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 ASP 1 - 63.9 - - - - - - - - - 179.1 - 34.3 - 2 PRO 2 - - - - - -85.1 - - - - - 175.2 - 39.7 - +* +* +* 3 ASN 3 A - 182.2 - - - - - - - - 177.5 - 34.1 - 4 ALA 4 ~l - - - - - - - - - - 175.8 - 29.6 - ** * ** 5 GLU 5 B - - -57.3 180.8 - - - - - - 181.2 - 35.2 - 6 PHE 6 B - - -58.1 - - - - - - - 177.9 -.5 35.7 - ** ** 7 ASP 7 B - 184.8 - - - - - - - - 182.3 -2.1 34.4 - 8 PRO 8 S - - - - - -91.3 - - - - - 176.0 - 38.3 - ** * ** 9 ASP 9 S A - 181.1 - - - - - - - - 180.2 - 34.1 - 10 LEU 10 g B - - -72.9 - - - - - - - 178.7 - 33.9 - 11 PRO 11 G - - - - - -60.1 - - - - - 179.1 - 38.3 - * * 12 GLY 12 G - - - - - - - - - - - 178.9 - - - 13 GLY 13 G - - - - - - - - - - - 182.6 -.8 - - +* +* 14 GLY 14 G - - - - - - - - - - - 182.9 -1.2 - - * * 15 LEU 15 g A - - -64.6 177.8 - - - - - - 186.7 -1.9 35.6 - * * 16 HIS 16 t B - - -46.8 - - - - - - - 178.1 -.5 34.3 - * +* +* 17 ARG 17 B B 54.7 - - - - - - - - - 169.3 -.6 33.8 - +* +* +* 18 CYS 18 t B - 174.1 - - - - - - - - 184.0 -2.1 33.8 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 19 LEU 19 T A - - -60.7 179.8 - - - - - - 177.8 -.7 34.0 - +* +* 20 ALA 20 T A - - - - - - - - - - 180.7 - 34.3 - 21 CYS 21 T A - - -61.6 - - - - - - - 180.5 -1.3 31.1 - 22 ALA 22 t l - - - - - - - - - - 183.2 -1.7 33.1 - 23 ARG 23 B - - -58.8 - - - - - - - 179.0 - 34.2 - 24 TYR 24 B B - - -75.8 - - - - - - - 183.3 - 34.9 - 25 PHE 25 B - - -58.4 - - - - - - - 184.8 -2.8 34.8 - 26 ILE 26 S A 60.8 - - 177.9 - - - - - - 180.5 - 33.3 - 27 ASP 27 h B - 181.2 - - - - - - - - 181.2 - 34.1 - 28 SER 28 H A - 179.4 - - - -62.4 -32.2 - - - 179.8 - 33.5 - 29 THR 29 H A - - -50.7 - - -66.1 -36.7 - - - 177.5 - 34.0 - * * 30 ASN 30 H A - - -76.4 - - -69.8 -39.2 - - - 176.1 - 34.0 - 31 LEU 31 H A - 168.7 - - - -64.6 -49.2 - - - 176.5 -2.0 32.8 - 32 LYS 32 H A - 180.0 - 174.1 - -59.7 -37.5 - - - 176.4 -3.4 33.1 - +* +* 33 THR 33 H A - - -59.3 - - -63.5 -29.8 - - - 176.9 -2.2 32.9 - 34 HIS 34 H A - 159.5 - - - -62.9 -28.7 - - - 181.8 -1.2 32.8 - * * * 35 PHE 35 h A - - -47.3 - - - - - - - 171.8 -1.0 32.4 - * * * * 36 ARG 36 T A - - -85.0 - - - - - - - 175.1 -1.5 32.1 - * * 37 SER 37 h B 46.4 - - - - - - - - - 185.4 -.9 34.8 - * +* +* 38 LYS 38 H A 63.2 - - - - -68.9 -33.0 - - - 183.1 -.8 30.5 - +* +* 39 ASP 39 H A - 183.2 - - - -72.7 -31.4 - - - 179.4 - 34.6 - 40 HIS 40 H A - 183.9 - - - -64.0 -51.4 - - - 182.0 - 35.3 - * * 41 LYS 41 H A - - -54.8 178.4 - -70.1 -29.8 - - - 172.8 -1.6 33.9 - * * 42 LYS 42 H A - 174.2 - 178.1 - -66.1 -39.9 - - - 180.5 -1.8 34.5 - 43 ARG 43 H A - 194.7 - - - -62.8 -32.4 - - - 180.6 -2.5 36.5 - 44 LEU 44 H A - - -57.4 182.5 - -75.6 -44.1 - - - 181.9 -1.6 36.5 - 45 LYS 45 H A - 186.0 - 181.9 - -65.8 -39.1 - - - 178.9 -2.4 34.4 - 46 GLN 46 H A 69.9 - - 182.6 - -78.1 -21.4 - - - 176.6 -3.0 33.0 - * +* * +* 47 LEU 47 H A - 183.7 - 165.9 - -76.6 -27.6 - - - 178.3 -.7 34.1 - * +* +* 48 SER 48 h B - - -56.5 - - - - - - - 184.7 -1.4 34.9 - 49 VAL 49 S A - 182.6 - - - - - - - - 185.9 - 34.4 - * * 50 GLU 50 S A - 181.3 - 179.1 - - - - - - 180.5 - 31.3 - 51 PRO 51 S - - - - - -74.8 - - - - - 180.9 - 38.5 - * * 52 TYR 52 S ~l - - -65.7 - - - - - - - 177.1 - 31.3 - ** ** 53 SER 53 t B - - -58.6 - - - - - - - 185.1 - 34.3 - 54 GLN 54 T b - 185.0 - 178.2 - - - - - - 175.0 -1.0 30.8 - * * 55 GLU 55 T a - - -68.3 177.5 - - - - - - 177.5 -2.5 34.7 - 56 GLU 56 T A - - -59.6 - - - - - - - 175.2 - 34.5 - 57 ALA 57 t B - - - - - - - - - - 181.6 -2.6 34.1 - 58 GLU 58 b - - -59.1 185.2 - - - - - - 172.7 - 32.0 - * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 59 ARG 59 ~l - 186.0 - 180.2 - - - - - - 181.4 - 33.1 - ** ** 60 ALA 60 ~l - - - - - - - - - - 180.6 -1.3 30.5 - ** * ** 61 ALA 61 A - - - - - - - - - - 180.6 - 34.1 - 62 GLY 62 - - - - - - - - - - - 182.3 - - - 63 MET 63 B - - -59.4 178.7 - - - - - - 179.7 - 34.5 - 64 GLY 64 - - - - - - - - - - - 179.0 - - - 65 SER 65 S b 53.5 - - - - - - - - - 182.8 - 34.2 - 66 TYR 66 B - 186.0 - - - - - - - - 181.4 -1.1 35.2 - * * 67 VAL 67 - - 180.7 - - - - - - - - - - 33.2 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * * * ** * +* +* ** +* ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.9 180.9 -61.4 178.7 -77.8 -67.6 -35.5 - - - 179.6 -1.6 34.0 * * Standard deviations: 7.9 7.2 9.0 4.2 13.6 5.4 7.8 - - - 3.5 .8 1.9 Numbers of values: 7 21 24 17 4 17 17 0 0 0 66 33 62 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 4 ---------------------------------------- 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 ASP 1 - 1.234 1.513 1.542 1.462 - 117.90 120.16 109.98 108.93 111.29 121.91 2 PRO 2 1.338 1.235 1.512 1.529 1.457 122.69 116.57 120.71 110.60 110.85 102.06 122.70 3 ASN 3 1.307 1.236 1.520 1.526 1.469 121.20 113.91 121.59 110.28 108.86 110.96 124.48 +* * +* 4 ALA 4 1.324 1.239 1.497 1.529 1.438 125.78 114.47 121.79 112.93 111.97 113.72 123.61 * * ** +* ** ** 5 GLU 5 1.304 1.237 1.501 1.482 1.390 123.88 114.58 121.66 108.98 107.47 111.07 123.64 +* * ** +*** * * +*** 6 PHE 6 1.254 1.242 1.500 1.542 1.438 123.23 116.98 119.93 108.96 107.99 110.65 123.08 *5.3* * * * *5.3* 7 ASP 7 1.303 1.235 1.529 1.526 1.442 120.69 118.34 120.16 110.00 108.76 111.00 121.48 +* * +* 8 PRO 8 1.343 1.240 1.542 1.518 1.451 122.25 117.55 120.29 111.30 114.74 102.40 122.16 * * * 9 ASP 9 1.304 1.233 1.501 1.525 1.458 120.67 114.73 121.71 109.89 108.76 111.61 123.52 +* * +* 10 LEU 10 1.299 1.231 1.521 1.544 1.435 122.59 117.58 120.37 110.17 109.85 111.50 121.99 ** * ** 11 PRO 11 1.336 1.251 1.537 1.536 1.465 122.69 115.74 121.08 110.28 112.04 104.03 123.16 * * 12 GLY 12 1.320 1.241 1.502 - 1.446 121.67 115.63 120.81 - 112.29 - 123.49 13 GLY 13 1.321 1.228 1.507 - 1.441 121.84 116.40 120.28 - 112.99 - 123.32 Residue-by-residue listing for refined_3 Page 5 ---------------------------------------- ................................................................................................................................... 