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 - - 189.4 - - - - - - - - 178.8 - 34.1 - 2 ALA 2 a - - - - - - - - - - 183.6 - 35.2 - 3 ASP 3 B - - -55.0 - - - - - - - 181.8 - 35.6 - 4 THR 4 A - - -56.9 - - - - - - - 185.7 -.8 34.7 - +* +* 5 GLY 5 - - - - - - - - - - - 175.4 - - - 6 GLU 6 S B 54.5 - - 174.4 - - - - - - 181.1 - 32.7 - 7 VAL 7 E B - - -63.7 - - - - - - - 177.2 -2.8 32.7 - 8 GLN 8 E B - 184.6 - 178.7 - - - - - - 181.6 - 35.6 - 9 PHE 9 E B - 189.0 - - - - - - - - 179.1 -2.5 35.3 - 10 MET 10 E B 59.2 - - 176.4 - - - - - - 180.1 - 33.4 - 11 LYS 11 e B 52.8 - - - - - - - - - 175.7 -1.0 30.9 - * * 12 PRO 12 - - - - - -54.9 - - - - - 181.2 - 39.0 - * * 13 PHE 13 B - - -90.9 - - - - - - - 176.4 -.6 33.3 - +* +* +* 14 ILE 14 t B - - -58.3 176.5 - - - - - - 188.2 - 35.4 - * * 15 SER 15 T A - - -34.1 - - - - - - - 185.8 -.7 38.5 - ** +* * ** 16 GLU 16 g A - 186.1 - 181.4 - - - - - - 184.4 - 35.5 - 17 LYS 17 G A - 184.9 - 190.8 - - - - - - 183.5 -.5 35.8 - ** ** 18 SER 18 G A - - -61.9 - - - - - - - 169.0 -2.9 32.5 - +* * +* 19 SER 19 G A - - -61.5 - - - - - - - 183.7 -.6 36.1 - +* +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 20 LYS 20 g a - 179.6 - - - - - - - - 188.7 -1.1 34.7 - +* * +* 21 SER 21 t B - - -55.6 - - - - - - - 180.1 -1.3 35.6 - 22 LEU 22 E B - 194.8 - 178.4 - - - - - - 181.3 -2.7 35.6 - 23 GLU 23 E B - 170.3 - 174.9 - - - - - - 176.7 - 33.7 - 24 ILE 24 E B - - -59.7 - - - - - - - 178.8 -2.5 36.0 - 25 PRO 25 h - - - - - -52.8 - - - - - 181.1 - 39.1 - * * * 26 LEU 26 H A - 189.1 - 169.1 - -55.4 -47.0 - - - 182.6 - 34.7 - 27 GLY 27 H - - - - - - -71.6 -13.0 - - - 180.0 - - - ** ** 28 PHE 28 H A - 194.5 - - - -89.5 -20.1 - - - 181.5 -1.1 33.4 - ** +* * ** 29 ASN 29 H A - 170.4 - - - -62.2 -48.1 - - - 182.3 -1.0 35.5 - * * 30 GLU 30 h A 57.7 - - - - - - - - - 183.6 -.8 30.4 - +* +* 31 TYR 31 T A - 182.1 - - - - - - - - 178.0 - 34.6 - 32 PHE 32 t b 66.9 - - - - - - - - - 173.5 -.7 30.7 - * +* +* 33 PRO 33 - - - - - -82.9 - - - - - 180.7 - 38.5 - +* * +* 34 ALA 34 B - - - - - - - - - - 170.1 - 35.5 - +* +* 35 PRO 35 - - - - - -54.2 - - - - - 185.0 - 38.6 - * * * 36 PHE 36 B 55.4 - - - - - - - - - 180.5 - 31.3 - 37 PRO 37 - - - - - -74.9 - - - - - 176.5 - 39.1 - * * 38 ILE 38 S A - - -57.8 - - - - - - - 179.7 - 33.1 - 39 THR 39 B 52.2 - - - - - - - - - 174.5 - 34.8 - 40 VAL 40 E B - - -61.3 - - - - - - - 181.8 -3.0 33.9 - * * 41 ASP 41 E B - - -65.8 - - - - - - - 176.7 -1.3 31.9 - * * 42 LEU 42 E B - - -59.3 176.6 - - - - - - 176.5 -3.2 36.8 - +* +* 43 LEU 43 E B - - -88.2 - - - - - - - 178.5 -2.8 33.3 - * * * 44 ASP 44 E B - 178.2 - - - - - - - - 182.7 -2.2 35.2 - 45 TYR 45 e A - 190.0 - - - - - - - - 179.1 -.7 34.3 - +* +* 46 SER 46 T A - - -50.1 - - - - - - - 176.8 - 34.2 - * * 47 GLY 47 t - - - - - - - - - - - 181.2 -1.7 - - 48 ARG 48 e B - 182.3 - 176.4 - - - - - - 179.6 - 33.0 - 49 SER 49 E B 58.9 - - - - - - - - - 