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 MET 1 - - 179.0 - 182.4 - - - - - - 180.6 - 35.0 - 2 THR 2 B - 181.7 - - - - - - - - 173.3 - 31.2 - * * 3 GLU 3 e B - 183.9 - 175.4 - - - - - - 185.2 -.7 33.1 - +* +* 4 VAL 4 E B - - -65.6 - - - - - - - 180.1 - 33.3 - 5 TYR 5 E B 65.6 - - - - - - - - - 178.0 -3.4 33.0 - +* +* 6 ASP 6 E B - - -66.7 - - - - - - - 180.5 - 34.2 - 7 LEU 7 E B - - -74.8 175.6 - - - - - - 173.4 -3.7 35.3 - * ** ** 8 GLU 8 E B - 179.8 - 183.7 - - - - - - 187.6 -2.1 35.6 - * * 9 ILE 9 E B - - -55.1 - - - - - - - 175.5 -3.5 34.2 - ** ** 10 THR 10 E B - 148.1 - - - - - - - - 182.6 -3.3 30.8 - ** +* ** 11 THR 11 E B - - -42.2 - - - - - - - 176.6 -1.2 34.6 - +* * +* 12 ASN 12 e A 59.5 - - - - - - - - - 177.4 -.7 33.3 - +* +* 13 ALA 13 S A - - - - - - - - - - 179.1 - 34.0 - 14 THR 14 B 54.4 - - - - - - - - - 181.6 - 35.2 - 15 ASP 15 S A - 182.7 - - - - - - - - 183.2 - 35.0 - 16 PHE 16 S B - - -57.7 - - - - - - - 178.7 - 34.4 - 17 PRO 17 - - - - - -70.7 - - - - - 181.3 - 38.5 - * * 18 MET 18 E B - - -54.8 - - - - - - - 178.1 -2.1 35.9 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 19 GLU 19 E B - - -64.7 - - - - - - - 179.5 - 33.3 - 20 LYS 20 E B - - -71.0 186.4 - - - - - - 182.4 -2.8 33.1 - * * 21 LYS 21 E B - 185.6 - - - - - - - - 176.2 - 36.5 - 22 TYR 22 E B - - -72.3 - - - - - - - 177.9 -2.8 32.5 - * * 23 PRO 23 E - - - - - -75.9 - - - - - 182.2 - 38.9 - * * 24 ALA 24 e A - - - - - - - - - - 181.7 -2.9 32.9 - * * 25 GLY 25 T - - - - - - - - - - - 181.4 -.7 - - +* +* 26 MET 26 t B - 188.7 - 184.1 - - - - - - 178.6 -1.2 35.1 - * * 27 SER 27 h B 54.9 - - - - - - - - - 175.1 - 36.2 - 28 LEU 28 H A - 193.5 - - - -66.2 -28.5 - - - 177.6 -.8 35.0 - +* +* 29 ASN 29 H A - - -63.1 - - -55.3 -47.5 - - - 181.3 - 34.9 - 30 ASP 30 H A - 187.4 - - - -68.6 -41.4 - - - 180.8 - 35.0 - 31 LEU 31 H A - 195.8 - 173.1 - -61.8 -43.8 - - - 174.9 -1.7 34.9 - 32 LYS 32 H A - - -89.7 - - -57.0 -52.4 - - - 182.0 -3.2 34.8 - +* * +* +* 33 LYS 33 H A - 197.6 - 175.9 - -61.9 -31.5 - - - 175.4 -2.5 35.8 - 34 LYS 34 H A - - -93.8 - - -72.9 -33.8 - - - 173.5 -2.1 33.4 - +* * +* 35 LEU 35 H A - - -73.3 180.7 - -71.8 -35.9 - - - 176.8 -1.9 34.3 - 36 GLU 36 H A - - -65.5 - - -62.9 -31.3 - - - 175.9 -2.8 34.5 - * * 37 LEU 37 H A - 183.1 - - - -69.0 -29.0 - - - 180.3 -1.0 34.7 - * * 38 VAL 38 H A - 181.2 - - - -84.9 -41.4 - - - 181.8 -.6 34.3 - +* +* +* 39 VAL 39 H A - 185.6 - - - -85.2 -27.8 - - - 180.2 -3.0 32.7 - +* * * +* 40 GLY 40 h - - - - - - - - - - - 181.8 -2.4 - - 41 THR 41 b - 184.7 - - - - - - - - 178.0 - 33.3 - 42 THR 42 g B - - -43.6 - - - - - - - 192.3 - 33.8 - +* ** ** 43 VAL 43 G A - 181.1 - - - - - - - - 184.1 - 