Residue-by-residue listing for refined_4 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 - - 178.4 - - - - - - - - 180.5 - 33.9 - 2 ALA 2 b - - - - - - - - - - 181.8 - 34.5 - 3 ASP 3 B - 190.3 - - - - - - - - 180.6 - 34.7 - 4 THR 4 A - - -53.9 - - - - - - - 183.4 -1.0 35.1 - * * 5 GLY 5 e - - - - - - - - - - - 179.8 - - - 6 GLU 6 E B 57.1 - - 160.9 - - - - - - 167.9 -1.2 34.8 - ** * ** 7 VAL 7 E B - - -57.2 - - - - - - - 184.5 -1.6 31.9 - 8 GLN 8 E B 61.3 - - - - - - - - - 172.6 - 35.7 - * * 9 PHE 9 E B 61.0 - - - - - - - - - 182.4 -2.0 32.0 - 10 MET 10 E B - 185.7 - 185.4 - - - - - - 180.7 - 35.1 - 11 LYS 11 E B - 194.1 - - - - - - - - 175.2 -2.3 35.5 - 12 PRO 12 E - - - - - -82.8 - - - - - 186.8 - 39.1 - +* * * +* 13 PHE 13 e B - - -75.6 - - - - - - - 176.3 -2.2 30.3 - * * 14 ILE 14 h B - - -61.5 - - - - - - - 186.4 - 35.0 - * * 15 SER 15 H A - - -56.9 - - -56.2 -22.0 - - - 180.4 - 34.5 - +* +* 16 GLU 16 H A - 193.3 - - - -61.2 -41.6 - - - 181.4 - 35.2 - 17 LYS 17 H A - 183.7 - - - -100.3 -36.8 - - - 183.9 -1.7 35.2 - +** +** 18 SER 18 H A - - -50.9 - - -79.2 8.5 - - - 175.2 -3.3 34.4 - * * **** +* **** Residue-by-residue listing for refined_4 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 52.2 - - - - - - - - - 184.4 -.6 34.6 - +* +* 20 LYS 20 T a - - -64.4 179.6 - - - - - - 179.8 -1.0 34.7 - * * 21 SER 21 t B 51.4 - - - - - - - - - 174.6 -1.1 33.8 - * * 22 LEU 22 E B - 196.7 - 179.1 - - - - - - 183.8 -2.4 35.0 - 23 GLU 23 E B - 185.1 - - - - - - - - 179.7 -.6 34.7 - +* +* 24 ILE 24 E B - - -59.7 178.6 - - - - - - 183.0 -1.9 33.5 - 25 PRO 25 h - - - - - -52.2 - - - - - 182.5 - 38.0 - * * * 26 LEU 26 H A - - -62.1 174.9 - -50.5 -40.0 - - - 183.0 - 35.5 - * * 27 GLY 27 H - - - - - - -64.6 -29.6 - - - 181.6 - - - 28 PHE 28 H A - - -64.0 - - -80.1 -25.6 - - - 176.6 -1.5 31.8 - * * * 29 ASN 29 H A - 187.3 - - - -65.0 -36.0 - - - 180.1 -1.1 35.9 - * * 30 GLU 30 H A - 183.3 - - - -78.9 -34.3 - - - 182.9 -1.3 35.3 - * * 31 TYR 31 H A - 181.2 - - - -69.0 -29.0 - - - 177.3 -1.7 33.9 - 32 PHE 32 h b 62.9 - - - - - - - - - 173.3 -1.6 29.6 - * * * 33 PRO 33 - - - - - -84.9 - - - - - 181.1 - 38.7 - +* * +* 34 ALA 34 B - - - - - - - - - - 170.9 - 35.2 - +* +* 35 PRO 35 - - - - - -64.3 - - - - - 187.6 - 38.7 - * * * 36 PHE 36 B 55.6 - - - - - - - - - 177.8 - 31.0 - 37 PRO 37 - - - - - -81.1 - - - - - 177.2 - 39.2 - * +* +* 38 ILE 38 S A - - -59.1 - - - - - - - 179.1 - 33.7 - 39 THR 39 B 45.4 - - - - - - - - - 179.0 - 31.9 - * * 40 VAL 40 E B - 176.6 - - - - - - - - 184.6 -3.5 35.3 - ** ** 41 ASP 41 E B - 188.5 - - - - - - - - 182.3 -1.2 33.9 - * * 42 LEU 42 E B - - -64.1 181.6 - - - - - - 183.1 -2.9 35.5 - * * 43 LEU 43 E B - - -66.4 - - - - - - - 175.1 -3.0 34.2 - * * 44 ASP 44 e B - 173.3 - - - - - - - - 183.0 -2.8 35.5 - 45 TYR 45 T A - 185.6 - - - - - - - - 180.7 - 33.9 - 46 SER 46 T A - 183.5 - - - - - - - - 180.9 - 34.1 - 47 GLY 47 t - - - - - - - - - - - 177.3 -1.9 - - 48 ARG 48 e B - - -60.7 181.8 - - - - - - 182.3 - 33.9 - 49 SER 49 E B 58.3 - - - - - - - - - 