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 - - 181.3 - - - - - - - - 179.8 - 34.4 - 2 ALA 2 b - - - - - - - - - - 177.6 - 33.6 - 3 ASP 3 b - 183.2 - - - - - - - - 178.7 -.8 33.3 - +* +* 4 THR 4 A - - -48.6 - - - - - - - 184.4 - 37.0 - * * 5 GLY 5 S - - - - - - - - - - - 176.8 - - - 6 GLU 6 B 57.1 - - 165.6 - - - - - - 174.6 -.8 34.6 - +* +* 7 VAL 7 E B - - -63.7 - - - - - - - 180.4 -2.4 32.8 - 8 GLN 8 E B 53.2 - - 184.3 - - - - - - 183.1 - 32.3 - 9 PHE 9 E B - 182.3 - - - - - - - - 182.4 -3.0 36.1 - * * 10 MET 10 E B 62.5 - - 180.6 - - - - - - 178.0 - 33.3 - 11 LYS 11 E B - - -67.7 - - - - - - - 170.2 -2.2 35.0 - +* +* 12 PRO 12 E - - - - - -78.2 - - - - - 179.7 - 39.3 - * +* +* 13 PHE 13 e B - 183.1 - - - - - - - - 179.7 -3.3 34.2 - +* +* 14 ILE 14 t B - - -59.1 177.3 - - - - - - 184.7 - 35.4 - 15 SER 15 T A - - -67.3 - - - - - - - 179.6 -.6 32.9 - +* +* 16 GLU 16 T A - 183.0 - 178.8 - - - - - - 179.9 - 34.8 - 17 LYS 17 T a - - -66.5 - - - - - - - 188.1 -1.2 30.7 - * * * 18 SER 18 T A - - -50.6 - - - - - - - 178.5 -2.4 34.2 - * * 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 SER 19 T A - 182.2 - - - - - - - - 180.8 - 34.0 - 20 LYS 20 T a 61.5 - - 181.6 - - - - - - 179.0 -2.3 33.1 - 21 SER 21 t B - - -55.7 - - - - - - - 177.3 -2.3 36.1 - 22 LEU 22 E B - 197.9 - 179.7 - - - - - - 181.4 -3.0 34.2 - * * 23 GLU 23 E B 56.0 - - 183.6 - - - - - - 179.8 -.7 33.9 - +* +* 24 ILE 24 E B - - -57.5 - - - - - - - 183.7 -1.7 35.0 - 25 PRO 25 h - - - - - -62.0 - - - - - 179.9 - 38.5 - * * 26 LEU 26 H A - - -68.7 - - -66.8 -25.7 - - - 178.3 - 32.2 - * * 27 GLY 27 H - - - - - - -66.5 -25.7 - - - 178.8 - - - * * 28 PHE 28 H A - 183.7 - - - -85.8 -23.8 - - - 178.7 -1.1 34.6 - +* * * +* 29 ASN 29 H A - - -85.7 - - -74.0 -44.8 - - - 180.5 -1.0 34.9 - * * * 30 GLU 30 h A - 184.4 - 178.8 - - - - - - 177.4 -2.5 33.7 - 31 TYR 31 T A - 179.9 - - - - - - - - 175.5 - 33.4 - 32 PHE 32 t b 66.8 - - - - - - - - - 171.7 -.9 31.1 - * +* +* 33 PRO 33 - - - - - -75.5 - - - - - 184.2 - 38.1 - * * 34 ALA 34 B - - - - - - - - - - 174.1 - 35.6 - * * 35 PRO 35 - - - - - -54.8 - - - - - 187.6 - 38.8 - * * * 36 PHE 36 B 65.8 - - - - - - - - - 176.6 - 33.0 - 37 PRO 37 - - - - - -81.4 - - - - - 172.6 - 39.1 - * * * * 38 ILE 38 e a - - -55.9 - - - - - - - 177.2 - 32.6 - 39 THR 39 E B 51.2 - - - - - - - - - 175.9 - 33.5 - 40 VAL 40 E B - - -63.5 - - - - - - - 185.0 -3.1 32.9 - * * 41 ASP 41 E B - 188.6 - - - - - - - - 182.0 -1.5 33.5 - 42 LEU 42 E B - - -55.6 182.3 - - - - - - 179.5 -3.2 35.9 - +* +* 43 LEU 43 E B - - -73.2 - - - - - - - 178.3 -2.9 33.6 - * * 44 ASP 44 E B - 154.6 - - - - - - - - 182.9 -2.8 35.0 - +* +* 45 TYR 45 e A 55.1 - - - - - - - - - 179.9 -.6 33.6 - +* +* 46 SER 46 S A - 187.7 - - - - - - - - 176.3 - 33.8 - 47 GLY 47 S - - - - - - - - - - - 182.4 - - - 48 ARG 48 e B - - -59.0 183.3 - - - - - - 177.8 - 33.1 - 49 SER 49 E B 58.2 - - - - - - - - - 