33.3 - 44 ASP 44 G A - 179.4 - - - - - - - - 185.3 - 34.2 - 45 SER 45 e A - - -55.8 - - - - - - - 186.4 -.5 37.5 - * ** * ** 46 MET 46 E B - 189.7 - - - - - - - - 184.1 -1.1 35.0 - * * 47 ARG 47 E B - - -80.0 - - - - - - - 181.6 -1.8 28.4 - +* +* 48 ILE 48 E B - - -58.7 - - - - - - - 178.2 - 35.7 - 49 GLN 49 E B - - -68.8 180.9 - - - - - - 180.3 -3.5 33.6 - +* +* 50 LEU 50 E B - 184.7 - 169.8 - - - - - - 177.7 -2.1 33.9 - 51 PHE 51 E B - - -66.4 - - - - - - - 175.1 -3.1 35.5 - * * 52 ASP 52 e ~b - 199.9 - - - - - - - - 184.1 -1.7 34.0 - ** ** 53 GLY 53 T - - - - - - - - - - - 174.7 - - - 54 ASP 54 T a - 174.1 - - - - - - - - 181.7 -2.8 36.4 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 55 ASP 55 t ~b - 180.5 - - - - - - - - 181.3 -1.0 36.1 - ** * ** 56 GLN 56 e b - - -56.8 174.4 - - - - - - 182.4 - 35.4 - 57 LEU 57 E B - 182.1 - - - - - - - - 172.5 - 35.8 - * * 58 LYS 58 E A - - -68.1 184.7 - - - - - - 179.6 -2.9 33.9 - * * 59 GLY 59 E - - - - - - - - - - - 179.1 -.9 - - * * 60 GLU 60 E B - 182.2 - 182.5 - - - - - - 181.4 - 35.3 - 61 LEU 61 e b 55.9 - - 171.9 - - - - - - 173.8 -1.3 27.1 - * +* +* 62 THR 62 l - 202.3 - - - - - - - - 179.9 - 27.4 - * +* +* 63 ASP 63 a - - -56.2 - - - - - - - 174.8 - 35.3 - 64 GLY 64 - - - - - - - - - - - 180.3 - - - 65 ALA 65 S a - - - - - - - - - - 178.8 - 33.5 - 66 LYS 66 S B 51.7 - - 203.6 - - - - - - 191.2 - 33.4 - * +* +* 67 SER 67 B B - - -49.9 - - - - - - - 176.4 - 35.8 - * * 68 LEU 68 T A - - -64.8 169.9 - - - - - - 181.6 -2.4 36.0 - 69 LYS 69 T A - 203.7 - - - - - - - - 179.1 -2.5 35.1 - * * 70 ASP 70 T A - 183.4 - - - - - - - - 176.4 - 35.8 - 71 LEU 71 T A - - -69.8 176.9 - - - - - - 179.6 -2.0 34.3 - 72 GLY 72 T - - - - - - - - - - - 178.3 -1.2 - - * * 73 VAL 73 t B - 187.1 - - - - - - - - 183.3 -2.7 34.7 - 74 ARG 74 t b - - -68.3 - - - - - - - 178.4 -1.0 33.3 - * * 75 ASP 75 T B 51.5 - - - - - - - - - 180.2 - 34.4 - 76 GLY 76 T - - - - - - - - - - - 178.8 -3.3 - - +* +* 77 TYR 77 e B - - -68.9 - - - - - - - 179.7 -1.1 35.2 - * * 78 ARG 78 E B 66.9 - - 229.1 - - - - - - 181.6 -2.7 30.8 - +** +** 79 ILE 79 E B - - -65.5 - - - - - - - 179.0 -2.2 33.6 - 80 HIS 80 E B - 171.6 - - - - - - - - 179.2 -3.2 33.2 - +* +* 81 ALA 81 E B - - - - - - - - - - 178.5 -3.3 36.0 - +* +* 82 VAL 82 E B 61.0 - - - - - - - - - 173.3 -1.9 34.2 - * * 83 ASP 83 E B - 182.1 - - - - - - - - 187.4 - 32.1 - * * 84 VAL 84 e A - 184.5 - - - - - - - - 184.2 -2.8 33.1 - * * 85 THR 85 S A 52.9 - - - - - - - - - 176.4 - 32.6 - 86 GLY 86 S - - - - - - - - - - - 183.0 - - - 87 GLY 87 - - - - - - - - - - - 180.3 - - - 88 ASN 88 B 67.8 - - - - - - - - - 166.5 - 35.2 - ** ** 89 GLU 89 a - - -77.5 - - - - - - - 180.1 - 