Residue-by-residue listing for refined_3 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 - - - -64.1 - - - - - - - 177.8 - 34.2 - 2 ALA 2 B - - - - - - - - - - 181.8 - 33.6 - 3 GLU 3 S l 58.8 - - 176.4 - - - - - - 180.1 -.9 27.8 - * +* +* 4 VAL 4 B 57.3 - - - - - - - - - 183.2 - 30.7 - 5 HIS 5 a 58.5 - - - - - - - - - 180.9 - 33.8 - 6 ASN 6 b - 181.9 - - - - - - - - 172.2 - 34.0 - * * 7 GLN 7 b - - -58.9 176.0 - - - - - - 177.8 -1.2 35.9 - * * 8 LEU 8 E B - - -65.2 - - - - - - - 185.9 -2.2 31.2 - * * 9 GLU 9 E B - - -58.5 177.9 - - - - - - 181.6 -1.3 33.4 - * * 10 ILE 10 E B - - -57.3 178.5 - - - - - - 171.7 -2.5 35.8 - * * 11 LYS 11 E B 67.0 - - 172.8 - - - - - - 186.6 -2.7 31.0 - * * 12 PHE 12 E B - - -57.0 - - - - - - - 174.9 - 35.8 - 13 ARG 13 E B - - -77.5 188.9 - - - - - - 180.6 -2.6 32.1 - 14 LEU 14 t B - - -68.3 - - - - - - - 178.1 -3.3 34.6 - +* +* 15 THR 15 T A - 183.2 - - - - - - - - 178.9 - 34.5 - 16 ASP 16 T A - 179.0 - - - - - - - - 179.9 - 34.3 - 17 GLY 17 t - - - - - - - - - - - 178.4 -1.7 - - 18 SER 18 B 48.2 - - - - - - - - - 181.3 - 35.3 - * * 19 ASP 19 B B 63.9 - - - - - - - - - 178.8 - 32.3 - Residue-by-residue listing for refined_3 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 ILE 20 B - - -58.0 178.9 - - - - - - 180.3 -2.4 35.8 - 21 GLY 21 - - - - - - - - - - - 183.3 - - - 22 PRO 22 - - - - - -62.8 - - - - - 182.7 - 37.2 - 23 LYS 23 E B - 191.9 - 184.4 - - - - - - 181.4 -2.5 36.5 - 24 ALA 24 E B - - - - - - - - - - 179.5 - 33.6 - 25 PHE 25 E B - - -57.0 - - - - - - - 168.8 -3.1 37.5 - +* * * +* 26 PRO 26 t - - - - - -72.0 - - - - - 179.8 - 39.7 - +* +* 27 ASP 27 T A - 188.9 - - - - - - - - 180.3 - 33.7 - 28 ALA 28 T A - - - - - - - - - - 179.2 - 34.2 - 29 THR 29 t B - 192.2 - - - - - - - - 177.6 -1.3 33.1 - 30 THR 30 h B 58.0 - - - - - - - - - 174.8 - 34.8 - 31 VAL 31 H A - 176.7 - - - -63.4 -30.1 - - - 176.7 -3.4 33.9 - +* +* 32 SER 32 H A - 183.4 - - - -62.4 -49.7 - - - 179.1 -1.8 34.5 - 33 ALA 33 H A - - - - - -67.7 -30.5 - - - 176.4 - 33.7 - 34 LEU 34 H A - 170.6 - - - -61.6 -47.0 - - - 180.1 -2.2 36.9 - 35 LYS 35 H A - - -63.0 176.3 - -72.0 -38.1 - - - 174.4 -2.5 31.1 - 36 GLU 36 H A - - -69.8 - - -56.0 -40.7 - - - 179.2 -2.7 35.0 - 37 THR 37 H A - - -56.5 - - -69.2 -46.7 - - - 181.6 -2.2 33.6 - 38 VAL 38 H A 72.6 - - - - -61.3 -41.0 - - - 179.2 -2.4 32.5 - 39 ILE 39 H A - - -61.2 172.8 - -62.1 -33.4 - - - 178.5 -2.9 33.8 - * * 40 SER 40 H A - - -58.2 - - -75.6 -35.9 - - - 179.9 -1.2 33.4 - * * 41 GLU 41 H A - - -56.2 - - -78.5 -25.5 - - - 180.8 -2.0 35.4 - * * * 42 TRP 42 h B - 185.8 - - - - - - - - 179.1 -2.2 35.9 - 43 PRO 43 t - - - - - -62.3 - - - - - 177.1 - 39.3 - +* +* 44 ARG 44 T A - - -71.6 - - - - - - - 178.5 - 31.3 - 45 GLU 45 T A - 182.2 - 183.4 - - - - - - 182.6 - 35.5 - 46 LYS 46 t b - 186.4 - - - - - - - - 175.7 -1.2 33.6 - * * 47 GLU 47 T B 51.6 - - 178.1 - - - - - - 184.0 -.6 33.3 - +* +* 48 