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 MET 1 - - - -58.5 183.0 - - - - - - 175.5 - 33.2 - 2 THR 2 B 48.1 - - - - - - - - - 188.2 - 33.9 - * * * 3 GLU 3 e B - 186.5 - 175.9 - - - - - - 185.7 -.8 36.0 - +* +* 4 VAL 4 E B - - -66.3 - - - - - - - 178.1 - 34.8 - 5 TYR 5 E B - - -63.4 - - - - - - - 172.0 -3.3 33.4 - * +* +* 6 ASP 6 E B - - -63.0 - - - - - - - 182.6 - 35.0 - 7 LEU 7 E B 42.1 - - - - - - - - - 186.5 -3.4 30.6 - * * +* +* 8 GLU 8 E B - 185.0 - 177.9 - - - - - - 184.2 -3.2 35.6 - +* +* 9 ILE 9 E B - - -58.5 - - - - - - - 173.1 -3.1 34.8 - * * * 10 THR 10 E B 46.3 - - - - - - - - - 181.8 -2.6 33.5 - * * 11 THR 11 E B - - -44.7 - - - - - - - 178.2 -.9 35.5 - * * * 12 ASN 12 e A 59.4 - - - - - - - - - 181.6 -.9 34.8 - +* +* 13 ALA 13 S A - - - - - - - - - - 180.0 - 33.6 - 14 THR 14 B 52.5 - - - - - - - - - 176.3 - 33.9 - 15 ASP 15 S A - 182.9 - - - - - - - - 177.8 - 33.6 - 16 PHE 16 S B - 180.7 - - - - - - - - 178.8 - 34.8 - 17 PRO 17 - - - - - -82.0 - - - - - 180.9 - 38.5 - * * * 18 MET 18 E B - 181.8 - - - - - - - - 179.7 -2.0 35.2 - 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 GLU 19 E B 59.3 - - 174.1 - - - - - - 178.9 - 32.2 - 20 LYS 20 E B - - -65.0 - - - - - - - 179.6 -3.1 36.7 - * * 21 LYS 21 E B - 183.0 - 179.1 - - - - - - 179.2 - 33.7 - 22 TYR 22 E B - - -67.8 - - - - - - - 176.9 -2.3 34.4 - 23 PRO 23 E - - - - - -61.5 - - - - - 179.9 - 38.8 - * * 24 ALA 24 e A - - - - - - - - - - 180.2 -2.8 34.1 - * * 25 GLY 25 T - - - - - - - - - - - 177.2 -.6 - - +* +* 26 MET 26 t B - 183.2 - - - - - - - - 180.6 -1.8 34.9 - 27 SER 27 h B 52.0 - - - - - - - - - 177.2 - 36.4 - 28 LEU 28 H A - 204.6 - 175.4 - -69.2 -22.2 - - - 178.0 -1.3 34.8 - * +* * +* 29 ASN 29 H A - 215.6 - - - -56.0 -44.6 - - - 179.7 - 36.9 - +* +* 30 ASP 30 H A - 185.4 - - - -70.4 -36.7 - - - 179.5 - 36.0 - 31 LEU 31 H A - 180.5 - - - -61.1 -48.3 - - - 178.0 -1.3 35.5 - 32 LYS 32 H A - - -56.9 187.3 - -63.5 -42.5 - - - 182.6 -3.1 34.6 - * * 33 LYS 33 H A - 190.7 - - - -57.8 -35.8 - - - 176.2 -2.1 36.2 - 34 LYS 34 H A - 185.1 - - - -67.8 -44.4 - - - 179.4 -1.7 36.8 - 35 LEU 35 H A - - -64.8 182.6 - -63.8 -46.5 - - - 178.3 -1.8 35.0 - 36 GLU 36 H A - - -66.6 - - -59.3 -31.7 - - - 178.2 -3.8 34.5 - ** ** 37 LEU 37 H A - 182.8 - - - -69.5 -32.5 - - - 180.9 -1.2 34.2 - * * 38 VAL 38 H A - 179.9 - - - -88.8 -42.0 - - - 183.2 -1.1 34.3 - +* * +* 39 VAL 39 H A - 188.5 - - - -83.4 -26.8 - - - 179.3 -3.6 32.3 - +* * ** ** 40 GLY 40 h - - - - - - - - - - - 180.2 -1.9 - - 41 THR 41 B - - -43.5 - - - - - - - 171.8 - 36.0 - +* * +* 42 THR 42 g B 52.0 - - - - - - - - - 192.4 - 33.5 - ** ** 43 VAL 43 G A - 179.9 - - - - - - - - 178.6 - 