Residue-by-residue listing for refined_9 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 GLU 1 - - 187.4 - - - - - - - - 182.8 - 33.2 - 2 ALA 2 B - - - - - - - - - - 180.8 - 34.6 - 3 GLU 3 t b - - -57.0 172.4 - - - - - - 170.3 - 37.4 - +* +* 4 VAL 4 T B - 177.9 - - - - - - - - 187.6 - 33.9 - * * 5 HIS 5 T l - - -60.5 - - - - - - - 173.0 - 30.3 - * * * 6 ASN 6 t B - - -60.0 - - - - - - - 186.2 -1.2 34.3 - * * * 7 GLN 7 e ~a - - -60.2 - - - - - - - 179.5 -.5 31.1 - ** ** ** 8 LEU 8 E B - - -66.0 - - - - - - - 173.1 -1.5 34.6 - * * 9 GLU 9 E B - - -60.8 188.3 - - - - - - 179.1 -2.8 34.1 - 10 ILE 10 E B - - -56.2 176.6 - - - - - - 172.3 -2.8 34.6 - * * * 11 LYS 11 E B 67.9 - - 171.5 - - - - - - 185.2 -2.2 31.7 - 12 PHE 12 E B - - -53.6 - - - - - - - 177.8 -1.2 35.2 - * * 13 ARG 13 E B - 177.4 - 181.4 - - - - - - 177.9 -2.5 33.3 - 14 LEU 14 e B - - -66.5 - - - - - - - 182.2 -3.4 34.8 - +* +* 15 THR 15 T A 53.2 - - - - - - - - - 179.3 - 34.0 - 16 ASP 16 T A - - -57.0 - - - - - - - 181.5 - 35.1 - 17 GLY 17 t - - - - - - - - - - - 179.1 -2.0 - - 18 SER 18 e B - - -48.7 - - - - - - - 179.1 - 36.9 - * * Residue-by-residue listing for refined_9 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 ASP 19 E B 63.1 - - - - - - - - - 175.4 - 33.9 - 20 ILE 20 E B - - -56.3 178.7 - - - - - - 184.4 -2.7 35.0 - 21 GLY 21 E - - - - - - - - - - - 180.9 - - - 22 PRO 22 E - - - - - -79.3 - - - - - 177.8 - 38.6 - * * * 23 LYS 23 E B - - -66.6 176.5 - - - - - - 180.6 -2.0 33.7 - 24 ALA 24 E B - - - - - - - - - - 178.1 - 33.2 - 25 PHE 25 E B - - -58.7 - - - - - - - 174.7 -3.9 35.7 - +** +** 26 PRO 26 t - - - - - -66.8 - - - - - 175.4 - 39.3 - +* +* 27 ASP 27 T A - - -62.9 - - - - - - - 182.3 - 36.4 - 28 ALA 28 T A - - - - - - - - - - 177.3 - 33.8 - 29 THR 29 t B - - -62.8 - - - - - - - 181.7 -2.3 33.5 - 30 THR 30 h B 56.2 - - - - - - - - - 176.6 - 33.7 - 31 VAL 31 H A - 179.0 - - - -66.8 -26.0 - - - 172.9 -3.0 32.8 - * * * * 32 SER 32 H A - - -60.9 - - -64.9 -46.6 - - - 178.6 -1.4 33.5 - 33 ALA 33 H A - - - - - -68.2 -25.8 - - - 175.1 - 33.3 - * * 34 LEU 34 H A - 174.3 - - - -65.2 -46.1 - - - 175.4 -1.7 35.8 - 35 LYS 35 H A - - -70.1 175.8 - -67.1 -36.8 - - - 175.1 -2.1 32.2 - 36 GLU 36 H A - - -63.6 - - -57.2 -41.8 - - - 178.9 -2.4 35.1 - 37 THR 37 H A - - -56.8 - - -61.3 -39.6 - - - 177.9 -2.1 34.4 - 38 VAL 38 H A - 180.4 - - - -62.1 -49.5 - - - 180.5 -1.4 34.4 - 39 ILE 39 H A - - -55.3 178.0 - -56.9 -38.8 - - - 181.4 -2.5 35.5 - 40 SER 40 H A - 176.6 - - - -64.6 -40.2 - - - 185.3 -2.2 34.5 - 41 GLU 41 H A - - -56.5 - - -93.6 -18.9 - - - 179.7 -1.6 35.1 - ** +* ** 42 TRP 42 h B - 195.7 - - - - - - - - 179.4 -2.3 36.0 - 43 PRO 43 t - - - - - -47.4 - - - - - 183.0 - 39.2 - +* +* +* 44 ARG 44 T A 65.2 - - 177.8 - - - - - - 185.2 - 35.1 - 45 GLU 45 T A - 188.8 - 179.2 - - - - - - 182.7 - 35.4 - 46 LYS 46 t B 82.1 - - - - - - - - - 174.7 -1.0 35.1 - * * * 47 GLU 47 