178.8 - 33.4 - 50 TRP 50 E B - - -69.9 - - - - - - - 176.6 -2.6 33.9 - 51 THR 51 E B - - -56.2 - - - - - - - 186.4 -.5 33.5 - * ** ** 52 VAL 52 E B - - -61.2 - - - - - - - 180.7 -3.0 34.4 - * * 53 ARG 53 e B - 189.3 - 182.6 - - - - - - 178.1 -1.4 36.9 - Residue-by-residue listing for refined_4 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 ----------------------------------------------------------------------------------------------------------------------------------- 54 MET 54 E B - 188.4 - 187.2 - - - - - - 185.1 -.6 34.7 - +* +* 55 LYS 55 E B - - -69.4 175.8 - - - - - - 175.3 -2.3 34.8 - 56 LYS 56 E B - - -52.4 - - - - - - - 188.9 - 37.9 - +* * +* 57 ARG 57 E b - 202.9 - 176.2 - - - - - - 182.1 -2.2 35.0 - * * 58 GLY 58 T - - - - - - - - - - - 181.1 - - - 59 GLU 59 T A 52.0 - - - - - - - - - 178.3 - 31.8 - 60 LYS 60 E B 55.1 - - - - - - - - - 178.6 -1.2 32.0 - * * 61 VAL 61 E B - 176.7 - - - - - - - - 175.2 -1.6 33.9 - 62 PHE 62 E B - - -67.1 - - - - - - - 171.6 -1.6 34.8 - * * 63 LEU 63 E B - 193.8 - 168.2 - - - - - - 189.9 -2.6 33.0 - +* +* 64 THR 64 e b 54.2 - - - - - - - - - 187.6 -1.1 34.4 - * * * 65 VAL 65 T B - 187.9 - - - - - - - - 186.0 - 32.8 - * * 66 GLY 66 h - - - - - - - - - - - 174.1 - - - * * 67 TRP 67 H A - 167.6 - - - -54.9 -30.1 - - - 185.4 -1.6 36.1 - 68 GLU 68 H A - 184.2 - 177.1 - -66.5 -25.9 - - - 178.1 - 32.0 - * * 69 ASN 69 H A - - -60.7 - - -67.9 -45.7 - - - 183.3 -1.6 34.5 - 70 PHE 70 H A - 178.1 - - - -73.1 -45.3 - - - 183.7 -.9 34.2 - * * 71 VAL 71 H A 75.6 - - - - -61.8 -44.9 - - - 177.7 -3.2 33.1 - +* +* 72 LYS 72 H A - - -61.1 - - -73.1 -41.5 - - - 185.4 -1.8 31.2 - 73 ASP 73 H A - 189.9 - - - -70.7 -40.0 - - - 180.0 -2.6 34.1 - 74 ASN 74 h A - 189.4 - - - - - - - - 181.0 -2.8 34.8 - * * 75 ASN 75 T l - 182.6 - - - - - - - - 180.7 - 30.8 - 76 LEU 76 t B - - -61.0 176.3 - - - - - - 183.5 -2.5 34.7 - 77 GLU 77 t B 59.5 - - 182.2 - - - - - - 176.2 - 33.5 - 78 ASP 78 T B - 186.8 - - - - - - - - 180.9 - 36.7 - 79 GLY 79 T - - - - - - - - - - - 178.9 -1.9 - - 80 LYS 80 e B - - -56.5 - - - - - - - 180.2 -2.2 34.1 - 81 TYR 81 E B - - -61.3 - - - - - - - 183.1 - 34.6 - 82 LEU 82 E B - - -55.2 182.1 - - - - - - 172.2 -1.9 35.3 - * * 83 GLN 83 E B - - -67.6 185.5 - - - - - - 178.1 -2.3 35.0 - 84 PHE 84 E B - - -60.1 - - - - - - - 182.2 -3.2 34.1 - +* +* 85 ILE 85 E B - - -52.6 176.7 - - - - - - 177.2 -2.8 36.2 - 86 TYR 86 E B 67.6 - - - - - - - - - 182.4 -3.1 30.1 - * * * 87 ASP 87 E b - 183.2 - - - - - - - - 176.2 -.8 32.5 - +* +* 88 ARG 88 e l - - -65.2 - - - - - - - 181.1 -1.5 32.5 - 89 ASP 89 S b - 197.9 - - - - - - - - 185.1 - 34.8 - 90 ARG 90 e A - - -62.3 147.6 - - - - - - 179.7 - 37.8 - +* * +* 91 THR 91 E B - - -51.7 - - - - - - - 182.6 - 37.1 - 92 PHE 92 E B - - -67.0 - - - - - - - 177.4 -1.9 34.0 - Residue-by-residue listing for refined_4 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 ----------------------------------------------------------------------------------------------------------------------------------- 93 