ASN 48 T l - - -62.0 - - - - - - - 180.7 - 32.6 - 49 GLY 49 t - - - - - - - - - - - 180.3 -.9 - - * * 50 PRO 50 - - - - - -70.3 - - - - - 173.7 - 40.5 - * +* +* 51 LYS 51 a - - -94.6 - - - - - - - 181.4 - 31.8 - +* +* 52 THR 52 t B 47.7 - - - - - - - - - 187.0 - 28.2 - * * +* +* 53 VAL 53 T A 57.1 - - - - - - - - - 182.6 - 33.3 - 54 LYS 54 T A - 185.4 - 177.4 - - - - - - 181.8 - 32.5 - 55 GLU 55 e A 46.1 - - - - - - - - - 173.6 -.8 27.0 - * * +* +* +* 56 VAL 56 E B 59.2 - - - - - - - - - 183.1 -1.2 32.2 - * * 57 LYS 57 E B - - -62.5 179.5 - - - - - - 176.7 -2.7 34.2 - 58 LEU 58 E B - - -74.4 - - - - - - - 181.0 -.5 33.7 - ** ** 59 ILE 59 E B - - -68.1 184.7 - - - - - - 176.3 -3.3 32.4 - +* +* Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 60 SER 60 E B - - -56.5 - - - - - - - 179.6 -2.4 35.5 - 61 ALA 61 T l - - - - - - - - - - 181.2 - 32.0 - 62 GLY 62 T - - - - - - - - - - - 179.7 - - - 63 LYS 63 E B - 177.5 - - - - - - - - 176.3 -1.2 34.9 - * * 64 VAL 64 E B - 180.8 - - - - - - - - 181.5 - 34.6 - 65 LEU 65 e B - - -58.9 178.9 - - - - - - 179.1 -3.1 35.0 - * * 66 GLU 66 t B - 188.6 - - - - - - - - 187.8 - 34.2 - * * 67 ASN 67 T A - - -57.6 - - - - - - - 184.0 -.5 33.7 - ** ** 68 SER 68 T A - - -47.8 - - - - - - - 178.1 - 33.4 - * * 69 LYS 69 t B - - -75.7 - - - - - - - 174.8 -2.3 34.6 - 70 THR 70 h B 49.4 - - - - - - - - - 180.9 - 35.0 - 71 VAL 71 H A - 180.9 - - - -59.5 -47.0 - - - 179.5 -2.8 33.7 - * * 72 LYS 72 H A - 182.4 - 177.1 - -58.9 -33.5 - - - 179.5 -2.2 34.0 - 73 ASP 73 H A - 184.6 - - - -72.3 -37.2 - - - 184.9 - 34.8 - 74 TYR 74 H A - 192.3 - - - -73.9 -41.7 - - - 181.1 -1.9 35.1 - 75 ARG 75 h B - - -55.9 183.6 - - - - - - 175.7 -2.8 36.3 - 76 SER 76 B - - -57.7 - - - - - - - 180.3 - 35.0 - 77 PRO 77 - - - - - -61.9 - - - - - 184.3 - 38.2 - * * 78 VAL 78 a 61.7 - - - - - - - - - 181.6 -.6 31.2 - +* +* 79 SER 79 B - - -58.5 - - - - - - - 175.9 - 35.3 - 80 ASN 80 b - 178.5 - - - - - - - - 181.8 - 33.6 - 81 LEU 81 B - - -62.0 179.8 - - - - - - 180.3 -1.2 36.8 - * * 82 ALA 82 S B - - - - - - - - - - 181.5 - 34.2 - 83 GLY 83 S - - - - - - - - - - - 181.8 - - - 84 ALA 84 e B - - - - - - - - - - 178.7 - 34.4 - 85 VAL 85 E B - 180.2 - - - - - - - - 178.9 - 33.9 - 86 THR 86 E B - - -52.3 - - - - - - - 181.0 -3.2 35.3 - +* +* 87 THR 87 E B - - -54.3 - - - - - - - 178.1 - 34.7 - 88 MET 88 E B - - -69.4 179.6 - - - - - - 185.9 -2.2 30.5 - * * 89 HIS 89 E B - 191.8 - - - - - - - - 180.8 -2.0 34.4 - 90 VAL 90 E B - 182.1 - - - - - - - - 178.0 -3.8 34.3 - ** ** 91 ILE 91 E B - - -73.5 - - - - - - - 184.0 -2.9 33.3 - * * 92 ILE 92 E B - - -72.3 - - - - - - - 171.3 -.5 33.9 - +* ** ** 93 GLN 93 e B - 176.9 - 177.5 - - - - - - 182.8 -2.4 34.5 - 94 ALA 94 B - - - - - - - - - - 177.9 -.7 33.0 - +* +* 95 PRO 95 - - - - - -78.2 - - - - - 180.7 - 39.1 - * * * 96 VAL 96 S b 60.1 - - - - - - - - - 175.8 - 29.0 - * * 97 THR 97 B 45.5 - - - - - - - - - 185.1 -2.2 36.0 - * * 98 GLU 98 B 62.0 - - 186.3 - - - - - - 175.5 - 36.5 - Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 99 LYS 99 S b 56.9 - - 180.9 - - - - - - 181.1 - 31.8 - 100 GLU 100 a 42.7 - - 174.8 - - - - - - 179.4 -1.5 30.0 - * * * 101 LYS 101 - 55.9 - - 178.4 - - - - - - - - 31.1 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * +* * * * +* ** +* ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.2 183.4 -63.1 179.3 -67.9 -66.3 -38.5 - - - 179.7 -2.0 34.0 Standard deviations: 7.6 5.5 9.0 4.0 6.7 6.9 7.2 - - - 3.4 .9 2.3 Numbers of values: 21 25 36 25 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_3 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 - 1.230 1.507 1.552 1.461 - 116.90 120.19 109.12 109.59 112.23 122.90 * * * 2 ALA 2 1.317 1.233 1.516 1.521 1.445 121.25 115.25 120.26 110.98 109.36 111.04 124.44 3 GLU 3 1.332 1.243 1.527 1.549 1.468 125.09 115.61 121.86 113.20 114.13 114.44 122.50 +* +* * ** ** 4 VAL 4 1.308 1.237 1.508 1.558 1.427 120.43 114.52 121.97 112.78 110.43 113.37 123.48 * +* +* * +* 5 HIS 5 1.281 1.237 1.505 1.559 1.451 122.88 114.46 121.51 111.54 108.91 110.82 124.00 *** * *** 6 ASN 6 1.319 1.240 1.520 1.540 1.440 122.94 114.84 121.45 109.74 110.73 111.50 123.54 7 GLN 7 1.293 1.236 1.520 1.530 1.428 123.17 119.62 119.32 111.08 105.01 108.72 121.05 +** +* +* ** * * +** 8 LEU 8 1.292 1.221 1.496 1.522 1.426 117.29 115.78 121.41 111.90 109.18 113.78 122.80 +** * +* ** +* +** 9 GLU 9 1.283 1.231 1.491 1.515 1.422 120.74 114.90 121.55 111.05 110.51 111.08 123.54 *** +* +* *** 10 ILE 10 1.281 1.238 1.504 1.567 1.425 122.35 116.28 120.39 108.36 109.01 111.17 123.30 *** * +* *** 11 LYS 11 1.301 1.247 1.503 1.528 1.413 121.09 116.53 120.58 111.54 108.17 114.96 122.90 ** * ** * +** +** 12 PHE 12 1.285 1.223 1.513 1.523 1.433 121.07 116.65 120.03 109.48 111.17 108.94 123.30 *** * *** Residue-by-residue listing for refined_3 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 1.320 1.215 1.498 1.527 1.448 122.14 115.84 120.68 109.86 111.45 113.63 123.47 * +* +* 14 LEU 14 1.299 1.235 1.526 1.551 1.444 123.13 115.88 121.03 109.19 110.85 111.12 123.08 ** * ** 15 THR 15 1.322 1.230 1.539 1.558 1.463 123.13 114.85 121.71 110.49 110.30 110.09 123.43 16 ASP 16 1.310 1.222 1.536 1.537 1.465 123.15 116.32 121.32 110.96 111.24 109.28 122.34 * * 17 GLY 17 1.319 1.240 1.510 - 1.454 120.94 115.66 121.08 - 112.27 - 123.26 18 SER 18 1.299 1.230 1.521 1.518 1.427 122.76 117.70 120.11 111.91 109.05 107.77 122.15 ** +* +* ** 19 ASP 19 1.304 1.238 1.512 1.544 1.421 120.62 115.02 121.48 111.74 111.65 111.64 123.47 +* +* +* 20 ILE 20 1.297 1.230 1.513 1.571 1.445 123.43 117.05 119.03 108.89 107.02 111.08 123.88 ** * * * ** 21 GLY 21 1.335 1.239 1.524 - 1.458 121.58 117.85 119.83 - 112.29 - 122.32 22 PRO 22 1.347 1.245 1.528 1.530 1.460 122.98 115.07 121.57 111.09 113.54 104.57 123.36 * * * 23 LYS 23 1.299 1.224 1.524 1.536 1.438 