Residue-by-residue listing for refined_13 Page 1 ---------------------------------------- This listing highlights the residues in the structure which may need investigation. The ideal values and standard deviations against which the structure has been compared are shown in the following table: <------------------------------- I D E A L V A L U E S -------------------------------> Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha ------------------------------------------------------------------------------------------ Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9 Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5 ------------------------------------------------------------------------------------------ In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above. Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*. The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing. Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments. Full print-out. ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 1 GLU 1 - - - -59.3 180.8 - - - - - - 176.5 - 33.8 - 2 ALA 2 b - - - - - - - - - - 186.0 - 34.1 - * * 3 GLU 3 b - 182.2 - 174.4 - - - - - - 173.5 - 31.4 - * * 4 VAL 4 b 65.3 - - - - - - - - - 174.8 -1.2 35.0 - * * 5 HIS 5 S A - 179.1 - - - - - - - - 174.6 - 33.6 - 6 ASN 6 b - 190.8 - - - - - - - - 180.1 - 33.8 - 7 GLN 7 B 54.3 - - 194.8 - - - - - - 189.4 - 31.2 - +* +* 8 LEU 8 E B - - -63.6 - - - - - - - 178.4 -2.0 34.2 - 9 GLU 9 E B - - -57.3 - - - - - - - 178.4 - 34.6 - 10 ILE 10 E B - - -55.2 179.2 - - - - - - 173.6 -3.2 35.8 - * * * 11 LYS 11 E B 70.3 - - - - - - - - - 184.4 -3.2 30.4 - +* +* 12 PHE 12 E B - - -56.8 - - - - - - - 174.8 -.6 36.1 - +* +* 13 ARG 13 E B - 194.5 - 181.4 - - - - - - 185.8 -3.2 33.0 - * * 14 LEU 14 E B - - -60.1 - - - - - - - 182.4 -3.4 34.3 - +* +* 15 THR 15 e A 46.1 - - - - - - - - - 179.9 -.7 34.8 - * +* +* 16 ASP 16 T A - - -76.3 - - - - - - - 177.9 - 31.7 - 17 GLY 17 t - - - - - - - - - - - 175.3 -1.3 - - 18 SER 18 e B - - -56.5 - - - - - - - 178.4 - 35.6 - Residue-by-residue listing for refined_13 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 ASP 19 E B 59.8 - - - - - - - - - 177.6 - 33.3 - 20 ILE 20 E B - - -58.8 178.6 - - - - - - 181.3 -2.9 35.5 - * * 21 GLY 21 E - - - - - - - - - - - 183.2 - - - 22 PRO 22 E - - - - - -60.6 - - - - - 181.6 - 37.4 - 23 LYS 23 E B - 182.3 - 183.1 - - - - - - 181.2 -2.5 36.3 - 24 ALA 24 E B - - - - - - - - - - 180.4 - 33.5 - 25 PHE 25 E B - - -48.2 - - - - - - - 171.0 -3.7 37.1 - * +* ** ** 26 PRO 26 t - - - - - -66.5 - - - - - 178.7 - 40.0 - +* +* 27 ASP 27 T A 61.4 - - - - - - - - - 178.1 - 32.5 - 28 ALA 28 T A - - - - - - - - - - 179.6 - 34.3 - 29 THR 29 t B - - -58.1 - - - - - - - 175.6 -1.4 35.2 - 30 THR 30 h B - 174.0 - - - - - - - - 179.1 - 33.8 - 31 VAL 31 H A - 181.8 - - - -64.6 -26.0 - - - 174.2 -3.4 32.8 - * +* +* 32 SER 32 H A - 184.3 - - - -58.5 -45.9 - - - 180.2 -.9 35.0 - +* +* 33 ALA 33 H A - - - - - -77.5 -22.9 - - - 175.0 - 33.0 - * * * 34 LEU 34 H A - 171.4 - - - -64.6 -44.3 - - - 174.4 -1.6 35.7 - 35 LYS 35 H A - - -90.7 - - -71.0 -30.0 - - - 176.6 -2.5 30.0 - +* * +* 36 GLU 36 H