Residue-by-residue listing for refined_12 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 - - - -63.7 - - - - - - - 186.4 - 33.7 - * * 2 ALA 2 l - - - - - - - - - - 188.3 - 31.3 - * * 3 GLU 3 b - 184.6 - 173.5 - - - - - - 180.6 - 34.0 - 4 VAL 4 B - 182.1 - - - - - - - - 181.4 - 34.9 - 5 HIS 5 S XX - 182.7 - - - - - - - - 180.0 - 31.8 - **** **** 6 ASN 6 B - - -63.0 - - - - - - - 172.2 - 34.2 - * * 7 GLN 7 B - - -89.3 - - - - - - - 176.5 -.9 34.8 - +* +* +* 8 LEU 8 E B 58.0 - - 167.1 - - - - - - 184.0 -2.0 29.2 - * * 9 GLU 9 E B - - -58.0 174.5 - - - - - - 182.2 -2.1 34.7 - 10 ILE 10 E B - - -57.9 178.6 - - - - - - 175.8 -2.9 34.5 - * * 11 LYS 11 E B 63.5 - - 176.6 - - - - - - 185.4 -2.8 32.1 - 12 PHE 12 E B - - -56.6 - - - - - - - 177.2 -.6 35.7 - +* +* 13 ARG 13 E B - 184.3 - 185.1 - - - - - - 177.3 -3.5 34.4 - ** ** 14 LEU 14 E B - - -70.4 - - - - - - - 178.4 -3.4 34.5 - +* +* 15 THR 15 e A 46.8 - - - - - - - - - 179.0 -1.3 34.8 - * * 16 ASP 16 T A - - -62.1 - - - - - - - 178.5 - 34.6 - 17 GLY 17 t - - - - - - - - - - - 177.2 -2.0 - - Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 18 SER 18 e B - - -56.1 - - - - - - - 181.6 - 35.8 - 19 ASP 19 E B 68.5 - - - - - - - - - 177.2 - 32.8 - 20 ILE 20 E B - - -59.8 179.0 - - - - - - 181.8 -3.0 35.2 - * * 21 GLY 21 E - - - - - - - - - - - 182.2 - - - 22 PRO 22 E - - - - - -65.0 - - - - - 178.1 - 38.0 - * * 23 LYS 23 E B - 184.4 - - - - - - - - 183.9 -2.3 34.7 - 24 ALA 24 E B - - - - - - - - - - 178.6 - 34.0 - 25 PHE 25 E B - - -54.2 - - - - - - - 173.3 -3.3 36.3 - * +* +* 26 PRO 26 t - - - - - -59.7 - - - - - 180.4 - 38.5 - * * 27 ASP 27 T A - 180.9 - - - - - - - - 180.3 - 35.2 - 28 ALA 28 T A - - - - - - - - - - 182.9 - 34.4 - 29 THR 29 t B - - -66.8 - - - - - - - 181.5 -2.3 30.9 - 30 THR 30 h B - 177.6 - - - - - - - - 177.6 - 33.7 - 31 VAL 31 H A - 180.1 - - - -64.3 -26.0 - - - 176.0 -3.3 33.9 - * +* +* 32 SER 32 H A - 180.8 - - - -56.3 -47.0 - - - 180.3 -.8 34.1 - +* +* 33 ALA 33 H A - - - - - -70.3 -27.1 - - - 177.2 -.5 33.9 - * ** ** 34 LEU 34 H A - 172.6 - - - -67.6 -45.1 - - - 177.6 -1.1 35.9 - * * 35 LYS 35 H A - - -63.5 168.1 - -71.0 -33.4 - - - 173.7 -2.9 32.8 - * * * 36 GLU 36 H A - - -67.8 - - -60.0 -44.2 - - - 180.8 -2.3 34.3 - 37 THR 37 H A - - -56.5 - - -64.7 -46.4 - - - 181.9 -2.1 33.9 - 38 VAL 38 H A 67.9 - - - - -60.1 -38.6 - - - 178.1 -2.2 32.2 - 39 ILE 39 H A - - -60.0 176.9 - -68.4 -37.1 - - - 180.7 -1.9 33.5 - 40 SER 40 H A - - -60.4 - - -72.2 -25.2 - - - 180.1 -1.8 33.5 - * * 41 GLU 41 H A - - -64.9 - - -83.5 -19.5 - - - 181.7 -1.7 34.3 - +* +* +* 42 TRP 42 h B - 196.1 - - - - - - - - 171.8 -.9 37.1 - * +* +* 43 PRO 43 t - - - - - -53.1 - - - - - 185.4 - 38.7 - * * * 44 ARG 44 T A - 182.9 - 179.1 - - - - - - 179.7 -.6 32.5 - +* +* 45 GLU 45 T A - 182.8 - 174.8 - - - - - - 174.0 - 33.0 - * * 46 LYS 46 t B - 180.7 - - - - - - - - 180.2 -.8 36.1 - +* +* 47 