33.2 - 44 ASP 44 G A - 174.1 - - - - - - - - 185.1 - 33.3 - 45 SER 45 e A - - -59.1 - - - - - - - 181.4 -.8 36.6 - +* +* 46 MET 46 E B - 195.0 - - - - - - - - 181.1 -.7 35.8 - +* +* 47 ARG 47 E B - - -68.9 188.1 - - - - - - 182.0 -3.5 29.8 - +* * +* 48 ILE 48 E B - - -60.9 - - - - - - - 178.3 - 35.3 - 49 GLN 49 E B - - -61.2 180.2 - - - - - - 182.0 -3.3 33.6 - +* +* 50 LEU 50 E B - 183.4 - 167.8 - - - - - - 175.0 -3.3 33.0 - +* +* 51 PHE 51 E B - - -62.5 - - - - - - - 183.5 -3.2 35.2 - +* +* 52 ASP 52 e b 75.5 - - - - - - - - - 181.0 -2.1 33.9 - 53 GLY 53 S - - - - - - - - - - - 178.7 - - - 54 ASP 54 S a - - -77.2 - - - - - - - 184.9 - 32.5 - 55 ASP 55 S ~a - 176.9 - - - - - - - - 189.8 - 34.1 - ** +* ** 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 ----------------------------------------------------------------------------------------------------------------------------------- 56 GLN 56 e B 54.9 - - 174.3 - - - - - - 176.2 - 31.3 - 57 LEU 57 E B - 177.1 - - - - - - - - 177.7 - 35.8 - 58 LYS 58 E A - - -66.8 - - - - - - - 177.7 -2.7 33.6 - 59 GLY 59 E - - - - - - - - - - - 179.9 -1.5 - - 60 GLU 60 E B - 182.9 - 178.4 - - - - - - 181.5 - 34.6 - 61 LEU 61 e a - - -61.2 176.6 - - - - - - 174.8 -2.5 32.5 - 62 THR 62 l - 199.0 - - - - - - - - 178.1 - 27.2 - +* +* 63 ASP 63 B - - -62.3 - - - - - - - 179.9 - 35.1 - 64 GLY 64 - - - - - - - - - - - 172.9 - - - * * 65 ALA 65 S A - - - - - - - - - - 178.0 - 34.0 - 66 LYS 66 S B - - -64.2 178.1 - - - - - - 180.2 - 35.6 - 67 SER 67 h B - - -48.0 - - - - - - - 175.6 - 37.4 - * * 68 LEU 68 H A - - -62.1 178.3 - -59.5 -34.8 - - - 181.7 -2.3 34.9 - 69 LYS 69 H A - 184.2 - - - -74.2 -36.6 - - - 181.6 -2.8 35.1 - * * 70 ASP 70 H A - 193.8 - - - -68.2 -34.5 - - - 179.2 - 36.2 - 71 LEU 71 H A - - -65.6 173.1 - -80.3 -13.4 - - - 178.9 -2.2 34.8 - * ** ** 72 GLY 72 h - - - - - - - - - - - 176.6 -.6 - - +* +* 73 VAL 73 t B - 182.6 - - - - - - - - 179.1 -3.3 35.6 - +* +* 74 ARG 74 t b - - -56.7 175.5 - - - - - - 179.9 - 35.3 - 75 ASP 75 T B 57.9 - - - - - - - - - 182.9 - 32.1 - 76 GLY 76 T - - - - - - - - - - - 181.1 -3.8 - - ** ** 77 TYR 77 e B - - -72.4 - - - - - - - 184.6 -.9 32.0 - +* +* 78 ARG 78 E B - - -64.0 175.4 - - - - - - 177.8 -2.4 34.4 - 79 ILE 79 E B - - -70.7 - - - - - - - 183.7 -2.7 31.8 - 80 HIS 80 E B - 172.8 - - - - - - - - 177.4 -3.5 34.9 - +* +* 81 ALA 81 E B - - - - - - - - - - 181.1 -3.3 34.2 - +* +* 82 VAL 82 E B 60.4 - - - - - - - - - 177.1 -2.5 33.7 - 83 ASP 83 E B - 173.6 - - - - - - - - 179.7 - 34.8 - 84 VAL 84 e A - 188.8 - - - - - - - - 184.7 -3.2 35.2 - +* +* 85 THR 85 T A - - -41.8 - - - - - - - 180.1 -.6 36.4 - +* +* +* 86 GLY 86 T - - - - - - - - - - - 