A - - -66.2 - - -56.2 -32.7 - - - 174.2 -1.3 33.6 - * * 37 THR 37 H A - - -55.7 - - -72.8 -49.2 - - - 182.8 -1.1 34.4 - * * 38 VAL 38 H A - 182.6 - - - -61.1 -43.0 - - - 181.1 -1.6 33.4 - 39 ILE 39 H A - - -51.2 176.2 - -63.3 -34.2 - - - 180.6 -3.8 33.9 - * ** ** 40 SER 40 H A - 178.1 - - - -76.0 -40.2 - - - 187.6 -.9 35.2 - * * * 41 GLU 41 H A - - -54.5 - - -91.9 -37.2 - - - 183.3 -2.6 34.2 - ** ** 42 TRP 42 h B - 183.8 - - - - - - - - 176.4 -3.0 34.5 - * * 43 PRO 43 t - - - - - -66.1 - - - - - 178.9 - 39.4 - +* +* 44 ARG 44 T A - 188.9 - 178.0 - - - - - - 177.8 - 34.7 - 45 GLU 45 T A - - -57.9 178.6 - - - - - - 175.8 - 34.1 - 46 LYS 46 t B - 184.9 - - - - - - - - 172.5 -1.5 38.2 - * * * 47 GLU 47 T B - - -74.4 - - - - - - - 187.3 - 32.2 - * * 48 ASN 48 T l - - -60.8 - - - - - - - 188.4 - 33.7 - * * 49 GLY 49 t - - - - - - - - - - - 175.7 -.6 - - +* +* 50 PRO 50 - - - - - -93.7 - - - - - 178.7 - 40.0 - +** +* +** 51 LYS 51 ~a - 183.5 - 183.5 - - - - - - 189.5 - 33.5 - ** +* ** 52 THR 52 B 51.9 - - - - - - - - - 189.8 - 29.4 - +* * +* 53 VAL 53 t A 54.0 - - - - - - - - - 191.3 - 33.1 - +* +* Residue-by-residue listing for refined_13 Page 3 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 54 LYS 54 T A - 182.7 - 180.6 - - - - - - 186.5 - 32.6 - * * 55 GLU 55 T A 62.3 - - 182.8 - - - - - - 175.1 - 29.0 - * * 56 VAL 56 t B 61.8 - - - - - - - - - 185.2 -1.0 33.2 - * * 57 LYS 57 E B - - -58.8 - - - - - - - 176.8 -1.5 33.6 - 58 LEU 58 E B - - -63.4 - - - - - - - 179.6 -.9 35.3 - +* +* 59 ILE 59 E B - - -67.6 - - - - - - - 177.2 -2.4 33.2 - 60 SER 60 E B - 182.0 - - - - - - - - 179.7 -2.8 33.8 - * * 61 ALA 61 T l - - - - - - - - - - 181.6 - 32.2 - 62 GLY 62 T - - - - - - - - - - - 180.3 - - - 63 LYS 63 E B - - -65.7 185.1 - - - - - - 182.0 -2.0 34.2 - 64 VAL 64 E B - 184.0 - - - - - - - - 180.2 - 34.2 - 65 LEU 65 E B - - -71.7 - - - - - - - 182.3 -3.4 32.8 - +* +* 66 GLU 66 t B - 185.2 - 179.1 - - - - - - 183.7 -.5 35.1 - +* +* 67 ASN 67 T A 67.3 - - - - - - - - - 180.7 - 33.6 - 68 SER 68 T A - 183.5 - - - - - - - - 181.3 - 33.8 - 69 LYS 69 t B - - -66.0 174.6 - - - - - - 183.9 -2.9 33.9 - * * 70 THR 70 h B 59.8 - - - - - - - - - 176.6 - 35.2 - 71 VAL 71 H A - 179.2 - - - -62.2 -35.2 - - - 177.9 -3.4 33.5 - +* +* 72 LYS 72 H A - - -65.7 180.0 - -56.2 -34.6 - - - 180.9 -1.1 34.4 - * * 73 ASP 73 H A - - -70.7 - - -63.3 -35.7 - - - 180.6 -.6 33.7 - +* +* 74 TYR 74 H A - - -68.6 - - -102.0 5.7 - - - 177.8 -.9 32.1 - *** +*** * +*** 75 ARG 75 h B - - -83.9 - - - - - - - 174.6 -.7 33.6 - * +* +* 76 SER 76 B - - -54.0 - - - - - - - 181.6 -.5 35.8 - ** ** 77 PRO 77 S - - - - - -51.5 - - - - - 178.4 - 37.8 - * * * 78 VAL 78 S b - 182.4 - - - - - - - - 175.9 - 32.1 - 79 SER 79 b - - -62.3 - - - - - - - 185.9 -.9 34.2 - * * * 80 ASN 80 b - - -57.7 - - - - - - - 178.6 - 33.0 - 81 LEU 81 b - - -66.4 179.0 - - - - - - 184.7 -1.5 35.3 - 82 ALA 82 S l - - - - - - - - - - 190.3 -1.0 31.5 - +* * +* 83 GLY 83 S - - - - - - - - - - - 174.0 - - - * * 84 ALA 84 S B - - - - - - - - - - 184.2 - 34.8 - 85 VAL 85 B 58.7 - - - - - - - - - 180.4 - 31.5 - 86 THR 86 E B - - -48.6 - - - - - - - 179.3 -3.2 35.9 - * +* +* 87 