GLU 47 B 55.9 - - - - - - - - - 178.7 -1.0 29.7 - * * * 48 ASN 48 S XX - 177.9 - - - - - - - - 177.2 - 29.2 - **** * **** 49 GLY 49 S - - - - - - - - - - - 173.2 -1.2 - - * * * 50 PRO 50 S - - - - - -86.1 - - - - - 181.9 - 39.7 - +* +* +* 51 LYS 51 B - - -89.5 - - - - - - - 178.1 - 32.1 - +* +* 52 THR 52 t B 40.1 - - - - - - - - - 187.7 - 33.5 - +* * +* Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 53 VAL 53 T A 61.7 - - - - - - - - - 178.0 - 32.9 - 54 LYS 54 T A - 177.2 - 190.4 - - - - - - 189.7 - 35.5 - +* +* 55 GLU 55 e a 54.0 - - 188.8 - - - - - - 179.5 -2.4 31.8 - 56 VAL 56 E B 62.4 - - - - - - - - - 179.4 -1.7 32.9 - 57 LYS 57 E B - - -73.2 - - - - - - - 176.7 -1.5 33.3 - 58 LEU 58 E B - - -67.9 - - - - - - - 183.0 - 34.1 - 59 ILE 59 E B - - -64.1 - - - - - - - 173.6 -2.8 35.2 - * * 60 SER 60 E B 62.9 - - - - - - - - - 182.2 -2.1 34.1 - 61 ALA 61 T l - - - - - - - - - - 179.5 - 32.6 - 62 GLY 62 T - - - - - - - - - - - 183.5 - - - 63 LYS 63 E B - - -58.0 175.2 - - - - - - 178.2 -1.6 37.0 - 64 VAL 64 E B - 187.5 - - - - - - - - 182.2 - 36.2 - 65 LEU 65 e B - - -66.0 - - - - - - - 174.8 -2.5 32.5 - 66 GLU 66 t B - - -71.4 - - - - - - - 184.8 - 32.7 - 67 ASN 67 T A - 186.7 - - - - - - - - 180.2 - 35.0 - 68 SER 68 T A - 180.1 - - - - - - - - 184.0 - 34.2 - 69 LYS 69 t B - - -67.5 167.8 - - - - - - 182.4 -.8 32.8 - +* +* 70 THR 70 B B 59.5 - - - - - - - - - 178.4 - 34.9 - 71 VAL 71 G A - 180.1 - - - - - - - - 176.9 -3.2 33.8 - +* +* 72 LYS 72 G A - 177.0 - 183.7 - - - - - - 181.7 -1.3 35.8 - * * 73 ASP 73 G A - - -67.7 - - - - - - - 177.2 -1.1 33.1 - * * 74 TYR 74 G A - - -75.1 - - - - - - - 174.3 -2.0 31.1 - 75 ARG 75 g b - - -65.0 - - - - - - - 176.4 -1.0 35.9 - * * 76 SER 76 B 50.2 - - - - - - - - - 181.0 - 33.6 - 77 PRO 77 S - - - - - -52.7 - - - - - 182.1 - 38.4 - * * * 78 VAL 78 S XX 68.3 - - - - - - - - - 178.9 - 26.1 - **** ** **** 79 SER 79 b - 191.6 - - - - - - - - 177.1 -2.4 35.2 - 80 ASN 80 a - 185.9 - - - - - - - - 190.5 - 32.8 - +* +* 81 LEU 81 B - - -77.2 - - - - - - - 182.4 - 31.6 - 82 ALA 82 b - - - - - - - - - - 177.2 - 35.4 - 83 GLY 83 S - - - - - - - - - - - 181.6 -1.9 - - 84 ALA 84 e B - - - - - - - - - - 178.1 - 34.7 - 85 VAL 85 E B - 180.8 - - - - - - - - 181.0 - 33.8 - 86 THR 86 E B - - -58.5 - - - - - - - 175.3 -3.3 35.4 - +* +* 87 THR 87 E B - - -55.5 - - - - - - - 184.9 -.6 34.7 - +* +* 88 MET 88 E B - 182.8 - 175.9 - - - - - - 181.8 -3.0 34.5 - * * 89 HIS 89 E B - - -63.2 - - - - - - - 177.1 -3.1 33.2 - * * 90 VAL 90 E B - 182.1 - - - - - - - - 181.8 -2.2 34.0 - 91 ILE 91 E B - - -73.7 - - - - - - - 175.9 -2.7 33.8 - 92 ILE 92 E b - - -58.3 - - - - - - - 186.9 -.6 34.7 - * +* +* 93 GLN 93 e B - 191.0 - - - - - - - - 181.3 -1.1 36.5 - * * Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 94 ALA 94 B - - - - - - - - - - 175.0 -.6 34.0 - +* +* 95 PRO 95 - - - - - -81.5 - - - - - 175.0 - 39.6 - * +* +* 