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 - - 179.3 - 180.0 - - - - - - 179.7 - 34.1 - 2 ALA 2 B - - - - - - - - - - 177.4 - 33.5 - 3 ASP 3 b - 185.2 - - - - - - - - 183.0 -.7 34.2 - +* +* 4 THR 4 A - - -56.3 - - - - - - - 180.6 - 34.6 - 5 GLY 5 - - - - - - - - - - - 176.2 - - - 6 GLU 6 b - 180.9 - 187.4 - - - - - - 174.3 - 34.5 - 7 VAL 7 E B - - -63.1 - - - - - - - 181.7 -1.2 32.3 - * * 8 GLN 8 E B - - -54.9 184.1 - - - - - - 181.0 - 36.0 - 9 PHE 9 E B - 185.9 - - - - - - - - 178.2 -2.5 34.8 - 10 MET 10 E B 62.5 - - 180.9 - - - - - - 182.7 - 33.6 - 11 LYS 11 E B - 175.2 - - - - - - - - 170.4 -2.2 36.1 - +* +* 12 PRO 12 E - - - - - -79.6 - - - - - 183.8 - 39.2 - * +* +* 13 PHE 13 e B - - -80.2 - - - - - - - 176.5 -1.9 29.9 - * * 14 ILE 14 h B - - -60.5 177.4 - - - - - - 186.2 - 36.0 - * * 15 SER 15 H A - 182.4 - - - -57.4 -30.4 - - - 181.4 -.7 34.3 - +* +* 16 GLU 16 H A - 182.6 - 176.8 - -60.3 -34.2 - - - 178.2 - 34.9 - 17 LYS 17 H A - - -72.0 177.2 - -103.0 -29.9 - - - 180.5 -1.6 32.0 - *** *** 18 SER 18 H A - 184.5 - - - -70.3 -11.2 - - - 176.7 -3.1 34.1 - ** * ** 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 SER 19 h A 52.4 - - - - - - - - - 181.3 -1.3 35.0 - * * 20 LYS 20 T a - - -71.1 - - - - - - - 181.4 -1.6 34.0 - 21 SER 21 t B 53.0 - - - - - - - - - 175.6 -2.1 33.8 - 22 LEU 22 E B - 193.9 - 179.5 - - - - - - 180.1 -3.0 35.8 - * * 23 GLU 23 E B 56.0 - - 170.6 - - - - - - 176.2 -.6 34.0 - +* +* 24 ILE 24 e B - - -61.7 - - - - - - - 179.0 -1.0 34.5 - * * 25 PRO 25 h - - - - - -50.8 - - - - - 186.1 - 39.0 - * * * * 26 LEU 26 H A - 196.3 - 174.5 - -58.5 -43.1 - - - 181.1 - 33.8 - 27 GLY 27 H - - - - - - -64.3 -32.3 - - - 178.9 - - - 28 PHE 28 H A - 185.2 - - - -82.8 -36.1 - - - 175.1 -.6 34.2 - * +* +* 29 ASN 29 H A - 168.4 - - - -59.9 -43.6 - - - 179.0 -2.9 36.0 - * * 30 GLU 30 h A - 179.6 - 183.4 - - - - - - 182.3 -3.0 35.7 - * * 31 TYR 31 T A - 176.9 - - - - - - - - 181.1 - 34.2 - 32 PHE 32 t b 65.7 - - - - - - - - - 171.6 -1.2 30.9 - * * * 33 PRO 33 - - - - - -81.7 - - - - - 183.7 - 38.4 - * * * 34 ALA 34 B - - - - - - - - - - 173.3 - 34.9 - * * 35 PRO 35 - - - - - -62.3 - - - - - 184.3 - 38.5 - * * 36 PHE 36 B 70.3 - - - - - - - - - 176.2 - 34.2 - 37 PRO 37 - - - - - -87.5 - - - - - 177.5 - 38.4 - +* * +* 38 ILE 38 e A - - -55.0 - - - - - - - 179.3 - 34.4 - 39 THR 39 E B 48.4 - - - - - - - - - 180.2 - 33.8 - 40 VAL 40 E B - 174.7 - - - - - - - - 181.6 -3.3 35.2 - +* +* 41 ASP 41 E B - - -65.5 - - - - - - - 178.5 -1.3 32.6 - 42 LEU 42 E B - - -56.8 180.8 - - - - - - 182.2 -2.9 36.2 - * * 43 LEU 43 E B - - -63.9 - - - - - - - 178.6 -3.3 34.7 - +* +* 44 ASP 44 E B - 169.6 - - - - - - - - 184.3 -2.8 33.6 - * * 45 