175.7 - 33.1 - 50 TRP 50 E B - - -70.2 - - - - - - - 178.8 -2.7 34.2 - 51 THR 51 E B - - -55.1 - - - - - - - 182.6 - 34.4 - 52 VAL 52 E B 58.8 - - - - - - - - - 180.8 -2.8 33.4 - 53 ARG 53 e B - - -58.4 177.9 - - - - - - 184.9 -2.9 34.4 - * * 54 MET 54 E B - 171.9 - 184.1 - - - - - - 179.1 -.6 36.9 - +* +* 55 LYS 55 E B - 185.3 - 175.2 - - - - - - 174.5 -1.2 35.3 - * * 56 LYS 56 E B - - -62.1 - - - - - - - 177.1 - 36.9 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 57 ARG 57 E b - 181.5 - 177.0 - - - - - - 179.8 -1.0 33.2 - * * 58 GLY 58 T - - - - - - - - - - - 182.5 - - - 59 GLU 59 T A - - -58.1 176.8 - - - - - - 184.2 - 35.8 - 60 LYS 60 E B - - -62.3 171.1 - - - - - - 177.4 -.6 36.3 - +* +* 61 VAL 61 E B - 183.3 - - - - - - - - 174.9 -.7 34.7 - +* +* 62 PHE 62 E B - - -66.6 - - - - - - - 173.7 -1.2 33.2 - * * * 63 LEU 63 E B - - -59.6 - - - - - - - 192.5 -2.2 32.7 - ** ** 64 THR 64 e a 51.2 - - - - - - - - - 182.7 -1.2 31.4 - * * 65 VAL 65 S B - 179.3 - - - - - - - - 177.6 - 33.9 - 66 GLY 66 h - - - - - - - - - - - 177.9 - - - 67 TRP 67 H A - 166.4 - - - -58.9 -26.2 - - - 180.4 - 34.6 - * * * 68 GLU 68 H A 55.5 - - 192.1 - -58.0 -36.0 - - - 180.4 -.6 34.7 - +* +* 69 ASN 69 H A - - -65.5 - - -72.8 -31.9 - - - 181.3 -1.5 33.2 - 70 PHE 70 H A - 184.4 - - - -70.4 -52.5 - - - 178.7 -.8 34.8 - * +* +* 71 VAL 71 H A - 160.0 - - - -65.4 -37.2 - - - 175.9 -2.6 29.2 - * * * 72 LYS 72 H A - - -63.2 - - -70.6 -43.4 - - - 181.7 -2.2 31.5 - 73 ASP 73 H A - - -83.8 - - -69.1 -39.8 - - - 180.5 -2.8 30.8 - * * * 74 ASN 74 H A - 184.7 - - - -91.4 -13.8 - - - 184.4 -2.9 34.0 - ** ** * ** 75 ASN 75 h l - 180.6 - - - - - - - - 180.9 -.9 30.8 - * * 76 LEU 76 t B - - -69.2 175.5 - - - - - - 176.7 -1.4 33.5 - 77 GLU 77 t B 38.6 - - - - - - - - - 182.1 - 29.1 - +* * +* 78 ASP 78 T B - 177.4 - - - - - - - - 181.9 - 35.8 - 79 GLY 79 T - - - - - - - - - - - 177.7 - - - 80 LYS 80 t B - - -70.7 - - - - - - - 182.9 -1.9 32.5 - 81 TYR 81 e B - - -63.3 - - - - - - - 177.6 - 35.0 - 82 LEU 82 E B 55.0 - - - - - - - - - 182.5 - 30.4 - * * 83 GLN 83 E B 61.0 - - 182.0 - - - - - - 177.5 -2.5 35.4 - 84 PHE 84 E B - - -60.2 - - - - - - - 172.5 -3.7 35.9 - * ** ** 85 ILE 85 E B - - -55.1 177.8 - - - - - - 180.3 -2.5 35.0 - 86 TYR 86 E B - 181.2 - - - - - - - - 181.9 -3.4 34.2 - +* +* 87 ASP 87 e A - - -69.1 - - - - - - - 177.6 -.6 33.8 - +* +* 88 ARG 88 S l - 182.1 - - - - - - - - 178.8 - 31.8 - 89 ASP 89 S ~a 58.0 - - - - - - - - - 178.2 - 31.0 - ** ** 90 ARG 90 e a - 191.3 - - - - - - - - 185.8 - 35.7 - 91 THR 91 E B - - -54.8 - - - - - - - 174.0 - 34.9 - * * 92 PHE 92 E B - - -63.1 - - - - - - - 179.2 -2.9 34.9 - * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 93 TYR 93 E B - - -54.0 - - - - - - - 183.6 -2.8 34.5 - 94 VAL 94 E B - 185.9 - - - - - - - - 176.3 -3.6 35.1 - ** ** 95 ILE 95 E B - - -60.7 - - - - - - - 178.4 -2.0 33.5 - 96 ILE 96 E B - - -51.4 - - - - - - - 179.3 - 36.8 - * * 97 TYR 97 e B - - -66.4 - - - - - - - 179.4 -2.9 34.2 - * * 98 GLY 98 S - - - - - - - - - - - 178.2 -.8 - - +* +* 99 HIS 99 S a - 186.6 - - - - - - - - 179.4 - 32.6 - 100 ASN 100 S a - - -66.5 - - - - - - - 177.7 - 32.8 - 101 MET 101 B 65.7 - - 179.7 - - - - - - 182.0 - 33.8 - 102 CYS 102 - - 182.0 - - - - - - - - - - 33.6 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** +* * ** +* ** ** ** ** * ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.3 182.2 -62.2 178.3 -63.9 -69.6 -34.1 - - - 179.8 -1.8 34.2 Standard deviations: 6.4 7.8 9.8 5.4 14.0 11.3 13.3 - - - 3.7 1.0 2.1 Numbers of values: 16 32 40 22 5 12 12 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_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 - 1.236 1.534 1.555 1.467 - 116.30 120.96 111.96 108.52 109.73 122.70 * * 2 ALA 2 1.319 1.235 1.506 1.514 1.455 122.56 114.11 122.13 110.22 107.92 109.67 123.75 * * * 3 ASP 3 1.298 1.233 1.513 1.536 1.437 123.72 116.20 120.84 109.96 109.16 109.44 122.92 ** * * ** 4 THR 4 1.301 1.238 1.515 1.543 1.435 121.36 115.43 121.15 109.95 111.18 110.18 123.40 +* * +* 5 GLY 5 1.299 1.240 1.499 - 1.437 120.64 116.30 120.32 - 109.20 - 123.38 ** * ** 6 GLU 6 1.287 1.238 1.511 1.537 1.438 121.73 116.51 121.01 111.21 109.51 112.27 122.47 +** * * +** 7 VAL 7 1.301 1.235 1.508 1.565 1.438 120.87 115.78 121.31 110.27 111.09 112.89 122.90 +* * +* 8 GLN 8 1.293 1.233 1.505 1.533 1.422 121.46 117.45 119.96 110.82 106.98 109.29 122.59 +** +* +* +** 9 PHE 9 1.294 1.221 1.511 1.547 1.445 120.68 116.82 120.31 110.91 109.16 108.97 122.86 ** ** 10 MET 10 1.299 1.229 1.504 1.542 1.451 121.68 116.74 120.28 110.35 109.81 112.07 122.96 ** ** 11 LYS 11 1.305 1.228 1.529 1.565 1.443 121.08 116.85 120.30 113.40 112.56 111.42 122.74 +* +* +* +* 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 1.353 1.237 1.537 1.530 1.478 123.64 115.94 121.05 109.31 112.62 103.79 123.00 13 PHE 13 1.310 1.231 1.500 1.517 1.453 122.90 116.12 120.74 109.96 113.26 111.04 123.13 * * * 14 ILE 14 1.321 1.243 1.500 1.556 1.425 121.62 116.12 119.87 109.72 104.75 111.49 124.01 * +* ** ** 15 SER 15 1.312 1.211 1.516 1.512 1.456 123.49 114.74 121.05 106.50 110.75 107.68 124.14 * +* +* +* 16 GLU 16 1.308 1.235 1.516 1.505 1.430 124.23 116.56 120.47 110.00 112.09 108.35 122.94 +* * * * * +* 17 LYS 17 1.319 1.237 1.490 1.525 1.451 120.74 114.38 122.08 109.52 108.77 109.61 123.51 +* +* 18 SER 18 1.280 1.215 1.522 1.494 1.395 121.93 116.62 120.44 114.05 112.79 108.21 122.93 +*** +* *** ** * +*** 19 SER 19 1.338 1.233 1.516 1.539 1.455 120.51 114.90 121.71 107.19 107.49 111.60 123.39 +* * +* 20 LYS 20 1.322 1.224 1.524 1.534 1.429 121.28 116.52 120.65 110.39 112.30 109.28 122.82 +* +* 21 SER 21 1.314 1.244 1.530 1.515 1.437 121.15 115.46 121.22 110.53 112.44 107.61 123.32 * * +* +* 22 LEU 22 1.311 1.239 1.523 1.552 1.448 122.95 116.05 120.31 110.69 107.15 