96 VAL 96 S b - 179.5 - - - - - - - - 178.3 - 33.6 - 97 THR 97 B - - -55.3 - - - - - - - 183.1 -.9 34.4 - * * 98 GLU 98 A - 181.5 - 177.3 - - - - - - 181.4 - 34.5 - 99 LYS 99 XX - 170.5 - 176.3 - - - - - - 175.4 - 29.6 - **** * **** 100 GLU 100 b - 179.2 - 178.0 - - - - - - 190.1 - 35.0 - +* +* 101 LYS 101 - - 178.1 - 182.6 - - - - - - - - 31.9 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** +* +* +* +* +* +* ** ** **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.6 181.9 -64.9 177.6 -66.3 -67.1 -35.4 - - - 179.9 -1.9 34.1 Standard deviations: 8.4 5.1 8.5 6.1 14.3 7.4 9.8 - - - 3.9 .9 2.2 Numbers of values: 14 32 36 21 6 11 11 0 0 0 100 55 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_12 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 - 1.229 1.502 1.550 1.456 - 116.15 119.65 110.84 108.29 111.64 124.20 * * * 2 ALA 2 1.335 1.240 1.510 1.530 1.466 123.92 114.97 121.69 112.11 108.53 113.51 123.27 * * ** ** 3 GLU 3 1.305 1.240 1.533 1.542 1.417 121.85 115.31 121.71 113.20 110.46 108.18 122.85 +* ** +* * ** 4 VAL 4 1.308 1.246 1.519 1.565 1.447 122.91 116.23 119.62 109.76 108.64 111.00 124.13 * * 5 HIS 5 1.344 1.239 1.526 1.567 1.475 124.68 116.35 120.94 112.22 109.59 112.48 122.66 * +* +* * * +* 6 ASN 6 1.301 1.220 1.523 1.539 1.441 121.52 116.20 120.96 109.36 111.54 111.22 122.79 +* +* 7 GLN 7 1.300 1.242 1.520 1.543 1.454 122.85 118.84 119.64 109.68 107.36 111.33 121.51 ** * * ** 8 LEU 8 1.308 1.221 1.502 1.547 1.438 118.60 115.46 121.45 112.26 110.84 115.51 123.09 +* * * +* * +** +** 9 GLU 9 1.290 1.222 1.499 1.513 1.428 121.86 115.67 121.04 110.82 109.49 109.63 123.28 +** * +* +** 10 ILE 10 1.282 1.236 1.506 1.569 1.433 122.34 116.08 120.59 109.86 109.46 111.52 123.27 *** * * *** 11 LYS 11 1.304 1.246 1.508 1.534 1.423 121.38 115.80 120.84 111.62 109.26 112.90 123.36 +* +* * +* Residue-by-residue listing for refined_12 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 1.291 1.214 1.511 1.531 1.440 122.13 117.29 120.10 109.46 110.32 109.37 122.60 +** +** 13 ARG 13 1.306 1.227 1.512 1.536 1.445 121.31 116.45 120.57 109.12 109.23 111.93 122.97 +* +* 14 LEU 14 1.300 1.236 1.513 1.547 1.448 121.87 116.07 120.48 108.75 109.68 112.14 123.43 ** ** 15 THR 15 1.311 1.231 1.539 1.532 1.457 123.02 115.48 121.51 110.50 111.46 109.01 122.97 * * * 16 ASP 16 1.321 1.234 1.520 1.530 1.462 123.14 116.17 121.25 109.68 111.07 110.24 122.58 17 GLY 17 1.316 1.222 1.510 - 1.442 121.27 116.82 120.24 - 113.03 - 122.94 18 SER 18 1.316 1.227 1.523 1.527 1.448 121.74 117.83 119.84 109.68 108.62 109.19 122.31 19 ASP 19 1.310 1.237 1.512 1.532 1.430 119.91 114.66 121.83 110.36 112.01 111.99 123.49 * * * 20 ILE 20 1.291 1.238 1.519 1.567 1.436 124.13 116.55 119.44 109.90 107.31 110.94 123.98 +** * * * +** 21 GLY 21 1.324 1.241 1.517 - 1.452 122.41 117.23 120.48 - 113.69 - 122.29 * * 22 PRO 22 1.341 1.243 1.520 1.532 1.456 123.05 