TYR 93 E B - - -59.5 - - - - - - - 184.0 -3.0 34.6 - * * 94 VAL 94 E B - 186.0 - - - - - - - - 175.1 -2.2 35.2 - 95 ILE 95 E B - 185.7 - 180.0 - - - - - - 183.1 -2.5 32.0 - 96 ILE 96 E B - - -56.0 - - - - - - - 175.8 - 35.8 - 97 TYR 97 e B - - -70.4 - - - - - - - 178.0 -1.7 33.6 - 98 GLY 98 t - - - - - - - - - - - 181.5 - - - 99 HIS 99 T XX - 180.0 - - - - - - - - 177.8 - 31.2 - **** **** 100 ASN 100 T A - 177.8 - - - - - - - - 179.7 -2.0 34.2 - 101 MET 101 t l - - -54.5 183.8 - - - - - - 179.0 -2.3 31.9 - 102 CYS 102 - - - -57.0 - - - - - - - - - 32.0 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * * +* +* +** **** ** ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.9 185.6 -60.9 177.4 -73.1 -69.0 -32.9 - - - 180.3 -1.9 34.3 Standard deviations: 7.3 7.2 5.8 8.9 14.2 11.7 13.0 - - - 4.1 .8 1.9 Numbers of values: 15 35 38 22 5 17 17 0 0 0 101 61 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_4 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 - 1.239 1.519 1.532 1.468 - 116.11 120.77 110.15 110.83 110.86 123.12 2 ALA 2 1.321 1.235 1.511 1.524 1.440 122.89 116.43 120.58 110.47 108.92 110.37 122.95 3 ASP 3 1.306 1.234 1.511 1.542 1.449 121.29 116.20 120.86 110.16 108.64 110.69 122.82 +* +* 4 THR 4 1.309 1.247 1.527 1.551 1.447 121.44 115.08 122.04 109.75 109.47 110.27 122.86 * * 5 GLY 5 1.295 1.234 1.476 - 1.409 120.76 113.50 121.97 - 110.43 - 124.52 ** ** +** * +** 6 GLU 6 1.265 1.242 1.531 1.536 1.443 124.09 115.71 121.40 108.15 112.84 111.07 122.86 *4.5* * * *4.5* 7 VAL 7 1.300 1.241 1.504 1.570 1.436 121.67 116.44 120.43 110.70 106.40 115.41 123.08 ** * * +* ** ** 8 GLN 8 1.275 1.240 1.507 1.541 1.398 122.36 115.50 121.11 109.34 111.38 109.64 123.39 +*** *** +*** 9 PHE 9 1.293 1.234 1.514 1.550 1.444 121.70 116.79 120.21 112.15 109.18 112.54 122.99 +** * * +** 10 MET 10 1.303 1.230 1.511 1.532 1.448 121.58 117.04 120.15 109.68 109.00 110.36 122.80 +* +* 11 LYS 11 1.307 1.235 1.551 1.569 1.441 120.84 118.52 119.67 112.23 108.17 107.66 121.69 +* * +* * * * +* +* 12 PRO 12 1.362 1.230 1.527 1.539 1.474 123.00 116.99 120.65 109.63 110.59 103.83 122.34 * * Residue-by-residue listing for refined_4 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 1.304 1.242 1.509 1.517 1.446 120.76 114.16 121.46 112.47 116.37 111.08 124.37 +* * * +* +* 14 ILE 14 1.342 1.238 1.529 1.586 1.443 124.60 117.37 119.81 108.45 106.27 112.95 122.83 +* +* +* +* 15 SER 15 1.331 1.213 1.539 1.528 1.478 123.17 117.08 120.07 108.32 113.40 110.90 122.84 * * 16 GLU 16 1.323 1.231 1.528 1.548 1.457 122.74 116.07 121.11 111.04 108.67 108.96 122.77 17 LYS 17 1.312 1.235 1.510 1.531 1.446 120.82 115.40 121.26 110.11 109.30 109.74 123.26 * * 18 SER 18 1.317 1.221 1.526 1.505 1.442 122.44 116.73 120.47 110.44 112.26 109.23 122.80 * * 19 SER 19 1.309 1.233 1.519 1.528 1.428 121.46 115.89 121.04 110.57 110.63 109.74 123.06 * +* +* 20 LYS 20 1.322 1.237 1.504 1.514 1.449 120.72 116.55 120.34 109.31 112.68 110.07 123.10 * * 21 SER 21 1.294 1.223 1.516 1.529 1.441 121.27 115.77 121.19 