TYR 45 e A 56.2 - - - - - - - - - 181.2 -.9 32.9 - +* +* 46 SER 46 T A - 187.2 - - - - - - - - 176.5 - 32.8 - 47 GLY 47 t - - - - - - - - - - - 181.7 -2.0 - - 48 ARG 48 e B - - -58.0 186.7 - - - - - - 176.9 - 33.7 - 49 SER 49 E B 57.1 - - - - - - - - - 178.8 - 34.2 - 50 TRP 50 E B - - -69.8 - - - - - - - 175.0 -2.3 34.2 - 51 THR 51 E B - - -55.3 - - - - - - - 182.7 - 34.7 - 52 VAL 52 E B - - -59.2 - - - - - - - 180.6 -3.4 33.6 - +* +* 53 ARG 53 E B - 188.5 - 173.8 - - - - - - 187.0 -2.5 34.7 - * * 54 MET 54 E B - 177.1 - - - - - - - - 180.9 -.6 34.8 - +* +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 55 LYS 55 E B - - -83.2 - - - - - - - 172.1 -2.5 33.5 - * * * 56 LYS 56 E B - 182.6 - 164.7 - - - - - - 187.8 - 32.5 - * * 57 ARG 57 E b - 187.3 - 182.7 - - - - - - 181.6 -1.9 35.2 - 58 GLY 58 T - - - - - - - - - - - 181.9 -.8 - - +* +* 59 GLU 59 T A - - -31.4 - - - - - - - 191.9 -.5 35.7 - ** ** ** ** 60 LYS 60 E B 59.7 - - 186.0 - - - - - - 180.7 -1.7 35.5 - 61 VAL 61 E B - - -58.1 - - - - - - - 175.1 - 34.4 - 62 PHE 62 E B - - -62.6 - - - - - - - 170.0 -2.3 34.5 - +* +* 63 LEU 63 E B - - -57.4 - - - - - - - 191.0 -2.1 33.2 - +* +* 64 THR 64 e a 53.3 - - - - - - - - - 185.0 -1.7 32.6 - 65 VAL 65 T B 60.8 - - - - - - - - - 184.6 - 31.4 - 66 GLY 66 h - - - - - - - - - - - 175.2 - - - 67 TRP 67 H A - 166.0 - - - -63.0 -25.6 - - - 180.8 -1.3 34.2 - * * * * 68 GLU 68 H A 64.8 - - 179.7 - -68.6 -26.3 - - - 177.4 -.5 31.7 - * ** ** 69 ASN 69 H A - - -65.0 - - -69.0 -31.6 - - - 179.9 -1.2 33.8 - * * 70 PHE 70 H A - 186.0 - - - -74.3 -52.0 - - - 182.6 -.8 34.7 - * +* +* 71 VAL 71 H A 69.3 - - - - -59.8 -46.8 - - - 180.0 -2.5 32.8 - 72 LYS 72 H A - - -60.9 - - -72.2 -43.4 - - - 184.6 -2.5 31.0 - 73 ASP 73 H A - 182.7 - - - -77.3 -40.1 - - - 181.0 -2.0 32.8 - * * 74 ASN 74 H A - 183.7 - - - -84.9 -18.5 - - - 180.5 -2.6 34.5 - +* +* +* 75 ASN 75 h l - 182.3 - - - - - - - - 174.6 -.8 30.9 - +* +* 76 LEU 76 t B 66.7 - - - - - - - - - 184.2 -1.4 31.1 - 77 GLU 77 t B 58.8 - - 185.2 - - - - - - 174.8 - 35.3 - 78 ASP 78 T B - 181.5 - - - - - - - - 184.3 - 34.8 - 79 GLY 79 T - - - - - - - - - - - 174.9 -.7 - - +* +* 80 LYS 80 e B - - -87.4 - - - - - - - 180.9 -2.8 34.0 - * * * 81 TYR 81 E B - - -56.3 - - - - - - - 180.1 -1.3 35.2 - * * 82 LEU 82 E B - - -58.3 185.0 - - - - - - 175.1 -2.2 34.1 - 83 GLN 83 E B - - -61.0 - - - - - - - 179.1 -2.1 36.0 - 84 PHE 84 E B - - -63.0 - - - - - - - 175.1 -3.6 34.8 - ** ** 85 ILE 85 E B - - -64.0 - - - - - - - 180.9 -2.6 33.4 - 86 TYR 86 E B - - -55.5 - - - - - - - 173.1 -3.3 36.4 - * +* +* 87 ASP 87 e a - - -65.2 - - - - - - - 179.4 -1.0 32.6 - * * 88 ARG 88 S a - 193.3 - - - - - - - - 185.3 - 36.7 - 89 ASP 89 