95 E B - - -63.5 - - - - - - - 172.6 -3.2 33.4 - * +* +* Residue-by-residue listing for refined_8 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 96 ILE 96 E B - - -55.6 - - - - - - - 183.5 -.7 36.8 - +* +* 97 TYR 97 e B - - -62.8 - - - - - - - 181.8 -1.3 32.4 - 98 GLY 98 G - - - - - - - - - - - 182.7 -.8 - - +* +* 99 HIS 99 G L - 192.7 - - - - - - - - 187.1 -.7 34.7 - * +* +* 100 ASN 100 g b - 180.1 - - - - - - - - 169.7 -.7 32.3 - +* +* +* 101 MET 101 a - 181.8 - 183.9 - - - - - - 176.2 -.9 35.3 - * * 102 CYS 102 - - 184.1 - - - - - - - - - - 34.0 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +* * +*** *4.6* +* ** +* *4.6* ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.4 182.6 -64.2 179.0 -71.3 -71.1 -31.9 - - - 179.7 -1.8 34.0 Standard deviations: 6.1 5.7 8.2 6.7 7.9 14.9 14.5 - - - 3.7 .9 2.0 Numbers of values: 17 31 40 25 5 16 16 0 0 0 101 65 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_8 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 - 1.222 1.501 1.539 1.461 - 116.88 120.03 108.68 109.08 110.46 123.09 * * 2 ALA 2 1.309 1.225 1.512 1.522 1.436 121.14 116.41 120.65 110.41 108.83 110.95 122.87 * * * 3 ASP 3 1.301 1.247 1.510 1.525 1.449 121.68 115.66 121.44 111.05 111.39 111.66 122.88 ** ** 4 THR 4 1.299 1.235 1.531 1.551 1.433 122.13 116.90 120.40 110.21 110.98 110.35 122.68 ** * ** 5 GLY 5 1.322 1.233 1.503 - 1.438 119.64 115.03 120.86 - 114.73 - 124.11 6 GLU 6 1.292 1.244 1.532 1.529 1.458 123.84 115.44 121.21 109.03 113.14 108.88 123.34 +** * +** 7 VAL 7 1.312 1.229 1.518 1.569 1.453 123.51 117.32 120.32 109.85 108.58 113.75 122.32 * * * * * 8 GLN 8 1.298 1.237 1.504 1.545 1.414 120.71 116.21 120.70 109.76 109.99 112.05 123.08 ** ** ** 9 PHE 9 1.299 1.226 1.501 1.542 1.433 121.26 115.65 120.76 111.64 110.64 112.10 123.55 ** * * ** 10 MET 10 1.295 1.231 1.510 1.536 1.438 122.76 116.72 120.29 111.10 109.51 110.56 122.98 ** * ** 11 LYS 11 1.298 1.231 1.514 1.554 1.444 121.89 118.24 119.65 110.54 109.60 111.48 122.07 ** * * ** Residue-by-residue listing for refined_8 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 1.337 1.238 1.524 1.543 1.450 122.05 116.84 120.67 109.96 109.98 104.24 122.48 * * * 13 PHE 13 1.295 1.232 1.492 1.524 1.447 120.68 115.44 121.26 111.25 111.77 112.73 123.30 ** +* * ** 14 ILE 14 1.298 1.228 1.503 1.548 1.424 121.60 116.78 120.06 110.39 107.34 110.71 123.16 ** * +* * ** 15 SER 15 1.303 1.229 1.535 1.522 1.453 122.43 116.53 120.36 113.07 113.22 110.03 123.06 +* +* +* 16 GLU 16 1.321 1.232 1.534 1.525 1.456 122.37 116.11 121.06 108.95 109.95 109.89 122.78 17 LYS 17 1.322 1.226 1.493 1.546 1.453 120.88 115.46 120.64 109.38 110.30 113.25 123.85 +* +* +* 18 SER 18 1.309 1.206 1.536 1.548 1.435 123.03 117.31 120.56 112.70 110.88 109.66 122.03 * * * * * 19 SER 19 1.329 1.243 1.540 1.528 1.456 120.23 116.83 120.94 110.64 111.71 111.09 122.20 20 LYS 20 1.318 1.237 1.524 1.538 1.439 120.29 117.39 119.99 112.51 113.20 111.37 122.61 * * * 21 SER 21 1.315 1.237 1.516 1.529 1.446 120.47 115.86 120.77 109.73 112.27 109.55 123.37 * * 22 