179.4 - 34.0 - 50 TRP 50 E B - - -59.1 - - - - - - - 175.4 -2.8 35.4 - * * 51 THR 51 E B - - -56.8 - - - - - - - 187.4 - 33.3 - * * 52 VAL 52 E B - - -58.3 - - - - - - - 181.8 -2.6 34.0 - 53 ARG 53 E B - 191.0 - 180.9 - - - - - - 181.1 -.8 35.4 - +* +* 54 MET 54 E B - 171.3 - 185.9 - - - - - - 178.9 -1.2 36.5 - * * 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 LYS 55 E B - - -70.5 185.3 - - - - - - 175.3 -2.2 34.1 - 56 LYS 56 E B - 177.0 - 167.7 - - - - - - 187.8 - 32.1 - * * 57 ARG 57 E B - - -50.8 180.5 - - - - - - 184.5 -1.6 35.4 - * * 58 GLY 58 T - - - - - - - - - - - 181.6 -.6 - - +* +* 59 GLU 59 T A - - -58.1 - - - - - - - 179.6 - 33.8 - 60 LYS 60 E B 58.2 - - 182.2 - - - - - - 178.3 -.9 34.7 - +* +* 61 VAL 61 E B - 175.0 - - - - - - - - 172.0 -1.3 34.7 - * * 62 PHE 62 E B - - -65.8 - - - - - - - 178.2 -2.2 33.8 - 63 LEU 63 E B - 197.6 - 171.6 - - - - - - 191.6 -2.2 34.4 - ** ** 64 THR 64 E b - 179.8 - - - - - - - - 190.0 -1.4 33.8 - +* +* 65 VAL 65 T B - - -63.4 - - - - - - - 194.3 - 31.1 - ** ** 66 GLY 66 h - - - - - - - - - - - 171.5 - - - * * 67 TRP 67 H A - 163.1 - - - -60.5 -31.6 - - - 182.1 -2.2 35.8 - * * 68 GLU 68 H A 42.9 - - - - -66.4 -25.6 - - - 173.6 - 25.3 - * * * ** ** 69 ASN 69 H A - - -63.3 - - -61.0 -41.2 - - - 183.0 -.9 34.6 - +* +* 70 PHE 70 H A - 178.1 - - - -64.5 -53.6 - - - 183.2 -.8 35.4 - * +* +* 71 VAL 71 H A - 172.1 - - - -71.7 -36.8 - - - 175.0 -1.9 28.4 - +* +* 72 LYS 72 H A - - -66.3 - - -71.5 -39.2 - - - 183.2 -2.7 31.8 - 73 ASP 73 H A - 179.1 - - - -77.1 -30.5 - - - 178.8 -2.8 31.9 - * * 74 ASN 74 H A - 192.3 - - - -91.9 -19.4 - - - 183.2 -2.3 34.4 - ** +* ** 75 ASN 75 h l - 182.9 - - - - - - - - 179.8 -1.1 31.7 - * * 76 LEU 76 t B 58.0 - - - - - - - - - 184.6 -1.0 30.1 - * * * 77 GLU 77 t B 57.8 - - 181.7 - - - - - - 176.4 - 34.2 - 78 ASP 78 T B - 182.6 - - - - - - - - 178.7 - 37.3 - 79 GLY 79 T - - - - - - - - - - - 178.3 -1.9 - - 80 LYS 80 e B - - -49.7 - - - - - - - 182.3 -1.5 34.5 - * * 81 TYR 81 E B - - -51.0 - - - - - - - 184.1 -1.2 33.9 - * * * 82 LEU 82 E B - - -57.4 176.4 - - - - - - 176.6 -2.8 35.5 - * * 83 GLN 83 E B - 185.3 - 185.3 - - - - - - 178.9 -2.5 36.4 - 84 PHE 84 E B - - -58.1 - - - - - - - 177.7 -3.8 35.4 - ** ** 85 ILE 85 E B - - -55.0 178.1 - - - - - - 179.4 -2.9 34.8 - * * 86 TYR 86 E B - 175.1 - - - - - - - - 181.7 -3.6 36.5 - ** ** 87 ASP 87 e a - 175.6 - - - - - - - - 177.9 -2.1 34.2 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 88 ARG 88 S ~b - 201.5 - - - - - - - - 190.1 - 36.6 - ** * +* ** 89 ASP 89 S b - 194.4 - - - - - - - - 187.3 - 36.3 - * * 90 ARG 90 e A - 198.4 - - - - - - - - 184.9 - 38.2 - * * 91 THR 91 E B - - -58.7 - - - - - - - 177.4 - 35.0 - 92 PHE 92 E B - - -63.7 - - - - - - - 178.5 -1.9 35.3 - 93 TYR 93 E B - - -50.4 - - - - - - - 184.4 -2.4 35.2 - * * 94 VAL 94 E B - 185.8 - - - - - - - - 173.0 -2.8 35.2 - * * * 95 ILE 95 E B - 185.2 - 178.6 - - - - - - 184.1 -1.7 32.0 - 96 ILE 96 E B - - -55.2 177.4 - - - - - - 176.6 - 35.7 - 97 TYR 97 E B - - -64.2 - - - - - - - 184.1 -3.3 34.1 - +* +* 98 GLY 98 S - - - - - - - - - - - 181.1 - - - 99 HIS 99 S b 54.8 - - - - - - - - - 177.4 - 29.0 - * * 100 ASN 100 a - 181.1 - - - - - - - - 178.7 -1.7 35.0 - 101 MET 101 B - 181.0 - 181.8 - - - - - - 181.2 - 34.8 - 102 CYS 102 - - - -57.1 - - - - - - - - -1.0 34.2 - * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * +* * * ** +* ** ** ** ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.3 182.7 -60.3 179.6 -70.4 -71.5 -33.2 - - - 180.2 -2.0 34.3 Standard deviations: 5.9 9.4 7.6 5.1 11.4 9.6 10.1 - - - 4.4 .9 2.2 Numbers of values: 15 36 37 25 5 12 12 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_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 - 1.232 1.512 1.529 1.460 - 116.73 120.74 110.09 109.74 110.59 122.52 2 ALA 2 1.307 1.229 1.515 1.524 1.438 120.89 116.40 120.69 110.85 110.57 110.86 122.84 +* * +* 3 ASP 3 1.312 1.224 1.508 1.540 1.454 121.45 115.64 121.06 110.07 109.86 112.33 123.26 * * * 4 THR 4 1.296 1.230 1.543 1.548 1.438 122.84 115.28 122.14 108.77 108.39 108.55 122.58 ** * * +* ** 5 GLY 5 1.309 1.232 1.460 - 1.426 121.36 113.12 121.84 - 109.12 - 125.00 * *** +* +* * * *** 6 GLU 6 1.263 1.250 1.518 1.541 1.436 123.55 115.97 121.16 108.75 109.97 111.81 122.87 *4.7* * * *4.7* 7 VAL 7 1.292 1.222 1.502 1.569 1.441 121.73 117.08 120.46 110.43 108.51 113.59 122.44 +** * * * +** 8 GLN 8 1.290 1.240 1.501 1.517 1.403 120.62 114.96 121.27 113.05 110.98 110.52 123.75 +** * +** +* +** 9 PHE 9 1.287 1.218 1.511 1.530 1.427 123.67 117.91 119.74 111.66 107.72 107.34 122.33 *** +* * * +* *** 10 MET 10 1.302 1.236 1.516 1.543 1.456 119.95 115.72 120.92 110.37 111.78 111.32 123.36 +* +* 11 LYS 11 1.315 1.235 1.514 1.549 1.450 123.05 117.89 120.13 107.59 110.36 112.26 121.94 * * * * 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 PRO 12 1.334 1.244 1.520 1.544 1.446 121.96 117.13 120.10 109.62 108.61 104.29 122.75 * * * * 13 PHE 13 1.304 1.244 1.521 1.540 1.442 120.83 116.70 120.23 110.94 108.96 110.47 123.04 +* +* 14 ILE 14 1.323 1.225 1.513 1.556 1.421 121.72 117.13 119.72 110.27 107.55 110.21 123.15 +* * +* 15 SER 15 1.328 1.222 1.533 1.530 1.470 122.79 116.38 120.60 110.07 113.09 111.48 123.01 16 GLU 16 1.322 1.237 1.536 1.527 1.446 122.16 117.53 120.46 110.23 111.28 109.45 122.01 17 LYS 17 1.336 1.234 1.487 1.541 1.479 118.63 115.50 120.83 109.26 113.43 115.19 123.56 +* * +* +** +** 18 SER 18 1.305 1.214 1.535 1.519 1.438 122.68 116.65 120.93 111.33 111.85 108.94 122.43 +* * +* 19 SER 19 1.317 1.235 1.545 1.537 1.444 121.46 116.96 120.68 111.36 110.58 109.69 122.36 20 LYS 20 1.332 1.237 1.525 1.540 1.457 120.41 116.45 120.89 111.06 111.52 110.98 122.65 21 SER 21 1.310 1.219 1.515 1.536 1.445 122.45 117.49 120.08 108.49 108.53 110.15 122.42 * * 22 LEU 22 1.292 1.245 