THR 87 E B - - -56.2 - - - - - - - 180.9 -.5 34.8 - ** ** 88 MET 88 E B 65.4 - - 181.5 - - - - - - 178.8 -2.3 32.5 - 89 HIS 89 E B - - -67.8 - - - - - - - 181.0 -2.1 33.9 - 90 VAL 90 E B - 182.6 - - - - - - - - 178.8 -2.7 33.7 - Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 91 ILE 91 E B - - -66.0 - - - - - - - 180.7 -3.2 35.2 - +* +* 92 ILE 92 B - - -63.1 - - - - - - - 180.6 -.8 33.7 - +* +* 93 GLN 93 B - 179.8 - 174.9 - - - - - - 180.4 -.6 35.2 - +* +* 94 ALA 94 B - - - - - - - - - - 181.1 - 33.6 - 95 PRO 95 - - - - - -63.8 - - - - - 180.1 - 38.9 - * * 96 VAL 96 S b 55.4 - - - - - - - - - 180.6 - 30.7 - 97 THR 97 b - - -57.2 - - - - - - - 184.3 -1.7 35.5 - 98 GLU 98 B - - -67.6 - - - - - - - 173.3 - 32.3 - * * 99 LYS 99 S ~a - - -70.8 180.9 - - - - - - 171.0 - 32.4 - ** +* ** 100 GLU 100 a 56.3 - - 174.7 - - - - - - 177.0 - 31.8 - 101 LYS 101 - - - -67.1 184.4 - - - - - - - - 34.6 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * +* +** *** +*** +* ** +* +*** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.4 182.7 -63.1 180.3 -67.0 -69.4 -33.7 - - - 179.9 -1.9 34.1 Standard deviations: 6.2 4.8 8.6 4.5 14.2 13.1 13.1 - - - 4.4 1.0 2.0 Numbers of values: 16 24 42 23 6 15 15 0 0 0 100 53 96 0 KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_13 Page 5 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 GLU 1 - 1.238 1.511 1.524 1.457 - 115.43 120.98 109.96 110.39 111.38 123.57 2 ALA 2 1.297 1.241 1.505 1.524 1.436 123.80 116.15 120.65 110.91 107.36 111.08 123.16 ** * * * ** 3 GLU 3 1.304 1.240 1.516 1.536 1.419 121.22 114.39 121.99 112.16 112.48 111.99 123.56 +* ** * ** 4 VAL 4 1.301 1.246 1.546 1.577 1.439 123.24 119.33 118.63 111.71 105.65 109.73 122.02 ** * +* * * +* * ** 5 HIS 5 1.329 1.229 1.520 1.542 1.459 120.60 115.67 120.25 111.01 108.45 111.37 124.06 6 ASN 6 1.331 1.241 1.519 1.536 1.466 123.51 116.73 120.24 109.53 108.65 112.34 123.00 * * * 7 GLN 7 1.313 1.219 1.533 1.541 1.441 121.85 118.18 119.76 115.07 110.18 110.16 122.06 * +** +** 8 LEU 8 1.310 1.212 1.517 1.546 1.472 120.26 117.20 120.32 108.82 112.42 111.49 122.43 * * 9 GLU 9 1.316 1.238 1.507 1.543 1.454 120.44 116.05 120.64 106.95 108.85 113.87 123.31 +* +* +* 10 ILE 10 1.297 1.235 1.520 1.565 1.439 122.59 117.33 119.81 108.51 108.30 111.13 122.79 ** * * ** 11 LYS 11 1.317 1.246 1.520 1.564 1.431 120.42 116.31 120.67 113.81 109.30 113.15 123.02 +* * +* +* +* 12 PHE 12 1.298 1.222 1.510 1.535 1.448 121.78 117.50 120.00 108.33 110.31 109.97 122.49 ** ** Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 13 ARG 13 1.309 1.233 1.518 1.525 1.436 120.18 115.96 120.92 110.98 108.11 112.44 123.10 * * * * * 14 LEU 14 1.292 1.239 1.521 1.536 1.430 122.67 115.44 120.92 110.38 111.75 110.01 123.62 +** * +** 15 THR 15 1.316 1.237 1.543 1.533 1.447 123.76 116.86 120.67 110.81 113.23 108.28 122.42 * +* +* 16 ASP 16 1.333 1.230 1.515 1.541 1.482 121.75 116.74 120.76 110.23 113.25 112.97 122.50 * * * 17 GLY 17 1.310 1.235 1.504 - 1.447 120.50 116.17 120.95 - 112.36 - 122.88 * * 18 SER 18 1.306 1.236 1.516 1.527 1.431 121.71 117.37 120.00 110.24 107.95 109.38 122.61 +* * * +* 19 ASP 19 1.293 1.229 1.495 1.530 1.421 