32.5 - 90 ASP 90 - - 180.6 - - - - - - - - - - 36.3 - ----------------------------------------------------------------------------------------------------------------------------------- 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 ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** ** +* +** +* * ** ** +* +** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.4 184.5 -65.5 182.2 -73.3 -68.1 -37.0 - - - 179.7 -2.1 34.2 Standard deviations: 6.2 9.9 11.4 13.8 3.7 9.6 8.1 - - - 4.0 .9 2.0 Numbers of values: 11 33 31 19 2 12 12 0 0 0 89 51 81 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 MET 1 - 1.231 1.505 1.530 1.462 - 117.18 120.43 109.13 109.39 110.88 122.39 2 THR 2 1.299 1.240 1.536 1.570 1.419 120.06 115.12 121.79 112.07 111.90 112.75 123.01 ** * ** * ** 3 GLU 3 1.303 1.217 1.503 1.550 1.433 123.07 117.00 120.02 112.18 106.19 112.08 122.93 +* * * * * +* +* 4 VAL 4 1.296 1.233 1.519 1.568 1.447 122.37 115.60 121.19 110.09 111.19 112.18 123.18 ** * ** 5 TYR 5 1.296 1.238 1.512 1.540 1.436 122.83 115.93 120.84 112.52 110.27 110.25 123.15 ** * * ** 6 ASP 6 1.303 1.226 1.495 1.530 1.449 121.87 115.34 121.13 109.47 109.69 111.68 123.53 +* * +* 7 LEU 7 1.272 1.221 1.485 1.515 1.418 123.86 115.14 121.05 108.61 111.05 110.65 123.81 **** +* ** * **** 8 GLU 8 1.283 1.220 1.509 1.518 1.421 122.23 115.76 121.28 111.19 104.84 109.18 122.86 *** +* ** *** 9 ILE 9 1.276 1.228 1.504 1.555 1.442 121.33 114.49 121.31 109.13 111.60 111.75 124.21 +*** +*** 10 THR 10 1.286 1.230 1.489 1.573 1.427 124.24 115.61 121.32 112.01 110.19 114.31 123.04 *** +* * +* * * +* *** 11 THR 11 1.274 1.219 1.521 1.559 1.440 122.52 116.80 120.48 109.43 107.52 112.10 122.66 +*** * +*** 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 ASN 12 1.282 1.227 1.524 1.536 1.441 122.01 115.36 121.74 111.09 109.52 111.35 122.91 *** *** 13 ALA 13 1.322 1.231 1.527 1.522 1.438 122.32 116.49 120.73 110.64 110.41 110.37 122.78 * * 14 THR 14 1.324 1.227 1.519 1.540 1.441 121.57 116.34 120.41 108.69 110.04 111.01 123.22 15 ASP 15 1.303 1.230 1.519 1.538 1.463 122.27 115.35 121.59 109.92 110.43 109.73 123.05 +* +* 16 PHE 16 1.306 1.236 1.527 1.529 1.441 122.28 117.45 120.31 110.85 110.78 109.56 122.22 +* +* 17 PRO 17 1.349 1.238 1.533 1.541 1.463 122.96 116.65 120.70 109.90 111.85 104.29 122.65 * * 18 MET 18 1.314 1.226 1.520 1.539 1.463 122.08 117.53 119.78 108.81 109.51 109.82 122.68 * * 19 GLU 19 1.321 1.238 1.512 1.538 1.462 120.84 116.04 120.61 108.81 110.26 113.31 123.34 +* +* 20 LYS 20 1.307 1.214 1.501 1.486 1.412 122.97 115.63 120.95 110.58 112.38 110.91 123.41 +* * ** ** ** 21 LYS 21 1.292 1.241 1.530 1.536 1.453 122.85 117.04 120.16 108.29 109.81 