S b - 192.8 - - - - - - - - 184.3 - 35.9 - 90 ARG 90 e a - - -60.0 - - - - - - - 177.3 - 35.1 - 91 THR 91 E B 47.9 - - - - - - - - - 181.2 - 34.5 - * * Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 92 PHE 92 E B - - -65.6 - - - - - - - 179.6 -2.0 36.0 - 93 TYR 93 E B - - -53.6 - - - - - - - 186.4 -2.5 34.8 - * * 94 VAL 94 E B - 185.9 - - - - - - - - 171.2 -3.2 35.2 - +* +* +* 95 ILE 95 E B - - -66.2 - - - - - - - 185.7 -1.8 32.7 - 96 ILE 96 E B - - -57.8 - - - - - - - 170.9 - 35.1 - +* +* 97 TYR 97 E B - - -61.2 - - - - - - - 178.7 -2.6 35.3 - 98 GLY 98 - - - - - - - - - - - 177.9 -.6 - - +* +* 99 HIS 99 S ~b - 188.5 - - - - - - - - 182.2 - 35.1 - ** ** 100 ASN 100 S ~a - 183.4 - - - - - - - - 174.3 - 35.2 - ** ** 101 MET 101 B 62.7 - - - - - - - - - 175.9 - 35.3 - 102 CYS 102 - - - -60.3 - - - - - - - - - 34.3 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * * ** +* *** ** ** ** +* *** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.2 182.8 -62.0 179.8 -72.4 -70.4 -34.1 - - - 179.7 -1.9 34.4 Standard deviations: 6.7 7.1 9.2 5.8 15.3 12.2 10.7 - - - 4.3 .9 1.7 Numbers of values: 18 32 38 20 5 16 16 0 0 0 101 62 95 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 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 - 1.226 1.517 1.539 1.456 - 116.43 120.97 110.46 109.94 110.77 122.56 2 ALA 2 1.304 1.236 1.513 1.521 1.438 121.20 115.55 120.98 110.96 110.65 110.84 123.42 +* * +* 3 ASP 3 1.306 1.228 1.495 1.535 1.452 122.71 116.39 120.46 109.85 108.19 111.78 123.12 +* * * +* 4 THR 4 1.301 1.235 1.519 1.533 1.438 121.33 115.36 121.56 110.50 110.30 109.86 123.05 ** * ** 5 GLY 5 1.281 1.242 1.480 - 1.403 120.77 115.43 120.67 - 110.98 - 123.87 *** ** *** *** 6 GLU 6 1.283 1.237 1.488 1.519 1.413 122.52 116.08 121.00 109.08 108.68 112.12 122.83 *** +* ** *** 7 VAL 7 1.278 1.240 1.496 1.562 1.414 119.91 116.78 120.51 111.95 107.45 113.26 122.64 +*** * ** * * * +*** 8 GLN 8 1.287 1.234 1.503 1.529 1.407 120.91 116.76 120.34 110.29 108.19 108.97 122.90 *** * +** * *** 9 PHE 9 1.293 1.224 1.526 1.548 1.446 120.98 116.87 120.34 111.17 109.96 109.08 122.78 +** +** 10 MET 10 1.317 1.230 1.514 1.534 1.454 121.76 116.80 120.55 110.27 109.55 111.78 122.65 11 LYS 11 1.295 1.237 1.532 1.551 1.444 121.49 117.84 120.02 110.14 110.78 108.09 122.08 ** * * ** 12 PRO 12 1.355 1.239 1.528 1.548 1.459 122.49 117.29 120.44 109.94 109.03 103.82 122.27 * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 13 PHE 13 1.303 1.220 1.485 1.513 1.445 120.22 114.45 121.64 111.61 115.66 112.75 123.90 +* +* +* * +* 14 ILE 14 1.316 1.238 1.512 1.562 1.413 123.61 116.75 119.79 110.46 104.87 109.88 123.43 ** * ** ** 15 SER 15 1.323 1.229 1.533 1.541 1.465 