1.518 1.544 1.430 120.24 115.07 121.06 111.33 106.00 111.21 123.83 +** * +* +** 23 GLU 23 1.294 1.252 1.550 1.535 1.432 123.19 115.69 121.60 112.60 111.30 108.39 122.68 +** * * * * * +** 24 ILE 24 1.316 1.244 1.529 1.543 1.449 122.20 117.39 120.31 108.86 108.92 111.39 122.30 25 PRO 25 1.337 1.247 1.530 1.528 1.468 123.22 115.72 121.41 110.03 114.10 103.62 122.86 26 LEU 26 1.321 1.229 1.520 1.543 1.461 122.22 116.09 120.78 110.48 111.34 112.85 123.10 * * 27 GLY 27 1.323 1.225 1.516 - 1.446 121.17 116.03 120.95 - 111.95 - 123.01 28 PHE 28 1.319 1.220 1.528 1.539 1.457 122.19 114.77 121.75 111.61 108.78 109.12 123.43 29 ASN 29 1.313 1.220 1.492 1.510 1.458 123.55 115.89 120.84 109.08 111.66 110.31 123.27 * +* * +* 30 GLU 30 1.311 1.238 1.534 1.533 1.443 121.58 115.55 121.38 112.02 109.67 109.73 123.05 * * * 31 TYR 31 1.330 1.238 1.532 1.546 1.443 122.06 116.83 120.20 111.85 109.86 110.44 122.95 32 PHE 32 1.342 1.230 1.544 1.572 1.464 121.75 118.14 121.42 111.30 112.39 113.21 120.34 ** +* +* ** 33 PRO 33 1.333 1.247 1.515 1.526 1.434 121.22 115.70 120.98 110.51 109.04 104.95 123.32 ** * +* ** 34 ALA 34 1.279 1.252 1.507 1.533 1.437 122.63 118.65 118.82 110.26 108.26 109.33 122.48 +*** * * * * * +*** 35 PRO 35 1.359 1.247 1.515 1.523 1.457 121.76 116.45 120.38 109.96 108.58 104.25 123.17 * * * * 36 PHE 36 1.294 1.235 1.525 1.531 1.397 121.89 116.66 121.24 112.32 111.91 109.97 122.05 +** *** * *** 37 PRO 37 1.320 1.229 1.518 1.528 1.439 122.60 117.46 120.39 110.53 109.95 103.29 121.95 * +* +* 38 ILE 38 1.299 1.223 1.526 1.554 1.435 119.04 116.46 121.09 111.23 108.15 112.97 122.43 ** * * * ** 39 THR 39 1.308 1.233 1.535 1.547 1.445 121.43 115.93 120.82 110.08 111.78 111.44 123.22 +* +* 40 VAL 40 1.314 1.237 1.520 1.569 1.454 124.20 118.31 119.55 110.64 107.39 113.50 122.14 * * * * * * * 41 ASP 41 1.303 1.243 1.522 1.535 1.457 119.60 115.81 120.90 111.70 110.89 109.97 123.28 +* * +* 42 LEU 42 1.316 1.237 1.510 1.543 1.444 122.43 116.29 120.54 107.87 109.05 111.03 123.17 * * 43 LEU 43 1.302 1.240 1.503 1.550 1.441 121.87 114.05 121.63 109.09 111.77 112.47 124.28 +* * * * * +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 44 ASP 44 1.288 1.235 1.513 1.529 1.438 124.55 114.66 121.16 110.58 110.46 109.17 124.17 +** * +* +** 45 TYR 45 1.310 1.229 1.529 1.547 1.448 124.41 117.09 120.55 111.20 112.33 110.03 122.36 * +* +* 46 SER 46 1.318 1.237 1.543 1.545 1.442 120.86 116.27 121.10 112.05 108.81 110.02 122.62 * * 47 GLY 47 1.322 1.233 1.518 - 1.448 120.74 116.82 120.47 - 113.31 - 122.71 48 ARG 48 1.314 1.231 1.529 1.531 1.456 121.99 116.35 121.00 110.97 111.84 110.89 122.59 * * 49 SER 49 1.305 1.240 1.525 1.536 1.439 121.97 116.73 120.68 111.15 109.46 110.43 122.57 +* * +* 50 TRP 50 1.300 1.231 1.511 1.536 1.456 121.49 117.16 120.41 108.16 110.13 111.08 122.43 ** * ** 51 THR 51 1.301 1.239 1.530 1.531 1.427 120.20 115.01 121.54 111.41 108.26 111.45 