122.94 118.33 119.17 110.62 106.56 107.98 122.49 ** * * +* * ** 24 ALA 24 1.311 1.227 1.523 1.521 1.455 120.92 116.29 120.75 110.78 111.05 110.53 122.96 * * 25 PHE 25 1.308 1.228 1.510 1.540 1.447 122.70 118.70 120.27 105.71 108.24 110.93 121.00 * * ** * * ** 26 PRO 26 1.311 1.224 1.525 1.535 1.445 120.79 118.14 119.79 109.04 107.96 104.12 122.08 +* * +* * +* 27 ASP 27 1.308 1.213 1.518 1.536 1.463 119.93 115.16 122.01 111.04 108.27 111.17 122.65 * * * 28 ALA 28 1.319 1.245 1.542 1.515 1.452 122.72 117.21 120.48 110.38 112.22 109.58 122.30 29 THR 29 1.325 1.246 1.533 1.574 1.448 121.34 116.61 120.53 110.13 109.40 112.99 122.77 * * 30 THR 30 1.307 1.245 1.525 1.547 1.436 121.24 116.37 120.57 108.80 110.26 111.45 123.06 +* * +* 31 VAL 31 1.319 1.221 1.531 1.555 1.449 121.94 115.64 121.29 110.67 108.64 111.34 123.03 32 SER 32 1.317 1.229 1.542 1.532 1.435 122.01 116.91 120.17 111.02 109.81 109.56 122.86 * * 33 ALA 33 1.342 1.235 1.527 1.517 1.470 122.03 115.74 121.06 110.48 110.81 110.62 123.19 34 LEU 34 1.322 1.237 1.522 1.525 1.423 123.85 115.05 121.53 110.54 108.91 106.81 123.38 +* * ** ** 35 LYS 35 1.309 1.209 1.513 1.512 1.424 122.03 117.07 120.10 114.16 111.79 110.48 122.76 * * +* ** ** 36 GLU 36 1.318 1.236 1.523 1.530 1.461 121.83 115.51 121.26 109.25 110.07 110.44 123.21 37 THR 37 1.311 1.232 1.544 1.538 1.427 121.78 117.62 119.84 110.68 111.27 110.85 122.50 * +* +* 38 VAL 38 1.349 1.201 1.524 1.579 1.471 120.89 115.92 120.48 110.69 110.04 113.09 123.51 * +* * +* 39 ILE 39 1.323 1.224 1.540 1.558 1.476 123.57 116.72 120.96 110.21 111.44 110.84 122.31 * * 40 SER 40 1.316 1.238 1.544 1.526 1.447 120.98 116.41 121.01 111.48 111.09 110.06 122.57 41 GLU 41 1.326 1.229 1.540 1.527 1.435 122.09 115.38 121.14 110.20 110.23 108.93 123.48 * * 42 TRP 42 1.316 1.237 1.535 1.543 1.453 124.25 118.03 120.36 110.81 109.35 107.87 121.56 * +* +* 43 PRO 43 1.338 1.223 1.528 1.535 1.463 122.39 116.40 121.07 109.21 112.46 103.71 122.53 44 ARG 44 1.313 1.226 1.525 1.544 1.460 121.62 115.21 121.80 111.49 110.83 113.29 122.97 * +* +* Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 45 GLU 45 1.309 1.238 1.553 1.543 1.447 123.18 116.50 120.84 110.62 110.00 108.40 122.66 * * * * 46 LYS 46 1.341 1.252 1.529 1.538 1.460 122.12 115.22 121.52 109.52 111.91 111.64 123.26 * * 47 GLU 47 1.306 1.236 1.503 1.517 1.416 122.38 115.59 120.61 111.48 109.22 111.20 123.79 +* * ** ** 48 ASN 48 1.315 1.234 1.522 1.550 1.482 123.52 115.95 121.12 110.28 111.05 112.57 122.91 * * * * * * 49 GLY 49 1.310 1.249 1.507 - 1.419 121.17 117.48 120.03 - 111.48 - 122.49 * +* +* 50 PRO 50 1.335 1.226 1.515 1.533 1.466 123.74 115.23 120.88 108.05 112.94 103.02 123.88 * * * * 51 LYS 51 1.317 1.219 1.527 1.552 1.455 123.17 117.17 120.26 110.21 111.48 113.75 122.57 * +* +* 52 THR 52 1.325 1.238 1.548 1.554 1.449 121.93 114.62 121.35 113.10 114.45 113.92 123.99 * +* * * +* 53 VAL 53 1.321 1.238 1.543 