109.18 123.64 * * * * 23 GLU 23 1.303 1.237 1.536 1.532 1.438 122.38 115.52 121.08 111.46 112.14 109.53 123.39 +* * +* 24 ILE 24 1.318 1.243 1.535 1.554 1.451 123.13 117.76 119.76 108.13 108.43 110.73 122.47 25 PRO 25 1.349 1.247 1.538 1.520 1.473 123.34 115.09 121.17 109.56 113.41 103.12 123.73 * * * 26 LEU 26 1.324 1.230 1.538 1.560 1.456 124.28 116.54 120.80 112.13 110.84 108.08 122.61 +* * * * +* 27 GLY 27 1.321 1.219 1.518 - 1.452 120.67 117.01 120.78 - 113.54 - 122.19 28 PHE 28 1.309 1.226 1.548 1.542 1.447 121.26 115.64 121.29 112.57 109.57 109.66 123.05 * * * * 29 ASN 29 1.334 1.250 1.529 1.543 1.482 123.49 116.31 120.59 109.14 112.88 108.99 123.10 * * 30 GLU 30 1.319 1.234 1.516 1.551 1.457 121.86 115.47 121.07 113.50 112.57 111.82 123.46 * +* +* 31 TYR 31 1.317 1.227 1.525 1.530 1.441 122.47 116.97 120.60 110.90 111.25 109.19 122.40 32 PHE 32 1.315 1.229 1.533 1.563 1.440 119.99 117.22 121.91 112.72 111.68 112.73 120.63 * +* * * * +* 33 PRO 33 1.321 1.233 1.508 1.518 1.433 122.36 114.31 121.71 109.81 111.30 104.58 123.98 * ** +* * * ** 34 ALA 34 1.274 1.244 1.501 1.529 1.436 124.09 119.67 118.46 110.22 107.04 109.74 121.86 +*** * * * +* * * +*** 35 PRO 35 1.343 1.245 1.524 1.534 1.451 121.05 117.70 119.86 110.11 108.40 104.57 122.43 * * * 36 PHE 36 1.305 1.229 1.520 1.533 1.401 120.47 116.77 120.87 113.32 111.71 111.42 122.32 +* *** +* *** 37 PRO 37 1.329 1.228 1.517 1.537 1.447 122.42 116.91 120.86 110.45 110.91 103.24 122.21 * * 38 ILE 38 1.292 1.228 1.512 1.554 1.427 119.95 115.97 120.84 110.95 108.27 112.65 123.12 +** +* * +** 39 THR 39 1.310 1.233 1.525 1.546 1.434 122.10 115.56 120.75 109.13 111.28 110.79 123.69 * * * 40 VAL 40 1.308 1.242 1.521 1.577 1.449 124.31 118.39 119.49 109.83 106.54 113.11 122.11 +* * * * +* +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 41 ASP 41 1.306 1.239 1.490 1.539 1.460 119.43 114.35 121.55 109.70 112.47 113.77 124.09 +* +* * +* +* 42 LEU 42 1.293 1.228 1.499 1.527 1.424 123.60 116.64 120.41 107.93 107.81 109.92 122.94 +** * +* * * * +** 43 LEU 43 1.285 1.215 1.485 1.546 1.441 121.35 115.84 120.58 110.20 109.86 112.54 123.57 *** +* * *** 44 ASP 44 1.282 1.239 1.491 1.530 1.435 121.94 115.97 120.38 109.83 108.17 110.38 123.63 *** +* * * *** 45 TYR 45 1.304 1.232 1.544 1.537 1.451 123.40 116.78 120.65 111.44 110.95 109.05 122.55 +* +* 46 SER 46 1.331 1.227 1.547 1.526 1.450 121.58 116.87 120.56 110.81 110.67 109.82 122.56 * * 47 GLY 47 1.340 1.228 1.526 - 1.454 120.34 118.09 119.80 - 114.83 - 122.10 48 ARG 48 1.317 1.236 1.534 1.546 1.467 120.35 117.35 119.94 111.86 110.05 110.78 122.69 49 SER 49 1.329 1.235 1.525 1.542 1.445 121.30 115.61 121.01 110.66 111.93 111.32 123.35 50 TRP 50 1.306 1.225 1.518 1.537 1.450 122.89 117.03 120.35 109.39 109.46 111.76 122.61 +* +* 51 THR 51 1.297 1.241 1.531 1.533 1.436 121.49 115.96 121.17 110.07 109.75 110.69 122.87 ** * ** 52 VAL 52 1.297 1.228 1.527 