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 ----------------------------------------------------------------------------------------------------------------------------------- 14 GLY 14 1.329 1.228 1.519 - 1.439 121.20 116.49 120.81 - 112.06 - 122.70 15 LEU 15 1.323 1.228 1.514 1.522 1.440 122.02 117.37 120.62 108.73 112.45 109.58 122.01 16 HIS 16 1.311 1.227 1.495 1.535 1.447 119.68 116.08 120.61 109.09 110.14 111.83 123.27 * * * * 17 ARG 17 1.295 1.235 1.489 1.538 1.434 121.65 114.79 121.43 107.69 112.31 113.30 123.76 ** +* * * +* ** 18 CYS 18 1.289 1.226 1.506 1.554 1.439 121.22 117.34 119.55 110.97 105.71 112.32 123.11 +** * +* * +** 19 LEU 19 1.309 1.225 1.510 1.521 1.465 122.02 115.29 121.35 110.26 110.91 110.61 123.35 * * 20 ALA 20 1.304 1.226 1.531 1.512 1.452 122.32 117.03 120.65 109.96 111.66 110.07 122.32 +* +* 21 CYS 21 1.326 1.226 1.517 1.541 1.446 120.34 116.25 120.28 113.01 113.06 111.25 123.47 +* +* 22 ALA 22 1.340 1.229 1.528 1.534 1.473 123.99 116.05 121.24 111.08 111.09 110.94 122.67 * * 23 ARG 23 1.317 1.248 1.489 1.533 1.438 121.49 114.80 120.90 109.29 110.37 111.78 124.30 +* * +* 24 TYR 24 1.293 1.234 1.502 1.504 1.406 123.64 115.38 120.89 110.71 110.13 109.33 123.73 +** * * +** * +** 25 PHE 25 1.293 1.238 1.510 1.534 1.434 122.49 116.31 120.15 110.63 109.11 109.88 123.53 +** * +** 26 ILE 26 1.324 1.229 1.534 1.543 1.447 123.16 117.05 120.59 109.98 113.21 111.25 122.36 27 ASP 27 1.314 1.240 1.513 1.542 1.454 121.32 116.78 119.82 110.77 109.17 110.68 123.40 * * 28 SER 28 1.325 1.215 1.524 1.546 1.453 122.48 117.03 120.34 111.44 110.68 110.47 122.57 29 THR 29 1.327 1.229 1.544 1.524 1.443 121.16 116.64 120.75 110.50 110.44 110.46 122.57 30 ASN 30 1.333 1.237 1.512 1.527 1.442 122.56 115.31 121.28 110.89 110.42 110.29 123.40 31 LEU 31 1.312 1.226 1.532 1.564 1.445 122.54 115.60 121.22 114.12 110.08 109.07 123.19 * +* ** ** 32 LYS 32 1.286 1.229 1.555 1.527 1.457 123.16 117.20 120.36 112.41 111.93 109.21 122.43 *** * * *** 33 THR 33 1.342 1.245 1.549 1.544 1.474 122.27 114.81 122.14 111.03 110.34 111.58 123.03 * * 34 HIS 34 1.310 1.230 1.532 1.562 1.450 123.73 117.76 120.23 112.19 111.86 110.45 122.00 * +* * * +* 35 PHE 35 1.326 1.204 1.526 1.528 1.449 118.99 117.81 120.77 109.29 110.88 113.81 121.42 * +* +* +* 36 ARG 36 1.319 1.232 1.529 1.523 1.479 119.52 115.28 121.35 110.93 110.53 112.55 123.37 * * * * 37 SER 37 1.309 1.248 1.551 1.534 1.422 124.13 116.43 121.21 112.71 109.70 107.49 122.34 * * +* * * +* +* 38 LYS 38 1.334 1.237 1.528 1.577 1.463 121.19 116.01 120.78 113.27 112.38 112.24 123.14 ** +* * ** 39 ASP 39 1.324 1.214 1.493 1.523 1.464 122.25 115.03 121.42 109.65 109.68 110.84 123.55 +* +* 40 HIS 40 1.304 1.211 1.482 1.511 1.457 122.47 115.38 120.99 108.52 110.69 110.64 123.63 +* * ** ** 41 LYS 41 1.282 1.219 1.510 1.486 1.425 121.60 115.99 121.03 112.21 109.65 108.96 122.96 *** ** +* * *** 42 LYS 42 1.318 1.223 1.516 1.518 1.437 121.23 115.70 120.70 109.51 109.41 111.12 123.58 * * 43 ARG 43 1.333 1.212 1.522 1.533 1.443 123.28 115.21 121.17 109.31 108.74 108.66 123.60 * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 44 LEU 44 1.322 1.236 1.524 1.530 1.435 123.42 114.63 121.85 108.89 109.26 109.02 123.51 * * 45 LYS 45 1.312 1.231 1.538 1.532 1.444 123.82 116.38 120.65 111.57 110.98 108.73 122.96 * * * * 46 GLN 46 1.328 1.230 1.528 1.512 1.456 121.95 115.75 121.40 111.08 110.95 110.96 122.84 47 LEU 47 1.320 1.237 1.526 1.540 1.446 122.42 115.11 121.29 113.07 108.64 108.49 123.58 +* * +* 48 SER 48 1.325 1.233 1.544 1.532 1.444 122.86 117.26 120.42 110.89 109.39 109.14 122.31 49 VAL 49 1.316 1.231 1.530 1.553 1.457 121.19 115.74 120.76 109.09 111.82 111.21 123.48 50 GLU 50 1.319 1.227 1.564 1.538 1.465 123.14 120.44 119.08 112.31 114.83 110.62 120.48 +* ** * * * +* ** 51 PRO 51 1.363 1.233 1.533 1.539 1.465 121.66 116.07 120.20 110.37 111.73 103.87 123.74 * * * 52 TYR 52 1.339 1.235 1.523 1.540 1.477 124.38 115.57 121.60 110.32 112.98 113.44 122.82 * * +* +* 53 SER 53 1.303 1.253 1.517 1.530 1.426 122.44 115.03 121.05 112.02 108.24 109.43 123.85 +* * +* * * +* 54 GLN 54 1.318 1.234 1.535 1.537 1.456 123.14 113.13 121.89 112.47 113.22 111.87 124.83 +* * * +* 55 GLU 55 1.311 1.230 1.501 1.547 1.467 128.08 113.76 122.09 108.31 105.47 113.29 124.11 * * +*** * ** +* +*** 56 GLU 56 1.310 1.226 1.512 1.522 1.444 123.02 115.63 121.34 110.55 109.36 110.13 123.03 * * 57 ALA 57 1.304 1.232 1.511 1.526 1.428 122.05 116.91 120.26 111.16 108.50 110.58 122.78 +* +* +* 58 GLU 58 1.318 1.232 1.513 1.538 1.440 121.03 115.28 120.57 110.31 111.74 113.23 123.86 +* +* 59 ARG 59 1.332 1.242 1.557 1.541 1.490 124.90 116.35 120.22 111.13 114.07 109.61 123.43 +* +* +* * +* 60 ALA 60 1.330 1.229 1.510 1.531 1.461 125.02 115.44 121.62 112.24 111.30 113.40 122.89 +* * +* +* 61 ALA 61 1.307 1.225 1.513 1.521 1.447 121.59 115.68 121.26 110.47 110.33 110.42 123.06 +* +* 62 GLY 62 1.319 1.235 1.515 - 1.457 121.75 115.48 121.19 - 111.83 - 123.33 63 MET 63 1.316 1.239 1.514 1.536 1.444 122.73 115.93 120.62 110.18 110.21 110.41 123.44 64 GLY 64 1.304 1.237 1.504 - 1.436 121.43 116.12 120.88 - 110.91 - 123.00 +* +* 65 SER 65 1.304 1.242 1.526 1.527 1.435 121.67 115.99 120.96 111.48 110.14 109.54 123.02 +* * +* 66 TYR 66 1.305 1.232 1.510 1.535 1.436 121.96 116.49 120.41 110.89 108.52 109.27 123.09 +* * +* 67 VAL 67 1.302 - 1.522 1.554 1.442 121.54 - - 110.53 110.01 112.11 - +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *5.3* * ** ** +*** +*** ** * ** ** ** +* *5.3* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 Page 7 ---------------------------------------- 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 62 1.254 1.342 1.314 .015 *5.3* * C-N (Pro) 1.341 .016 4 1.336 1.363 1.345 .011 * C-O C-O 1.231 .020 66 1.204 1.253 1.232 .009 * * CA-C CH1E-C (except Gly) 1.525 .021 62 1.482 1.564 1.520 .017 ** +* CH2G*-C (Gly) 1.516 .018 5 1.502 1.519 1.509 .007 CA-CB CH1E-CH3E (Ala) 1.521 .033 6 1.512 1.534 1.525 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 5 1.524 1.554 1.544 .011 CH1E-CH2E (the rest) 1.530 .020 51 1.482 1.577 1.532 .016 ** ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 58 1.390 1.490 1.447 .017 +*** +* NH1-CH2G* (Gly) 1.451 .016 5 1.436 1.457 1.444 .008 N-CH1E (Pro) 1.466 .015 4 1.451 1.465 1.460 .006 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 Page 8 ---------------------------------------- +-----------------+ | 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 57 113.13 120.44 116.01 1.24 +* ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.48 116.49 116.02 .40 CH1E-C-N (Pro) 116.9 1.5 4 115.74 117.55 116.48 .68 O-C-N O-C-NH1 (except Pro) 123.0 1.6 62 120.48 124.83 123.08 .74 +* * O-C-N (Pro) 122.0 1.4 4 122.16 123.74 122.94 .58 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 57 118.99 128.08 122.43 1.53 +* +*** C-NH1-CH2G* (Gly) 120.6 1.7 5 121.20 121.84 121.58 .23 C-N-CH1E (Pro) 122.6 5.0 4 121.66 122.69 122.32 .42 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 61 119.08 122.14 120.87 .63 * CH2G*-C-O (Gly) 120.8 2.1 5 120.28 121.19 120.79 .29 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 6 109.96 112.93 111.31 1.01 +* CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 5 109.09 111.03 110.23 .66 CH2E-CH1E-C (the rest) 110.1 1.9 51 107.69 114.12 110.66 1.38 * ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 58 105.47 114.83 110.33 1.80 ** * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.91 112.99 112.02 .68 N-CH1E-C (Pro) 111.8 2.5 4 110.85 114.74 112.34 1.45 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 6 110.07 113.72 111.52 1.47 ** NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 5 110.46 112.11 111.32 .54 N-CH1E-CH2E (Pro) 103.0 1.1 4 102.06 104.03 103.09 .87 NH1-CH1E-CH2E (the rest) 110.5 1.7 47 107.49 113.81 110.67 1.45 +* +* ------------------------------------------------------------------------------------------------------------- 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 9 ---------------------------------------- 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] 47 83.9% Residues in additional allowed regions [a,b,l,p] 5 8.9% Residues in generously allowed regions [~a,~b,~l,~p] 4 7.1% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 56 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 5 Number of proline residues 4 ---- Total number of residues 67 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 56 83.9 83.8 10.0 .0 Inside b. Omega angle st dev 66 3.5 6.0 3.0 -.8 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 62 1.9 3.1 1.6 -.8 Inside e. H-bond energy st dev 33 .8 .8 .2 -.2 Inside f. Overall G-factor 67 .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 7 7.9 18.1 6.5 -1.6 BETTER b. Chi-1 trans st dev 21 7.2 19.0 5.3 -2.2 BETTER c. Chi-1 gauche plus st dev 24 9.0 17.5 4.9 -1.7 BETTER d. Chi-1 pooled st dev 52 9.3 18.2 4.8 -1.8 BETTER e. Chi-2 trans st dev 17 4.2 20.4 5.0 -3.2 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 83.9 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 10.5 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .89 3 Residue-by-residue listing for refined_3 Page 10 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.50 Chi1-chi2 distribution -.20 Chi1 only .10 Chi3 & chi4 .13 Omega -.04 ------ -.18 ===== Main-chain covalent forces:- Main-chain bond lengths .04 Main-chain bond angles .37 ------ .23 ===== OVERALL AVERAGE -.03 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.