110.37 112.94 110.23 123.04 ** ** 22 LEU 22 1.301 1.240 1.517 1.539 1.435 121.62 115.77 120.69 110.70 105.19 110.65 123.52 ** * ** ** 23 GLU 23 1.291 1.235 1.533 1.547 1.440 122.71 116.06 120.78 113.33 109.75 107.14 123.11 +** +* +* +** 24 ILE 24 1.316 1.246 1.546 1.559 1.444 122.08 116.66 120.68 111.51 109.73 110.73 122.61 * * * 25 PRO 25 1.357 1.251 1.545 1.530 1.485 124.41 114.56 121.61 110.31 115.41 103.43 123.81 * * +* * * +* 26 LEU 26 1.344 1.239 1.528 1.541 1.475 124.93 116.26 120.71 108.20 112.48 110.04 123.02 * +* * +* 27 GLY 27 1.320 1.227 1.507 - 1.445 121.37 117.15 120.34 - 113.68 - 122.50 28 PHE 28 1.313 1.222 1.516 1.518 1.439 120.42 116.38 120.61 112.26 111.39 111.52 122.97 * * * * 29 ASN 29 1.328 1.234 1.531 1.537 1.472 121.37 114.18 121.97 108.36 108.14 110.35 123.84 * * * 30 GLU 30 1.322 1.234 1.535 1.563 1.449 124.31 116.05 120.73 112.50 109.57 107.32 123.19 +* * * +* +* 31 TYR 31 1.330 1.242 1.533 1.548 1.460 122.22 117.58 120.15 110.83 111.88 110.04 122.25 32 PHE 32 1.322 1.226 1.533 1.572 1.446 119.74 117.68 121.66 112.69 113.04 113.56 120.53 ** * * +* +* ** 33 PRO 33 1.332 1.235 1.513 1.517 1.432 121.09 114.72 121.62 109.62 111.04 104.46 123.67 ** * * * ** 34 ALA 34 1.274 1.242 1.512 1.534 1.440 123.70 119.47 118.95 110.28 107.97 109.89 121.57 +*** * +* * * +*** 35 PRO 35 1.339 1.245 1.521 1.530 1.451 120.81 117.24 119.88 110.09 106.99 104.61 122.88 +* * +* 36 PHE 36 1.304 1.236 1.520 1.532 1.399 121.48 116.35 121.32 113.09 113.21 111.38 122.29 +* *** +* *** 37 PRO 37 1.332 1.235 1.521 1.532 1.446 123.09 116.72 120.66 110.39 110.59 103.11 122.59 * * 38 ILE 38 1.300 1.220 1.518 1.558 1.435 120.43 116.28 121.17 110.44 108.82 112.10 122.54 ** * ** 39 THR 39 1.308 1.239 1.520 1.538 1.431 120.68 114.09 121.96 110.94 113.44 112.18 123.95 +* * * +* 40 VAL 40 1.298 1.230 1.521 1.564 1.437 125.52 118.39 119.50 110.84 106.04 110.13 122.10 ** * ** * +* ** 41 ASP 41 1.295 1.244 1.524 1.527 1.439 119.68 115.83 120.73 112.28 110.56 108.97 123.43 ** * * * ** Residue-by-residue listing for refined_4 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 1.315 1.226 1.496 1.536 1.454 123.05 115.86 120.61 108.31 109.76 110.95 123.53 * * 43 LEU 43 1.297 1.243 1.512 1.553 1.440 121.99 114.32 121.39 109.02 111.77 111.67 124.27 ** * ** 44 ASP 44 1.306 1.246 1.510 1.547 1.451 124.28 115.64 120.51 109.75 107.98 110.10 123.84 +* * * +* 45 TYR 45 1.307 1.222 1.553 1.541 1.459 124.11 117.65 120.33 111.08 112.83 109.33 122.01 +* * * +* 46 SER 46 1.325 1.235 1.536 1.537 1.457 121.24 116.81 120.77 110.42 111.13 110.32 122.42 47 GLY 47 1.313 1.229 1.507 - 1.441 119.98 116.72 120.54 - 112.47 - 122.73 * * 48 ARG 48 1.320 1.237 1.510 1.533 1.450 120.79 117.14 119.99 110.31 108.38 111.69 122.87 * * 49 SER 49 1.301 1.242 1.523 1.528 1.431 120.67 115.59 120.99 111.55 111.72 110.06 123.38 +* * +* 50 TRP 50 1.306 1.232 1.503 1.541 1.461 122.86 116.30 120.64 109.13 111.28 111.98 123.06 +* * +* 51 THR 51 1.299 1.237 1.529 1.528 1.417 120.97 114.53 121.77 111.91 108.66 110.68 123.68 ** ** * ** 52 VAL 52 1.291 1.225 1.517 1.551 1.439 124.57 117.53 120.31 109.60 110.03 111.33 122.14 +** * +* +** 53 ARG 53 1.296 1.219 1.526 1.534 1.438 119.95 117.37 120.18 108.45 108.04 109.01 122.45 ** * * ** 54 MET 54 1.316 1.227 1.489 1.528 1.463 121.55 117.15 120.01 108.32 107.53 112.65 122.83 +* * * +* 55 LYS 55 1.301 1.233 1.494 1.507 1.407 120.66 115.40 121.03 110.29 112.28 109.28 123.56 +* * * +** +** 56 LYS 56 1.297 1.236 1.496 1.518 1.421 122.57 117.53 119.76 108.56 102.63 108.48 122.67 ** * +* *** * *** 57 ARG 57 1.278 1.239 1.516 1.545 1.435 119.37 115.42 121.42 111.91 109.52 108.38 123.12 +*** * * * +*** 58 GLY 58 1.307 1.233 1.509 - 1.429 120.65 116.04 120.91 - 111.23 - 123.03 +* * +* 59 GLU 59 1.298 1.237 1.527 1.548 1.444 122.57 116.56 120.58 111.59 112.73 111.94 122.84 ** ** 60 LYS 60 1.310 1.233 1.517 1.544 1.432 122.56 116.31 120.89 110.46 110.82 113.51 122.78 * * +* +* 61 VAL 61 1.303 1.232 1.507 1.562 1.436 121.53 116.05 120.99 109.76 109.37 112.32 122.93 +* * +* 62 PHE 62 1.293 1.248 1.477 1.535 1.418 121.20 116.26 120.70 108.13 108.60 112.85 123.03 +** ** ** * * +** 63 LEU 63 1.285 1.215 1.506 1.538 1.408 118.67 114.28 121.30 114.10 103.55 111.14 124.31 *** +** +* ** +** *** 64 THR 64 1.289 1.243 1.554 1.544 1.436 124.59 115.74 121.14 111.72 113.61 107.85 123.12 +** * * +* * ** +** 65 VAL 65 1.336 1.233 1.530 1.556 1.453 123.47 115.59 121.36 111.12 110.88 111.67 123.03 66 GLY 66 1.302 1.230 1.473 - 1.424 120.92 114.09 121.52 - 108.63 - 124.37 +* ** +* * * ** 67 TRP 67 1.330 1.235 1.508 1.537 1.450 123.76 114.81 121.45 109.31 109.71 109.05 123.63 * * 68 GLU 68 1.310 1.227 1.534 1.529 1.442 121.41 116.15 121.23 112.25 110.56 111.58 122.61 * * * 69 ASN 69 1.316 1.197 1.500 1.534 1.453 121.84 115.55 120.96 109.60 109.33 111.22 123.38 +* * +* Residue-by-residue listing for refined_4 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 PHE 70 1.303 1.231 1.509 1.541 1.441 123.09 116.34 120.27 110.47 110.83 110.51 123.37 +* +* 71 VAL 71 1.333 1.217 1.521 1.581 1.452 120.98 115.44 121.42 111.09 109.41 112.19 123.13 +* +* 72 LYS 72 1.306 1.228 1.523 1.519 1.439 121.84 117.64 119.91 111.54 113.57 112.15 122.44 +* * +* 73 ASP 73 1.341 1.227 1.517 1.527 1.483 120.14 116.41 120.91 109.44 111.04 111.07 122.62 * * 74 ASN 74 1.317 1.234 1.528 1.542 1.460 121.27 114.05 121.51 110.74 108.65 109.71 124.38 * * 75 ASN 75 1.334 1.240 1.515 1.532 1.452 125.57 114.70 121.81 112.52 111.57 112.54 123.44 ** * * ** 76 LEU 76 1.307 1.234 1.510 1.527 1.437 123.44 115.80 120.76 110.51 109.48 110.05 123.43 +* * +* 77 GLU 77 1.303 1.242 1.510 1.521 1.435 122.58 114.89 120.92 110.48 111.16 111.15 124.13 +* * +* 78 ASP 78 1.312 1.246 1.516 1.535 1.461 124.00 115.75 120.64 107.80 109.25 109.67 123.60 * * * * 79 GLY 79 1.308 1.232 1.505 - 1.432 120.79 116.57 120.54 - 111.78 - 122.90 +* * +* 80 LYS 80 1.327 1.253 1.530 1.546 1.457 121.01 116.24 120.66 109.55 109.69 111.68 123.10 * * 81 TYR 81 1.316 1.241 1.496 1.536 1.443 122.30 116.73 120.25 109.89 108.26 111.31 123.01 * * * 82 LEU 