Residue-by-residue listing for refined_5 Page 1 ---------------------------------------- This listing highlights the residues in the structure which may need investigation. The ideal values and standard deviations against which the structure has been compared are shown in the following table: <------------------------------- I D E A L V A L U E S -------------------------------> Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha ------------------------------------------------------------------------------------------ Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9 Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5 ------------------------------------------------------------------------------------------ In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above. Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*. The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing. Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments. Full print-out. ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 1 GLU 1 - - - -70.5 - - - - - - - 177.8 - 31.5 - 2 ALA 2 b - - - - - - - - - - 184.4 - 33.5 - 3 GLU 3 b - 187.8 - 175.7 - - - - - - 179.9 - 33.9 - 4 VAL 4 B - 185.4 - - - - - - - - 181.7 -.9 34.9 - * * 5 HIS 5 b 60.0 - - - - - - - - - 175.8 -.5 32.7 - ** ** 6 ASN 6 S a - 188.3 - - - - - - - - 181.2 - 34.4 - 7 GLN 7 S b - - -60.1 - - - - - - - 178.0 - 36.6 - 8 LEU 8 E B - - -62.0 - - - - - - - 180.5 -2.0 34.6 - 9 GLU 9 E B - - -61.3 180.3 - - - - - - 179.9 -3.0 33.5 - * * 10 ILE 10 E B - - -69.4 - - - - - - - 173.9 -3.1 34.3 - * * * 11 LYS 11 E B 60.0 - - 157.1 - - - - - - 183.1 -2.5 33.0 - * * 12 PHE 12 E B - - -55.9 - - - - - - - 180.6 -.9 34.7 - +* +* 13 ARG 13 E B - 180.3 - - - - - - - - 181.1 -3.4 35.1 - +* +* 14 LEU 14 E B - - -55.7 178.7 - - - - - - 174.1 -2.8 36.1 - * * 15 THR 15 e A - 181.7 - - - - - - - - 179.7 -2.0 34.2 - 16 ASP 16 T A - 175.3 - - - - - - - - 180.0 - 35.5 - 17 GLY 17 t - - - - - - - - - - - 178.6 -2.0 - - 18 SER 18 e B - - -55.5 - - - - - - - 179.0 - 35.6 - 19 ASP 19 E B 63.7 - - - - - - - - - 179.9 - 31.6 - 20 ILE 20 E B - - -57.7 177.8 - - - - - - 182.9 -2.7 35.8 - Residue-by-residue listing for refined_5 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 21 GLY 21 E - - - - - - - - - - - 182.5 - - - 22 PRO 22 E - - - - - -58.5 - - - - - 179.9 - 37.6 - * * 23 LYS 23 E B - 189.0 - - - - - - - - 183.3 -2.9 37.3 - * * 24 ALA 24 E B - - - - - - - - - - 178.5 - 33.0 - 25 PHE 25 E B - - -48.7 - - - - - - - 172.2 -3.5 36.9 - * * +* +* 26 PRO 26 t - - - - - -65.4 - - - - - 181.9 - 39.2 - +* +* 27 ASP 27 T A 64.3 - - - - - - - - - 180.5 - 33.0 - 28 ALA 28 T A - - - - - - - - - - 177.9 - 33.6 - 29 THR 29 t B - - -59.5 - - - - - - - 183.5 -1.8 33.8 - 30 THR 30 h B 58.5 - - - - - - - - - 179.2 - 33.5 - 31 VAL 31 H A - 181.8 - - - -65.1 -25.8 - - - 176.5 -3.4 33.4 - * +* +* 32 SER 32 H A - 182.3 - - - -54.4 -47.9 - - - 179.8 -2.0 34.2 - 33 ALA 33 H A - - - - - -74.6 -30.0 - - - 177.5 -.6 33.6 - +* +* 34 LEU 34 H A - 174.0 - - - -61.8 -49.2 - - - 177.7 -1.4 35.8 - 35 LYS 35 H A - - -67.4 176.4 - -64.9 -39.4 - - - 177.1 -3.3 33.1 - +* +* 36 GLU 36 H A - - -72.8 - - -61.9 -34.1 - - - 177.2 -2.0 32.8 - 37 THR 37 H A - - -56.7 - - -66.5 -39.4 - - - 176.2 -2.0 34.3 - 38 VAL 38 H A - 180.4 - - - -57.4 -51.6 - - - 182.3 -1.6 35.3 - * * 39 ILE 39 H A - - -48.2 - - -61.5 -37.8 - - - 181.8 -2.4 35.1 - * * 40 SER 40 H A - 184.4 - - - -66.2 -37.1 - - - 180.3 -2.2 34.4 - 41 GLU 41 H A - - -66.0 - - -90.3 -5.3 - - - 186.5 -2.0 35.9 - ** *** * *** 42 TRP 42 h B - 192.4 - - - - - - - - 171.5 -.8 35.0 - * +* +* 43 PRO 43 t - - - - - -59.1 - - - - - 185.6 - 39.6 - +* +* 44 ARG 44 T A - 190.4 - 167.6 - - - - - - 179.0 -.6 32.4 - +* +* 45 GLU 45 T A - 186.2 - 178.6 - - - - - - 180.2 - 33.3 - 46 LYS 46 t b - 187.0 - - - - - - - - 178.9 -1.5 34.5 - 47 GLU 47 T B 44.2 - - - - - - - - - 184.3 -1.0 28.3 - * * +* +* 48 ASN 48 T l - - -71.0 - - - - - - - 178.5 - 29.9 - * * 49 GLY 49 t - - - - - - - - - - - 178.8 -1.0 - - * * 50 PRO 50 - - - - - -79.0 - - - - - 170.4 - 39.2 - * +* +* +* 51 LYS 51 S a - - -65.7 - - - - - - - 178.6 - 34.4 - 52 THR 52 g B 55.4 - - - - - - - - - 179.9 - 34.7 - 53 VAL 53 G A - 181.2 - - - - - - - - 184.3 - 32.1 - 54 LYS 54 G A - - -61.7 177.0 - - - - - - 179.4 - 35.0 - 55 GLU 55 e A 56.7 - - - - - - - - - 179.9 -1.0 28.6 - * +* +* 56 VAL 56 E B 62.3 - - - - - - - - - 179.8 -1.2 32.9 - * * 57 LYS 57 E B - - -58.3 184.9 - - - - - - 178.9 -2.8 34.3 - * * Residue-by-residue listing for refined_5 Page 3 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 58 LEU 58 E B - 190.2 - - - - - - - - 182.9 - 35.2 - 59 ILE 59 E B - - -67.5 - - - - - - - 176.1 -3.3 33.7 - +* +* 60 SER 60 E B - 180.8 - - - - - - - - 180.9 -2.9 34.1 - * * 61 ALA 61 T l - - - - - - - - - - 181.4 - 32.7 - 62 GLY 62 T - - - - - - - - - - - 181.0 - - - 63 LYS 63 E B - - -74.4 - - - - - - - 174.5 -1.7 35.5 - 64 VAL 64 E B 57.6 - - - - - - - - - 188.7 - 32.0 - +* +* 65 LEU 65 e B - - -52.5 187.8 - - - - - - 175.8 -2.6 34.0 - 66 GLU 66 t B 53.5 - - 183.3 - - - - - - 188.6 - 31.7 - * * 67 ASN 67 T A 67.6 - - - - - - - - - 184.2 - 33.1 - 68 SER 68 T A - 186.1 - - - - - - - - 176.8 - 32.8 - 69 LYS 69 t B - - -68.1 - - - - - - - 177.0 -2.0 34.8 - 70 THR 70 B B 56.1 - - - - - - - - - 176.5 - 35.5 - 71 VAL 71 g A - 180.0 - - - - - - - - 180.5 -2.6 34.7 - 72 LYS 72 G A - 185.1 - - - - - - - - 184.2 -2.3 33.5 - 73 ASP 73 G A - 187.2 - - - - - - - - 179.8 - 33.3 - 74 TYR 74 G A - - -65.9 - - - - - - - 176.9 -.8 32.9 - +* +* 75 ARG 75 g B - 170.1 - 180.5 - - - - - - 180.4 -.7 35.1 - +* +* 76 SER 76 t B - 186.1 - - - - - - - - 174.3 - 35.6 - 77 PRO 77 T - - - - - -60.7 - - - - - 184.7 - 37.7 - * * 78 VAL 78 T ~b 69.6 - - - - - - - - - 172.3 -1.0 34.3 - ** * * ** 79 SER 79 t b - - -56.7 - - - - - - - 183.6 -1.8 34.1 - 80 ASN 80 B - - -66.5 - - - - - - - 181.9 - 33.9 - 81 LEU 81 S B - - -63.9 180.8 - - - - - - 183.6 - 35.5 - 82 ALA 82 S l - - - - - - - - - - 186.2 - 31.4 - * * 83 GLY 83 S - - - - - - - - - - - 183.9 - - - 84 ALA 84 e B - - - - - - - - - - 177.7 - 33.7 - 85 VAL 85 E B - 181.6 - - - - - - - - 180.9 -.8 34.1 - +* +* 86 THR 86 E B - - -54.2 - - - - - - - 178.5 -3.8 35.6 - ** ** 87 THR 87 E B - - -54.9 - - - - - - - 180.5 - 35.1 - 88 MET 88 E B - - -64.8 179.8 - - - - - - 183.6 -2.8 32.6 - * * 89 HIS 89 E B - - -66.2 - - - - - - - 180.8 -2.7 32.7 - 90 VAL 90 E B - 182.8 - - - - - - - - 182.5 -3.3 33.8 - +* +* 91 ILE 91 E B - - -66.6 - - - - - - - 179.6 -3.1 34.3 - * * 92 ILE 92 E B - - -65.5 - - - - - - - 176.9 -.6 34.5 - +* +* 93 GLN 93 e B - - -60.2 182.5 - - - - - - 179.6 -1.3 34.4 - * * 94 ALA 94 B - - - - - - - - - - 180.6 - 34.1 - 95 PRO 95 - - - - - -67.2 - - - - - 179.0 - 38.7 - * * 96 VAL 96 S A - 183.1 - - - - - - - - 175.9 - 34.9 - 97 THR 97 S B - - -56.3 - - - - - - - 180.6 - 35.3 - Residue-by-residue listing for refined_5 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 98 GLU 98 B - 179.3 - - - - - - - - 177.1 -.5 33.4 - +* +* 99 LYS 99 S XX - 180.5 - 182.0 - - - - - - 180.3 -.5 32.5 - **** +* **** 100 GLU 100 B - - -57.9 178.9 - - - - - - 181.6 -2.4 34.8 - 101 LYS 101 - - 197.1 - - - - - - - - - - 35.7 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * * * ** *** +* ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.2 183.8 -61.8 178.3 -65.0 -65.9 -36.2 - - - 179.8 -2.0 34.3 Standard deviations: 6.4 5.5 6.5 6.8 7.7 9.6 12.9 - - - 3.4 1.0 1.9 Numbers of values: 14 31 37 18 6 11 11 0 0 0 100 56 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_5 Page 5 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 GLU 1 - 1.243 1.514 1.547 1.460 - 114.80 121.50 111.62 111.68 112.65 123.69 * * 2 ALA 2 1.310 1.243 1.510 1.528 1.437 123.97 115.46 121.38 111.14 107.94 111.59 123.04 * * * * * 3 GLU 3 1.301 1.236 1.517 1.528 1.417 121.69 115.69 121.03 112.15 110.29 109.39 123.18 ** ** * ** 4 VAL 4 1.312 1.237 1.510 1.549 1.440 121.79 116.08 120.93 108.55 108.33 112.15 122.99 * * * 5 HIS 5 1.289 1.230 1.516 1.558 1.435 121.74 116.04 121.20 111.54 110.97 111.63 122.68 +** * * +** 6 ASN 6 1.300 1.231 1.528 1.541 1.463 121.52 113.82 122.70 111.59 108.23 109.65 123.47 ** * * * ** 7 GLN 7 1.311 1.237 1.523 1.546 1.431 124.59 117.31 120.05 108.99 107.66 109.33 122.62 * * +* * +* 8 LEU 8 1.309 1.222 1.507 1.552 1.445 120.76 117.24 120.38 108.88 107.87 112.50 122.35 * * * * * 9 GLU 9 1.296 1.219 1.492 1.503 1.439 120.43 115.52 121.06 109.58 110.80 111.93 123.41 ** +* * ** 10 ILE 10 1.281 1.229 1.501 1.591 1.433 122.46 116.21 120.65 108.70 108.98 113.23 123.14 *** * +* * * *** 11 LYS 11 1.295 1.249 1.490 1.532 1.426 120.78 116.03 120.67 109.14 108.19 114.44 123.29 ** +* +* * ** ** Residue-by-residue listing for refined_5 Page 6 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 12 PHE 12 1.288 1.224 1.506 1.528 1.421 120.61 115.84 120.78 111.21 109.71 109.34 123.38 +** +* +** 13 ARG 13 1.303 1.228 1.507 1.539 1.440 122.74 116.39 120.45 110.01 108.85 110.23 123.15 +* +* 14 LEU 14 1.302 1.238 1.512 1.530 1.440 121.44 115.60 120.88 107.68 110.15 110.57 123.49 +* * +* 15 THR 15 1.317 1.231 1.540 1.549 1.462 123.23 114.50 121.76 110.04 110.18 110.82 