123.45 +* +* * * +* 52 VAL 52 1.293 1.232 1.524 1.553 1.440 123.20 117.59 120.22 110.41 110.53 110.97 122.19 +** +** 53 ARG 53 1.316 1.221 1.520 1.532 1.447 120.28 116.01 120.82 109.11 108.92 110.38 123.16 54 MET 54 1.297 1.202 1.496 1.539 1.446 123.00 117.63 119.51 108.57 108.58 109.73 122.86 ** * * ** 55 LYS 55 1.311 1.242 1.495 1.501 1.431 120.86 115.83 120.85 108.67 112.32 111.59 123.31 * * * * * 56 LYS 56 1.308 1.233 1.467 1.503 1.427 120.98 112.99 122.30 111.92 108.33 112.69 124.71 +* +** * +* +* * * * +** 57 ARG 57 1.250 1.241 1.503 1.543 1.425 123.19 115.53 121.10 110.73 107.73 109.55 123.33 *5.7* * +* * *5.7* 58 GLY 58 1.296 1.248 1.515 - 1.422 120.70 116.34 120.91 - 110.68 - 122.69 ** +* ** 59 GLU 59 1.307 1.229 1.518 1.531 1.451 121.64 115.32 121.21 111.15 109.90 110.48 123.46 +* +* 60 LYS 60 1.318 1.237 1.538 1.531 1.429 123.56 116.58 120.80 110.98 110.06 109.36 122.61 +* * +* 61 VAL 61 1.317 1.237 1.509 1.585 1.458 122.49 116.36 120.49 108.21 108.93 112.97 123.11 +* +* 62 PHE 62 1.299 1.244 1.489 1.534 1.423 121.06 115.97 120.66 110.12 107.88 112.46 123.35 ** +* +* * * ** 63 LEU 63 1.286 1.212 1.528 1.543 1.416 120.84 115.25 121.26 114.14 105.34 108.21 123.47 *** ** ** ** * *** 64 THR 64 1.292 1.230 1.566 1.570 1.450 123.82 117.44 119.93 113.33 111.93 107.85 122.62 +** +* * * +* ** +** 65 VAL 65 1.347 1.225 1.513 1.552 1.472 123.40 114.58 122.17 110.95 112.79 113.35 123.25 * * * 66 GLY 66 1.289 1.223 1.483 - 1.413 121.67 113.74 122.02 - 106.12 - 124.22 +** +* ** * ** +** 67 TRP 67 1.334 1.238 1.503 1.535 1.440 123.74 115.07 121.64 109.48 109.08 109.58 123.25 * * * 68 GLU 68 1.307 1.214 1.513 1.553 1.428 120.09 116.29 120.43 116.57 112.67 115.07 123.23 +* * +* *** +** *** 69 ASN 69 1.333 1.184 1.507 1.539 1.465 121.89 116.07 120.78 108.17 109.88 112.32 123.08 ** * * ** 70 PHE 70 1.304 1.225 1.507 1.555 1.455 123.46 115.94 120.98 109.96 109.81 109.66 123.04 +* * +* 71 VAL 71 1.307 1.224 1.528 1.553 1.435 120.71 117.31 120.35 114.77 113.00 112.96 122.32 +* * +** +** 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 ----------------------------------------------------------------------------------------------------------------------------------- 72 LYS 72 1.319 1.233 1.527 1.537 1.454 120.38 117.13 120.33 111.07 111.78 112.63 122.53 * * 73 ASP 73 1.328 1.235 1.515 1.540 1.483 120.71 116.77 120.88 111.51 112.74 111.65 122.35 * * 74 ASN 74 1.304 1.228 1.518 1.526 1.451 120.05 114.79 121.01 110.22 109.35 110.61 124.13 +* +* 75 ASN 75 1.330 1.234 1.528 1.540 1.472 125.04 116.64 121.21 111.51 112.03 112.18 122.10 +* +* 76 LEU 76 1.313 1.240 1.527 1.560 1.443 120.61 115.85 120.82 113.91 112.35 111.97 123.33 * * ** ** 77 GLU 77 1.312 1.243 1.504 1.517 1.446 122.97 114.97 120.66 109.55 111.28 111.03 124.33 * * 78 ASP 78 1.327 1.249 1.517 1.535 1.472 123.58 115.54 121.10 107.52 110.49 108.74 123.34 * * * * 79 GLY 79 1.312 1.231 1.497 - 