Residue-by-residue listing for refined_6 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 - - 181.8 - 183.4 - - - - - - 181.3 - 35.0 - 2 ALA 2 b - - - - - - - - - - 179.4 - 34.9 - 3 ASP 3 B - 185.4 - - - - - - - - 175.8 - 33.1 - 4 THR 4 a - - -57.5 - - - - - - - 182.1 -1.2 35.1 - * * 5 GLY 5 - - - - - - - - - - - 175.5 - - - 6 GLU 6 b 54.8 - - 181.5 - - - - - - 184.5 - 31.6 - 7 VAL 7 E B - - -63.2 - - - - - - - 181.3 -2.9 33.0 - * * 8 GLN 8 E B 50.8 - - 181.1 - - - - - - 178.6 - 33.0 - 9 PHE 9 E B - 183.5 - - - - - - - - 179.8 -1.8 35.3 - 10 MET 10 E B 60.0 - - - - - - - - - 177.8 - 33.3 - 11 LYS 11 E B 70.8 - - - - - - - - - 176.2 -1.2 33.2 - * * 12 PRO 12 E - - - - - -81.3 - - - - - 178.9 - 39.0 - * * * 13 PHE 13 e B 52.7 - - - - - - - - - 182.2 -.6 32.2 - +* +* 14 ILE 14 h B - - -59.9 178.1 - - - - - - 186.0 - 34.2 - * * 15 SER 15 H A - - -48.8 - - -55.9 -25.8 - - - 180.8 - 34.3 - * * * 16 GLU 16 H A - 186.2 - 175.0 - -60.4 -28.9 - - - 175.2 - 35.3 - 17 LYS 17 H a - - -72.1 - - -112.6 -41.4 - - - 186.1 -2.5 31.7 - +*** * +*** 18 SER 18 H A - 183.7 - - - -56.5 -21.6 - - - 179.6 -3.2 33.4 - +* +* +* 19 SER 19 h A - - -60.6 - - - - - - - 181.6 -1.6 33.0 - Residue-by-residue listing for refined_6 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 ----------------------------------------------------------------------------------------------------------------------------------- 20 LYS 20 T a - 185.8 - 176.8 - - - - - - 184.3 -2.8 33.5 - * * 21 SER 21 t B 54.7 - - - - - - - - - 177.9 -3.1 35.0 - * * 22 LEU 22 E B - - -70.7 181.6 - - - - - - 175.8 -1.1 32.2 - * * 23 GLU 23 E B 57.6 - - 183.7 - - - - - - 182.3 - 34.2 - 24 ILE 24 E B - - -61.8 177.3 - - - - - - 179.9 -2.2 33.1 - 25 PRO 25 t - - - - - -57.0 - - - - - 181.9 - 38.8 - * * 26 LEU 26 T A - - -67.3 - - - - - - - 179.9 - 33.8 - 27 GLY 27 g - - - - - - - - - - - 178.7 - - - 28 PHE 28 G A - 194.6 - - - - - - - - 174.8 - 34.2 - 29 ASN 29 G A - 170.0 - - - - - - - - 181.7 -.5 33.5 - +* +* 30 GLU 30 G A - 184.8 - 180.0 - - - - - - 183.1 -1.2 35.1 - * * 31 TYR 31 G A - 180.0 - - - - - - - - 179.8 -.8 35.2 - +* +* 32 PHE 32 g B - - -64.1 - - - - - - - 181.6 -1.5 32.5 - 33 PRO 33 S - - - - - -69.0 - - - - - 181.6 - 39.4 - +* +* 34 ALA 34 S B - - - - - - - - - - 176.7 - 34.5 - 35 PRO 35 S - - - - - -50.2 - - - - - 176.8 - 39.2 - * +* +* 36 PHE 36 S B - - -69.1 - - - - - - - 178.3 - 33.7 - 37 PRO 37 - - - - - -86.6 - - - - - 180.4 - 38.7 - +* * +* 38 ILE 38 e A - - -58.7 - - - - - - - 180.1 - 33.0 - 39 THR 39 E B - - -49.3 - - - - - - - 183.7 - 34.9 - * * 40 VAL 40 E B - 176.4 - - - - - - - - 178.7 -3.1 35.5 - * * 41 ASP 41 E B - - -69.3 - - - - - - - 179.6 -1.2 32.8 - * * 42 LEU 42 E B - - -62.8 177.9 - - - - - - 177.3 -3.2 35.2 - +* +* 43 LEU 43 E B - - -63.5 - - - - - - - 183.6 -3.6 33.9 - ** ** 44 ASP 44 E B - 150.8 - - - - - - - - 180.5 -2.5 34.0 - +* +* 45 TYR 45 e A - 180.5 - - - - - - - - 180.5 -2.1 34.6 - 46 SER 46 S A - 183.4 - - - - - - - - 176.3 - 33.2 - 47 GLY 47 S - - - - - - - - - - - 180.1 - - - 48 ARG 48 e B - - -69.6 - - - - - - - 173.2 - 33.9 - * * 49 SER 49 E B 56.4 - - - - - - - - - 180.2 - 33.5 - 50 TRP 50 E B - - -53.9 - - - - - - - 175.1 -2.6 36.6 - 51 THR 51 E B - - -55.9 - - - - - - - 189.2 - 35.3 - +* +* 52 VAL 52 E B - 185.1 - - - - - - - - 178.0 -3.1 34.6 - * * 53 ARG 53 E B - 178.9 - 171.8 - - - - - - 185.1 -2.8 33.3 - * * 54 MET 54 E B - - -59.6 181.0 - - - - - - 175.0 -.9 36.8 - +* +* Residue-by-residue listing for refined_6 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 - - -66.5 185.3 - - - - - - 172.3 -2.3 32.9 - * * 56 LYS 56 E B - - -58.0 - - - - - - - 185.8 - 34.8 - * * 57 ARG 57 E b - 174.9 - 179.8 - - - - - - 180.7 -2.6 34.1 - 58 GLY 58 T - - - - - - - - - - - 181.1 -.7 - - +* +* 59 GLU 59 T A - - -53.3 180.3 - - - - - - 185.6 -.6 36.3 - +* +* 60 LYS 60 E B 56.0 - - 179.6 - - - - - - 182.4 -2.2 33.1 - 61 VAL 61 E B - 182.7 - - - - - - - - 175.7 -1.7 34.7 - 62 PHE 62 E B - - -67.7 - - - - - - - 179.1 -2.5 33.3 - 63 LEU 63 E B - 195.1 - - - - - - - - 187.4 -2.1 35.9 - * * 64 THR 64 e a 56.3 - - - - - - - - - 185.9 -1.5 31.1 - * * 65 VAL 65 T B - - -61.7 - - - - - - - 184.7 - 31.2 - 66 GLY 66 h - - - - - - - - - - - 175.7 - - - 67 TRP 67 H A - 172.3 - - - -65.9 -26.9 - - - 181.5 -.6 34.7 - * +* +* 68 GLU 68 H A - 189.3 - 175.2 - -69.6 -26.7 - - - 175.4 - 30.6 - * * 69 ASN 69 H A - - -58.9 - - -73.9 -29.8 - - - 181.8 -.7 34.4 - +* +* 70 PHE 70 H A - 191.2 - - - -73.6 -51.5 - - - 181.4 -1.0 35.8 - * * * 71 VAL 71 H A 68.6 - - - - -60.9 -40.2 - - - 178.7 -3.4 33.3 - +* +* 72 LYS 72 H A - - -60.1 - - -70.4 -35.0 - - - 183.6 -1.8 32.6 - 73 ASP 73 H A - 185.5 - - - -77.6 -42.1 - - - 181.1 -1.5 32.5 - * * 74 ASN 74 H A - - -67.9 - - -108.2 13.7 - - - 181.0 -2.8 31.5 - +*** *4.7* * *4.7* 75 ASN 75 h XX - 185.3 - - - - - - - - 178.4 -.8 32.0 - **** +* **** 76 LEU 76 l - - -76.6 - - - - - - - 176.1 -2.3 30.7 - 77 GLU 77 t B - 183.5 - 177.2 - - - - - - 181.7 - 33.5 - 78 ASP 78 T B - 175.1 - - - - - - - - 181.6 - 34.5 - 79 GLY 79 T - - - - - - - - - - - 178.3 - - - 80 LYS 80 e B - - -63.4 180.2 - - - - - - 183.6 -1.3 33.0 - 81 TYR 81 E B - - -57.2 - - - - - - - 179.4 -1.1 35.0 - * * 82 LEU 82 E B - - -63.3 180.4 - - - - - - 175.5 -1.3 34.3 - 83 GLN 83 E B - 181.0 - 182.1 - - - - - - 183.9 -3.1 35.9 - * * 84 PHE 84 E B - 181.4 - - - - - - - - 179.9 -3.4 35.6 - +* +* 85 ILE 85 E B - - -54.3 - - - - - - - 181.3 -3.2 35.0 - +* +* 86 TYR 86 E B - 179.2 - - - - - - - - 173.6 -3.2 37.0 - * +* +* 87 ASP 87 a 56.9 - - - - - - - - - 175.7 -.5 29.0 - ** * ** 88 ARG 88 S a - 203.1 - - - - - - - - 182.6 - 34.7 - * * 89 ASP 89 S b - 187.7 - - - - - - - - 183.3 - 35.0 - 90 ARG 90 e A - 178.6 - 181.5 - - - - - - 179.3 - 35.7 - Residue-by-residue listing for refined_6 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 ----------------------------------------------------------------------------------------------------------------------------------- 91 THR 