1.564 1.441 122.37 116.58 120.70 111.54 109.81 111.00 122.71 ** * ** 53 ARG 53 1.302 1.229 1.520 1.527 1.425 121.86 114.79 121.44 112.14 109.46 108.80 123.77 +* +* * +* 54 MET 54 1.305 1.212 1.509 1.531 1.452 124.25 117.63 119.77 109.25 109.92 107.84 122.60 +* * +* +* 55 LYS 55 1.317 1.231 1.523 1.519 1.439 120.53 116.96 120.29 110.16 110.59 108.99 122.72 56 LYS 56 1.327 1.237 1.505 1.499 1.430 121.58 116.07 120.45 105.50 107.42 111.80 123.44 +* * ** * ** 57 ARG 57 1.264 1.230 1.519 1.533 1.441 122.28 116.73 120.36 111.32 109.93 111.17 122.89 *4.6* *4.6* 58 GLY 58 1.306 1.233 1.511 - 1.440 120.30 116.37 120.48 - 112.05 - 123.15 +* +* 59 GLU 59 1.317 1.226 1.517 1.524 1.462 122.03 116.25 120.67 108.45 110.94 109.84 123.09 60 LYS 60 1.313 1.232 1.514 1.531 1.436 122.83 117.18 120.23 109.87 109.14 108.44 122.58 * * * * 61 VAL 61 1.307 1.232 1.498 1.565 1.448 120.63 116.82 120.38 108.08 107.98 113.32 122.76 +* * * * +* 62 PHE 62 1.284 1.239 1.483 1.538 1.416 120.30 115.72 121.10 110.40 109.55 112.62 123.14 *** ** ** * *** 63 LEU 63 1.289 1.225 1.492 1.551 1.422 120.06 115.06 120.73 111.91 104.78 113.57 124.17 +** +* * +* ** +* +** 64 THR 64 1.296 1.225 1.538 1.546 1.438 122.87 116.06 120.96 111.95 115.89 110.60 122.97 ** * * +* ** 65 VAL 65 1.291 1.234 1.522 1.560 1.457 123.04 116.91 120.15 110.47 110.83 110.97 122.93 +** +** 66 GLY 66 1.320 1.232 1.486 - 1.445 120.09 115.61 120.66 - 113.29 - 123.73 +* +* 67 TRP 67 1.325 1.242 1.514 1.541 1.462 122.97 113.64 122.02 110.51 109.57 110.10 124.27 * * 68 GLU 68 1.294 1.209 1.527 1.527 1.442 123.69 116.24 120.92 111.98 110.33 108.20 122.73 ** * * * ** 69 ASN 69 1.315 1.192 1.510 1.534 1.443 121.97 116.38 120.83 111.24 110.92 111.03 122.71 +* +* 70 PHE 70 1.300 1.237 1.522 1.547 1.452 123.06 115.89 120.92 110.56 109.01 110.05 123.17 ** ** 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 1.326 1.225 1.517 1.567 1.451 121.31 117.38 120.32 113.60 112.24 113.60 122.28 ** * ** 72 LYS 72 1.316 1.238 1.532 1.535 1.446 119.66 117.21 120.12 111.67 111.36 112.64 122.63 * * * 73 ASP 73 1.339 1.224 1.506 1.536 1.483 121.28 117.69 120.07 110.13 114.64 113.59 122.24 * * +* +* 74 ASN 74 1.299 1.232 1.523 1.541 1.464 119.95 114.68 121.39 110.99 109.76 110.34 123.85 ** ** 75 ASN 75 1.326 1.232 1.523 1.538 1.462 124.29 115.48 121.85 112.46 111.22 112.81 122.58 * * * * 76 LEU 76 1.299 1.233 1.487 1.523 1.440 121.32 114.88 121.19 109.77 111.54 111.87 123.93 ** +* ** 77 GLU 77 1.290 1.254 1.523 1.562 1.411 123.01 115.61 120.32 115.03 111.62 112.70 124.00 +** * +* ** +** * +** 78 ASP 78 1.320 1.238 1.530 1.534 1.460 124.15 116.35 120.67 109.31 110.79 109.08 122.98 * * 79 GLY 79 1.318 1.234 1.517 - 1.446 121.06 116.53 120.90 - 111.60 - 122.57 80 LYS 80 1.324 1.231 1.509 1.551 1.463 121.09 116.82 120.52 110.20 110.03 113.31 122.65 * +* +* 81 TYR 81 1.303 1.241 1.485 1.541 1.429 121.40 115.92 120.43 109.15 108.56 111.55 123.63 +* +* +* +* 82 LEU 82 1.287 1.242 1.510 1.560 1.407 121.80 115.81 120.63 113.99 110.71 112.56 123.54 *** * +** ** * *** 83 GLN 83 1.296 1.234 1.524 1.537 1.442 122.56 116.31 120.35 109.78 109.86 109.62 123.33 ** ** 84 PHE 84 1.305 1.235 1.510 1.535 1.443 122.62 116.79 120.15 107.45 109.63 111.23 123.03 +* * +* 85 ILE 85 1.299 1.237 1.515 1.556 1.444 121.39 117.08 119.97 108.59 106.64 112.54 122.90 ** +* ** 86 TYR 86 1.302 1.238 1.525 1.547 1.446 120.92 116.15 120.91 111.97 109.80 109.19 122.93 +* +* 87 ASP 87 1.323 1.238 1.515 1.537 1.469 121.95 115.50 120.69 109.35 111.18 111.71 123.80 88 ARG 88 1.336 1.234 1.560 1.567 1.479 124.00 117.11 121.26 112.64 112.15 110.87 121.61 +* +* * * * +* 89 ASP 89 1.316 1.236 1.541 1.542 1.441 120.90 117.21 120.59 112.73 112.49 111.75 122.20 * * 90 ARG 90 1.304 1.234 1.529 1.537 1.433 121.89 116.06 121.38 110.06 108.60 109.26 122.56 +* * +* 91 THR 91 1.316 1.231 1.533 1.542 1.436 120.56 115.58 121.11 109.85 112.38 109.49 123.29 * * * 92 PHE 92 1.318 1.242 1.517 1.536 1.439 122.80 116.89 120.55 109.42 107.86 111.25 122.53 * * 93 TYR 93 1.299 1.231 1.508 1.530 1.444 120.95 116.28 120.37 110.20 108.27 110.93 123.34 ** * ** 94 VAL 94 1.299 1.237 1.522 1.552 1.435 122.22 115.96 120.99 108.79 109.95 111.22 123.01 ** * ** 95 ILE 95 1.303 1.234 1.525 1.594 1.445 121.71 116.81 119.99 109.30 108.04 113.90 123.19 +* +* * * +* 96 ILE 96 1.317 1.232 1.521 1.572 1.459 122.22 117.37 119.90 107.48 106.81 110.77 122.73 * +* +* 97 TYR 97 1.314 1.237 1.513 1.534 1.449 120.86 116.01 120.70 109.45 110.20 111.53 123.28 * * 98 GLY 98 1.305 1.239 1.497 - 1.436 121.25 116.75 120.23 - 110.85 - 123.02 +* * +* 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 1.308 1.231 1.532 1.550 1.438 120.96 117.36 120.23 112.63 109.95 110.84 122.38 * * * * 100 ASN 100 1.319 1.236 1.513 1.551 1.471 121.42 116.27 120.91 110.15 110.47 112.79 122.82 * * * 101 MET 101 1.313 1.234 1.509 1.543 1.453 121.92 116.86 119.94 110.18 108.50 111.97 123.20 * * 102 CYS 102 1.303 - 1.521 1.533 1.436 121.58 - - 111.42 109.74 110.61 - +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *4.6* +* ** +* *** * +* * +** ** +* * *4.6* ----------------------------------------------------------------------------------------------------------------------------------- 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 1.264 1.340 1.308 .014 *4.6* * C-N (Pro) 1.341 .016 5 1.321 1.353 1.339 .012 * C-O C-O 1.231 .020 101 1.192 1.254 1.233 .009 +* * CA-C CH1E-C (except Gly) 1.525 .021 95 1.483 1.560 1.518 .015 ** +* CH2G*-C (Gly) 1.516 .018 7 1.486 1.526 1.508 .013 +* CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.514 1.529 1.522 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.533 1.594 1.558 .014 +* CH1E-CH2E (the rest) 1.530 .020 75 1.494 1.567 1.536 .014 +* +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.395 1.483 1.444 .016 *** * NH1-CH2G* (Gly) 