S B - - -61.8 184.2 - - - - - - 185.4 - 31.2 - 48 ASN 48 S l - - -67.1 - - - - - - - 182.4 - 32.3 - 49 GLY 49 S - - - - - - - - - - - 177.7 - - - 50 PRO 50 - - - - - -43.7 - - - - - 177.4 - 40.9 - +* ** ** 51 LYS 51 a - 180.5 - 186.1 - - - - - - 189.7 - 34.7 - +* +* 52 THR 52 t B 60.6 - - - - - - - - - 177.1 - 32.5 - 53 VAL 53 T A - 177.4 - - - - - - - - 185.2 - 37.4 - * * 54 LYS 54 T A - 184.5 - 182.9 - - - - - - 183.1 - 35.3 - 55 GLU 55 e A - - -64.4 - - - - - - - 186.2 -2.1 34.2 - * * 56 VAL 56 E B - 179.4 - - - - - - - - 171.7 -.6 35.4 - * +* +* 57 LYS 57 E B - - -68.6 188.3 - - - - - - 178.7 -2.1 33.3 - 58 LEU 58 E B - - -66.0 - - - - - - - 177.8 - 33.5 - 59 ILE 59 E B - - -69.8 - - - - - - - 175.3 -2.5 34.1 - 60 SER 60 E B 55.9 - - - - - - - - - 180.6 -2.7 33.8 - 61 ALA 61 T l - - - - - - - - - - 181.8 - 32.6 - 62 GLY 62 T - - - - - - - - - - - 181.2 - - - Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 63 LYS 63 E B - 182.7 - 180.6 - - - - - - 180.8 -1.6 34.5 - 64 VAL 64 E B - 184.0 - - - - - - - - 177.1 - 35.6 - 65 LEU 65 e B - - -66.9 - - - - - - - 174.1 -2.8 34.5 - * * * 66 GLU 66 t B - 178.7 - 186.4 - - - - - - 183.5 -.5 35.5 - +* +* 67 ASN 67 T A 63.6 - - - - - - - - - 181.8 - 30.8 - 68 SER 68 T A - - -56.7 - - - - - - - 174.5 - 32.9 - 69 LYS 69 t B - - -69.3 - - - - - - - 178.1 -1.9 34.3 - 70 THR 70 h B - - -40.3 - - - - - - - 179.4 - 36.2 - +* +* 71 VAL 71 H A - 175.7 - - - -63.1 -38.0 - - - 179.1 -2.8 32.8 - * * 72 LYS 72 H A - 189.2 - 175.9 - -62.4 -34.0 - - - 180.6 -2.6 34.7 - 73 ASP 73 H A - - -67.3 - - -74.9 -34.0 - - - 184.8 - 35.3 - 74 TYR 74 H A - 187.5 - - - -76.3 -34.2 - - - 182.0 -1.8 33.6 - 75 ARG 75 h B - - -56.8 201.9 - - - - - - 178.8 -2.0 33.6 - * * 76 SER 76 B 49.0 - - - - - - - - - 178.8 - 35.2 - 77 PRO 77 S - - - - - -47.2 - - - - - 184.8 - 39.2 - +* +* +* 78 VAL 78 S l 61.0 - - - - - - - - - 182.0 - 25.3 - ** ** 79 SER 79 b - 182.8 - - - - - - - - 182.7 - 35.7 - 80 ASN 80 B 61.8 - - - - - - - - - 180.8 - 32.4 - 81 LEU 81 B 64.4 - - 174.8 - - - - - - 181.6 - 34.5 - 82 ALA 82 S ~b - - - - - - - - - - 187.4 -1.0 35.3 - ** * * ** 83 GLY 83 S - - - - - - - - - - - 184.5 -1.9 - - 84 ALA 84 E B - - - - - - - - - - 181.0 -1.8 34.2 - 85 VAL 85 E B - 183.7 - - - - - - - - 180.0 - 33.9 - 86 THR 86 E B - - -52.1 - - - - - - - 179.9 -3.5 36.0 - ** ** 87 THR 87 E B - - -54.3 - - - - - - - 179.8 - 34.6 - 88 MET 88 E B - - -64.5 180.9 - - - - - - 182.0 -2.6 31.8 - 89 HIS 89 E B - - -58.9 - - - - - - - 184.4 -3.0 34.3 - * * 90 VAL 90 E B - 182.8 - - - - - - - - 176.3 -3.4 33.8 - +* +* 91 ILE 91 E B - - -72.2 - - - - - - - 183.7 -2.5 33.6 - 92 ILE 92 E B - - -66.5 - - - - - - - 172.6 -.6 34.0 - * +* +* 93 GLN 93 e B - - -60.2 - - - - - - - 184.6 -2.6 35.2 - 94 ALA 94 B - - - - - - - - - - 184.5 -.6 34.2 - +* +* 95 PRO 95 - - - - - -78.3 - - - - - 176.4 - 38.7 - * * * 96 VAL 96 B - 181.1 - - - - - - - - 179.1 - 35.0 - 97 