1.571 1.470 126.79 118.23 119.85 110.73 114.77 110.04 121.92 * +** * * +** 54 LYS 54 1.310 1.235 1.526 1.541 1.446 119.84 116.60 120.70 111.28 111.02 111.87 122.66 * * * 55 GLU 55 1.316 1.238 1.536 1.542 1.453 120.38 117.10 120.92 113.56 114.98 114.55 121.98 +* * ** ** 56 VAL 56 1.308 1.231 1.537 1.579 1.452 120.79 116.99 121.08 111.92 108.71 112.71 121.88 +* * * +* 57 LYS 57 1.307 1.229 1.512 1.520 1.439 120.76 115.53 120.94 110.02 111.99 110.36 123.53 +* * +* 58 LEU 58 1.311 1.240 1.510 1.563 1.452 122.62 116.21 120.44 110.25 108.86 112.17 123.33 * +* +* 59 ILE 59 1.305 1.242 1.519 1.570 1.441 122.32 114.99 121.40 111.11 112.04 112.06 123.56 +* * +* 60 SER 60 1.310 1.229 1.526 1.514 1.423 123.66 116.58 119.88 110.44 108.13 109.11 123.43 * +* * * +* 61 ALA 61 1.336 1.232 1.539 1.530 1.482 123.82 116.05 121.13 111.55 112.42 111.36 122.72 * * * 62 GLY 62 1.310 1.238 1.519 - 1.451 121.18 116.43 120.74 - 112.54 - 122.83 * * 63 LYS 63 1.312 1.239 1.530 1.533 1.442 121.93 116.04 120.51 110.48 110.62 109.36 123.43 * * 64 VAL 64 1.330 1.240 1.520 1.562 1.459 122.51 115.76 120.65 108.89 108.92 112.12 123.59 65 LEU 65 1.308 1.243 1.525 1.524 1.442 123.21 115.63 120.76 109.63 111.22 109.69 123.62 +* +* 66 GLU 66 1.308 1.233 1.534 1.554 1.440 122.79 115.99 120.55 113.75 107.59 108.22 123.46 +* * +* * * +* 67 ASN 67 1.333 1.242 1.539 1.543 1.493 124.41 118.02 119.94 107.72 115.08 111.98 122.03 +* +* * * +* 68 SER 68 1.317 1.236 1.527 1.516 1.457 120.89 116.23 120.97 111.09 112.01 110.15 122.80 69 LYS 69 1.304 1.231 1.493 1.523 1.436 121.96 115.17 121.39 109.01 110.73 111.33 123.43 +* +* * +* 70 THR 70 1.280 1.245 1.500 1.525 1.388 122.89 116.84 119.70 110.96 107.75 109.94 123.46 +*** * +*** * +*** 71 VAL 71 1.313 1.225 1.536 1.557 1.449 121.10 115.37 120.98 111.18 109.32 110.91 123.55 * * 72 LYS 72 1.316 1.224 1.534 1.535 1.464 124.19 117.80 120.01 110.50 112.71 109.82 122.18 * * Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 73 ASP 73 1.333 1.234 1.503 1.547 1.474 120.10 114.78 121.79 107.85 109.26 112.55 123.42 * * * * 74 TYR 74 1.308 1.239 1.530 1.527 1.426 121.93 116.33 120.62 110.35 110.70 109.21 123.04 +* +* +* 75 ARG 75 1.320 1.228 1.505 1.513 1.418 122.47 116.63 120.66 108.43 110.19 109.49 122.71 ** ** 76 SER 76 1.295 1.240 1.536 1.515 1.420 120.84 118.14 119.89 111.55 108.68 108.61 121.91 ** ** * ** 77 PRO 77 1.352 1.235 1.513 1.517 1.460 122.12 116.15 121.15 109.71 110.67 104.95 122.68 +* +* 78 VAL 78 1.290 1.228 1.512 1.570 1.442 120.62 115.85 120.79 112.16 112.39 112.53 123.35 +** * * +** 79 SER 79 1.288 1.235 1.519 1.541 1.449 123.04 116.39 120.56 109.01 110.13 110.44 123.05 +** +** 80 ASN 80 1.307 1.245 1.521 1.536 1.449 121.65 115.37 121.42 110.83 108.96 111.41 123.08 +* +* 81 LEU 81 1.304 1.228 1.523 1.498 1.386 123.56 115.89 120.82 110.23 110.83 106.87 123.28 +* +* +*** * ** +*** 82 ALA 82 1.306 1.232 1.500 1.520 1.408 123.91 115.79 120.79 