180.0 - - - 87 GLY 87 t - - - - - - - - - - - 181.2 -1.7 - - 88 ASN 88 T B 55.5 - - - - - - - - - 177.6 - 34.2 - 89 GLU 89 T L - - -56.6 - - - - - - - 182.0 - 35.1 - 90 ASP 90 t - 63.0 - - - - - - - - - - -.5 32.8 - ** ** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * +* +* * +* ** ** ** +* ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 55.7 185.3 -61.3 178.0 -71.7 -68.3 -35.8 - - - 179.9 -2.2 34.4 Standard deviations: 8.2 9.1 8.1 4.9 14.5 9.5 9.3 - - - 3.5 1.0 1.8 Numbers of values: 14 30 31 19 2 16 16 0 0 0 89 51 81 0 Residue-by-residue listing for refined_3 Page 4 ---------------------------------------- KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_3 Page 5 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - 1.238 1.520 1.531 1.470 - 117.02 120.62 110.41 110.13 111.84 122.36 2 THR 2 1.329 1.231 1.517 1.548 1.433 121.25 116.17 121.28 111.36 108.47 110.91 122.56 * * * 3 GLU 3 1.299 1.230 1.511 1.537 1.431 121.40 116.07 120.50 112.46 107.71 106.79 123.40 ** * * * ** ** 4 VAL 4 1.308 1.229 1.510 1.569 1.455 123.54 116.15 120.62 108.76 109.94 111.75 123.21 +* * * +* 5 TYR 5 1.297 1.244 1.505 1.538 1.441 121.73 115.69 120.72 110.11 111.21 111.82 123.53 ** ** 6 ASP 6 1.318 1.218 1.493 1.530 1.452 121.61 116.38 120.78 107.77 106.83 113.01 122.84 +* * +* * +* 7 LEU 7 1.255 1.224 1.507 1.535 1.417 122.62 116.19 120.70 114.32 111.73 111.30 123.10 *5.3* ** ** *5.3* 8 GLU 8 1.288 1.223 1.503 1.517 1.428 121.94 115.34 121.25 111.29 108.99 107.95 123.39 +** * +* * +** 9 ILE 9 1.296 1.250 1.513 1.559 1.441 121.89 114.34 121.55 108.34 111.39 111.80 124.11 ** ** 10 THR 10 1.286 1.232 1.500 1.536 1.426 123.99 116.81 120.84 110.01 108.60 112.77 122.33 *** * +* * *** 11 THR 11 1.277 1.213 1.505 1.559 1.413 121.95 116.37 120.51 109.74 105.70 111.16 123.09 +*** ** +* +*** 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 ----------------------------------------------------------------------------------------------------------------------------------- 12 ASN 12 1.261 1.224 1.519 1.535 1.443 122.89 115.19 121.48 109.41 109.66 110.87 123.32 *4.8* *4.8* 13 ALA 13 1.310 1.230 1.528 1.515 1.428 122.05 116.89 120.78 111.28 111.86 109.84 122.33 * +* +* 14 THR 14 1.315 1.224 1.523 1.548 1.438 121.15 116.66 121.15 109.83 111.24 111.46 122.17 * * 15 ASP 15 1.296 1.239 1.522 1.537 1.450 121.10 114.55 122.09 111.55 108.48 110.81 123.33 ** ** 16 PHE 16 1.318 1.244 1.536 1.541 1.439 123.00 117.38 120.86 110.56 109.53 109.82 121.74 * * 17 PRO 17 1.330 1.236 1.521 1.514 1.444 122.43 115.93 121.20 110.36 111.97 103.63 122.86 * * 18 MET 18 1.298 1.231 1.513 1.541 1.448 121.69 117.17 120.12 110.01 108.86 110.03 122.69 ** ** 19 GLU 19 1.315 1.240 1.520 1.532 1.445 120.47 115.23 121.00 110.96 111.41 112.40 123.73 * * 20 LYS 20 1.304 1.225 1.514 1.519 1.417 124.65 117.67 119.86 108.48 107.96 109.35 122.46 +* ** +* * ** 21 LYS 21 1.300 1.233 1.513 1.525 1.442 120.24 116.20 120.56 110.73 110.35 110.80 123.24 ** ** 22 TYR 22 1.309 1.235 1.507 1.540 1.446 122.58 118.01 119.77 109.69 109.34 111.43 122.18 * * 23 PRO 23 1.341 1.229 1.512 1.531 1.456 122.28 116.20 120.80 109.65 111.28 104.25 123.00 * * 24 ALA 24 1.308 1.235 1.517 1.497 1.449 121.98 114.57 121.89 110.84 111.22 109.45 123.50 +* +* 25 GLY 25 1.296 1.234 1.511 - 1.436 122.03 116.57 120.60 - 112.52 - 122.82 ** ** 26 MET 26 1.315 1.235 1.522 1.535 1.441 121.53 115.98 120.56 110.35 108.22 110.16 123.46 * * 27 SER 27 1.290 1.244 1.500 1.516 1.421 123.44 115.81 121.22 110.56 110.06 107.33 122.97 +** * +* +* +** 28 LEU 28 1.316 1.209 1.539 1.539 1.450 121.24 114.45 122.19 111.85 106.67 109.09 123.33 * +* +* 29 ASN 29 1.314 1.235 1.534 1.532 1.471 124.63 115.26 121.34 108.61 109.22 108.36 123.37 * +* * +* 30 ASP 30 1.333 1.239 1.520 1.521 1.471 123.35 114.49 121.59 109.03 109.74 109.09 123.90 31 LEU 31 1.321 1.235 1.517 1.565 1.459 124.05 115.06 121.29 112.29 108.35 107.69 123.64 +* * * * +* +* 32 LYS 32 1.313 1.169 1.491 1.522 1.452 122.07 117.20 119.76 108.00 110.41 112.23 123.02 * *** +* * * *** 33 LYS 33 1.313 1.241 1.548 1.530 1.446 123.19 116.51 120.33 110.76 110.42 107.06 123.16 * * ** ** 34 LYS 34 1.334 1.229 1.526 1.532 1.454 122.37 114.90 121.56 108.09 108.99 109.19 123.53 * * 35 LEU 35 1.315 1.224 1.517 1.525 1.440 123.48 115.34 120.95 110.70 110.44 109.02 123.68 36 GLU 36 1.306 1.219 1.500 1.523 1.429 124.84 116.19 120.85 111.01 111.56 109.20 122.96 +* * +* +* +* 37 LEU 37 1.304 1.231 1.533 1.530 1.441 121.70 116.37 120.88 110.44 110.30 110.41 122.73 +* +* 38 VAL 38 1.311 1.237 1.539 1.560 1.453 121.73 116.82 120.72 109.54 111.30 111.06 122.43 * * 39 VAL 39 1.321 1.239 1.526 1.561 1.456 121.60 116.56 120.93 111.19 111.29 112.21 122.49 40 GLY 40 1.319 1.240 1.508 - 1.442 120.23 116.46 120.44 - 112.44 - 123.10 Residue-by-residue listing for refined_3 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 41 THR 41 1.312 1.249 1.553 1.554 1.458 121.40 116.26 120.82 108.92 109.70 109.61 122.87 * * * * 42 THR 42 1.309 1.240 1.529 1.542 1.423 122.90 116.27 120.13 111.60 107.79 111.38 123.50 * +* * * +* 43 VAL 43 1.321 1.234 1.540 1.564 1.464 123.37 117.87 119.83 110.83 113.52 110.42 122.27 44 ASP 44 1.318 1.239 1.524 1.534 1.476 120.69 115.83 121.20 109.59 111.60 111.88 122.92 45 SER 45 1.307 1.233 1.531 1.494 1.422 123.08 116.56 120.65 109.52 112.44 107.09 122.79 +* +* +* ** ** 