THR 97 b - 180.6 - - - - - - - - 180.6 -.6 30.1 - +* * +* 98 GLU 98 S B - 183.8 - 174.4 - - - - - - 192.1 -.8 33.8 - ** +* ** 99 LYS 99 S l - 185.5 - 182.9 - - - - - - 184.9 - 31.5 - 100 GLU 100 B - 185.7 - 182.2 - - - - - - 177.8 - 35.4 - 101 LYS 101 - - 189.6 - - - - - - - - - - 35.3 - ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * +* * +* ** +* ** +** ** +** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 61.8 182.6 -61.0 180.7 -60.4 -67.0 -36.7 - - - 180.1 -2.0 34.4 Standard deviations: 8.1 4.9 6.4 6.5 16.4 9.1 8.3 - - - 4.1 .8 2.1 Numbers of values: 13 28 41 24 6 15 15 0 0 0 100 52 96 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_9 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 GLU 1 - 1.237 1.520 1.559 1.446 - 115.54 121.13 114.08 107.60 109.41 123.20 * ** * ** 2 ALA 2 1.329 1.236 1.517 1.523 1.444 122.69 116.01 120.40 110.13 109.78 110.33 123.59 3 GLU 3 1.313 1.241 1.512 1.532 1.433 124.67 116.30 120.65 107.53 107.44 109.47 123.05 * * +* * * +* 4 VAL 4 1.308 1.235 1.536 1.561 1.443 121.14 117.06 119.51 111.40 106.66 111.38 123.42 +* * +* +* 5 HIS 5 1.338 1.229 1.520 1.530 1.470 125.00 115.81 121.41 111.78 110.73 114.25 122.78 +* ** ** 6 ASN 6 1.316 1.244 1.504 1.537 1.441 122.21 116.42 120.26 110.01 106.30 112.13 123.30 * +* +* 7 GLN 7 1.306 1.248 1.507 1.545 1.437 122.16 115.86 121.21 111.96 113.49 112.14 122.94 +* * +* 8 LEU 8 1.281 1.199 1.500 1.533 1.442 121.07 117.33 120.20 107.97 111.22 112.14 122.46 *** +* * * *** 9 GLU 9 1.297 1.221 1.483 1.514 1.423 120.62 116.99 120.24 107.87 107.64 114.04 122.77 ** ** +* * * ** ** 10 ILE 10 1.274 1.238 1.495 1.555 1.429 120.59 115.80 120.52 108.93 109.36 112.14 123.64 +*** * +* +*** 11 LYS 11 1.298 1.248 1.502 1.546 1.434 120.50 116.68 120.26 110.64 107.84 114.93 123.05 ** * * * +** +** Residue-by-residue listing for refined_9 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 PHE 12 1.291 1.223 1.504 1.530 1.434 120.73 116.92 120.19 110.06 110.06 109.61 122.88 +** * * +** 13 ARG 13 1.308 1.227 1.519 1.539 1.446 121.19 115.89 120.62 110.57 110.53 111.60 123.47 +* +* 14 LEU 14 1.310 1.236 1.520 1.553 1.449 123.03 116.73 120.24 108.99 109.13 111.62 122.98 * * * 15 THR 15 1.320 1.237 1.539 1.538 1.459 122.62 115.90 121.48 110.22 112.30 110.16 122.61 16 ASP 16 1.322 1.228 1.518 1.534 1.467 122.37 116.18 120.98 108.34 110.38 111.07 122.83 17 GLY 17 1.321 1.227 1.504 - 1.442 121.07 115.34 121.12 - 110.94 - 123.55 18 SER 18 1.313 1.229 1.520 1.522 1.432 123.04 117.59 119.87 109.38 108.36 107.98 122.53 * * * * * 19 ASP 19 1.299 1.238 1.497 1.524 1.427 120.70 114.55 121.29 109.44 111.15 111.82 124.13 ** * +* ** 20 ILE 20 1.296 1.242 1.522 1.560 1.430 123.78 116.40 119.37 110.04 106.46 111.27 124.22 ** * * +* ** 21 GLY 21 1.326 1.242 1.524 - 1.453 123.20 118.00 120.18 - 114.32 - 121.82 +* +* 22 PRO 22 1.344 1.237 1.519 1.544 1.440 122.39 115.65 121.21 109.86 111.86 104.50 