122.98 115.13 121.33 110.40 111.04 109.97 123.46 16 GLU 16 1.316 1.229 1.528 1.519 1.446 123.91 116.80 120.81 110.69 111.21 108.78 122.39 * * * 17 LYS 17 1.319 1.237 1.513 1.525 1.450 120.11 115.84 120.75 112.12 111.50 111.43 123.34 * * 18 SER 18 1.325 1.222 1.531 1.533 1.451 122.44 116.07 120.81 110.57 110.79 110.22 123.12 19 SER 19 1.316 1.241 1.542 1.529 1.438 122.90 116.49 120.52 110.82 111.57 108.49 122.99 * * * 20 LYS 20 1.337 1.225 1.526 1.524 1.462 121.81 118.60 119.27 108.64 114.20 111.09 122.11 * * * 21 SER 21 1.322 1.231 1.527 1.534 1.455 119.76 115.46 121.35 110.43 113.35 109.96 123.18 * * 22 LEU 22 1.307 1.247 1.519 1.554 1.445 122.80 116.23 120.49 109.81 106.14 110.08 123.27 +* * +* +* 23 GLU 23 1.302 1.241 1.537 1.538 1.441 121.77 116.37 121.14 110.23 111.16 110.70 122.47 +* +* 24 ILE 24 1.307 1.236 1.529 1.553 1.441 121.17 117.62 119.82 109.70 108.52 111.49 122.53 +* +* 25 PRO 25 1.354 1.234 1.532 1.523 1.479 123.50 115.91 120.61 110.33 112.09 102.71 123.47 * * 26 LEU 26 1.324 1.222 1.542 1.561 1.460 123.63 116.91 120.26 112.20 111.23 109.06 122.80 +* * * +* 27 GLY 27 1.320 1.235 1.526 - 1.464 121.19 116.21 120.98 - 112.82 - 122.81 28 PHE 28 1.318 1.208 1.530 1.540 1.457 122.02 115.45 121.17 111.59 108.54 109.81 123.37 * * 29 ASN 29 1.313 1.233 1.538 1.532 1.472 124.00 115.73 121.27 110.11 110.65 107.89 122.99 * * +* +* 30 GLU 30 1.324 1.232 1.537 1.534 1.467 123.68 115.17 121.89 109.76 110.57 108.76 122.93 * * * 31 TYR 31 1.299 1.238 1.537 1.533 1.433 123.21 117.76 120.26 112.34 111.75 108.19 121.95 ** * * * ** 32 PHE 32 1.326 1.229 1.542 1.570 1.450 119.38 117.84 121.50 112.12 113.05 112.43 120.52 +* * * * +* +* 33 PRO 33 1.336 1.242 1.518 1.522 1.434 121.57 115.63 121.33 110.14 110.25 104.66 123.04 ** +* ** 34 ALA 34 1.283 1.241 1.514 1.531 1.446 122.31 118.55 119.48 110.29 109.71 109.85 121.97 *** * *** 35 PRO 35 1.349 1.242 1.532 1.541 1.460 122.00 117.41 120.06 110.63 109.17 104.02 122.53 * * 36 PHE 36 1.312 1.239 1.541 1.542 1.420 121.23 117.15 121.21 111.08 110.93 109.75 121.55 * ** ** 37 PRO 37 1.324 1.251 1.525 1.525 1.433 122.48 116.07 121.44 110.94 111.21 103.60 122.43 * ** ** 38 ILE 38 1.288 1.237 1.517 1.549 1.427 120.80 115.34 121.16 110.31 108.02 111.28 123.45 +** +* * +** 39 THR 39 1.311 1.239 1.533 1.551 1.431 122.79 115.77 120.82 110.46 110.49 111.13 123.41 * * * 40 VAL 40 1.306 1.229 1.521 1.569 1.449 124.24 117.88 119.76 110.26 107.85 110.33 122.35 +* * * * +* 41 ASP 41 1.308 1.240 1.494 1.535 1.447 120.18 114.94 121.29 110.25 111.54 112.63 123.77 +* * * +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 42 LEU 42 1.300 1.236 1.498 1.530 1.429 122.69 116.28 120.44 108.63 107.30 110.33 123.28 ** * +* * ** 43 LEU 43 1.294 1.239 1.512 1.555 1.433 121.28 115.80 120.78 109.48 109.79 111.22 123.42 +** * * +** 44 ASP 44 1.303 1.238 1.499 1.531 1.447 122.87 114.74 121.01 110.46 110.31 111.44 124.24 +* * +* 45 TYR 45 1.305 1.235 1.537 1.538 1.453 124.40 118.03 119.69 111.09 114.28 110.17 122.28 +* +* * +* 46 SER 46 1.326 1.239 1.546 1.546 1.442 120.59 116.96 120.67 112.09 110.57 110.68 122.36 * * * 47 GLY 47 1.337 1.232 1.521 - 1.456 119.80 117.56 120.07 - 114.67 - 122.37 48 ARG 48 1.318 1.235 1.517 1.528 1.462 120.64 116.46 120.66 109.15 111.23 112.06 122.88 49 SER 49 1.313 1.227 1.528 1.535 1.438 121.57 116.74 120.57 111.08 110.09 110.02 122.69 * * * 50 TRP 50 1.304 1.231 1.506 1.544 1.453 121.97 116.39 120.41 108.90 110.36 112.09 123.19 +* +* 51 THR 51 1.302 1.239 1.531 1.539 1.430 121.42 116.03 120.95 110.52 108.11 110.48 122.98 +* * * +* 52 VAL 52 1.304 1.228 1.512 1.555 1.440 122.75 116.83 120.56 110.24 110.11 111.89 122.60 +* +* 53 ARG 53 1.296 1.228 1.532 1.531 1.432 121.17 115.85 121.02 112.79 107.72 108.21 123.11 ** * * * * ** 54 MET 54 1.314 1.231 1.508 1.554 1.462 122.89 116.45 120.30 112.07 110.10 108.24 123.23 * * * * * 55 LYS 55 1.324 1.240 1.505 1.556 1.451 122.36 115.48 121.05 108.57 112.06 113.02 123.46 * * * 56 LYS 56 1.314 1.230 1.472 1.505 1.424 121.53 113.40 122.05 111.95 107.12 112.51 124.54 * +** * +* * * * +** 57 ARG 57 1.243 1.245 1.503 1.523 1.426 123.40 115.72 121.07 110.59 109.28 109.28 123.16 *6.1* * +* *6.1* 58 GLY 58 1.298 1.237 1.503 - 1.427 120.68 116.36 120.64 - 111.16 - 122.97 ** +* ** 59 GLU 59 1.305 1.215 1.521 1.553 1.436 121.18 116.81 120.44 106.99 110.00 112.02 122.58 +* * * +* +* 60 LYS 60 1.318 1.226 1.520 1.533 1.457 121.99 116.39 120.64 110.31 111.93 108.24 122.93 * * 61 VAL 61 1.326 1.239 1.518 1.561 1.456 122.05 116.02 120.62 107.69 110.51 113.08 123.35 62 PHE 62 1.307 1.242 1.509 1.544 1.441 122.16 116.51 120.50 108.63 109.77 112.26 122.94 +* * +* 63 LEU 63 1.309 1.219 1.506 1.559 1.457 120.06 116.92 120.24 110.26 105.10 113.99 122.79 * * ** ** ** 64 THR 64 1.294 1.242 1.537 1.541 1.434 120.72 116.17 121.27 111.18 114.85 110.38 122.51 ** * * ** 65 VAL 65 1.306 1.237 1.521 1.563 1.435 121.50 115.67 121.69 112.66 110.59 112.50 122.61 +* * +* +* 66 GLY 66 1.301 1.227 1.481 - 1.427 120.31 115.21 120.97 - 109.94 - 123.80 ** +* * ** 67 TRP 67 1.328 1.240 1.508 1.540 1.451 122.56 114.90 121.84 111.16 109.23 110.30 123.15 68 GLU 68 1.310 1.219 1.533 1.514 1.428 120.61 116.01 121.22 111.81 110.57 112.42 122.75 * +* * +* 69 ASN 69 1.324 1.198 1.500 1.541 1.455 122.02 115.74 121.05 110.34 109.58 111.49 123.19 +* * +* 70 PHE 70 1.298 1.227 1.513 1.543 1.436 122.94 115.97 120.61 110.42 108.81 110.52 123.41 ** * ** 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 ----------------------------------------------------------------------------------------------------------------------------------- 71 VAL 71 1.339 1.219 1.518 1.582 1.460 121.67 115.69 120.83 110.71 110.45 112.60 123.48 +* +* 72 LYS 72 1.309 1.234 1.523 1.532 1.446 122.16 117.86 119.88 111.64 113.89 112.18 122.26 * * 73 ASP 73 1.334 1.230 1.509 1.523 1.476 119.08 116.53 120.87 110.13 112.22 111.80 122.56 * * 74 ASN 74 1.307 1.233 1.526 1.538 1.453 120.85 114.63 121.24 110.93 109.58 109.83 124.11 +* +* 75 ASN 75 1.325 1.233 1.520 1.538 1.465 125.21 115.91 121.61 110.89 112.82 113.56 122.44 +* +* +* 76 LEU 76 1.299 1.230 1.506 1.561 1.431 120.64 116.20 120.45 113.89 108.50 112.54 123.33 ** +* * +* * ** 77 GLU 77 1.283 1.240 1.491 1.521 1.438 122.56 116.37 119.44 109.93 108.73 109.95 124.16 *** +* * *** 78 ASP 78 1.320 1.240 1.525 1.543 1.479 121.55 116.46 120.41 109.83 108.11 110.68 123.07 * * * 79 GLY 79 1.306 1.226 1.512 - 1.439 120.89 116.02 120.76 - 110.64 - 123.22 +* +* 80 LYS 80 1.327 1.244 1.520 1.550 1.459 122.20 116.34 120.62 109.18 109.80 112.31 123.04 * * 81 TYR 81 1.314 1.243 1.495 1.540 1.443 121.68 117.16 119.95 109.01 107.70 111.44 122.88 * * * * 82 LEU 82 1.301 1.236 1.502 1.532 1.436 120.34 115.32 120.73 109.18 111.09 111.73 123.94 +* * * +* 83 GLN 83 1.307 1.230 1.493 1.532 1.443 122.65 116.34 120.08 107.99 107.18 111.28 123.56 +* +* * * +* 84 PHE 84 1.292 1.235 1.499 1.529 1.427 122.02 115.90 120.85 109.16 109.72 111.18 123.21 +** * +* +** 85 ILE 85 1.290 1.231 1.514 1.580 1.432 121.84 116.52 120.30 110.13 107.13 113.56 123.11 +** * * * * +** 86 TYR 86 1.300 1.239 1.518 1.534 1.451 121.56 117.27 119.86 108.02 109.78 109.81 122.86 ** * ** 87 ASP 87 1.326 1.228 1.518 1.556 1.462 119.92 115.77 121.43 108.67 109.69 114.79 122.75 * +** +** 88 ARG 88 1.312 1.226 1.528 1.544 1.441 122.43 115.29 121.83 109.92 106.81 108.37 122.85 * +* * +* 89 ASP 89 1.323 1.229 1.534 1.543 1.441 122.24 116.83 120.19 110.80 107.68 108.35 122.93 * * * 90 ARG 90 1.304 1.236 1.525 1.560 1.444 124.07 116.10 121.12 109.19 109.22 110.99 122.78 +* +* * +* 91 THR 91 1.310 1.241 1.535 1.544 1.436 121.33 115.59 121.33 110.67 110.35 109.98 123.07 * * * 92 PHE 92 1.328 1.231 1.519 1.551 1.456 122.72 116.87 120.41 108.07 109.01 110.72 122.71 * * * 93 TYR 93 1.299 1.231 1.507 1.532 1.456 121.73 116.68 120.09 110.76 107.74 109.98 123.21 ** * ** 94 VAL 94 1.311 1.233 1.537 1.555 1.444 121.59 115.79 121.03 108.60 112.06 110.50 123.14 * * 95 ILE 95 1.321 1.235 1.532 1.591 1.463 123.10 116.87 120.05 110.14 107.40 114.41 123.08 +* * +* +* 96 ILE 96 1.321 1.236 1.522 1.593 1.456 122.45 116.16 120.64 