46 MET 46 1.295 1.228 1.523 1.525 1.449 121.51 117.26 120.34 109.50 108.76 109.44 122.40 ** ** 47 ARG 47 1.302 1.229 1.494 1.503 1.446 121.90 114.64 121.44 111.22 113.87 114.00 123.89 +* * * ** ** 48 ILE 48 1.307 1.233 1.527 1.547 1.448 122.62 116.18 120.55 108.44 110.66 110.87 123.26 +* +* 49 GLN 49 1.305 1.225 1.510 1.513 1.441 122.42 116.61 120.31 110.61 110.11 111.09 123.07 +* +* 50 LEU 50 1.299 1.245 1.522 1.567 1.451 121.48 114.83 121.45 112.39 111.14 110.29 123.72 ** +* * ** 51 PHE 51 1.302 1.244 1.521 1.537 1.442 123.78 118.13 119.59 109.59 106.49 110.89 122.28 +* * +* +* 52 ASP 52 1.313 1.240 1.515 1.527 1.438 120.27 114.94 121.40 109.65 111.27 111.37 123.66 * * * 53 GLY 53 1.309 1.242 1.511 - 1.444 121.70 116.06 120.54 - 112.20 - 123.41 * * 54 ASP 54 1.319 1.247 1.507 1.533 1.442 122.36 117.65 119.88 110.29 112.22 112.36 122.45 * * 55 ASP 55 1.343 1.227 1.514 1.533 1.458 120.43 116.64 119.82 108.53 114.23 111.14 123.54 * * 56 GLN 56 1.317 1.245 1.510 1.519 1.455 122.07 113.34 122.41 110.12 115.44 112.61 124.25 * +* * +* 57 LEU 57 1.305 1.232 1.502 1.539 1.426 123.39 116.41 120.61 109.68 108.43 109.76 122.96 +* * +* +* 58 LYS 58 1.293 1.233 1.499 1.522 1.431 120.58 115.59 121.33 110.98 109.38 111.17 123.07 +** * * +** 59 GLY 59 1.293 1.242 1.485 - 1.418 120.13 115.64 120.65 - 112.04 - 123.70 +** +* ** +** 60 GLU 60 1.290 1.242 1.513 1.525 1.414 122.42 116.04 120.73 111.54 108.56 109.56 123.22 +** ** +** 61 LEU 61 1.303 1.201 1.495 1.543 1.429 121.38 114.52 120.56 111.86 110.63 111.62 124.88 +* * * +* * +* 62 THR 62 1.296 1.236 1.538 1.598 1.482 127.67 115.82 121.03 113.21 112.54 116.30 123.13 ** ** * *** +* +** *** 63 ASP 63 1.324 1.229 1.501 1.539 1.455 122.38 116.95 120.29 108.40 109.02 111.73 122.76 * * 64 GLY 64 1.299 1.217 1.490 - 1.439 119.64 116.76 120.27 - 113.24 - 122.96 ** * ** 65 ALA 65 1.312 1.230 1.518 1.521 1.452 121.07 113.86 122.37 110.93 107.72 110.85 123.76 * * * * 66 LYS 66 1.311 1.247 1.512 1.521 1.421 124.18 116.14 120.68 109.70 109.14 109.58 123.18 * +* * +* 67 SER 67 1.301 1.241 1.509 1.518 1.410 121.95 116.68 120.06 108.56 107.78 108.43 123.26 +* +** * * +** 68 LEU 68 1.306 1.223 1.524 1.532 1.451 121.74 115.36 121.54 109.93 109.25 110.19 122.98 +* +* Residue-by-residue listing for refined_3 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 69 LYS 69 1.310 1.226 1.520 1.526 1.443 122.30 115.63 121.04 110.34 109.87 109.36 123.30 * * 70 ASP 70 1.327 1.233 1.529 1.522 1.453 122.77 114.89 121.67 110.00 109.05 108.06 123.40 * * 71 LEU 71 1.322 1.226 1.528 1.521 1.461 123.28 117.06 120.33 109.55 112.68 109.46 122.60 72 GLY 72 1.312 1.242 1.517 - 1.451 120.23 116.13 120.82 - 112.82 - 