123.14 +* * +* 23 LYS 23 1.296 1.217 1.465 1.532 1.450 122.40 116.31 120.05 109.65 108.74 112.80 123.64 ** +** * +** 24 ALA 24 1.275 1.232 1.506 1.523 1.445 120.44 115.52 121.08 110.59 110.37 111.62 123.41 +*** +*** 25 PHE 25 1.295 1.237 1.507 1.534 1.420 123.04 116.67 120.94 108.76 107.86 110.91 122.29 ** ** * ** 26 PRO 26 1.301 1.231 1.532 1.525 1.451 123.15 116.00 120.74 109.07 112.60 103.82 123.24 +** * +** 27 ASP 27 1.331 1.229 1.520 1.523 1.476 123.57 116.35 120.51 106.18 111.38 110.90 123.13 * ** ** 28 ALA 28 1.331 1.226 1.525 1.521 1.452 122.17 116.90 120.60 110.36 111.70 110.40 122.50 29 THR 29 1.311 1.234 1.530 1.551 1.440 121.34 116.99 120.66 111.71 109.25 110.67 122.29 * * * 30 THR 30 1.306 1.231 1.509 1.538 1.425 120.47 116.10 120.73 109.96 111.39 111.57 123.17 +* +* +* 31 VAL 31 1.311 1.231 1.548 1.546 1.445 121.99 116.34 121.35 112.23 109.29 111.06 122.31 * * * * 32 SER 32 1.333 1.216 1.530 1.537 1.449 121.14 116.49 120.39 110.84 109.04 111.38 123.02 33 ALA 33 1.344 1.235 1.532 1.516 1.465 122.18 115.77 121.15 110.97 110.85 110.64 123.08 * * 34 LEU 34 1.321 1.231 1.535 1.531 1.418 123.68 115.61 121.18 112.04 108.27 107.25 123.16 ** * * * +* ** 35 LYS 35 1.330 1.225 1.529 1.536 1.449 122.19 116.69 120.16 112.42 111.25 110.94 123.14 * * 36 GLU 36 1.336 1.235 1.532 1.532 1.467 122.47 115.66 121.19 108.49 110.02 110.99 123.14 37 THR 37 1.330 1.238 1.541 1.552 1.454 122.52 115.87 120.98 109.88 110.17 110.79 123.13 38 VAL 38 1.331 1.221 1.526 1.560 1.457 122.07 115.66 120.48 109.21 109.24 112.00 123.80 39 ILE 39 1.335 1.232 1.532 1.562 1.479 123.40 115.60 121.19 108.35 110.43 110.73 123.20 * * 40 SER 40 1.318 1.240 1.531 1.538 1.443 122.46 117.09 120.28 110.00 112.86 109.64 122.62 41 GLU 41 1.316 1.236 1.524 1.510 1.426 121.41 115.81 120.98 110.78 111.75 108.25 123.21 * +* * +* 42 TRP 42 1.311 1.247 1.529 1.540 1.443 122.61 118.06 119.37 110.35 107.70 108.70 122.51 * * * * 43 PRO 43 1.356 1.210 1.525 1.530 1.471 123.09 116.77 120.51 110.21 111.55 102.81 122.72 * * Residue-by-residue listing for refined_9 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 ARG 44 1.318 1.228 1.527 1.544 1.466 121.96 114.81 121.77 109.13 110.09 110.45 123.42 45 GLU 45 1.304 1.233 1.540 1.525 1.439 123.82 116.02 120.87 111.85 110.85 106.98 123.11 +* * ** ** 46 LYS 46 1.334 1.248 1.536 1.557 1.442 123.44 116.56 121.02 109.99 110.86 109.71 122.39 * * 47 GLU 47 1.293 1.245 1.488 1.509 1.400 121.05 114.62 120.68 112.30 109.27 113.38 124.67 +** +* * *** * +* * *** 48 ASN 48 1.309 1.229 1.519 1.543 1.474 123.85 115.98 121.38 110.84 110.85 112.51 122.58 * * * * 49 GLY 49 1.312 1.239 1.500 - 1.417 120.69 117.22 119.54 - 111.82 - 123.22 * ** ** 50 PRO 50 1.351 1.227 1.524 1.516 1.482 125.02 116.12 121.24 108.36 114.31 101.58 122.64 * * * * 51 LYS 51 1.305 1.212 1.506 1.542 1.435 120.77 116.22 120.88 108.52 110.60 111.79 122.89 +* * +* 52 THR 52 1.305 1.232 1.526 