121.30 115.16 120.86 110.27 110.48 112.06 123.96 +** * +* +** 20 ILE 20 1.291 1.239 1.511 1.560 1.432 123.50 116.61 119.40 109.52 106.95 110.86 123.98 +** * * +* +** 21 GLY 21 1.330 1.243 1.516 - 1.456 121.56 117.78 119.83 - 112.66 - 122.39 22 PRO 22 1.342 1.248 1.518 1.527 1.454 122.94 114.68 121.58 111.03 113.41 104.43 123.74 * * * * 23 LYS 23 1.294 1.224 1.508 1.536 1.431 123.77 117.84 119.56 110.37 106.52 108.70 122.58 ** * * +* * ** 24 ALA 24 1.299 1.235 1.517 1.511 1.437 120.73 115.84 120.94 111.07 110.81 110.56 123.22 ** * ** 25 PHE 25 1.303 1.237 1.515 1.540 1.439 123.34 118.14 120.20 106.05 107.61 111.28 121.61 +* ** * ** 26 PRO 26 1.316 1.233 1.537 1.534 1.456 121.85 116.83 120.62 109.10 110.23 103.17 122.56 +* +* 27 ASP 27 1.313 1.227 1.529 1.536 1.474 121.99 115.97 121.12 110.65 111.63 111.93 122.89 * * 28 ALA 28 1.317 1.236 1.527 1.522 1.468 122.54 115.89 121.01 109.84 111.30 110.34 123.10 29 THR 29 1.310 1.226 1.525 1.547 1.439 122.31 116.53 120.67 109.81 110.22 109.90 122.76 * * * 30 THR 30 1.298 1.232 1.526 1.565 1.432 121.59 117.34 120.17 110.98 108.77 111.45 122.49 ** * ** 31 VAL 31 1.317 1.233 1.529 1.547 1.453 121.82 115.39 121.45 111.51 109.38 111.82 123.14 * * 32 SER 32 1.324 1.224 1.549 1.544 1.439 122.09 116.09 120.97 110.95 108.73 109.29 122.84 * * * 33 ALA 33 1.337 1.232 1.526 1.511 1.459 122.61 116.36 120.59 110.82 111.36 111.03 123.05 34 LEU 34 1.328 1.235 1.526 1.537 1.424 123.10 114.95 122.06 112.30 107.48 107.43 122.93 +* * * +* +* 35 LYS 35 1.310 1.209 1.500 1.497 1.427 121.87 118.40 118.72 112.02 113.72 113.04 122.88 * * * +* +* * * * * +* 36 GLU 36 1.330 1.245 1.527 1.522 1.469 121.24 115.93 121.31 110.14 110.35 111.29 122.76 37 THR 37 1.313 1.222 1.542 1.544 1.427 121.31 116.54 120.66 110.15 109.52 110.83 122.72 * +* +* 38 VAL 38 1.330 1.208 1.537 1.554 1.463 122.25 117.34 120.16 109.48 111.79 112.10 122.49 * * 39 ILE 39 1.333 1.234 1.539 1.582 1.478 121.68 115.43 121.17 109.66 108.95 112.29 123.36 +* * +* 40 SER 40 1.326 1.223 1.536 1.544 1.444 122.52 117.16 120.51 110.13 112.24 108.92 122.31 41 GLU 41 1.321 1.231 1.528 1.519 1.434 121.06 117.07 120.10 110.24 113.66 109.49 122.82 * * 42 TRP 42 1.317 1.246 1.518 1.540 1.457 121.88 117.12 120.28 110.10 110.32 110.33 122.58 Residue-by-residue listing for refined_13 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 PRO 43 1.334 1.216 1.515 1.538 1.447 122.60 116.85 120.84 109.17 110.45 104.15 122.30 * * * 44 ARG 44 1.297 1.235 1.532 1.525 1.451 121.43 113.97 122.50 111.54 107.54 109.28 123.46 ** * * * ** 45 GLU 45 1.325 1.216 1.546 1.518 1.445 124.11 116.49 120.67 110.91 111.37 109.49 122.83 * * * 46 LYS 46 1.323 1.238 1.540 1.551 1.471 123.42 118.45 119.18 107.17 108.35 108.19 122.36 * * +* * * +* 47 GLU 47 1.350 1.236 1.524 1.533 1.466 120.62 116.11 120.07 110.89 110.24 112.64 123.82 +* * +* 48 ASN 48 1.345 1.217 1.518 1.561 1.492 123.84 113.77 120.85 108.84 107.77 113.54 125.25 * +* +* * * * +* * +* 49 GLY 49 1.348 1.233 1.510 - 1.465 126.96 116.89 120.77 - 117.33 - 122.31 * +*** +* +*** 50 PRO 50 1.333 1.242 1.525 1.526 1.430 123.41 117.33 120.36 110.28 109.43 102.13 122.31 ** ** 51 LYS 51 1.313 1.248 1.533 