91 E B 48.1 - - - - - - - - - 184.5 - 33.7 - * * 92 PHE 92 E B - - -55.0 - - - - - - - 181.1 -2.0 34.3 - 93 TYR 93 E B - - -61.4 - - - - - - - 178.9 -1.4 34.4 - 94 VAL 94 E B 61.4 - - - - - - - - - 177.7 -3.4 32.8 - +* +* 95 ILE 95 E B - - -55.8 177.1 - - - - - - 181.4 -3.0 34.3 - * * 96 ILE 96 E B - - -61.7 - - - - - - - 173.9 -.5 34.5 - * ** ** 97 TYR 97 E B - - -62.4 - - - - - - - 184.3 -3.2 34.3 - +* +* 98 GLY 98 S - - - - - - - - - - - 181.6 -.8 - - +* +* 99 HIS 99 B - 183.8 - - - - - - - - 176.6 - 34.0 - 100 ASN 100 B - 188.0 - - - - - - - - 184.9 -1.0 34.3 - * * 101 MET 101 B - - -61.2 177.8 - - - - - - 179.0 - 33.9 - 102 CYS 102 - - - -59.7 - - - - - - - - -.6 31.6 - +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +* * +* +*** *4.7* +* ** +* *4.7* ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.5 182.6 -61.6 179.4 -68.8 -73.8 -29.7 - - - 180.1 -1.9 34.1 Standard deviations: 6.2 8.6 6.1 3.0 15.5 18.5 16.2 - - - 3.4 1.0 1.8 Numbers of values: 14 34 40 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_6 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 - 1.242 1.507 1.531 1.457 - 116.14 120.63 109.82 108.80 110.34 123.21 2 ALA 2 1.306 1.237 1.503 1.523 1.436 122.34 116.77 120.50 109.87 109.20 110.42 122.72 +* * * +* 3 ASP 3 1.307 1.234 1.493 1.529 1.441 120.13 115.36 121.38 109.74 109.49 113.09 123.12 +* * +* +* 4 THR 4 1.273 1.230 1.508 1.542 1.415 121.92 115.26 121.31 109.99 107.84 110.71 123.30 +*** ** * +*** 5 GLY 5 1.304 1.221 1.493 - 1.413 120.55 116.27 120.56 - 110.70 - 123.11 +* * ** ** 6 GLU 6 1.288 1.237 1.505 1.539 1.426 122.02 115.09 122.14 113.22 108.78 112.25 122.69 +** +* +* * +** 7 VAL 7 1.285 1.233 1.513 1.562 1.428 121.73 116.00 121.15 111.30 110.43 111.71 122.83 *** +* * *** 8 GLN 8 1.294 1.234 1.507 1.526 1.422 121.61 115.84 120.97 111.99 111.17 110.45 123.13 ** +* ** 9 PHE 9 1.297 1.235 1.512 1.546 1.438 121.93 116.82 120.11 110.73 108.16 109.43 123.07 ** * * ** 10 MET 10 1.297 1.243 1.502 1.553 1.443 121.83 116.03 120.64 110.07 109.80 112.57 123.30 ** * * * ** 11 LYS 11 1.301 1.248 1.516 1.564 1.430 121.60 118.22 119.67 110.38 108.77 112.90 122.10 +* +* * * * +* Residue-by-residue listing for refined_6 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 1.329 1.240 1.518 1.543 1.436 122.36 116.18 121.05 110.15 109.91 104.08 122.76 +* +* 13 PHE 13 1.288 1.237 1.514 1.542 1.431 121.45 115.68 121.20 112.68 110.02 111.42 123.08 +** * * +** 14 ILE 14 1.290 1.239 1.521 1.556 1.428 122.35 116.08 120.47 112.09 108.82 109.76 123.44 +** +* * * +** 15 SER 15 1.327 1.233 1.526 1.523 1.474 124.01 115.37 120.83 110.16 112.59 109.59 123.75 * * 16 GLU 16 1.299 1.224 1.523 1.515 1.440 124.00 116.48 120.99 111.42 110.09 107.75 122.53 ** * +* ** 17 LYS 17 1.320 1.236 1.494 1.541 1.452 120.11 115.17 120.81 109.73 110.88 114.60 123.92 * ** ** 18 SER 18 1.324 1.218 1.524 1.542 1.453 123.78 117.29 120.08 111.49 112.42 109.93 122.59 * * 19 SER 19 1.327 1.235 1.542 1.525 1.445 120.25 118.05 