109.39 122.79 +** +** 22 TYR 22 1.317 1.219 1.525 1.539 1.457 122.01 118.43 119.92 111.14 111.28 111.77 121.62 * * 23 PRO 23 1.349 1.228 1.518 1.537 1.457 122.54 116.63 120.54 109.46 111.02 104.48 122.80 * * 24 ALA 24 1.315 1.234 1.526 1.515 1.455 121.78 115.48 121.62 111.65 112.15 110.21 122.86 * * 25 GLY 25 1.292 1.239 1.511 - 1.445 121.11 116.52 120.71 - 112.97 - 122.77 +** +** 26 MET 26 1.309 1.237 1.536 1.534 1.444 121.76 116.72 120.58 110.56 109.17 109.34 122.69 * * 27 SER 27 1.302 1.245 1.516 1.513 1.426 122.63 115.63 121.29 109.68 110.52 108.16 123.09 +* +* * +* 28 LEU 28 1.318 1.211 1.525 1.548 1.456 121.95 115.18 121.02 112.18 107.55 108.47 123.75 * * * * * 29 ASN 29 1.329 1.238 1.524 1.545 1.482 123.02 115.89 121.02 107.69 110.75 111.94 123.09 * * * 30 ASP 30 1.327 1.221 1.514 1.523 1.459 121.95 115.44 121.04 109.32 110.04 110.34 123.49 31 LEU 31 1.319 1.226 1.532 1.559 1.468 122.90 115.21 121.19 112.39 107.59 108.36 123.56 * * * * * 32 LYS 32 1.317 1.185 1.493 1.525 1.456 123.42 117.25 119.59 109.32 112.07 110.24 123.15 ** +* ** 33 LYS 33 1.306 1.228 1.537 1.472 1.431 122.80 116.21 121.16 111.27 111.05 106.37 122.62 +* +** * ** +** 34 LYS 34 1.316 1.233 1.533 1.520 1.421 123.07 116.02 120.98 113.24 110.93 108.57 122.99 +* +* * +* 35 LEU 35 1.317 1.223 1.521 1.528 1.444 123.19 115.93 120.96 110.84 110.19 109.87 123.10 36 GLU 36 1.312 1.210 1.506 1.507 1.434 123.87 116.33 120.78 110.34 110.84 109.78 122.88 * * * * * * 37 LEU 37 1.306 1.222 1.533 1.528 1.451 121.92 115.91 121.41 110.06 109.77 110.11 122.67 +* +* 38 VAL 38 1.312 1.233 1.539 1.559 1.453 121.92 116.58 120.70 109.41 110.65 111.43 122.72 * * 39 VAL 39 1.326 1.232 1.523 1.560 1.464 121.56 116.23 121.04 110.95 111.73 111.72 122.70 40 GLY 40 1.305 1.235 1.508 - 1.439 121.01 116.86 120.56 - 111.94 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 41 THR 41 1.321 1.244 1.528 1.561 1.451 119.70 116.22 120.52 111.51 110.05 111.04 123.22 * * * 42 THR 42 1.298 1.243 1.536 1.527 1.429 121.96 115.17 120.97 110.47 108.23 111.68 123.75 ** +* * ** 43 VAL 43 1.301 1.225 1.532 1.561 1.462 124.21 116.91 119.96 110.23 113.83 110.88 123.09 ** * ** 44 ASP 44 1.313 1.237 1.535 1.530 1.472 122.29 116.53 120.66 110.07 112.78 109.77 122.74 * * 45 SER 45 1.316 1.235 1.522 1.489 1.443 123.49 116.50 120.65 108.01 112.99 106.98 122.85 ** * ** ** 46 MET 46 1.285 1.233 1.529 1.525 1.437 120.96 116.12 120.93 112.74 110.33 106.95 122.95 *** * * ** *** 47 ARG 47 1.319 1.232 1.522 1.536 1.461 122.43 114.81 121.70 112.04 114.97 114.45 123.45 * * ** ** 48 ILE 48 1.322 1.241 1.540 1.558 1.454 123.18 116.39 120.58 108.80 110.53 110.10 123.03 49 GLN 49 1.318 1.231 1.524 1.512 1.446 122.60 