82 1.304 1.239 1.503 1.534 1.438 120.37 115.43 120.81 108.36 111.02 110.85 123.75 +* * * +* 83 GLN 83 1.302 1.240 1.491 1.521 1.438 122.42 116.23 120.31 107.76 107.75 112.81 123.44 +* +* * * * * +* 84 PHE 84 1.284 1.236 1.489 1.523 1.422 121.29 115.55 120.76 111.33 108.40 110.51 123.66 *** +* +* * *** 85 ILE 85 1.293 1.234 1.507 1.555 1.431 122.08 117.61 119.83 108.31 108.44 110.66 122.53 +** * +** 86 TYR 86 1.308 1.248 1.516 1.552 1.457 118.68 115.71 121.16 112.40 111.40 113.92 123.13 +* * +* * ** ** 87 ASP 87 1.318 1.234 1.527 1.553 1.459 121.93 114.60 121.26 111.91 111.03 111.23 123.85 * * 88 ARG 88 1.344 1.237 1.537 1.539 1.487 125.46 117.69 120.05 110.78 114.66 110.63 122.18 * +* ** * ** 89 ASP 89 1.319 1.225 1.535 1.566 1.434 120.81 115.43 120.86 111.19 108.12 109.98 123.65 +* * * +* 90 ARG 90 1.283 1.224 1.525 1.522 1.452 126.62 115.76 121.23 109.25 109.72 106.36 123.01 *** +** ** *** 91 THR 91 1.302 1.236 1.531 1.547 1.430 122.25 116.99 120.15 109.01 107.31 108.56 122.86 +* * * +* +* 92 PHE 92 1.320 1.234 1.509 1.539 1.454 121.22 115.58 121.23 109.54 111.43 111.35 123.19 93 TYR 93 1.294 1.239 1.507 1.536 1.438 122.39 116.58 120.24 110.87 107.64 110.40 123.15 ** * * ** 94 VAL 94 1.309 1.238 1.517 1.550 1.441 121.24 116.60 120.70 108.33 110.44 111.29 122.69 * * 95 ILE 95 1.304 1.245 1.536 1.573 1.438 120.39 115.86 120.93 111.87 108.72 113.15 123.15 +* * * * +* 96 ILE 96 1.308 1.235 1.525 1.594 1.447 122.85 117.12 120.16 107.54 108.33 112.24 122.71 +* ** * ** 97 TYR 97 1.314 1.240 1.516 1.522 1.451 121.15 115.92 121.03 109.29 111.22 112.01 123.05 * * Residue-by-residue listing for refined_4 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 ----------------------------------------------------------------------------------------------------------------------------------- 98 GLY 98 1.309 1.232 1.504 - 1.434 121.00 116.01 120.13 - 112.37 - 123.86 * * * 99 HIS 99 1.340 1.228 1.539 1.558 1.480 124.31 117.01 120.39 112.99 111.56 111.60 122.59 * * * +* +* 100 ASN 100 1.315 1.231 1.515 1.539 1.462 121.94 114.46 121.28 110.80 109.03 110.45 124.24 101 MET 101 1.329 1.232 1.513 1.540 1.461 124.70 114.90 120.81 110.41 111.21 113.39 124.22 +* +* +* 102 CYS 102 1.326 - 1.541 1.535 1.454 124.42 - - 112.85 111.61 110.57 - +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *4.5* +* ** ** *** +** +* * ** *** ** +* *4.5* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_4 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 1.265 1.344 1.309 .016 *4.5* * * C-N (Pro) 1.341 .016 5 1.332 1.362 1.344 .013 * C-O C-O 1.231 .020 101 1.197 1.253 1.234 .008 +* * CA-C CH1E-C (except Gly) 1.525 .021 95 1.477 1.554 1.519 .014 ** * CH2G*-C (Gly) 1.516 .018 7 1.473 1.509 1.497 .015 ** * CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.524 1.534 1.529 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.528 1.594 1.559 .016 ** CH1E-CH2E (the rest) 1.530 .020 75 1.505 1.572 1.536 .013 * ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.398 1.487 1.445 .016 *** +* NH1-CH2G* (Gly) 