1.451 .016 7 1.436 1.454 1.444 .007 N-CH1E (Pro) 1.466 .015 5 1.433 1.478 1.456 .017 ** ------------------------------------------------------------------------------------------------------------- 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 89 113.64 119.67 116.29 .94 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 7 115.61 118.09 116.67 .71 CH1E-C-N (Pro) 116.9 1.5 5 114.31 117.70 115.99 1.22 +* O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.63 124.27 122.99 .59 * O-C-N (Pro) 122.0 1.4 5 122.21 123.98 123.07 .70 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.43 124.31 121.93 1.20 * * C-NH1-CH2G* (Gly) 120.6 1.7 7 120.09 121.25 120.62 .39 C-N-CH1E (Pro) 122.6 5.0 5 121.05 123.64 122.56 .91 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 118.46 122.13 120.69 .60 * CH2G*-C-O (Gly) 120.8 2.1 7 119.80 120.90 120.45 .35 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.22 110.22 110.22 .00 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 107.48 113.60 109.87 1.46 ** CH2E-CH1E-C (the rest) 110.1 1.9 75 105.50 115.03 110.64 1.68 ** +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.75 115.89 110.04 1.98 ** +* NH1-CH2G*-C (Gly) 112.5 2.9 7 109.20 114.83 112.19 1.74 * N-CH1E-C (Pro) 111.8 2.5 5 108.40 113.41 111.33 1.72 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.67 109.74 109.71 .04 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.49 113.90 111.66 1.28 * * N-CH1E-CH2E (Pro) 103.0 1.1 5 103.12 104.58 103.86 .63 * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 107.61 113.77 110.61 1.60 +* +* ------------------------------------------------------------------------------------------------------------- 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] 77 87.5% Residues in additional allowed regions [a,b,l,p] 10 11.4% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.1% 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 87.5 83.8 10.0 .4 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 2.1 3.1 1.6 -.7 Inside e. H-bond energy st dev 56 1.0 .8 .2 .8 Inside f. Overall G-factor 102 .0 -.4 .3 1.1 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 16 6.4 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 32 7.8 19.0 5.3 -2.1 BETTER c. Chi-1 gauche plus st dev 40 9.8 17.5 4.9 -1.6 BETTER d. Chi-1 pooled st dev 88 9.7 18.2 4.8 -1.8 BETTER e. Chi-2 trans st dev 22 5.4 20.4 5.0 -3.0 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% 87.5 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 10.8 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 1.00 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 -.45 Chi1-chi2 distribution -.33 Chi1 only -.06 Chi3 & chi4 .52 Omega -.06 ------ -.16 ===== Main-chain covalent forces:- Main-chain bond lengths -.11 Main-chain bond angles .39 ------ .18 ===== OVERALL AVERAGE -.05 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.