115.09 121.52 110.48 113.18 104.24 123.37 * * * 23 LYS 23 1.293 1.219 1.516 1.565 1.434 123.47 118.15 119.44 113.26 105.96 108.66 122.40 +** +* * +* +* * +** 24 ALA 24 1.302 1.231 1.506 1.522 1.445 120.44 115.14 121.44 110.33 111.06 110.63 123.42 +* +* 25 PHE 25 1.294 1.232 1.492 1.537 1.424 122.41 118.10 119.89 107.51 106.75 111.55 121.88 ** +* +* * +* ** 26 PRO 26 1.310 1.240 1.530 1.528 1.447 121.55 115.00 121.07 110.62 111.07 103.77 123.93 +* * * * +* 27 ASP 27 1.303 1.237 1.548 1.540 1.472 124.62 115.71 121.52 111.65 111.23 107.35 122.72 +* * +* +* +* 28 ALA 28 1.323 1.237 1.545 1.522 1.452 122.74 117.92 120.00 109.70 113.20 109.69 122.08 29 THR 29 1.319 1.228 1.538 1.554 1.458 121.31 115.37 121.39 113.02 113.24 111.36 123.20 +* +* 30 THR 30 1.322 1.243 1.539 1.567 1.446 123.33 115.01 121.46 110.41 112.55 110.70 123.53 * * 31 VAL 31 1.330 1.221 1.528 1.554 1.456 124.09 116.52 120.77 110.66 109.88 110.91 122.71 * * 32 SER 32 1.324 1.220 1.547 1.541 1.449 121.51 116.91 120.45 111.37 109.69 109.88 122.50 * * 33 ALA 33 1.338 1.234 1.526 1.513 1.469 121.93 115.51 121.35 110.49 110.61 110.37 123.13 34 LEU 34 1.310 1.234 1.545 1.529 1.417 123.71 115.58 121.38 112.38 108.84 106.42 122.98 * ** * * ** ** 35 LYS 35 1.320 1.221 1.532 1.531 1.457 123.07 116.87 120.73 112.80 111.11 109.68 122.39 * * 36 GLU 36 1.320 1.240 1.531 1.533 1.456 121.23 115.40 121.11 110.01 110.14 110.69 123.46 37 THR 37 1.319 1.229 1.542 1.547 1.440 122.80 117.15 120.08 110.81 111.36 110.31 122.72 38 VAL 38 1.342 1.234 1.539 1.576 1.472 121.45 115.76 121.02 111.31 111.04 112.32 123.17 * * * 39 ILE 39 1.322 1.223 1.539 1.562 1.463 122.16 116.92 120.72 109.98 110.94 111.80 122.35 40 SER 40 1.321 1.238 1.540 1.531 1.458 121.56 116.77 120.65 110.64 112.25 110.39 122.58 41 GLU 41 1.321 1.235 1.528 1.520 1.439 122.14 116.81 120.66 110.19 112.25 109.79 122.53 42 TRP 42 1.300 1.222 1.527 1.546 1.450 121.73 119.29 119.01 109.22 107.30 108.24 121.58 ** +* * * * ** 43 PRO 43 1.349 1.230 1.539 1.531 1.465 121.72 116.46 120.77 110.24 110.05 103.81 122.74 44 ARG 44 1.324 1.236 1.524 1.534 1.457 121.69 116.42 121.00 111.01 112.03 111.63 122.58 Residue-by-residue listing for refined_12 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 1.317 1.233 1.531 1.531 1.445 121.22 115.56 121.33 112.73 109.45 110.06 123.11 * * 46 LYS 46 1.321 1.217 1.519 1.550 1.440 122.36 117.40 120.28 109.43 106.72 109.84 122.24 * +* +* 47 GLU 47 1.297 1.238 1.513 1.557 1.419 120.21 116.21 120.17 113.92 111.30 113.13 123.52 ** * ** ** +* ** 48 ASN 48 1.331 1.242 1.518 1.544 1.487 124.28 114.64 121.34 113.25 113.51 112.90 124.00 +* * +* * +* 49 GLY 49 1.283 1.231 1.516 - 1.448 123.07 118.15 120.30 - 110.47 - 121.55 *** * *** 50 PRO 50 1.337 1.243 1.518 1.513 1.434 121.99 114.75 121.61 109.13 110.91 103.36 123.54 ** * * ** 51 LYS 51 1.288 1.222 1.468 1.558 1.367 125.75 112.20 122.44 112.16 105.84 