116.43 120.60 109.82 111.68 111.28 122.97 50 LEU 50 1.318 1.244 1.530 1.565 1.465 121.78 115.91 120.88 111.90 110.35 109.64 123.21 +* +* 51 PHE 51 1.313 1.235 1.532 1.552 1.451 122.83 116.94 120.02 108.60 109.08 110.87 123.03 * * * 52 ASP 52 1.324 1.233 1.509 1.528 1.471 123.66 116.93 119.72 108.91 107.62 112.97 123.34 * * * * 53 GLY 53 1.319 1.230 1.493 - 1.453 123.41 113.56 122.07 - 109.94 - 124.34 * +* * +* 54 ASP 54 1.274 1.234 1.496 1.543 1.426 124.47 113.73 121.33 109.43 106.40 109.66 124.75 +*** * +* +* * +* * +*** 55 ASP 55 1.323 1.224 1.498 1.530 1.457 125.90 113.37 122.25 108.27 106.26 110.82 124.36 * ** * +* ** 56 GLN 56 1.313 1.244 1.534 1.517 1.439 124.00 115.62 120.97 110.64 111.31 108.05 123.41 * * * * * 57 LEU 57 1.319 1.238 1.523 1.542 1.452 123.63 115.94 120.82 109.26 111.53 109.10 123.21 * * 58 LYS 58 1.314 1.230 1.510 1.535 1.448 121.38 115.57 121.53 109.70 109.12 112.13 122.88 * * 59 GLY 59 1.311 1.247 1.498 - 1.429 120.53 115.60 120.68 - 112.43 - 123.71 * * * 60 GLU 60 1.306 1.243 1.512 1.530 1.431 122.71 116.47 120.69 110.14 108.11 109.87 122.83 +* * * +* 61 LEU 61 1.304 1.212 1.502 1.572 1.432 120.14 115.41 119.98 114.42 112.92 115.12 124.53 +* * ** * ** +** +** 62 THR 62 1.296 1.230 1.549 1.606 1.478 126.99 115.52 121.21 113.84 111.84 115.79 123.24 ** * ** * +** ** +** +** 63 ASP 63 1.344 1.223 1.529 1.541 1.479 123.90 115.93 121.23 108.69 110.60 110.31 122.83 * * * * 64 GLY 64 1.321 1.209 1.506 - 1.459 122.23 118.21 119.13 - 116.07 - 122.66 * * * 65 ALA 65 1.322 1.228 1.543 1.517 1.472 121.61 114.34 121.99 111.20 110.67 110.11 123.67 66 LYS 66 1.299 1.252 1.531 1.548 1.426 126.43 118.74 118.85 114.94 105.70 108.82 122.40 ** * +* +** * * +** +* +** 67 SER 67 1.317 1.223 1.490 1.521 1.431 120.76 114.90 121.23 108.23 110.95 110.31 123.86 +* * +* 68 LEU 68 1.281 1.233 1.512 1.516 1.434 123.32 114.76 121.63 110.79 109.34 107.73 123.55 *** * +* *** 69 LYS 69 1.311 1.223 1.513 1.534 1.439 122.07 114.12 121.78 111.37 106.99 109.22 124.05 * * * +* +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 70 ASP 70 1.321 1.232 1.530 1.510 1.449 124.06 115.11 121.49 110.47 110.24 107.74 123.38 * * +* +* 71 LEU 71 1.317 1.230 1.523 1.540 1.474 123.17 116.87 120.41 108.72 112.09 111.42 122.72 72 GLY 72 1.311 1.237 1.507 - 1.445 120.49 116.20 120.88 - 112.13 - 122.92 * * 73 VAL 73 1.314 1.234 1.515 1.551 1.438 121.42 116.12 121.00 109.39 107.28 112.00 122.82 * * * * 74 ARG 74 1.298 1.231 1.503 1.529 1.436 121.21 114.25 121.67 109.85 113.03 111.52 124.07 ** * * ** 75 ASP 75 1.304 1.230 1.492 1.530 1.435 123.88 114.68 121.50 110.10 111.14 110.51 123.82 +* +* * * +* 76 GLY 76 1.287 1.229 1.529 - 1.455 121.70 116.58 120.37 - 113.14 - 123.05 *** *** 77 TYR 77 1.312 1.240 1.520 1.550 1.467 123.31 117.82 120.28 110.13 109.03 109.83 121.88 * * * 78 ARG 78 1.310 1.239 1.514 1.544 1.435 119.22 115.14 121.53 113.03 111.14 112.54 123.30 * * * +* * +* 79 ILE 79 1.297 1.234 1.505 1.560 1.429 122.61 115.35 121.27 110.52 109.87 111.85 123.36 ** +* ** 80 HIS 80 1.289 1.223 1.506 1.539 1.420 122.23 115.19 121.21 111.65 110.09 111.01 123.60 +** +* +** 81 ALA 81 1.281 1.230 1.509 1.511 1.420 122.88 117.28 120.24 110.55 108.69 108.24 122.44 *** ** * *** 82 VAL 82 1.299 1.230 1.522 1.570 1.430 120.19 116.39 121.02 110.62 111.30 110.43 122.59 ** * * ** 83 ASP 83 1.310 1.238 1.471 1.520 1.440 120.33 116.11 120.76 110.92 107.32 114.13 123.08 * +** * ** +** 84 VAL 84 1.269 1.237 1.530 1.538 1.404 120.04 118.11 120.25 112.33 112.86 109.57 121.58 **** +** * * **** 85 THR 85 1.319 1.229 1.526 1.533 1.447 118.59 116.34 121.00 110.64 113.52 111.27 122.63 +* +* 86 GLY 86 1.284 1.229 1.474 - 1.435 121.91 114.17 121.45 - 109.26 - 124.39 *** ** * * *** 87 GLY 87 1.308 1.236 1.483 - 1.415 121.58 115.79 120.61 - 111.45 - 123.56 * +* ** ** 88 ASN 88 1.291 1.231 1.523 1.541 1.434 121.93 114.69 120.94 108.83 111.74 110.44 124.32 +** * +** 89 GLU 89 1.301 1.234 1.514 1.534 1.467 125.32 111.99 123.44 112.40 106.03 112.28 124.55 +* ** ** +* * +* * ** 90 ASP 90 1.311 - 1.503 1.528 1.432 125.84 - - 109.82 108.07 108.71 - * * * ** * * ** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** ** +** +** +** +** ** +* +** ** +** * **** ----------------------------------------------------------------------------------------------------------------------------------- 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 87 1.269 1.344 1.306 .015 **** * +* C-N (Pro) 1.341 .016 2 1.349 1.349 1.349 .000 C-O C-O 1.231 .020 89 1.185 1.252 1.231 .010 ** * CA-C CH1E-C (except Gly) 1.525 .021 81 1.471 1.549 1.518 .015 +** * CH2G*-C (Gly) 1.516 .018 9 1.474 1.529 1.501 .015 ** CA-CB CH1E-CH3E (Ala) 1.521 .033 4 1.511 1.522 1.517 .004 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.527 1.606 1.558 .017 ** CH1E-CH2E (the rest) 1.530 .020 59 1.472 1.572 1.531 .017 +** ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 79 1.404 1.482 1.445 .017 +** * NH1-CH2G* (Gly) 1.451 .016 9 1.415 1.459 1.442 .013 ** N-CH1E (Pro) 1.466 .015 2 1.457 1.463 1.460 .003 ------------------------------------------------------------------------------------------------------------- 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 78 111.99 118.74 115.90 1.11 ** * CH2G*-C-NH1 (Gly) 116.4 2.1 9 113.56 118.21 115.94 1.32 * CH1E-C-N (Pro) 116.9 1.5 2 116.63 116.65 116.64 .01 O-C-N O-C-NH1 (except Pro) 123.0 1.6 