123.04 * * 73 VAL 73 1.311 1.225 1.519 1.560 1.445 122.20 117.01 120.11 108.61 107.65 111.38 122.87 * * * 74 ARG 74 1.311 1.239 1.519 1.523 1.450 121.92 117.04 120.16 108.90 108.40 110.70 122.80 * * 75 ASP 75 1.315 1.233 1.495 1.532 1.448 121.35 114.57 121.53 110.78 111.26 112.87 123.89 * * * * 76 GLY 76 1.289 1.230 1.522 - 1.441 122.03 116.98 120.52 - 112.22 - 122.50 +** +** 77 TYR 77 1.323 1.233 1.501 1.539 1.456 121.09 116.37 120.54 111.96 110.70 111.99 123.09 * * 78 ARG 78 1.302 1.233 1.500 1.518 1.435 121.46 115.07 121.42 109.97 111.14 110.47 123.51 +* * * +* 79 ILE 79 1.291 1.238 1.512 1.578 1.423 122.40 114.69 121.64 111.72 108.53 113.85 123.64 +** * +* * * +** 80 HIS 80 1.286 1.222 1.513 1.533 1.426 123.39 116.13 120.64 110.86 111.17 109.03 123.22 *** +* *** 81 ALA 81 1.296 1.234 1.520 1.515 1.432 121.86 117.48 120.33 111.50 108.92 109.72 122.14 ** * ** 82 VAL 82 1.304 1.230 1.533 1.551 1.433 120.72 115.45 121.13 111.04 112.53 110.09 123.40 +* * +* 83 ASP 83 1.316 1.222 1.513 1.536 1.461 122.56 116.49 120.56 109.77 109.85 110.39 122.94 84 VAL 84 1.306 1.237 1.539 1.553 1.454 121.54 115.82 121.49 109.30 109.74 110.44 122.64 +* +* 85 THR 85 1.319 1.233 1.542 1.539 1.456 122.78 115.82 121.18 108.27 110.43 109.35 122.97 * * 86 GLY 86 1.321 1.239 1.516 - 1.447 121.11 116.56 120.33 - 112.80 - 123.10 87 GLY 87 1.335 1.229 1.512 - 1.462 121.69 115.54 121.41 - 112.17 - 123.05 88 ASN 88 1.298 1.240 1.509 1.548 1.441 122.49 116.00 120.14 110.90 110.07 110.38 123.82 ** ** 89 GLU 89 1.345 1.237 1.535 1.531 1.474 123.42 115.37 121.15 110.18 109.80 109.22 123.48 * * 90 ASP 90 1.321 - 1.521 1.541 1.436 124.09 - - 111.93 111.59 110.72 - * * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *5.3* *** +* ** +** *** * ** +* +** * *5.3* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 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 1.255 1.345 1.308 .015 *5.3* * +* C-N (Pro) 1.341 .016 2 1.330 1.341 1.336 .005 C-O C-O 1.231 .020 89 1.169 1.250 1.232 .011 *** CA-C CH1E-C (except Gly) 1.525 .021 81 1.491 1.553 1.518 .013 +* * CH2G*-C (Gly) 1.516 .018 9 1.485 1.522 1.508 .012 +* CA-CB CH1E-CH3E (Ala) 1.521 .033 4 1.497 1.521 1.512 .009 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.536 1.598 1.557 .014 ** CH1E-CH2E (the rest) 1.530 .020 59 1.494 1.567 1.530 .012 +* +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 79 1.410 1.482 1.444 .015 +** * NH1-CH2G* (Gly) 1.451 .016 9 1.418 1.462 1.442 .011 ** N-CH1E (Pro) 1.466 .015 2 1.444 1.456 1.450 .006 * * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 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 78 113.34 118.13 116.00 1.01 * CH2G*-C-NH1 (Gly) 