1.560 1.439 119.71 115.40 121.33 111.39 111.52 110.42 123.04 * * * * * 52 THR 52 1.302 1.234 1.553 1.517 1.425 123.02 113.66 121.89 113.36 116.34 111.22 124.33 +* * +* * +* +* +* 53 VAL 53 1.318 1.226 1.542 1.570 1.460 127.34 116.77 120.53 110.82 116.57 109.48 122.71 * *** +* * *** 54 LYS 54 1.306 1.232 1.534 1.533 1.452 121.70 118.28 119.84 111.27 114.97 110.10 121.86 +* * * +* 55 GLU 55 1.313 1.239 1.536 1.542 1.477 118.71 115.59 121.32 113.47 114.36 112.55 123.00 * * +* +* * * +* 56 VAL 56 1.310 1.238 1.543 1.552 1.457 123.09 117.47 120.30 111.12 108.04 111.97 122.13 * * * 57 LYS 57 1.312 1.235 1.530 1.555 1.447 120.76 116.40 120.71 110.03 111.54 111.49 122.88 * * * 58 LEU 58 1.320 1.206 1.534 1.573 1.460 121.92 118.49 119.67 108.65 108.26 111.50 121.83 * ** * * ** 59 ILE 59 1.315 1.219 1.515 1.592 1.469 121.34 116.07 120.94 109.40 110.47 113.37 122.98 +* * +* 60 SER 60 1.298 1.242 1.511 1.538 1.431 122.17 115.64 120.27 111.14 108.09 111.18 123.94 ** * * ** 61 ALA 61 1.336 1.235 1.523 1.534 1.474 124.55 115.49 121.40 111.41 111.16 111.80 123.06 +* +* 62 GLY 62 1.313 1.231 1.512 - 1.436 121.47 116.64 120.81 - 111.94 - 122.55 * * 63 LYS 63 1.311 1.233 1.500 1.517 1.409 121.67 116.24 120.39 111.26 109.89 110.03 123.36 * * +** +** 64 VAL 64 1.303 1.229 1.515 1.556 1.437 121.37 115.50 121.27 109.55 109.21 112.01 123.23 +* * +* 65 LEU 65 1.292 1.234 1.497 1.544 1.424 122.93 114.95 121.26 111.30 109.71 112.25 123.78 +** * +* * +** 66 GLU 66 1.298 1.226 1.514 1.515 1.420 122.32 115.62 120.46 111.03 109.05 109.00 123.92 ** +* ** 67 ASN 67 1.313 1.225 1.538 1.538 1.482 125.15 117.56 120.37 109.85 114.27 110.37 122.06 * * +* * +* 68 SER 68 1.314 1.234 1.549 1.543 1.449 121.17 116.59 120.50 111.35 111.07 109.91 122.90 * * * 69 LYS 69 1.321 1.225 1.533 1.525 1.447 123.61 117.32 120.13 111.96 110.26 109.28 122.55 * * Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 70 THR 70 1.312 1.238 1.525 1.546 1.437 122.43 117.07 120.20 109.06 110.54 110.57 122.73 * * * 71 VAL 71 1.337 1.229 1.535 1.566 1.455 121.30 116.02 120.67 110.42 109.41 112.08 123.26 72 LYS 72 1.347 1.230 1.520 1.528 1.473 123.04 116.43 120.29 108.10 111.76 111.79 123.27 * * * 73 ASP 73 1.326 1.227 1.519 1.534 1.445 122.66 116.71 120.82 110.60 111.86 110.49 122.46 74 TYR 74 1.316 1.234 1.524 1.517 1.441 121.75 116.31 120.65 111.81 112.87 110.89 123.04 75 ARG 75 1.317 1.235 1.506 1.519 1.432 122.38 115.22 121.35 110.08 112.47 110.94 123.42 * * 76 SER 76 1.295 1.240 1.532 1.521 1.411 122.23 117.96 119.79 110.97 107.40 108.45 122.21 ** ** * * ** 77 PRO 77 1.349 1.233 1.514 1.518 1.471 123.20 115.85 121.32 111.14 113.06 103.50 122.82 78 VAL 78 1.285 1.234 1.518 1.530 1.428 121.09 114.24 122.19 110.60 110.29 113.31 123.36 *** +* * *** 79 SER 79 1.278 1.238 1.507 1.539 1.443 124.44 116.35 120.75 110.70 107.45 111.26 122.88 +*** +* * +*** 80 ASN 80 1.302 1.232 1.505 1.539 1.438 121.04 115.51 121.32 110.92 111.11 111.59 123.11 +* * +* 81 LEU 81 1.307 1.236 1.519 1.496 1.390 123.12 117.00 119.26 111.89 109.07 107.78 123.74 +* +* +*** +* +*** 82 ALA 82 1.341 1.243 1.521 1.536 1.471 122.99 114.68 122.08 112.43 108.57 112.77 123.19 * +* +* 83 GLY 