1.433 120.61 116.85 120.35 - 112.98 - 122.79 * * * * 80 LYS 80 1.314 1.241 1.523 1.543 1.451 120.38 117.82 119.92 110.01 107.68 111.32 122.26 * * * 81 TYR 81 1.308 1.234 1.497 1.536 1.445 119.92 116.63 120.38 110.61 108.44 111.48 122.98 +* * +* 82 LEU 82 1.291 1.241 1.515 1.529 1.433 121.11 115.94 120.47 110.02 110.69 109.01 123.58 +** * +** 83 GLN 83 1.313 1.231 1.503 1.523 1.447 122.32 116.62 120.11 107.17 107.26 111.15 123.27 * * +* * +* 84 PHE 84 1.289 1.229 1.500 1.537 1.425 121.96 116.31 120.64 109.95 108.68 110.03 123.02 +** * +* +** 85 ILE 85 1.291 1.228 1.508 1.552 1.431 121.31 116.21 120.50 109.13 108.17 112.00 123.30 +** * * +** 86 TYR 86 1.284 1.233 1.503 1.544 1.426 122.76 116.11 119.91 110.93 106.92 107.81 123.96 *** * +* +* +* *** 87 ASP 87 1.327 1.227 1.509 1.546 1.465 122.10 114.27 120.95 109.99 110.72 110.87 124.78 * * 88 ARG 88 1.310 1.241 1.520 1.547 1.456 126.11 114.00 122.59 108.66 103.04 110.45 123.39 * ** * * +** +** 89 ASP 89 1.329 1.214 1.538 1.549 1.431 122.76 117.25 119.91 111.10 107.17 107.69 122.75 * * +* +* 90 ARG 90 1.299 1.235 1.543 1.524 1.453 123.65 115.81 121.11 108.37 109.97 106.39 123.08 ** * ** ** 91 THR 91 1.309 1.249 1.544 1.549 1.444 122.50 115.56 120.95 110.41 111.80 108.97 123.47 * * * 92 PHE 92 1.331 1.228 1.525 1.533 1.453 123.24 116.76 120.55 108.28 109.66 111.13 122.69 93 TYR 93 1.307 1.228 1.518 1.537 1.460 121.99 117.44 119.89 109.66 107.52 110.46 122.65 +* * +* 94 VAL 94 1.307 1.233 1.533 1.557 1.452 120.97 116.46 120.66 108.60 111.50 110.77 122.87 +* +* 95 ILE 95 1.316 1.241 1.530 1.579 1.449 122.04 116.63 120.37 111.28 107.93 113.98 122.97 * * * * 96 ILE 96 1.310 1.234 1.511 1.550 1.447 122.15 116.15 120.46 109.09 109.92 110.03 123.37 * * 97 TYR 97 1.307 1.246 1.496 1.511 1.439 121.71 115.55 120.54 109.55 109.52 111.71 123.90 +* * +* 98 GLY 98 1.301 1.235 1.497 - 1.416 121.17 117.04 120.07 - 109.18 - 122.86 +* * ** * ** 99 HIS 99 1.308 1.233 1.521 1.553 1.445 120.93 114.43 122.17 113.43 112.71 113.64 123.31 +* * +* +* +* Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 100 ASN 100 1.302 1.228 1.509 1.541 1.443 123.04 115.29 121.55 109.99 108.52 110.40 123.15 +* +* 101 MET 101 1.308 1.236 1.505 1.520 1.432 122.06 116.06 121.09 109.88 108.89 110.56 122.82 +* * +* 102 CYS 102 1.281 - 1.508 1.529 1.423 121.53 - - 111.55 108.82 109.94 - *** +* *** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *5.7* ** *** ** *** ** +* * *** +** +** +* *5.7* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 1.250 1.347 1.308 .016 *5.7* * * C-N (Pro) 1.341 .016 5 1.320 1.359 1.337 .013 * * C-O C-O 1.231 .020 101 1.184 1.252 1.233 .010 ** * CA-C CH1E-C (except Gly) 1.525 .021 95 1.467 1.566 1.518 .015 +** +* CH2G*-C (Gly) 1.516 .018 7 1.460 1.518 1.498 .020 *** CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.524 1.533 1.529 .004 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.531 1.585 