LEU 22 1.309 1.240 1.522 1.561 1.442 121.42 115.85 120.57 111.98 107.25 110.53 123.56 * +* * +* 23 GLU 23 1.313 1.252 1.545 1.537 1.448 122.61 115.97 121.22 110.70 112.49 110.06 122.81 * * * 24 ILE 24 1.316 1.232 1.540 1.560 1.457 122.07 118.07 119.97 110.07 109.35 111.49 121.94 25 PRO 25 1.357 1.245 1.540 1.535 1.472 122.71 114.99 121.22 110.28 113.24 104.08 123.75 * * * 26 LEU 26 1.332 1.226 1.515 1.553 1.469 124.43 116.06 120.47 108.79 111.47 111.54 123.46 * +* +* 27 GLY 27 1.326 1.234 1.515 - 1.450 121.70 116.48 120.90 - 113.05 - 122.61 28 PHE 28 1.311 1.222 1.512 1.523 1.442 120.77 115.45 121.00 112.28 110.69 111.29 123.51 * * * 29 ASN 29 1.319 1.237 1.539 1.548 1.466 123.26 115.47 121.47 110.68 110.07 109.07 122.97 30 GLU 30 1.327 1.233 1.533 1.524 1.460 122.85 116.71 120.64 110.46 112.46 110.65 122.65 31 TYR 31 1.315 1.231 1.512 1.533 1.465 121.07 116.51 120.76 109.68 111.24 112.97 122.73 * * 32 PHE 32 1.306 1.228 1.525 1.553 1.435 121.16 116.73 121.48 113.68 112.19 112.68 121.73 +* * * +* * +* 33 PRO 33 1.337 1.240 1.520 1.539 1.451 123.00 115.68 120.40 110.30 111.62 104.13 123.92 * * * 34 ALA 34 1.321 1.231 1.516 1.535 1.460 124.05 118.95 119.24 109.41 108.09 111.21 121.80 * * * * 35 PRO 35 1.343 1.236 1.531 1.535 1.463 121.81 116.04 121.27 110.92 110.37 104.25 122.69 * * 36 PHE 36 1.305 1.232 1.518 1.535 1.429 121.99 117.47 120.53 111.61 108.08 112.11 121.93 +* * * +* 37 PRO 37 1.330 1.239 1.520 1.523 1.459 122.28 116.28 120.79 110.38 111.98 103.28 122.92 38 ILE 38 1.307 1.214 1.520 1.562 1.434 121.31 118.09 119.81 111.68 110.00 112.89 121.98 +* * * +* 39 THR 39 1.311 1.243 1.512 1.543 1.436 119.89 114.13 121.83 110.57 113.37 112.46 124.03 * * * * * 40 VAL 40 1.289 1.250 1.529 1.568 1.416 124.28 117.27 120.25 111.58 107.02 110.54 122.45 +** * ** * * * +** 41 ASP 41 1.301 1.235 1.493 1.533 1.440 120.60 115.17 121.34 110.92 111.44 112.15 123.48 +* +* +* 42 LEU 42 1.305 1.240 1.503 1.549 1.436 122.35 115.45 120.84 109.78 109.47 112.26 123.69 +* * * * +* Residue-by-residue listing for refined_8 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 1.301 1.210 1.495 1.548 1.441 122.99 114.74 121.25 110.01 111.27 111.65 124.00 ** * * ** 44 ASP 44 1.279 1.245 1.517 1.539 1.442 124.50 117.09 119.92 109.89 107.53 109.51 122.98 +*** +* * +*** 45 TYR 45 1.316 1.223 1.544 1.538 1.453 122.75 116.61 120.83 110.90 110.87 109.32 122.54 46 SER 46 1.320 1.236 1.555 1.544 1.452 122.49 117.06 120.76 111.14 111.44 108.89 122.17 * * 47 GLY 47 1.332 1.243 1.522 - 1.465 120.44 115.68 121.03 - 112.83 - 123.29 48 ARG 48 1.319 1.230 1.524 1.536 1.463 123.19 117.15 120.05 111.03 108.73 108.17 122.79 * * 49 SER 49 1.306 1.231 1.529 1.531 1.453 120.66 115.68 120.86 110.78 112.09 109.69 123.42 +* +* 50 TRP 50 1.312 1.251 1.513 1.511 1.427 123.97 116.51 120.44 108.01 109.57 108.02 123.05 * +* * * * +* 51 THR 51 1.294 1.235 1.526 1.543 1.430 121.61 117.15 120.40 109.96 106.99 109.99 122.43 +** * +* +** 52 VAL 52 1.314 1.227 1.518 1.568 1.445 120.58 115.76 120.89 110.55 111.08 111.06 123.32 * * * 53 ARG 53 1.306 1.250 