114.43 125.10 +** +** * *4.8* ** ** * +* ** * *4.8* 52 THR 52 1.214 1.231 1.540 1.529 1.417 125.62 116.03 120.53 112.53 111.78 108.92 123.42 *8.2* ** ** +* +* *8.2* 53 VAL 53 1.330 1.239 1.552 1.569 1.479 125.22 116.98 120.45 110.75 113.96 110.74 122.57 * * * +* +* 54 LYS 54 1.313 1.230 1.535 1.526 1.449 122.41 117.73 120.38 108.38 111.89 110.06 121.89 * * 55 GLU 55 1.314 1.234 1.544 1.541 1.457 119.50 118.04 119.95 112.81 115.66 109.21 121.90 * * * +* +* 56 VAL 56 1.322 1.240 1.538 1.567 1.470 120.35 115.88 120.99 110.06 111.23 112.47 123.10 57 LYS 57 1.326 1.238 1.516 1.549 1.450 122.57 115.28 120.91 109.41 111.14 112.62 123.81 * * 58 LEU 58 1.310 1.238 1.512 1.556 1.445 123.12 116.56 120.13 110.13 108.04 111.98 123.30 * * * * 59 ILE 59 1.309 1.240 1.528 1.558 1.456 122.54 115.76 120.88 108.88 111.55 110.47 123.36 * * 60 SER 60 1.307 1.249 1.513 1.527 1.417 122.81 116.66 119.40 110.98 107.09 111.28 123.85 +* ** * ** 61 ALA 61 1.330 1.238 1.534 1.536 1.473 123.59 115.55 121.36 111.60 110.43 111.39 123.06 * * 62 GLY 62 1.329 1.233 1.518 - 1.450 122.05 116.84 120.29 - 113.28 - 122.85 63 LYS 63 1.316 1.243 1.526 1.515 1.431 122.73 116.81 119.93 109.15 109.72 107.66 123.25 * +* +* 64 VAL 64 1.329 1.219 1.519 1.561 1.458 121.74 118.07 119.96 106.80 106.89 112.25 121.96 * +* +* 65 LEU 65 1.290 1.237 1.523 1.538 1.444 120.42 116.35 120.58 110.28 112.27 112.30 123.05 +** * +** 66 GLU 66 1.337 1.228 1.517 1.539 1.453 121.33 115.05 121.05 109.44 110.37 113.60 123.88 +* +* 67 ASN 67 1.302 1.234 1.547 1.535 1.461 124.59 116.79 120.83 110.82 112.69 108.04 122.38 +* * +* * +* 68 SER 68 1.320 1.241 1.540 1.541 1.463 121.85 116.08 120.96 110.49 111.41 109.91 122.92 69 LYS 69 1.310 1.233 1.520 1.533 1.447 122.44 116.43 120.70 113.05 111.28 109.53 122.83 * +* +* 70 THR 70 1.297 1.236 1.528 1.541 1.414 122.73 117.27 119.80 110.34 110.00 109.91 122.92 ** ** ** 71 VAL 71 1.337 1.234 1.534 1.557 1.469 121.92 115.20 120.93 109.79 109.93 111.80 123.84 72 LYS 72 1.331 1.230 1.535 1.532 1.472 124.66 116.45 120.94 108.93 111.74 108.96 122.61 +* +* 73 ASP 73 1.321 1.228 1.522 1.521 1.441 122.60 116.46 120.95 111.20 112.24 110.44 122.59 74 TYR 74 1.314 1.240 1.502 1.512 1.434 121.95 114.66 121.55 113.21 111.86 111.37 123.79 * * * +* +* Residue-by-residue listing for refined_12 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 1.302 1.237 1.517 1.523 1.401 124.58 117.83 119.58 110.95 106.57 108.63 122.57 +* *** +* +* * *** 76 SER 76 1.291 1.235 1.551 1.525 1.430 121.34 118.09 119.71 112.74 110.04 109.02 122.17 +** * * * +** 77 PRO 77 1.363 1.240 1.542 1.530 1.480 123.50 114.39 121.06 110.13 114.24 103.37 124.54 * +* +* +* 78 VAL 78 1.341 1.241 1.528 1.596 1.485 127.76 115.97 120.25 113.35 113.71 116.75 123.76 ** * *** +* *** *** 79 SER 79 1.297 1.246 1.518 1.547 1.454 124.98 118.43 119.29 109.12 107.12 111.36 122.24 ** +* * * ** 80 ASN 80 1.327 1.235 1.523 