123.74 16 ASP 16 1.308 1.222 1.542 1.542 1.455 124.15 117.15 120.82 110.13 111.61 108.45 121.96 +* * * +* 17 GLY 17 1.320 1.234 1.516 - 1.457 119.84 115.53 121.51 - 112.00 - 122.96 18 SER 18 1.297 1.226 1.523 1.540 1.431 122.34 118.33 119.69 110.85 107.56 108.92 121.93 ** * * * ** 19 ASP 19 1.310 1.238 1.498 1.536 1.436 119.72 114.54 121.38 110.58 112.06 113.44 124.08 * * * * +* +* 20 ILE 20 1.294 1.240 1.514 1.565 1.432 123.70 116.45 119.49 109.78 106.87 110.20 124.04 ** * * +* ** 21 GLY 21 1.327 1.241 1.518 - 1.451 122.08 117.30 120.25 - 113.41 - 122.45 22 PRO 22 1.343 1.237 1.521 1.534 1.459 123.28 114.54 121.62 110.91 113.41 104.26 123.83 +* * * +* 23 LYS 23 1.292 1.224 1.520 1.532 1.428 124.20 118.55 119.39 109.63 105.40 107.90 122.06 +** +* * * ** +* +** 24 ALA 24 1.300 1.234 1.516 1.520 1.456 119.75 116.15 120.62 110.90 111.68 111.07 123.22 ** * ** 25 PHE 25 1.318 1.239 1.516 1.536 1.450 122.86 118.41 119.98 106.23 108.01 111.22 121.55 * ** * ** 26 PRO 26 1.324 1.239 1.531 1.533 1.459 121.85 116.96 120.57 109.90 109.78 103.57 122.47 * * 27 ASP 27 1.316 1.237 1.527 1.543 1.473 121.53 116.27 120.66 110.25 111.72 111.80 123.04 28 ALA 28 1.323 1.237 1.531 1.520 1.455 121.87 117.11 120.41 110.44 112.06 110.53 122.48 29 THR 29 1.320 1.240 1.536 1.543 1.446 121.57 116.56 120.60 111.48 109.77 110.26 122.82 * * 30 THR 30 1.318 1.245 1.532 1.553 1.439 121.45 115.11 121.49 109.67 112.39 111.77 123.40 31 VAL 31 1.317 1.223 1.538 1.554 1.444 123.82 116.49 120.74 110.94 110.42 111.20 122.76 * * 32 SER 32 1.327 1.238 1.547 1.543 1.456 122.25 116.63 120.62 111.11 110.19 109.83 122.66 * * 33 ALA 33 1.333 1.229 1.525 1.519 1.460 121.74 116.17 120.83 110.77 110.45 110.62 122.98 34 LEU 34 1.324 1.229 1.533 1.527 1.424 123.39 115.57 121.10 111.65 108.85 107.32 123.26 +* +* +* 35 LYS 35 1.322 1.220 1.515 1.525 1.454 122.64 116.89 120.40 111.04 111.36 110.96 122.70 36 GLU 36 1.325 1.235 1.521 1.525 1.456 121.36 116.41 120.38 110.54 111.75 111.63 123.21 37 THR 37 1.317 1.232 1.535 1.540 1.446 122.00 115.68 120.88 110.65 109.17 110.51 123.40 38 VAL 38 1.336 1.214 1.524 1.564 1.459 122.59 115.62 120.74 108.45 109.07 111.48 123.58 39 ILE 39 1.334 1.225 1.539 1.573 1.474 123.09 115.67 121.29 108.81 110.29 110.97 123.02 * * 40 SER 40 1.323 1.232 1.545 1.548 1.452 123.03 116.62 120.83 111.15 111.07 109.31 122.55 41 GLU 41 1.321 1.233 1.527 1.522 1.447 122.35 116.96 120.58 108.56 111.76 109.33 122.45 42 TRP 42 1.300 1.242 1.525 1.537 1.437 120.94 117.39 120.26 110.15 111.12 109.45 122.24 ** * ** 43 PRO 43 1.355 1.223 1.521 1.529 1.460 122.81 116.38 120.90 109.40 110.33 103.35 122.72 44 ARG 44 1.295 1.220 1.528 1.526 1.447 121.84 116.48 121.45 113.00 111.59 109.86 122.08 ** +* ** 45 GLU 45 1.310 1.240 1.565 1.534 1.445 121.24 116.73 120.86 112.31 110.99 109.41 122.40 * +* * +* Residue-by-residue listing for refined_5 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 46 LYS 46 1.342 1.232 1.548 1.548 1.475 122.21 116.68 120.92 109.72 110.96 110.44 122.38 * * 47 GLU 47 1.316 1.227 1.526 1.551 1.435 121.54 115.57 