110.85 107.38 111.14 123.35 +* * +** * * +** 83 GLY 83 1.288 1.235 1.510 - 1.443 120.92 115.50 121.43 - 110.53 - 123.06 +** +** 84 ALA 84 1.313 1.242 1.511 1.522 1.437 121.95 116.23 120.63 110.43 110.10 110.19 123.14 * * * 85 VAL 85 1.305 1.226 1.520 1.562 1.442 121.94 116.12 121.03 109.91 109.01 112.15 122.80 +* +* 86 THR 86 1.285 1.227 1.527 1.538 1.426 122.30 117.16 120.48 110.72 108.22 109.42 122.32 *** +* * * *** 87 THR 87 1.298 1.232 1.525 1.541 1.431 121.18 116.40 120.65 110.17 110.09 110.21 122.92 ** * ** 88 MET 88 1.316 1.240 1.511 1.531 1.460 121.87 115.95 120.69 112.83 111.44 112.75 123.33 * * * 89 HIS 89 1.316 1.228 1.526 1.538 1.449 122.05 115.60 120.93 111.03 110.53 109.50 123.47 90 VAL 90 1.305 1.247 1.503 1.551 1.448 123.28 114.11 121.93 109.05 110.20 112.03 123.95 +* * * +* 91 ILE 91 1.278 1.239 1.504 1.560 1.414 123.78 114.93 121.28 111.72 108.22 111.80 123.76 +*** * ** * * * +*** 92 ILE 92 1.294 1.238 1.512 1.585 1.421 122.52 115.54 120.88 110.23 111.02 111.63 123.54 +** +* +* +** 93 GLN 93 1.297 1.227 1.504 1.532 1.414 122.28 116.11 120.76 111.38 105.55 110.72 123.01 ** ** ** ** 94 ALA 94 1.292 1.241 1.525 1.514 1.439 121.34 116.90 120.85 111.06 111.75 110.82 122.25 +** +** 95 PRO 95 1.339 1.252 1.527 1.531 1.452 122.70 116.81 120.59 110.57 110.69 102.95 122.60 * * 96 VAL 96 1.315 1.235 1.547 1.574 1.443 120.60 113.70 122.91 113.54 112.14 113.97 123.09 * * * * ** * ** 97 THR 97 1.303 1.233 1.512 1.536 1.399 125.93 117.75 119.31 109.76 106.41 109.93 122.92 +* *** ** +* *** 98 GLU 98 1.306 1.240 1.514 1.525 1.448 121.17 116.21 120.68 109.10 110.46 108.30 123.11 +* * +* 99 LYS 99 1.315 1.238 1.531 1.542 1.419 121.51 115.66 121.80 112.32 110.20 112.24 122.43 ** * * ** 100 GLU 100 1.299 1.233 1.535 1.545 1.428 121.37 117.33 119.86 114.18 112.60 111.66 122.78 ** +* ** ** Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 101 LYS 101 1.310 - 1.513 1.561 1.452 123.51 - - 112.03 109.69 113.70 - * +* * * +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** +* +* +* +*** +** +* * ** ** +** * +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 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 1.349 1.310 .014 +*** * * C-N (Pro) 1.341 .016 6 1.311 1.352 1.337 .013 +* C-O C-O 1.231 .020 100 1.201 1.252 1.234 .009 +* * CA-C CH1E-C (except Gly) 1.525 .021 96 1.491 1.553 1.522 .013 +* * CH2G*-C (Gly) 1.516 .018 5 1.507 1.524 1.514 .006 CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.514 1.530 1.520 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.525 1.585 1.559 .015 +* CH1E-CH2E (the rest) 1.530 .020 62 1.498 1.563 1.534 .013 +* +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.386 1.493 1.442 .020 +*** +* NH1-CH2G* (Gly) 1.451 .016 5 1.419 1.458 1.445 .014 +* N-CH1E (Pro) 1.466 .015 6 1.445 1.466 1.458 .007 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 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 