120.13 110.63 112.28 111.04 121.82 20 LYS 20 1.338 1.235 1.530 1.529 1.454 119.00 117.80 120.10 110.40 113.60 110.28 122.10 * * 21 SER 21 1.314 1.221 1.506 1.531 1.454 119.77 116.57 120.54 109.81 112.26 109.41 122.87 * * * 22 LEU 22 1.303 1.247 1.492 1.527 1.448 120.27 114.28 121.20 109.25 111.85 113.92 124.51 +* +* ** ** 23 GLU 23 1.303 1.245 1.531 1.549 1.424 123.28 116.24 121.11 112.20 107.89 109.69 122.55 +* +* * * +* 24 ILE 24 1.298 1.245 1.538 1.546 1.434 121.25 116.79 120.56 111.59 111.25 110.70 122.60 ** * * ** 25 PRO 25 1.354 1.242 1.538 1.530 1.476 123.78 114.90 121.68 109.77 114.04 103.33 123.39 * * 26 LEU 26 1.319 1.229 1.521 1.554 1.456 123.58 116.53 120.80 109.86 111.13 111.55 122.66 * * * 27 GLY 27 1.319 1.226 1.505 - 1.448 120.40 115.57 121.07 - 111.48 - 123.33 28 PHE 28 1.325 1.221 1.544 1.539 1.460 123.02 115.95 121.52 111.79 108.90 109.43 122.53 29 ASN 29 1.329 1.232 1.534 1.542 1.463 122.46 116.17 120.75 110.55 111.54 110.93 123.02 30 GLU 30 1.327 1.229 1.537 1.538 1.474 122.84 114.56 122.01 110.85 110.17 108.64 123.38 * * 31 TYR 31 1.294 1.229 1.546 1.538 1.444 124.13 116.79 121.05 112.45 110.82 106.78 122.15 ** * * * ** ** 32 PHE 32 1.325 1.235 1.531 1.536 1.459 120.97 117.62 120.22 110.70 111.40 112.04 122.15 33 PRO 33 1.361 1.243 1.522 1.545 1.471 122.92 114.91 121.44 109.49 112.51 103.42 123.65 * * * * 34 ALA 34 1.299 1.244 1.523 1.525 1.443 122.71 117.18 119.92 110.28 110.83 110.04 122.87 ** ** 35 PRO 35 1.355 1.238 1.525 1.527 1.473 123.61 116.42 121.05 109.87 111.65 103.09 122.53 36 PHE 36 1.311 1.224 1.520 1.510 1.400 122.12 117.40 120.85 111.07 110.68 110.42 121.65 * * *** *** 37 PRO 37 1.333 1.243 1.523 1.530 1.439 122.03 116.48 120.99 110.75 110.67 103.48 122.53 +* +* 38 ILE 38 1.298 1.232 1.514 1.556 1.433 120.68 117.04 120.97 110.69 110.14 112.36 121.99 ** * ** 39 THR 39 1.306 1.240 1.529 1.544 1.437 120.22 115.42 120.74 110.58 109.20 109.85 123.83 +* * +* 40 VAL 40 1.301 1.235 1.529 1.581 1.456 124.63 117.51 120.10 109.64 108.02 110.53 122.38 +* +* +* * +* 41 ASP 41 1.308 1.239 1.506 1.539 1.451 121.04 115.43 121.16 110.06 111.10 112.62 123.40 +* * +* Residue-by-residue listing for refined_6 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 1.306 1.240 1.505 1.541 1.437 122.50 115.59 120.83 108.85 108.95 111.25 123.57 +* * +* 43 LEU 43 1.293 1.210 1.508 1.554 1.426 122.51 115.92 120.67 110.27 108.07 112.25 123.41 +** * * +* * * +** 44 ASP 44 1.270 1.233 1.510 1.531 1.445 124.17 115.04 120.93 111.66 111.98 109.07 124.03 **** * **** 45 TYR 45 1.317 1.237 1.535 1.539 1.450 123.94 116.80 120.64 110.71 111.50 109.20 122.56 * * 46 SER 46 1.319 1.235 1.544 1.543 1.440 121.36 117.02 120.49 112.02 110.15 110.33 122.49 * * 47 GLY 47 1.321 1.229 1.523 - 1.450 120.58 117.30 120.38 - 113.90 - 122.32 48 ARG 48 1.313 1.233 1.517 1.539 1.464 121.56 116.03 121.00 107.97 111.11 113.10 122.93 * * +* +* 49 SER 49 1.299 1.232 1.524 1.540 1.431 121.29 116.15 120.73 111.84 109.37 110.55 123.10 ** * ** 