120.77 114.76 112.98 113.13 123.57 * * ** +* ** 48 ASN 48 1.340 1.223 1.496 1.542 1.483 124.62 114.72 121.59 111.48 111.00 115.13 123.64 * * +* +** +** 49 GLY 49 1.288 1.248 1.492 - 1.401 121.61 117.73 120.11 - 109.86 - 122.15 +** * *** *** 50 PRO 50 1.308 1.228 1.520 1.537 1.439 122.75 115.04 121.37 109.34 112.64 103.97 123.54 ** +* * * ** 51 LYS 51 1.299 1.226 1.503 1.560 1.453 123.10 113.07 122.53 108.79 105.79 113.43 124.40 ** * * +* * +* +* ** 52 THR 52 1.307 1.236 1.536 1.532 1.410 125.76 117.02 120.49 109.94 108.52 110.88 122.49 +* +** ** +** 53 VAL 53 1.305 1.232 1.532 1.547 1.451 122.68 115.61 121.38 110.87 110.65 112.91 122.99 +* +* 54 LYS 54 1.322 1.232 1.523 1.520 1.458 123.19 117.41 120.32 109.32 112.17 109.69 122.24 55 GLU 55 1.319 1.243 1.531 1.534 1.452 118.82 116.99 120.54 112.13 114.31 114.46 122.41 +* * * ** ** 56 VAL 56 1.316 1.236 1.534 1.565 1.451 121.05 116.68 121.12 110.71 110.69 112.17 122.18 57 LYS 57 1.304 1.234 1.517 1.526 1.434 120.92 116.36 120.47 109.95 110.19 110.91 123.16 +* * +* 58 LEU 58 1.311 1.233 1.535 1.566 1.445 121.80 116.61 120.31 112.04 107.17 108.70 123.08 * +* * * * +* 59 ILE 59 1.320 1.237 1.535 1.590 1.457 122.82 115.50 121.16 109.34 111.54 112.34 123.34 +* +* 60 SER 60 1.310 1.236 1.519 1.539 1.439 123.52 116.52 119.83 111.00 107.59 110.97 123.55 * * * * 61 ALA 61 1.343 1.237 1.536 1.535 1.479 123.79 116.11 121.17 111.21 111.54 111.10 122.68 * * * * 62 GLY 62 1.324 1.232 1.517 - 1.449 121.03 116.33 120.95 - 112.05 - 122.72 63 LYS 63 1.312 1.233 1.504 1.523 1.418 122.88 116.28 120.37 109.79 110.84 109.28 123.34 * * ** ** 64 VAL 64 1.316 1.237 1.527 1.575 1.442 121.01 115.97 121.30 112.46 107.81 112.96 122.72 * +* * +* 65 LEU 65 1.301 1.235 1.511 1.525 1.437 121.50 115.86 120.82 109.82 111.92 110.85 123.31 +* * +* 66 GLU 66 1.306 1.237 1.527 1.523 1.441 121.73 115.22 121.04 112.99 110.62 111.18 123.74 +* +* +* 67 ASN 67 1.316 1.236 1.538 1.546 1.474 124.50 117.78 119.78 109.78 114.92 110.92 122.44 +* * +* 68 SER 68 1.317 1.230 1.547 1.540 1.450 120.75 117.25 120.75 112.02 111.96 110.25 121.99 * * * 69 LYS 69 1.318 1.224 1.503 1.522 1.450 121.00 116.90 120.19 108.82 109.42 111.37 122.91 * * 70 THR 70 1.301 1.246 1.525 1.533 1.421 121.64 116.72 120.24 109.32 109.56 110.03 123.04 +* +* +* 71 VAL 71 1.325 1.233 1.535 1.562 1.457 121.72 115.06 121.65 109.69 109.09 111.04 123.25 72 LYS 72 1.322 1.227 1.532 1.545 1.446 123.46 117.39 119.90 112.33 111.99 109.16 122.69 * * 73 ASP 73 1.329 1.237 1.530 1.536 1.479 121.76 116.70 120.95 109.87 112.35 111.44 122.35 * * 74 TYR 74 1.318 1.235 1.522 1.508 1.441 121.03 115.86 120.77 111.37 112.17 110.51 123.37 * * Residue-by-residue listing for refined_5 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 75 ARG 75 1.314 1.236 1.521 1.520 1.438 123.11 115.68 120.94 110.68 110.17 108.83 123.37 * * * 76 SER 76 1.289 1.249 1.536 1.544 1.422 122.08 118.43 119.72 110.97 108.53 108.62 121.79 +** +* * * +** 77 PRO 77 1.358 1.235 1.522 1.508 1.454 121.98 113.42 121.86 110.38 110.44 105.01 124.64 * * ** +* +* ** 