107.62 111.00 112.34 123.19 +* +* 97 TYR 97 1.312 1.238 1.502 1.524 1.445 121.77 116.95 119.48 107.78 107.62 112.14 123.55 * * * * * 98 GLY 98 1.318 1.232 1.511 - 1.443 120.53 115.91 120.47 - 111.17 - 123.60 Residue-by-residue listing for refined_3 Page 9 ---------------------------------------- ................................................................................................................................... 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 ----------------------------------------------------------------------------------------------------------------------------------- 99 HIS 99 1.326 1.224 1.509 1.548 1.477 124.37 113.87 121.75 108.38 107.56 111.96 124.37 * * * * * 100 ASN 100 1.305 1.224 1.500 1.540 1.464 125.10 113.54 122.46 109.61 105.90 111.12 123.99 +* * +* * +* +* 101 MET 101 1.308 1.246 1.512 1.549 1.425 124.19 117.19 119.58 109.12 106.64 111.54 123.19 +* +* * +* +* 102 CYS 102 1.294 - 1.522 1.526 1.438 121.24 - - 110.89 108.85 110.26 - ** * ** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *6.1* +* +** +* *** +* * +* ** +** +* *6.1* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 Page 10 ---------------------------------------- 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 96 1.243 1.339 1.309 .015 *6.1* * C-N (Pro) 1.341 .016 5 1.324 1.355 1.344 .012 * C-O C-O 1.231 .020 101 1.198 1.251 1.233 .008 +* CA-C CH1E-C (except Gly) 1.525 .021 95 1.472 1.546 1.518 .015 +** * CH2G*-C (Gly) 1.516 .018 7 1.480 1.526 1.505 .017 ** CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.521 1.531 1.526 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.533 1.593 1.560 .017 +* CH1E-CH2E (the rest) 1.530 .020 75 1.505 1.570 1.538 .013 * +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.407 1.479 1.445 .015 +** * NH1-CH2G* (Gly) 1.451 .016 7 1.403 1.464 1.437 .019 *** N-CH1E (Pro) 1.466 .015 5 1.433 1.479 1.453 .017 ** ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 Page 11 ---------------------------------------- +-----------------+ | BOND ANGLES | +-----------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Angle X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 89 113.40 118.60 116.24 .97 * * CH2G*-C-NH1 (Gly) 116.4 2.1 7 115.21 117.56 116.10 .71 CH1E-C-N (Pro) 116.9 1.5 5 115.63 117.41 116.46 .74 O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.52 124.54 123.02 .60 +* O-C-N (Pro) 122.0 1.4 5 122.27 123.47 122.75 .44 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.08 125.21 121.99 1.27 * +* C-NH1-CH2G* (Gly) 120.6 1.7 7 119.80 121.19 120.60 .41 C-N-CH1E (Pro) 122.6 5.0 5 121.57 123.50 122.41 .65 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 119.27 