1.524 1.531 1.430 122.60 115.80 121.07 111.74 108.94 110.21 123.13 +* * +* 54 MET 54 1.303 1.223 1.510 1.537 1.443 122.28 116.03 120.92 110.51 110.58 110.01 123.05 +* +* 55 LYS 55 1.305 1.220 1.507 1.528 1.447 122.09 117.10 120.01 107.16 110.75 110.15 122.88 +* +* +* 56 LYS 56 1.313 1.235 1.485 1.521 1.442 120.51 115.82 120.76 107.71 107.16 113.86 123.39 * +* * * +* +* 57 ARG 57 1.268 1.236 1.496 1.542 1.424 120.89 115.23 121.13 111.57 108.50 113.26 123.59 **** * +* +* **** 58 GLY 58 1.302 1.236 1.506 - 1.424 120.94 116.12 120.75 - 111.50 - 123.09 +* +* +* 59 GLU 59 1.310 1.237 1.532 1.526 1.451 121.81 117.31 120.45 109.31 112.17 109.70 122.23 * * 60 LYS 60 1.315 1.238 1.529 1.546 1.457 120.26 116.03 121.01 110.55 111.77 109.56 122.93 * * 61 VAL 61 1.319 1.242 1.500 1.542 1.444 121.78 114.99 121.46 108.45 111.48 114.00 123.55 * * * 62 PHE 62 1.293 1.249 1.505 1.539 1.420 122.08 116.46 120.46 108.61 108.54 110.64 123.05 +** +* +** 63 LEU 63 1.300 1.227 1.508 1.527 1.451 120.50 116.85 119.95 110.13 107.54 112.00 123.20 ** * ** 64 THR 64 1.311 1.237 1.535 1.543 1.449 120.88 116.91 120.74 111.27 113.61 110.91 122.33 * * 65 VAL 65 1.318 1.234 1.521 1.571 1.446 120.79 115.62 121.16 112.53 109.83 113.01 123.15 * +* +* 66 GLY 66 1.306 1.223 1.492 - 1.429 121.63 115.19 121.55 - 109.88 - 123.26 +* * * +* 67 TRP 67 1.318 1.218 1.507 1.543 1.436 122.54 115.48 121.40 111.06 108.74 111.08 123.04 * * 68 GLU 68 1.310 1.210 1.547 1.551 1.442 121.19 115.86 121.41 115.27 108.59 109.53 122.62 * * * * +** +** 69 ASN 69 1.328 1.205 1.501 1.552 1.470 122.91 114.84 121.31 107.65 108.48 111.81 123.79 * * * * * 70 PHE 70 1.305 1.242 1.518 1.553 1.445 124.06 115.38 120.61 110.36 108.79 108.25 123.99 +* * * * +* Residue-by-residue listing for refined_8 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 1.336 1.201 1.508 1.579 1.448 122.52 116.36 120.96 110.49 110.40 112.93 122.67 +* * +* 72 LYS 72 1.301 1.228 1.519 1.527 1.441 120.67 116.93 120.41 110.69 111.22 111.38 122.64 ** ** 73 ASP 73 1.327 1.227 1.546 1.521 1.469 119.79 117.80 120.23 111.11 113.56 109.75 121.97 * * 74 ASN 74 1.325 1.235 1.517 1.535 1.494 121.03 115.77 120.81 111.72 113.01 113.49 123.42 +* +* +* 75 ASN 75 1.325 1.230 1.529 1.515 1.490 125.17 115.94 120.53 111.70 112.69 111.86 123.53 +* +* +* 76 LEU 76 1.316 1.243 1.518 1.531 1.495 123.20 115.66 121.42 111.84 115.33 113.95 122.86 +* * ** ** 77 GLU 77 1.290 1.233 1.515 1.522 1.432 121.24 114.88 120.93 111.62 109.51 108.79 124.19 +** * * +** 78 ASP 78 1.300 1.236 1.528 1.540 1.463 124.24 116.02 120.75 110.25 111.97 111.30 123.09 ** * ** 79 GLY 79 1.316 1.219 1.493 - 1.449 121.27 115.46 121.36 - 112.06 - 123.18 * * 80 LYS 80 1.296 1.232 1.514 1.528 1.438 123.03 117.13 120.04 113.27 109.62 108.63 122.83 ** * +* * ** 81 TYR 81 1.316 1.243 1.487 1.535 1.437 121.21 114.47 121.14 109.15 111.16 111.85 124.38 +* * +* 82 LEU 82 1.292 1.238 1.507 1.559 1.413 123.28 115.12 121.10 112.90 110.06 113.15 123.75 +** * ** * +* +** 83 GLN 83 1.303 1.227 1.509 1.530 1.435 122.96 116.15 120.50 109.84 108.65 109.29 