78 VAL 78 1.285 1.238 1.527 1.553 1.441 126.37 113.81 122.31 110.82 106.54 111.27 123.87 *** +** * +* *** 79 SER 79 1.312 1.234 1.526 1.535 1.431 124.05 115.30 121.52 111.11 107.16 111.06 122.90 * * * * * 80 ASN 80 1.306 1.234 1.509 1.536 1.451 122.21 115.95 120.32 110.01 111.34 111.00 123.72 +* +* 81 LEU 81 1.331 1.241 1.520 1.492 1.416 124.17 115.25 120.64 110.03 112.81 108.09 124.09 +* ** * * ** 82 ALA 82 1.336 1.246 1.511 1.528 1.459 124.25 115.00 121.47 112.35 109.68 112.65 123.45 * * +* +* 83 GLY 83 1.312 1.231 1.502 - 1.433 121.50 114.89 121.33 - 108.46 - 123.76 * * * * 84 ALA 84 1.326 1.237 1.514 1.519 1.441 122.92 115.16 121.35 110.54 112.18 110.36 123.49 85 VAL 85 1.304 1.225 1.514 1.563 1.434 122.69 116.27 120.74 109.79 107.57 112.61 122.95 +* * * +* 86 THR 86 1.286 1.235 1.531 1.546 1.423 122.84 116.76 120.80 110.00 109.07 109.45 122.42 *** +* * *** 87 THR 87 1.298 1.231 1.521 1.542 1.428 121.23 116.68 120.68 109.75 108.42 110.66 122.64 ** +* ** 88 MET 88 1.304 1.233 1.501 1.531 1.441 121.34 116.16 120.68 111.91 110.01 111.45 123.14 +* * +* 89 HIS 89 1.304 1.231 1.497 1.534 1.444 121.51 115.40 121.01 110.88 111.19 111.94 123.58 +* * +* 90 VAL 90 1.295 1.246 1.504 1.547 1.429 122.40 114.12 121.83 110.68 109.18 111.47 124.05 ** * +* * ** 91 ILE 91 1.280 1.239 1.505 1.542 1.414 123.47 114.67 121.40 111.41 110.20 109.86 123.92 +*** ** * +*** 92 ILE 92 1.297 1.234 1.507 1.578 1.427 122.81 116.40 120.51 108.82 108.51 112.82 123.08 ** * +* ** 93 GLN 93 1.295 1.245 1.496 1.528 1.422 121.49 116.09 120.19 109.72 107.87 111.92 123.71 ** * +* * ** 94 ALA 94 1.297 1.243 1.518 1.515 1.439 122.30 117.52 120.53 110.64 109.69 110.40 121.90 ** ** 95 PRO 95 1.333 1.239 1.519 1.538 1.455 122.49 116.17 120.56 110.27 111.33 103.85 123.28 96 VAL 96 1.318 1.236 1.518 1.546 1.452 122.23 115.02 121.70 109.59 108.11 111.12 123.25 * * 97 THR 97 1.298 1.241 1.534 1.543 1.427 122.63 117.04 120.46 109.93 108.30 110.17 122.48 ** +* * ** 98 GLU 98 1.316 1.245 1.518 1.538 1.446 121.03 115.21 120.48 110.55 110.90 111.32 124.30 99 LYS 99 1.333 1.230 1.528 1.541 1.462 124.65 116.75 120.60 111.96 111.51 110.92 122.62 +* +* 100 GLU 100 1.307 1.244 1.513 1.531 1.442 122.50 116.47 120.35 109.87 108.34 110.82 123.17 +* * +* 101 LYS 101 1.297 - 1.521 1.559 1.434 121.95 - - 111.19 106.07 109.02 - ** * * +* ** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** +* +* *** +** ** * ** ** +** +* +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 9 ---------------------------------------- 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 1.280 1.343 1.311 .014 +*** * * C-N (Pro) 1.341 .016 6 1.308 1.358 1.337 .018 ** * C-O C-O 1.231 .020 100 1.214 1.249 1.234 .007 CA-C CH1E-C (except Gly) 1.525 .021 96 1.490 1.565 1.522 .014 +* +* CH2G*-C (Gly) 1.516 .018 5 1.492 1.518 1.509 .011 * CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.515 1.535 1.523 .006 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.532 1.591 1.556 .016 +* CH1E-CH2E (the rest) 1.530 .020 62 1.492 1.566 1.535 .013 +* +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.410 1.483 1.444 .016 +** * NH1-CH2G* (Gly) 1.451 .016 5 1.401 1.457 1.438 .020 *** N-CH1E (Pro) 1.466 .015 6 1.439 1.460 1.454 .007 +* ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 10 ---------------------------------------- +-----------------+ | 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 89 113.07 118.55 116.15 1.03 +* * CH2G*-C-NH1 (Gly) 116.4 2.1 5 114.89 117.73 116.36 1.06 CH1E-C-N (Pro) 116.9 1.5 6 113.42 116.96 115.42 1.21 ** O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.55 124.40 123.01 .61 O-C-N (Pro) 122.0 1.4 6 122.47 124.64 123.41 .72 +* * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.82 126.37 122.34 1.31 +* +** C-NH1-CH2G* (Gly) 120.6 1.7 5 119.84 122.08 121.21 .76 C-N-CH1E (Pro) 122.6 5.0 6 121.85 123.28 122.53 .49 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.39 122.70 120.82 .61 * CH2G*-C-O (Gly) 120.8 2.1 5 120.11 121.51 120.83 .56 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 110.44 112.35 111.00 .57 * CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.45 112.46 110.01 .97 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 106.23 114.76 110.56 1.36 ** ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.40 114.92 109.98 1.89 ** * NH1-CH2G*-C (Gly) 112.5 2.9 5 108.46 113.41 111.16 1.76 * N-CH1E-C (Pro) 111.8 2.5 6 109.78 113.41 111.32 1.31 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 110.36 112.65 111.04 .73 +* NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 109.45 113.23 111.32 1.04 * * N-CH1E-CH2E (Pro) 103.0 1.1 6 103.35 105.01 104.00 .54 +* NH1-CH1E-CH2E (the rest) 110.5 1.7 56 107.32 115.13 110.67 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_5 Page 11 ---------------------------------------- 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] 11 12.5% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.1% Residues in disallowed regions [XX] 1 1.1% ---- ------ Number of non-glycine and non-proline residues 88 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 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 1.9 3.1 1.6 -.8 Inside e. H-bond energy st dev 56 1.0 .8 .2 .8 Inside f. Overall G-factor 101 .0 -.4 .3 1.3 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 14 6.4 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 31 5.5 19.0 5.3 -2.6 BETTER c. Chi-1 gauche plus st dev 37 6.5 17.5 4.9 -2.2 BETTER d. Chi-1 pooled st dev 82 7.2 18.2 4.8 -2.3 BETTER e. Chi-2 trans st dev 18 6.8 20.4 5.0 -2.7 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 85.2 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.2 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .97 3 Residue-by-residue listing for refined_5 Page 12 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.43 Chi1-chi2 distribution -.30 Chi1 only -.02 Chi3 & chi4 .33 Omega .03 ------ -.13 ===== Main-chain covalent forces:- Main-chain bond lengths .00 Main-chain bond angles .39 ------ .23 ===== OVERALL AVERAGE -.01 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.