83 1.304 1.234 1.511 - 1.442 121.56 113.97 122.13 - 107.75 - 123.89 +* * +* +* 84 ALA 84 1.312 1.246 1.509 1.518 1.433 124.17 117.08 119.86 110.39 106.84 110.52 123.06 * * * +* +* 85 VAL 85 1.305 1.238 1.520 1.562 1.441 120.91 115.19 121.73 111.77 111.67 112.71 123.08 +* * +* 86 THR 86 1.294 1.231 1.520 1.536 1.427 121.91 116.76 120.58 109.09 108.28 110.06 122.63 +** +* * +** 87 THR 87 1.285 1.225 1.511 1.540 1.417 121.12 116.84 120.69 110.64 108.26 110.33 122.44 *** ** * *** 88 MET 88 1.303 1.231 1.512 1.533 1.434 120.04 115.98 120.78 111.52 111.21 111.54 123.23 +* * +* 89 HIS 89 1.305 1.222 1.500 1.534 1.447 122.21 116.25 121.10 109.72 109.37 112.09 122.65 +* * +* 90 VAL 90 1.279 1.240 1.494 1.550 1.436 121.15 114.54 121.50 110.57 109.73 111.71 123.96 +*** * * +*** 91 ILE 91 1.286 1.242 1.493 1.540 1.407 122.58 114.65 121.41 110.30 107.99 110.30 123.93 *** +* +** * *** 92 ILE 92 1.287 1.235 1.501 1.546 1.409 121.99 114.97 121.18 111.11 109.51 111.29 123.84 *** * +** *** 93 GLN 93 1.290 1.239 1.512 1.531 1.405 123.26 116.20 120.06 111.74 107.52 108.83 123.67 +** +** * +** 94 ALA 94 1.307 1.246 1.529 1.521 1.442 122.08 117.10 120.49 111.06 110.71 110.42 122.41 +* +* 95 PRO 95 1.346 1.241 1.526 1.539 1.469 123.29 116.32 120.56 109.97 112.23 103.63 123.11 96 VAL 96 1.322 1.239 1.558 1.575 1.461 122.05 114.87 121.66 112.76 112.37 112.30 123.39 +* * +* +* 97 THR 97 1.332 1.229 1.553 1.589 1.469 126.23 118.49 119.91 107.71 106.91 112.45 121.58 * +* +** * +* +** 98 GLU 98 1.324 1.222 1.527 1.546 1.467 120.10 113.89 121.12 109.06 114.14 113.00 124.99 * * * * * 99 LYS 99 1.326 1.227 1.513 1.551 1.463 128.71 115.25 120.94 109.46 105.66 115.71 123.79 * +*** +* *** +*** Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 100 GLU 100 1.324 1.229 1.526 1.542 1.452 123.21 115.62 121.10 111.72 109.02 113.05 123.23 * * 101 LYS 101 1.320 - 1.501 1.526 1.446 124.22 - - 108.16 108.37 112.67 - * * * * * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** * +* ** +*** +*** +* * +** +* *** * +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_13 Page 10 ---------------------------------------- A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S +------------------+ | BOND LENGTHS | +------------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Bond X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- C-N C-NH1 (except Pro) 1.329 .014 94 1.278 1.350 1.313 .016 +*** +* * C-N (Pro) 1.341 .016 6 1.316 1.349 1.337 .011 +* C-O C-O 1.231 .020 100 1.206 1.248 1.233 .009 * CA-C CH1E-C (except Gly) 1.525 .021 96 1.493 1.558 1.522 .014 +* +* CH2G*-C (Gly) 1.516 .018 5 1.504 1.516 1.511 .004 CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.511 1.536 1.522 .009 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.517 1.592 1.555 .018 +* CH1E-CH2E (the rest) 1.530 .020 62 1.496 1.573 1.535 .014 +* ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.390 1.492 1.445 .020 +*** +* NH1-CH2G* (Gly) 1.451 .016 5 1.436 1.465 1.449 .010 N-CH1E (Pro) 1.466 .015 6 1.430 1.471 1.455 .014 ** ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_13 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 89 113.66 119.33 