1.537 1.422 120.81 113.44 121.86 109.93 114.68 111.83 124.69 +* +* * * * +* 53 VAL 53 1.329 1.231 1.540 1.576 1.475 127.72 115.97 121.20 108.11 111.06 108.15 122.82 * *** +* *** 54 LYS 54 1.315 1.235 1.530 1.528 1.431 122.99 116.19 120.92 111.27 110.42 108.08 122.84 * * * * 55 GLU 55 1.324 1.238 1.523 1.540 1.461 121.19 116.71 120.51 108.22 112.19 112.04 122.78 56 VAL 56 1.307 1.229 1.528 1.565 1.452 121.41 116.87 120.41 108.92 111.69 110.12 122.69 +* +* 57 LYS 57 1.322 1.236 1.516 1.520 1.441 121.78 116.19 120.46 109.22 110.50 112.77 123.36 * * 58 LEU 58 1.317 1.240 1.513 1.557 1.454 122.19 116.00 120.45 109.74 109.63 112.71 123.46 * * * 59 ILE 59 1.315 1.243 1.531 1.582 1.445 122.98 115.88 120.75 109.72 110.14 111.82 123.36 * +* +* 60 SER 60 1.310 1.233 1.519 1.528 1.432 123.00 116.42 119.81 111.22 108.79 110.74 123.66 * * * 61 ALA 61 1.332 1.244 1.529 1.533 1.477 124.15 115.31 121.47 111.34 111.03 111.38 123.15 * * * 62 GLY 62 1.317 1.230 1.513 - 1.436 121.67 116.62 120.73 - 111.93 - 122.65 63 LYS 63 1.314 1.241 1.524 1.537 1.438 121.65 116.10 120.63 111.01 109.57 109.72 123.27 * * * 64 VAL 64 1.314 1.235 1.525 1.563 1.450 122.34 117.05 120.30 108.34 109.04 111.20 122.63 * * 65 LEU 65 1.308 1.239 1.512 1.535 1.431 121.18 116.54 120.30 108.45 110.23 112.15 123.15 * * * 66 GLU 66 1.314 1.231 1.521 1.530 1.444 121.30 117.92 119.74 109.30 107.46 110.48 122.34 * * * 67 ASN 67 1.327 1.229 1.520 1.551 1.463 120.37 116.33 120.67 111.18 112.24 113.77 122.96 * +* +* 68 SER 68 1.308 1.232 1.541 1.517 1.441 122.19 116.91 120.76 112.20 112.61 109.53 122.33 * * * 69 LYS 69 1.315 1.245 1.519 1.526 1.431 121.66 115.92 120.97 109.95 109.70 111.07 123.11 * * * 70 THR 70 1.299 1.247 1.529 1.538 1.432 121.68 118.38 119.21 109.31 106.60 109.77 122.40 ** * * +* * ** 71 VAL 71 1.328 1.228 1.530 1.566 1.463 120.23 115.40 121.29 110.98 109.35 112.42 123.24 72 LYS 72 1.320 1.226 1.541 1.533 1.453 122.86 116.93 120.52 110.27 111.07 109.61 122.54 73 ASP 73 1.332 1.222 1.489 1.523 1.446 121.75 115.86 120.76 107.26 111.22 111.85 123.38 +* * +* Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 74 TYR 74 1.304 1.235 1.525 1.535 1.434 121.47 117.16 120.21 111.33 111.39 110.18 122.63 +* * +* 75 ARG 75 1.331 1.243 1.519 1.515 1.412 121.18 115.12 121.47 109.87 111.74 111.37 123.41 ** ** 76 SER 76 1.291 1.242 1.547 1.524 1.419 123.03 117.56 119.68 112.01 110.26 107.36 122.73 +** * ** * +* +** 77 PRO 77 1.368 1.237 1.538 1.523 1.484 124.38 115.17 120.91 109.65 113.98 102.76 123.89 +* * * * +* 78 VAL 78 1.328 1.242 1.518 1.567 1.465 124.89 112.47 123.23 114.61 113.17 116.61 124.22 * +* +* * +** *** *** 79 SER 79 1.286 1.231 1.518 1.548 1.435 125.15 117.50 120.17 109.96 106.78 109.95 122.33 *** * +* +* *** 80 ASN 80 1.303 1.246 1.515 1.550 1.452 120.34 115.34 121.09 111.25 111.83 111.78 123.54 +* +* 81 LEU 81 1.316 1.243 1.507 1.519 1.392 124.36 113.22 121.76 109.29 113.25 