87 121.58 124.75 123.17 .61 * O-C-N (Pro) 122.0 1.4 2 122.65 122.80 122.73 .08 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 78 118.59 126.99 122.51 1.52 +* +** C-NH1-CH2G* (Gly) 120.6 1.7 9 120.49 123.41 121.55 .87 +* C-N-CH1E (Pro) 122.6 5.0 2 122.54 122.96 122.75 .21 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 80 118.85 123.44 120.92 .66 * +* CH2G*-C-O (Gly) 120.8 2.1 9 119.13 122.07 120.72 .75 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 4 110.55 111.65 111.01 .45 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.69 113.84 110.56 1.34 ** CH2E-CH1E-C (the rest) 110.1 1.9 59 107.69 114.94 110.39 1.57 * +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 79 104.84 114.97 110.14 2.00 ** * NH1-CH2G*-C (Gly) 112.5 2.9 9 109.26 116.07 112.15 1.85 * * N-CH1E-C (Pro) 111.8 2.5 2 111.02 111.85 111.43 .41 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 4 108.24 110.37 109.73 .87 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.57 115.79 111.77 1.41 * +** N-CH1E-CH2E (Pro) 103.0 1.1 2 104.29 104.48 104.39 .09 * * * NH1-CH1E-CH2E (the rest) 110.5 1.7 57 106.37 115.12 110.29 1.80 ** +** ------------------------------------------------------------------------------------------------------------- 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] 66 85.7% Residues in additional allowed regions [a,b,l,p] 9 11.7% Residues in generously allowed regions [~a,~b,~l,~p] 2 2.6% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 77 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 9 Number of proline residues 2 ---- Total number of residues 90 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 77 85.7 83.8 10.0 .2 Inside b. Omega angle st dev 89 4.0 6.0 3.0 -.7 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 81 2.0 3.1 1.6 -.7 Inside e. H-bond energy st dev 51 .9 .8 .2 .6 Inside f. Overall G-factor 90 -.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 11 6.2 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 33 9.9 19.0 5.3 -1.7 BETTER c. Chi-1 gauche plus st dev 31 11.4 17.5 4.9 -1.3 BETTER d. Chi-1 pooled st dev 75 10.4 18.2 4.8 -1.6 BETTER e. Chi-2 trans st dev 19 13.8 20.4 5.0 -1.3 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% 85.7 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 11.4 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .94 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 -.49 Chi1-chi2 distribution -.48 Chi1 only -.05 Chi3 & chi4 .24 Omega -.04 ------ -.24 ===== Main-chain covalent forces:- Main-chain bond lengths -.22 Main-chain bond angles .32 ------ .10 ===== OVERALL AVERAGE -.12 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.