50 TRP 50 1.307 1.237 1.511 1.525 1.426 123.20 116.23 120.47 109.02 109.65 108.74 123.27 +* +* * +* 51 THR 51 1.291 1.236 1.525 1.536 1.430 122.41 116.46 120.79 110.91 106.85 109.50 122.73 +** * +* * +** 52 VAL 52 1.308 1.231 1.520 1.556 1.440 121.13 115.54 121.31 109.79 111.82 110.35 123.15 +* +* 53 ARG 53 1.303 1.241 1.519 1.545 1.434 122.39 115.90 120.91 112.34 108.50 110.66 123.19 +* * * +* 54 MET 54 1.308 1.227 1.485 1.531 1.448 121.81 116.80 120.13 106.91 109.43 110.61 123.06 * +* +* +* 55 LYS 55 1.303 1.239 1.510 1.527 1.441 120.03 115.74 121.16 109.51 112.27 112.53 123.09 +* * +* 56 LYS 56 1.313 1.233 1.504 1.531 1.423 121.71 116.18 120.72 109.32 105.51 112.25 123.08 * * +* ** * ** 57 ARG 57 1.268 1.238 1.517 1.539 1.440 122.23 115.63 121.06 111.56 110.79 109.46 123.30 **** **** 58 GLY 58 1.312 1.226 1.498 - 1.432 121.10 115.79 120.81 - 111.81 - 123.38 * * * * 59 GLU 59 1.303 1.232 1.523 1.527 1.442 122.26 116.11 120.96 108.62 109.83 109.32 122.93 +* +* 60 LYS 60 1.316 1.229 1.523 1.534 1.438 121.92 116.76 120.93 111.74 111.50 110.38 122.30 * * 61 VAL 61 1.310 1.241 1.529 1.567 1.442 121.13 116.00 120.82 109.72 110.23 110.91 123.15 * * 62 PHE 62 1.317 1.240 1.506 1.536 1.448 122.81 116.14 120.87 109.82 109.60 112.66 122.97 * * 63 LEU 63 1.298 1.228 1.531 1.515 1.444 121.10 118.65 119.07 109.65 107.57 109.15 122.28 ** * * * ** 64 THR 64 1.330 1.238 1.556 1.549 1.458 119.52 117.10 120.88 110.97 116.16 111.78 122.02 * * +* +* 65 VAL 65 1.323 1.228 1.505 1.548 1.464 121.49 115.63 120.87 110.75 112.14 113.75 123.51 * * 66 GLY 66 1.310 1.226 1.486 - 1.433 121.45 114.56 121.47 - 109.19 - 123.93 * +* * * +* 67 TRP 67 1.321 1.223 1.499 1.548 1.434 123.35 116.05 121.23 109.66 108.86 111.32 122.68 * * * 68 GLU 68 1.310 1.205 1.545 1.532 1.422 119.36 116.70 121.07 113.80 109.62 112.45 122.10 * * +* * +* * +* 69 ASN 69 1.328 1.220 1.511 1.539 1.471 121.48 114.78 121.80 109.37 108.95 111.56 123.39 Residue-by-residue listing for refined_6 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 1.307 1.242 1.538 1.554 1.436 123.62 115.80 120.70 110.93 108.13 108.53 123.48 +* * * * * * +* 71 VAL 71 1.349 1.211 1.511 1.576 1.466 122.88 116.19 121.25 109.95 110.43 112.63 122.57 * * * 72 LYS 72 1.299 1.232 1.521 1.536 1.441 120.73 117.73 120.11 110.61 111.03 112.41 122.15 ** * ** 73 ASP 73 1.340 1.234 1.540 1.533 1.474 118.37 117.82 120.19 109.87 113.95 111.88 121.98 +* +* 74 ASN 74 1.318 1.234 1.521 1.542 1.483 120.49 116.55 120.10 110.89 113.14 112.61 123.35 * * * 75 ASN 75 1.334 1.226 1.522 1.533 1.507 124.48 115.24 120.90 110.37 111.92 112.72 123.85 +** +* * +** 76 LEU 76 1.307 1.250 1.514 1.534 1.478 123.97 115.97 121.26 111.15 114.27 112.86 122.77 +* * * * * +* 77 GLU 77 1.297 1.252 1.519 1.536 1.428 120.63 115.35 120.52 111.81 108.67 110.79 124.13 ** * +* ** 78 ASP 78 1.304 1.233 1.524 1.532 1.469 124.02 115.63 121.06 109.85 111.69 109.97 123.29 +* * +* 79 GLY 79 1.314 1.234 1.505 - 1.440 121.66 115.27 121.37 - 110.60 - 123.36 * * 80 LYS 80 1.307 1.243 1.524 1.535 1.448 122.82 117.20 120.24 112.01 109.72 110.85 122.55 +* * +* 81 TYR 81 1.316 1.236 1.514 1.542 1.457 121.69 117.32 119.81 109.36 108.95 110.90 122.88 82 LEU 82 1.317 1.240 1.507 1.531 1.452 120.95 115.31 120.73 108.48 111.58 111.87 123.93 83 GLN 83 1.307 1.228 1.508 1.529 1.436 123.13 115.83 120.75 109.60 106.43 109.85 123.40 +* * +* +* 84 PHE 84 1.288 1.232 1.516 1.539 1.435 122.36 116.56 120.02 111.21 109.53 108.09 123.41 +** * * +** 85 ILE 85 1.317 1.237 1.518 1.558 1.448 121.95 115.87 120.83 108.59 108.84 111.91 123.30 86 TYR 86 1.298 1.236 1.520 1.548 1.438 122.79 117.02 120.14 110.06 109.06 107.40 122.83 ** * +* ** 87 ASP 87 1.314 1.233 1.521 1.575 1.444 120.11 117.65 120.05 113.86 110.00 114.68 122.23 * ** +* ** ** 88 ARG 88 1.309 1.231 1.543 1.543 1.435 120.91 116.85 120.67 110.16 109.83 110.24 122.47 * * * 89 ASP 89 1.333 1.234 1.548 1.567 1.438 122.80 116.21 120.78 112.34 109.02 108.21 123.01 * +* * * * +* 90 ARG 90 1.292 1.225 1.541 1.540 1.447 124.67 115.52 121.93 111.40 109.24 107.65 122.54 +** +* +* +** 91 THR 91 1.300 1.230 1.515 1.547 1.435 122.13 117.08 120.28 111.37 109.17 110.95 122.60 ** * * ** 92 PHE 92 1.317 1.225 1.494 1.522 1.449 120.24 115.95 120.58 109.94 110.97 110.66 123.47 * * 93 TYR 93 1.305 1.235 1.507 1.536 1.442 122.08 116.33 120.71 110.15 109.80 110.75 122.95 +* +* 94 VAL 94 1.295 1.240 1.537 1.564 1.438 121.34 116.01 121.27 111.29 110.69 111.72 122.66 ** * ** 95 ILE 95 1.309 1.238 1.524 1.560 1.441 121.88 116.35 120.61 109.85 108.27 111.88 123.02 * * * 96 ILE 96 1.304 1.239 1.519 1.592 1.450 122.02 116.47 120.70 108.84 109.28 112.53 122.78 +* +* +* 97 TYR 97 1.307 1.235 1.507 1.524 1.437 121.01 115.92 120.47 109.85 107.72 111.70 123.61 +* * * +* 98 GLY 98 1.298 1.236 1.503 - 1.429 121.06 116.06 120.80 - 109.96 - 123.12 ** * ** Residue-by-residue listing for refined_6 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 1.308 1.233 1.512 1.547 1.442 122.07 115.98 120.66 110.69 110.05 110.87 123.33 +* +* 100 ASN 100 1.303 1.235 1.514 1.541 1.441 121.24 116.78 120.02 111.03 106.91 110.84 123.16 +* +* +* 101 MET 101 1.300 1.230 1.515 1.526 1.444 122.17 115.03 120.58 110.63 111.63 110.29 124.39 ** ** 102 CYS 102 1.330 - 1.530 1.539 1.462 124.84 - - 112.10 111.79 111.82 - +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +* ** *** +* * * +* ** ** * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_6 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 1.268 1.349 1.308 .014 **** * * C-N (Pro) 1.341 .016 5 1.329 1.361 1.346 .013 * C-O C-O 1.231 .020 101 1.205 1.252 1.234 .008 * * CA-C CH1E-C (except Gly) 1.525 .021 95 1.485 1.556 1.520 .014 +* * CH2G*-C (Gly) 1.516 .018 7 1.486 1.523 1.502 .011 +* CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.523 1.525 1.524 .001 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.536 1.592 1.558 .014 +* CH1E-CH2E (the rest) 1.530 .020 75 1.510 1.575 1.537 .011 * ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.400 1.507 1.445 .016 *** +** NH1-CH2G* (Gly) 1.451 .016 7 1.413 1.450 1.435 .012 ** N-CH1E (Pro) 1.466 .015 5 1.436 1.476 1.459 .018 +* ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_6 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 89 114.28 118.65 116.29 .84 * CH2G*-C-NH1 (Gly) 116.4 2.1 7 114.56 117.30 115.83 .79 CH1E-C-N (Pro) 116.9 1.5 5 114.90 116.48 115.78 .72 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 121.65 124.51 122.98 .57 O-C-N (Pro) 122.0 1.4 5 122.53 123.65 122.97 .46 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.37 124.84 121.96 1.36 +* +* C-NH1-CH2G* (Gly) 120.6 1.7 7 120.40 121.66 120.97 .45 C-N-CH1E (Pro) 122.6 5.0 5 122.03 123.78 122.94 .68 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 119.07 122.14 120.76 .51 * CH2G*-C-O (Gly) 120.8 2.1 7 120.38 121.47 120.92 .37 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 109.87 110.28 110.08 .20 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.59 112.09 110.44 .92 * CH2E-CH1E-C (the rest) 110.1 1.9 75 106.91 113.86 110.59 1.26 +* +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.51 116.16 110.14 1.78 ** +* NH1-CH2G*-C (Gly) 112.5 2.9 7 109.19 113.90 111.09 1.41 * N-CH1E-C (Pro) 111.8 2.5 5 109.91 114.04 111.76 1.44 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 110.04 110.42 110.23 .19 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.50 113.75 111.31 1.10 * * N-CH1E-CH2E (Pro) 103.0 1.1 5 103.09 104.08 103.48 .33 NH1-CH1E-CH2E (the rest) 110.5 1.7 70 106.78 114.68 110.80 1.68 ** ** ------------------------------------------------------------------------------------------------------------- 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_6 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] 76 86.4% Residues in additional allowed regions [a,b,l,p] 11 12.5% 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 86.4 83.8 10.0 .3 Inside b. Omega angle st dev 101 3.4 6.0 3.0 -.9 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 1.8 3.1 1.6 -.8 Inside e. H-bond energy st dev 61 1.0 .8 .2 .8 Inside f. Overall G-factor 102 -.1 -.4 .3 1.1 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 14 6.2 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 34 8.6 19.0 5.3 -2.0 BETTER c. Chi-1 gauche plus st dev 40 6.1 17.5 4.9 -2.3 BETTER d. Chi-1 pooled st dev 88 8.4 18.2 4.8 -2.0 BETTER e. Chi-2 trans st dev 25 3.0 20.4 5.0 -3.5 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% 86.4 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.0 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .98 3 Residue-by-residue listing for refined_6 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.59 Chi1-chi2 distribution -.26 Chi1 only .05 Chi3 & chi4 .38 Omega -.01 ------ -.19 ===== Main-chain covalent forces:- Main-chain bond lengths -.08 Main-chain bond angles .42 ------ .21 ===== OVERALL AVERAGE -.05 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.