1.533 1.447 118.88 117.26 120.28 109.75 113.86 111.78 122.44 +* +* 81 LEU 81 1.319 1.240 1.499 1.499 1.411 121.28 112.77 122.18 110.49 115.63 111.88 125.02 * +* ** +* +* * ** 82 ALA 82 1.316 1.228 1.528 1.524 1.441 125.35 117.19 120.05 109.49 108.58 110.09 122.70 ** ** 83 GLY 83 1.319 1.237 1.508 - 1.467 121.10 115.85 121.36 - 112.48 - 122.79 84 ALA 84 1.299 1.229 1.501 1.518 1.435 121.88 116.62 120.22 110.37 109.59 110.12 123.15 ** * * ** 85 VAL 85 1.301 1.233 1.514 1.554 1.440 121.37 115.86 120.83 109.95 108.74 112.27 123.30 ** ** 86 THR 86 1.289 1.224 1.531 1.550 1.430 122.86 116.78 120.72 109.69 110.15 109.86 122.48 +** * +** 87 THR 87 1.302 1.233 1.527 1.548 1.430 120.72 116.72 120.52 110.38 107.13 110.99 122.75 +* * * +* 88 MET 88 1.303 1.227 1.511 1.527 1.444 121.45 116.71 120.30 111.31 110.20 109.25 122.99 +* +* 89 HIS 89 1.315 1.232 1.504 1.536 1.449 121.11 115.42 120.76 109.47 111.25 112.63 123.81 * * * 90 VAL 90 1.306 1.242 1.497 1.548 1.442 122.68 114.52 121.57 109.74 108.49 112.37 123.89 +* * +* 91 ILE 91 1.278 1.248 1.505 1.567 1.420 122.89 115.15 121.31 111.02 110.38 111.12 123.52 +*** * ** +*** 92 ILE 92 1.304 1.236 1.523 1.560 1.415 121.61 114.87 121.67 111.32 106.07 110.67 123.40 +* ** * +* ** 93 GLN 93 1.306 1.225 1.515 1.544 1.427 123.00 116.23 120.66 111.91 108.28 106.40 123.10 +* +* * ** ** 94 ALA 94 1.303 1.238 1.522 1.520 1.441 121.50 117.29 120.70 110.39 111.14 110.48 121.96 +* +* 95 PRO 95 1.334 1.238 1.518 1.534 1.456 122.88 116.61 120.42 110.37 109.70 102.56 122.95 96 VAL 96 1.307 1.235 1.525 1.549 1.452 121.28 115.90 121.20 109.21 109.64 112.89 122.78 +* +* 97 THR 97 1.300 1.235 1.523 1.554 1.431 122.74 115.92 120.94 110.45 107.97 111.28 123.10 ** * * ** 98 GLU 98 1.304 1.242 1.523 1.528 1.438 122.09 115.39 120.63 111.38 110.15 109.19 123.92 +* * +* 99 LYS 99 1.332 1.237 1.519 1.552 1.466 124.06 113.56 122.29 111.36 113.99 114.33 124.15 * * * ** ** 100 GLU 100 1.293 1.229 1.499 1.529 1.423 125.36 116.50 119.09 111.21 104.16 110.49 124.39 +** * +* ** * +** +** 101 LYS 101 1.334 - 1.530 1.542 1.469 123.58 - - 111.40 109.28 113.09 - * +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *8.2* +** ** *4.8* *** ** * ** +** *** +* *8.2* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 1.214 1.344 1.311 .018 *8.2* * * C-N (Pro) 1.341 .016 6 1.310 1.363 1.339 .016 +* * 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 1.468 1.552 1.523 .015 +** * CH2G*-C (Gly) 1.516 .018 5 1.508 1.518 1.514 .004 CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.513 1.536 1.523 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.529 1.596 1.558 .013 ** CH1E-CH2E (the rest) 1.530 .020 62 1.499 1.567 1.536 .013 +* +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.367 1.487 1.445 .020 *4.8* +* NH1-CH2G* (Gly) 1.451 .016 5 1.442 1.467 1.452 .008 N-CH1E (Pro) 1.466 .015 6 1.434 1.480 1.457 .014 ** ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 89 112.20 119.29 116.25 1.19 ** +* CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.85 118.15 116.98 .74 CH1E-C-N (Pro) 116.9 1.5 6 114.39 116.61 115.38 .84 +* * O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.51 125.10 123.01 .70 * O-C-N (Pro) 122.0 1.4 6 122.74 124.54 123.51 .60 +* * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.60 127.76 122.49 1.56 +* *** C-NH1-CH2G* (Gly) 120.6 1.7 5 121.10 123.07 121.98 .73 * C-N-CH1E (Pro) 122.6 5.0 6 121.55 123.50 122.45 .73 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.01 122.44 120.71 .71 * CH2G*-C-O (Gly) 120.8 2.1 5 120.24 121.36 120.54 .42 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 109.49 112.11 110.56 .83 * CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 106.80 113.35 110.40 1.27 * +* CH2E-CH1E-C (the rest) 110.1 1.9 62 107.51 113.92 110.79 1.42 * ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.16 115.66 110.19 2.21 +** +* NH1-CH2G*-C (Gly) 112.5 2.9 5 110.47 113.69 112.59 1.13 N-CH1E-C (Pro) 111.8 2.5 6 109.70 114.24 111.53 1.64 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 109.69 113.51 110.78 1.13 ** NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 108.92 116.75 111.33 1.47 +* *** N-CH1E-CH2E (Pro) 103.0 1.1 6 102.56 104.24 103.52 .52 * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 106.40 115.51 110.67 1.96 ** +** ------------------------------------------------------------------------------------------------------------- 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_12 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] 73 83.0% Residues in additional allowed regions [a,b,l,p] 11 12.5% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 4 4.5% ---- ------ 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 83.0 83.8 10.0 -.1 Inside b. Omega angle st dev 100 3.9 6.0 3.0 -.7 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 96 2.2 3.1 1.6 -.6 Inside e. H-bond energy st dev 55 .9 .8 .2 .5 Inside f. Overall G-factor 101 -.1 -.4 .3 .9 Inside 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 8.4 18.1 6.5 -1.5 BETTER b. Chi-1 trans st dev 32 5.1 19.0 5.3 -2.6 BETTER c. Chi-1 gauche plus st dev 36 8.5 17.5 4.9 -1.8 BETTER d. Chi-1 pooled st dev 82 7.7 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 21 6.1 20.4 5.0 -2.9 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% 83.0 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.7 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .92 3 Residue-by-residue listing for refined_12 Page 12 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.64 Chi1-chi2 distribution -.36 Chi1 only .02 Chi3 & chi4 .28 Omega -.12 ------ -.25 ===== Main-chain covalent forces:- Main-chain bond lengths -.10 Main-chain bond angles .29 ------ .13 ===== OVERALL AVERAGE -.12 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.