89 113.70 119.62 116.19 1.06 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.50 117.85 116.58 .95 CH1E-C-N (Pro) 116.9 1.5 6 115.07 118.14 116.30 1.03 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.00 124.44 122.98 .62 * O-C-N (Pro) 122.0 1.4 6 122.08 123.88 122.85 .59 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 117.29 126.79 122.22 1.38 ** +** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.92 121.58 121.16 .24 C-N-CH1E (Pro) 122.6 5.0 6 120.79 123.74 122.45 .90 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.03 122.91 120.79 .68 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.83 121.43 120.62 .61 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 110.38 111.55 110.81 .37 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.36 113.54 110.65 1.30 ** CH2E-CH1E-C (the rest) 110.1 1.9 62 105.71 114.18 110.60 1.55 ** ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.01 115.08 110.24 1.90 ** * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.53 112.54 111.82 .74 N-CH1E-C (Pro) 111.8 2.5 6 107.96 113.54 111.38 1.87 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 109.58 111.36 110.66 .54 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 109.42 113.97 111.60 1.25 * * N-CH1E-CH2E (Pro) 103.0 1.1 6 102.95 104.95 103.89 .74 +* NH1-CH1E-CH2E (the rest) 110.5 1.7 56 106.81 114.96 110.73 1.97 ** +** ------------------------------------------------------------------------------------------------------------- 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_3 Page 12 ---------------------------------------- R A M A C H A N D R A N P L O T S T A T I S T I C S Residues in most favoured regions [A,B,L] 75 85.2% Residues in additional allowed regions [a,b,l,p] 13 14.8% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% 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 85.2 83.8 10.0 .1 Inside b. Omega angle st dev 100 3.4 6.0 3.0 -.9 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 96 2.3 3.1 1.6 -.5 Inside e. H-bond energy st dev 53 .9 .8 .2 .3 Inside f. Overall G-factor 101 .0 -.4 .3 1.2 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 21 7.6 18.1 6.5 -1.6 BETTER b. Chi-1 trans st dev 25 5.5 19.0 5.3 -2.5 BETTER c. Chi-1 gauche plus st dev 36 9.0 17.5 4.9 -1.7 BETTER d. Chi-1 pooled st dev 82 8.8 18.2 4.8 -1.9 BETTER e. Chi-2 trans st dev 25 4.0 20.4 5.0 -3.3 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 85.2 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.7 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .88 3 Residue-by-residue listing for refined_3 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.48 Chi1-chi2 distribution -.11 Chi1 only -.32 Chi3 & chi4 .30 Omega .09 ------ -.12 ===== Main-chain covalent forces:- Main-chain bond lengths -.09 Main-chain bond angles .35 ------ .17 ===== OVERALL AVERAGE -.02 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.