123.34 +* * +* 84 PHE 84 1.298 1.231 1.498 1.530 1.436 122.23 116.81 120.03 108.18 109.09 109.89 123.14 ** * * * ** 85 ILE 85 1.297 1.245 1.515 1.556 1.438 120.94 115.52 120.82 111.48 108.48 112.73 123.63 ** * * ** 86 TYR 86 1.307 1.239 1.519 1.539 1.431 122.55 114.64 121.46 110.89 111.22 109.46 123.90 +* * +* 87 ASP 87 1.297 1.234 1.525 1.552 1.448 123.83 119.22 118.87 111.06 105.12 108.98 121.91 ** * * +* * ** ** 88 ARG 88 1.314 1.235 1.509 1.528 1.455 120.16 113.58 122.28 113.28 113.11 114.07 124.10 * * +* ** ** 89 ASP 89 1.298 1.217 1.523 1.559 1.423 126.10 119.15 118.98 110.68 102.60 108.84 121.87 ** * +* ** * * *** *** 90 ARG 90 1.279 1.228 1.507 1.533 1.458 121.61 114.28 122.19 111.09 108.33 111.73 123.50 +*** * +*** 91 THR 91 1.301 1.232 1.540 1.544 1.417 122.86 116.42 120.60 109.70 109.73 109.09 122.96 ** ** * ** 92 PHE 92 1.314 1.235 1.506 1.542 1.454 122.20 116.54 120.48 107.26 108.52 112.26 122.96 * * * * 93 TYR 93 1.293 1.236 1.505 1.531 1.439 121.40 116.51 120.10 111.41 108.39 111.17 123.37 +** * +** 94 VAL 94 1.312 1.237 1.510 1.553 1.439 121.51 116.02 121.12 109.11 109.95 111.80 122.85 * * 95 ILE 95 1.300 1.236 1.525 1.589 1.429 121.45 115.42 121.01 109.38 109.95 113.44 123.55 ** +* +* * ** 96 ILE 96 1.309 1.242 1.500 1.565 1.449 123.30 117.81 119.64 107.66 104.63 111.21 122.54 * * ** ** 97 TYR 97 1.294 1.227 1.506 1.526 1.439 119.62 114.84 121.54 111.73 110.58 111.61 123.56 ** * * ** 98 GLY 98 1.315 1.243 1.508 - 1.436 121.96 115.77 120.39 - 111.33 - 123.84 Residue-by-residue listing for refined_8 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 1.362 1.220 1.536 1.556 1.485 123.83 114.54 122.06 111.73 107.24 109.24 123.37 ** * * * * ** 100 ASN 100 1.326 1.230 1.513 1.540 1.452 123.23 114.75 121.53 110.84 113.98 111.45 123.63 101 MET 101 1.293 1.234 1.506 1.528 1.431 122.58 113.64 121.66 109.66 105.34 111.08 124.68 +** * * ** * +** 102 CYS 102 1.319 - 1.527 1.541 1.427 125.12 - - 111.60 106.14 111.08 - +* +* +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** +* +* +* ** ** +* * +** *** ** * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_8 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 1.268 1.362 1.309 .013 **** ** * C-N (Pro) 1.341 .016 5 1.330 1.357 1.341 .009 C-O C-O 1.231 .020 101 1.201 1.252 1.233 .010 +* * CA-C CH1E-C (except Gly) 1.525 .021 95 1.485 1.555 1.518 .015 +* * CH2G*-C (Gly) 1.516 .018 7 1.492 1.522 1.506 .010 * CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.522 1.535 1.528 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.542 1.589 1.559 .013 +* CH1E-CH2E (the rest) 1.530 .020 75 1.511 1.561 1.537 .011 +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.413 1.495 1.445 .016 ** +* NH1-CH2G* (Gly) 1.451 .016 7 1.424 1.465 1.442 .013 +* N-CH1E (Pro) 1.466 .015 5 1.450 1.472 1.459 .008 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_8 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 89 113.58 119.22 116.20 1.12 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 7 115.03 116.48 115.67 .47 CH1E-C-N (Pro) 116.9 1.5 5 