122.46 120.73 .64 CH2G*-C-O (Gly) 120.8 2.1 7 120.07 120.98 120.65 .29 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.29 110.96 110.62 .34 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 107.62 112.66 110.21 1.22 +* CH2E-CH1E-C (the rest) 110.1 1.9 75 106.99 113.89 110.24 1.27 +* +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.87 115.66 109.80 2.09 ** +* NH1-CH2G*-C (Gly) 112.5 2.9 7 109.94 114.67 111.63 1.48 N-CH1E-C (Pro) 111.8 2.5 5 109.03 112.09 110.35 1.18 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.85 110.84 110.34 .50 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.86 114.41 111.61 1.37 +* N-CH1E-CH2E (Pro) 103.0 1.1 5 102.71 104.66 103.76 .63 +* NH1-CH1E-CH2E (the rest) 110.5 1.7 70 107.89 114.79 110.77 1.55 +* +** ------------------------------------------------------------------------------------------------------------- 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 12 ---------------------------------------- R A M A C H A N D R A N P L O T S T A T I S T I C S Residues in most favoured regions [A,B,L] 75 85.2% Residues in additional allowed regions [a,b,l,p] 11 12.5% Residues in generously allowed regions [~a,~b,~l,~p] 2 2.3% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 88 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 7 Number of proline residues 5 ---- Total number of residues 102 Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good quality model would be expected to have over 90% in the most favoured regions [E,H,L]. S T E R E O C H E M I S T R Y O F M A I N - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. %-tage residues in A, B, L 88 85.2 83.8 10.0 .1 Inside b. Omega angle st dev 101 4.3 6.0 3.0 -.6 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 1.7 3.1 1.6 -.9 Inside e. H-bond energy st dev 62 .9 .8 .2 .4 Inside f. Overall G-factor 102 -.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 18 6.7 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 32 7.1 19.0 5.3 -2.3 BETTER c. Chi-1 gauche plus st dev 38 9.2 17.5 4.9 -1.7 BETTER d. Chi-1 pooled st dev 88 8.8 18.2 4.8 -1.9 BETTER e. Chi-2 trans st dev 20 5.8 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% 85.2 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 10.3 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .91 3 Residue-by-residue listing for refined_3 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.55 Chi1-chi2 distribution -.44 Chi1 only -.17 Chi3 & chi4 .29 Omega -.18 ------ -.29 ===== Main-chain covalent forces:- Main-chain bond lengths -.09 Main-chain bond angles .41 ------ .20 ===== OVERALL AVERAGE -.12 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.