1.451 .016 7 1.409 1.445 1.431 .011 +** * N-CH1E (Pro) 1.466 .015 5 1.432 1.485 1.457 .019 ** * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_4 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 89 114.05 119.47 116.14 1.05 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 7 113.50 117.15 115.73 1.28 * CH1E-C-N (Pro) 116.9 1.5 5 114.56 117.24 116.04 1.16 +* O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.53 124.52 123.09 .65 +* O-C-N (Pro) 122.0 1.4 5 122.34 123.81 123.06 .58 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.67 126.62 122.13 1.60 +* +** C-NH1-CH2G* (Gly) 120.6 1.7 7 119.98 121.37 120.78 .39 C-N-CH1E (Pro) 122.6 5.0 5 120.81 124.41 122.48 1.35 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 118.95 122.04 120.77 .59 * CH2G*-C-O (Gly) 120.8 2.1 7 120.13 121.97 120.85 .62 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.28 110.47 110.37 .09 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 107.54 111.91 110.16 1.33 * CH2E-CH1E-C (the rest) 110.1 1.9 75 107.76 114.10 110.45 1.49 * ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 102.63 116.37 110.03 2.28 *** +* NH1-CH2G*-C (Gly) 112.5 2.9 7 108.63 113.68 111.51 1.51 * N-CH1E-C (Pro) 111.8 2.5 5 106.99 115.41 110.92 2.68 +* * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.89 110.37 110.13 .24 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 107.85 115.41 111.43 1.67 ** ** N-CH1E-CH2E (Pro) 103.0 1.1 5 103.11 104.61 103.89 .58 * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 106.36 113.92 110.64 1.50 ** ** ------------------------------------------------------------------------------------------------------------- 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_4 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] 77 87.5% Residues in additional allowed regions [a,b,l,p] 10 11.4% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 1 1.1% ---- ------ 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 87.5 83.8 10.0 .4 Inside b. Omega angle st dev 101 4.1 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 1.9 3.1 1.6 -.7 Inside e. H-bond energy st dev 61 .8 .8 .2 -.2 Inside f. Overall G-factor 102 -.1 -.4 .3 1.0 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 15 7.3 18.1 6.5 -1.7 BETTER b. Chi-1 trans st dev 35 7.2 19.0 5.3 -2.2 BETTER c. Chi-1 gauche plus st dev 38 5.8 17.5 4.9 -2.4 BETTER d. Chi-1 pooled st dev 88 8.2 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 22 8.9 20.4 5.0 -2.3 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% 87.5 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.3 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .77 2 Residue-by-residue listing for refined_4 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.49 Chi1-chi2 distribution -.33 Chi1 only -.13 Chi3 & chi4 .40 Omega -.11 ------ -.21 ===== Main-chain covalent forces:- Main-chain bond lengths -.13 Main-chain bond angles .34 ------ .14 ===== OVERALL AVERAGE -.09 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.