114.99 116.84 115.96 .61 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 121.73 124.68 123.06 .63 * O-C-N (Pro) 122.0 1.4 5 122.48 123.92 123.15 .58 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.62 126.10 122.11 1.35 * ** C-NH1-CH2G* (Gly) 120.6 1.7 7 119.64 121.96 121.08 .76 C-N-CH1E (Pro) 122.6 5.0 5 121.81 123.00 122.37 .43 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 118.87 122.28 120.74 .63 * CH2G*-C-O (Gly) 120.8 2.1 7 120.39 121.55 120.98 .36 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 109.41 110.41 109.91 .50 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 107.66 112.53 110.27 1.16 +* CH2E-CH1E-C (the rest) 110.1 1.9 75 107.16 115.27 110.66 1.49 +* +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 102.60 115.33 110.02 2.24 *** * NH1-CH2G*-C (Gly) 112.5 2.9 7 109.88 114.73 112.20 1.42 N-CH1E-C (Pro) 111.8 2.5 5 109.98 113.24 111.44 1.17 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 110.95 111.21 111.08 .13 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.09 114.00 111.80 1.37 * * N-CH1E-CH2E (Pro) 103.0 1.1 5 103.28 104.25 104.00 .36 * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 108.02 114.07 110.85 1.51 * ** ------------------------------------------------------------------------------------------------------------- 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_8 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] 74 84.1% Residues in additional allowed regions [a,b,l,p] 13 14.8% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 1 1.1% ---- ------ Number of non-glycine and non-proline residues 88 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 7 Number of proline residues 5 ---- Total number of residues 102 Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good quality model would be expected to have over 90% in the most favoured regions [E,H,L]. S T E R E O C H E M I S T R Y O F M A I N - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. %-tage residues in A, B, L 88 84.1 83.8 10.0 .0 Inside b. Omega angle st dev 101 3.7 6.0 3.0 -.8 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 2.0 3.1 1.6 -.7 Inside e. H-bond energy st dev 65 .9 .8 .2 .6 Inside f. Overall G-factor 102 -.1 -.4 .3 1.0 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 17 6.1 18.1 6.5 -1.9 BETTER b. Chi-1 trans st dev 31 5.7 19.0 5.3 -2.5 BETTER c. Chi-1 gauche plus st dev 40 8.2 17.5 4.9 -1.9 BETTER d. Chi-1 pooled st dev 88 7.9 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 25 6.7 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% 84.1 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.5 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .97 3 Residue-by-residue listing for refined_8 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.50 Chi1-chi2 distribution -.35 Chi1 only -.22 Chi3 & chi4 .38 Omega -.11 ------ -.23 ===== Main-chain covalent forces:- Main-chain bond lengths -.05 Main-chain bond angles .37 ------ .19 ===== OVERALL AVERAGE -.08 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.