110.51 125.00 *** * * * *** 82 ALA 82 1.309 1.235 1.519 1.534 1.464 125.85 115.71 121.13 109.15 107.48 110.80 123.11 * ** * ** 83 GLY 83 1.333 1.223 1.508 - 1.439 120.47 115.74 121.09 - 109.93 - 123.17 84 ALA 84 1.314 1.224 1.512 1.513 1.447 121.85 116.65 120.50 110.66 110.71 109.90 122.84 * * 85 VAL 85 1.309 1.230 1.518 1.553 1.445 121.11 115.47 121.25 109.27 110.00 112.35 123.28 * * 86 THR 86 1.288 1.238 1.524 1.544 1.422 123.53 117.11 120.54 109.61 107.84 109.56 122.33 +** +* * * * +** 87 THR 87 1.292 1.227 1.512 1.533 1.421 120.71 116.59 120.76 110.37 109.25 110.49 122.63 +** +* +** 88 MET 88 1.300 1.239 1.494 1.527 1.431 120.49 115.19 121.16 112.27 110.72 111.99 123.62 ** * * * ** 89 HIS 89 1.301 1.237 1.495 1.536 1.437 122.00 116.11 120.30 110.80 108.07 110.92 123.58 +* * * * +* 90 VAL 90 1.292 1.236 1.496 1.551 1.429 121.95 114.13 121.74 109.97 110.71 111.80 124.12 +** * +* * +** 91 ILE 91 1.277 1.244 1.504 1.541 1.417 123.51 114.66 121.27 112.43 108.45 110.32 124.03 +*** * ** * +* +*** 92 ILE 92 1.298 1.243 1.514 1.582 1.421 122.63 115.38 121.24 109.59 110.84 112.21 123.35 ** +* +* ** 93 GLN 93 1.299 1.234 1.488 1.527 1.401 122.63 115.88 120.07 110.08 105.56 111.06 124.06 ** +* *** ** *** 94 ALA 94 1.290 1.231 1.522 1.524 1.461 122.62 116.88 120.90 110.33 110.45 110.27 122.22 +** +** 95 PRO 95 1.333 1.243 1.511 1.524 1.442 122.45 115.19 121.70 110.32 112.78 103.49 123.11 +* * +* 96 VAL 96 1.283 1.229 1.497 1.546 1.423 122.04 117.22 120.21 109.36 107.21 111.76 122.55 *** * +* * *** 97 THR 97 1.287 1.239 1.510 1.577 1.406 120.29 113.79 122.73 114.15 108.88 113.77 123.26 +** * +** * * ** * +** 98 GLU 98 1.299 1.243 1.515 1.510 1.418 122.40 115.25 120.38 113.68 108.01 108.43 124.37 ** ** +* * * ** 99 LYS 99 1.323 1.235 1.524 1.546 1.446 123.82 114.57 121.97 111.79 107.12 114.27 123.28 * * ** ** 100 GLU 100 1.303 1.238 1.516 1.538 1.435 123.17 116.19 120.64 110.69 109.64 108.88 123.14 +* * +* 101 LYS 101 1.293 - 1.524 1.528 1.420 122.26 - - 111.19 107.99 108.82 - +** +* * +** Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** +* +** +* *** *** +* * +** ** *** * +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 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 94 1.274 1.344 1.311 .016 +*** * * C-N (Pro) 1.341 .016 6 1.301 1.368 1.342 .021 +** +* C-O C-O 1.231 .020 100 1.199 1.248 1.234 .009 +* CA-C CH1E-C (except Gly) 1.525 .021 96 1.465 1.548 1.519 .015 +** * CH2G*-C (Gly) 1.516 .018 5 1.500 1.524 1.510 .008 CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.513 1.534 1.523 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.533 1.582 1.556 .014 +* CH1E-CH2E (the rest) 1.530 .020 62 1.509 1.559 1.533 .012 * * N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.392 1.479 1.441 .018 *** * NH1-CH2G* (Gly) 1.451 .016 5 1.417 1.453 1.437 .012 ** N-CH1E (Pro) 1.466 .015 6 1.440 1.484 1.462 .018 +* * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 