1.557 .013 +* CH1E-CH2E (the rest) 1.530 .020 75 1.501 1.572 1.536 .012 * ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.397 1.483 1.444 .015 *** * NH1-CH2G* (Gly) 1.451 .016 7 1.413 1.448 1.429 .013 ** * N-CH1E (Pro) 1.466 .015 5 1.434 1.468 1.449 .013 ** * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 89 112.99 118.65 116.20 1.04 +* * CH2G*-C-NH1 (Gly) 116.4 2.1 7 113.12 117.04 115.71 1.48 +* CH1E-C-N (Pro) 116.9 1.5 5 115.70 117.46 116.49 .72 O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.34 125.00 123.02 .68 +* * O-C-N (Pro) 122.0 1.4 5 121.95 123.32 122.81 .47 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.63 126.11 121.98 1.36 +* ** C-NH1-CH2G* (Gly) 120.6 1.7 7 120.61 121.67 121.06 .36 C-N-CH1E (Pro) 122.6 5.0 5 121.22 123.22 122.15 .69 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 118.82 122.59 120.77 .63 * * CH2G*-C-O (Gly) 120.8 2.1 7 120.07 122.02 120.95 .69 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.26 110.85 110.56 .29 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.21 114.77 110.44 1.62 +** CH2E-CH1E-C (the rest) 110.1 1.9 75 107.17 116.57 110.46 1.61 +* *** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 103.04 113.43 109.87 1.92 +** NH1-CH2G*-C (Gly) 112.5 2.9 7 106.12 113.31 110.48 2.36 ** N-CH1E-C (Pro) 111.8 2.5 5 108.58 114.10 110.06 2.08 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.33 110.86 110.10 .77 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 107.85 113.98 111.50 1.79 ** * N-CH1E-CH2E (Pro) 103.0 1.1 5 103.29 104.95 104.08 .58 +* NH1-CH1E-CH2E (the rest) 110.5 1.7 70 106.39 115.19 110.67 1.60 ** +** ------------------------------------------------------------------------------------------------------------- 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 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] 12 13.6% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.1% 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 4.4 6.0 3.0 -.5 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 2.2 3.1 1.6 -.6 Inside e. H-bond energy st dev 61 .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 15 5.9 18.1 6.5 -1.9 BETTER b. Chi-1 trans st dev 36 9.4 19.0 5.3 -1.8 BETTER c. Chi-1 gauche plus st dev 37 7.6 17.5 4.9 -2.0 BETTER d. Chi-1 pooled st dev 88 9.6 18.2 4.8 -1.8 BETTER e. Chi-2 trans st dev 25 5.1 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% 85.2 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 10.0 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .88 3 Residue-by-residue listing for refined_12 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.57 Chi1-chi2 distribution -.28 Chi1 only .03 Chi3 & chi4 .36 Omega -.15 ------ -.23 ===== Main-chain covalent forces:- Main-chain bond lengths -.16 Main-chain bond angles .35 ------ .13 ===== OVERALL AVERAGE -.11 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.