116.28 1.18 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 5 113.97 117.78 116.29 1.27 * CH1E-C-N (Pro) 116.9 1.5 6 114.68 117.33 116.31 .86 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.58 125.25 123.02 .66 * O-C-N (Pro) 122.0 1.4 6 122.30 123.74 122.81 .51 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.71 128.71 122.30 1.54 +* +*** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.50 126.96 122.41 2.31 +*** * C-N-CH1E (Pro) 122.6 5.0 6 121.85 123.41 122.88 .53 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 118.63 122.50 120.67 .71 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.83 122.13 120.90 .73 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 109.84 112.43 110.99 .70 * CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 107.71 113.36 110.40 1.24 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 106.05 115.07 110.48 1.53 ** +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.65 116.57 110.10 2.27 +* +* NH1-CH2G*-C (Gly) 112.5 2.9 5 107.75 117.33 112.41 3.04 +* +* N-CH1E-C (Pro) 111.8 2.5 6 109.43 113.41 111.47 1.51 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 110.34 112.77 111.06 .79 +* NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 108.28 113.37 111.29 1.20 +* * N-CH1E-CH2E (Pro) 103.0 1.1 6 102.13 104.43 103.50 .74 * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 107.43 115.71 110.99 1.67 +* *** ------------------------------------------------------------------------------------------------------------- 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_13 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] 72 81.8% Residues in additional allowed regions [a,b,l,p] 14 15.9% 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 5 Number of proline residues 6 ---- Total number of residues 101 Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good quality model would be expected to have over 90% in the most favoured regions [E,H,L]. S T E R E O C H E M I S T R Y O F M A I N - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. %-tage residues in A, B, L 88 81.8 83.8 10.0 -.2 Inside b. Omega angle st dev 100 4.4 6.0 3.0 -.5 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 96 2.0 3.1 1.6 -.7 Inside e. H-bond energy st dev 53 1.0 .8 .2 1.2 WORSE f. Overall G-factor 101 -.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 16 6.2 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 24 4.8 19.0 5.3 -2.7 BETTER c. Chi-1 gauche plus st dev 42 8.6 17.5 4.9 -1.8 BETTER d. Chi-1 pooled st dev 82 7.8 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 23 4.5 20.4 5.0 -3.2 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 81.8 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.4 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 1.06 3 Residue-by-residue listing for refined_13 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.57 Chi1-chi2 distribution -.14 Chi1 only -.11 Chi3 & chi4 .35 Omega -.20 ------ -.22 ===== Main-chain covalent forces:- Main-chain bond lengths -.03 Main-chain bond angles .31 ------ .17 ===== OVERALL AVERAGE -.08 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.