116.4 2.1 9 115.54 116.98 116.30 .46 CH1E-C-N (Pro) 116.9 1.5 2 115.93 116.20 116.06 .13 O-C-N O-C-NH1 (except Pro) 123.0 1.6 87 121.74 124.88 123.11 .53 * O-C-N (Pro) 122.0 1.4 2 122.86 123.00 122.93 .07 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 78 120.24 127.67 122.33 1.23 *** C-NH1-CH2G* (Gly) 120.6 1.7 9 119.64 122.03 120.98 .88 C-N-CH1E (Pro) 122.6 5.0 2 122.28 122.43 122.35 .07 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 80 119.59 122.41 120.86 .62 CH2G*-C-O (Gly) 120.8 2.1 9 120.27 121.41 120.62 .32 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 4 110.84 111.50 111.14 .27 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.27 113.21 110.04 1.38 +* CH2E-CH1E-C (the rest) 110.1 1.9 59 107.77 114.32 110.28 1.23 * ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 79 105.70 115.44 110.03 1.80 +* +* NH1-CH2G*-C (Gly) 112.5 2.9 9 112.04 113.24 112.49 .37 N-CH1E-C (Pro) 111.8 2.5 2 111.28 111.97 111.62 .34 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 4 109.45 110.85 109.96 .53 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.35 116.30 111.49 1.57 * +** N-CH1E-CH2E (Pro) 103.0 1.1 2 103.63 104.25 103.94 .31 * NH1-CH1E-CH2E (the rest) 110.5 1.7 57 106.79 114.00 110.24 1.61 ** ** ------------------------------------------------------------------------------------------------------------- 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 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] 71 92.2% Residues in additional allowed regions [a,b,l,p] 5 6.5% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.3% 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 92.2 83.8 10.0 .8 Inside b. Omega angle st dev 89 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 81 1.8 3.1 1.6 -.8 Inside e. H-bond energy st dev 51 1.0 .8 .2 1.0 WORSE f. Overall G-factor 90 .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 8.2 18.1 6.5 -1.5 BETTER b. Chi-1 trans st dev 30 9.1 19.0 5.3 -1.9 BETTER c. Chi-1 gauche plus st dev 31 8.1 17.5 4.9 -1.9 BETTER d. Chi-1 pooled st dev 75 10.0 18.2 4.8 -1.7 BETTER e. Chi-2 trans st dev 19 4.9 20.4 5.0 -3.1 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% 92.2 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.7 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 1.03 3 Residue-by-residue listing for refined_3 Page 12 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.25 Chi1-chi2 distribution -.28 Chi1 only -.39 Chi3 & chi4 .51 Omega .04 ------ -.08 ===== Main-chain covalent forces:- Main-chain bond lengths -.12 Main-chain bond angles .42 ------ .20 ===== OVERALL AVERAGE .01 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.