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 89 112.47 118.38 116.08 1.01 +* * CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.34 118.00 116.58 .97 CH1E-C-N (Pro) 116.9 1.5 6 115.17 116.77 115.82 .56 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.82 125.00 123.13 .59 * O-C-N (Pro) 122.0 1.4 6 122.64 123.89 123.12 .41 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 120.23 127.72 122.28 1.37 *** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.47 123.20 121.42 .98 +* C-N-CH1E (Pro) 122.6 5.0 6 122.39 125.02 123.41 .97 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.21 123.23 120.77 .66 * CH2G*-C-O (Gly) 120.8 2.1 5 119.54 121.12 120.53 .60 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 109.15 111.34 110.44 .61 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.11 114.61 110.25 1.61 +** CH2E-CH1E-C (the rest) 110.1 1.9 62 106.18 114.08 110.19 1.53 ** ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.56 114.68 109.86 1.81 ** * NH1-CH2G*-C (Gly) 112.5 2.9 5 109.93 114.32 111.79 1.46 N-CH1E-C (Pro) 111.8 2.5 6 111.55 114.31 112.85 1.01 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 109.90 111.62 110.67 .54 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 108.15 116.61 111.38 1.52 +* *** N-CH1E-CH2E (Pro) 103.0 1.1 6 101.58 104.50 103.16 .92 * * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 106.98 114.93 110.87 1.84 ** +** ------------------------------------------------------------------------------------------------------------- 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_9 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] 9 10.2% Residues in generously allowed regions [~a,~b,~l,~p] 2 2.3% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 88 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 5 Number of proline residues 6 ---- Total number of residues 101 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 100 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 96 2.1 3.1 1.6 -.6 Inside e. H-bond energy st dev 52 .8 .8 .2 .1 Inside f. Overall G-factor 101 .0 -.4 .3 1.2 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 13 8.1 18.1 6.5 -1.5 BETTER b. Chi-1 trans st dev 28 4.9 19.0 5.3 -2.7 BETTER c. Chi-1 gauche plus st dev 41 6.4 17.5 4.9 -2.3 BETTER d. Chi-1 pooled st dev 82 7.4 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 24 6.5 20.4 5.0 -2.8 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 8.6 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .84 2 Residue-by-residue listing for refined_9 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.48 Chi1-chi2 distribution -.07 Chi1 only .17 Chi3 & chi4 .22 Omega -.11 ------ -.15 ===== Main-chain covalent forces:- Main-chain bond lengths -.10 Main-chain bond angles .36 ------ .16 ===== OVERALL AVERAGE -.04 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.