Residue-by-residue listing for refined_11 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 - - 181.9 - 175.6 - - - - - - 178.5 - 33.6 - 2 ALA 2 B - - - - - - - - - - 178.1 - 34.8 - 3 GLU 3 B - - -67.9 - - - - - - - 179.6 - 31.6 - 4 VAL 4 B - 179.4 - - - - - - - - 179.5 -1.1 36.0 - * * 5 HIS 5 b - 184.1 - - - - - - - - 176.8 - 32.5 - 6 ASN 6 B - - -59.0 - - - - - - - 182.7 -1.9 33.8 - 7 GLN 7 S a - - -57.8 - - - - - - - 170.3 -.8 33.2 - +* +* +* 8 LEU 8 E B - 183.8 - - - - - - - - 174.7 -1.5 33.0 - 9 GLU 9 E B - - -60.7 193.9 - - - - - - 182.9 -1.5 31.0 - 10 ILE 10 E B - - -60.2 177.7 - - - - - - 171.9 -2.5 35.8 - * * 11 LYS 11 E B 60.9 - - 177.6 - - - - - - 183.6 -2.6 33.4 - 12 PHE 12 E B - - -59.1 - - - - - - - 178.9 -.5 35.7 - ** ** 13 ARG 13 E B - 188.8 - 172.2 - - - - - - 183.9 -2.5 32.7 - 14 LEU 14 E B - - -61.5 178.6 - - - - - - 176.0 -3.1 35.4 - * * 15 THR 15 e A - 187.5 - - - - - - - - 179.2 -1.9 34.9 - 16 ASP 16 T A - 187.1 - - - - - - - - 177.0 - 35.1 - 17 GLY 17 t - - - - - - - - - - - 176.3 -1.8 - - 18 SER 18 e B 56.6 - - - - - - - - - 184.1 - 33.2 - 19 ASP 19 E B 65.9 - - - - - - - - - 177.3 - 34.5 - 20 ILE 20 E B - - -58.4 177.8 - - - - - - 179.4 -3.5 35.5 - ** ** 21 GLY 21 E - - - - - - - - - - - 182.7 - - - Residue-by-residue listing for refined_11 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 ----------------------------------------------------------------------------------------------------------------------------------- 22 PRO 22 E - - - - - -75.1 - - - - - 180.0 - 38.0 - * * 23 LYS 23 E B - - -65.5 169.4 - - - - - - 180.0 -2.8 35.0 - 24 ALA 24 E B - - - - - - - - - - 177.6 - 34.1 - 25 PHE 25 E B - - -55.1 - - - - - - - 177.2 -3.8 35.0 - ** ** 26 PRO 26 t - - - - - -65.4 - - - - - 181.8 - 38.0 - * * 27 ASP 27 T A - - -56.7 - - - - - - - 181.3 - 35.1 - 28 ALA 28 T A - - - - - - - - - - 179.1 - 33.7 - 29 THR 29 t B - - -55.5 - - - - - - - 181.6 -1.7 34.5 - 30 THR 30 h B 53.2 - - - - - - - - - 180.1 - 33.7 - 31 VAL 31 H A - 180.5 - - - -64.2 -25.9 - - - 175.4 -3.2 32.4 - * +* +* 32 SER 32 H A - - -55.6 - - -55.2 -49.0 - - - 181.0 -.7 35.0 - +* +* 33 ALA 33 H A - - - - - -72.4 -28.8 - - - 177.3 -.6 33.5 - +* +* 34 LEU 34 H A - 172.1 - - - -64.6 -47.6 - - - 176.4 -1.5 35.1 - 35 LYS 35 H A - - -64.8 180.2 - -72.4 -34.3 - - - 174.8 -3.0 31.4 - * * 36 GLU 36 H A - - -76.1 - - -56.6 -29.8 - - - 176.8 -2.5 34.0 - 37 THR 37 H A - - -56.5 - - -65.8 -44.0 - - - 178.4 -1.3 33.9 - 38 VAL 38 H A - 182.2 - - - -63.4 -46.4 - - - 182.0 -1.0 36.0 - * * 39 ILE 39 H A - - -55.0 171.4 - -61.7 -49.5 - - - 184.6 -2.8 35.6 - * * 40 SER 40 H A - - -51.9 - - -75.4 -39.9 - - - 183.9 -2.8 34.6 - * * 41 GLU 41 h A - - -63.4 - - - - - - - 178.0 -2.5 34.8 - 42 TRP 42 t B - 192.4 - - - - - - - - 180.3 -.6 35.1 - +* +* 43 PRO 43 t - - - - - -57.7 - - - - - 180.7 - 38.4 - * * 44 ARG 44 T A - - -59.9 179.5 - - - - - - 175.1 - 32.2 - 45 GLU 45 T A - - -54.0 - - - - - - - 177.4 - 34.9 - 46 LYS 46 t B - - -74.7 - - - - - - - 175.5 -1.2 36.1 - * * 47 GLU 47 B 55.6 - - 178.1 - - - - - - 179.6 - 34.2 - 48 ASN 48 S b - 192.6 - - - - - - - - 178.3 - 31.7 - 49 GLY 49 - - - - - - - - - - - 173.1 -2.3 - - * * 50 PRO 50 - - - - - -56.1 - - - - - 178.7 - 40.6 - +* +* 51 LYS 51 a - - -61.9 176.1 - - - - - - 182.7 -.6 34.3 - +* +* 52 THR 52 t B 60.7 - - - - - - - - - 180.4 - 32.7 - 53 VAL 53 T A 60.8 - - - - - - - - - 179.8 - 34.7 - 54 LYS 54 T A - 173.8 - 182.3 - - - - - - 189.5 - 36.3 - +* +* 55 GLU 55 e A - - -53.5 174.5 - - - - - - 177.8 -2.0 34.4 - 56 VAL 56 E B - 180.0 - - - - - - - - 179.2 -.7 34.9 - +* +* 57 LYS 57 E B - - -58.0 - - - - - - - 182.9 -3.0 33.0 - * * 58 LEU 58 E B - 197.6 - - - - - - - - 183.9 -.9 38.2 - +* * +* Residue-by-residue listing for refined_11 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 ----------------------------------------------------------------------------------------------------------------------------------- 59 ILE 59 E B - - -61.3 180.6 - - - - - - 178.5 -1.8 33.2 - 60 SER 60 E B - 185.9 - - - - - - - - 179.3 -2.2 34.4 - 61 ALA 61 T l - - - - - - - - - - 180.2 - 32.5 - 62 GLY 62 T - - - - - - - - - - - 179.5 - - - 63 LYS 63 E B - - -72.3 - - - - - - - 177.3 -2.0 34.2 - 64 VAL 64 E B - 182.6 - - - - - - - - 178.0 - 34.6 - 65 LEU 65 E B - - -67.6 - - - - - - - 180.8 -3.2 33.8 - +* +* 66 GLU 66 t B - 188.2 - 170.4 - - - - - - 186.1 - 32.6 - * * 67 ASN 67 T A 60.3 - - - - - - - - - 183.4 - 33.6 - 68 SER 68 T A 61.0 - - - - - - - - - 180.3 - 33.0 - 69 LYS 69 t B - - -77.6 - - - - - - - 179.4 -2.3 31.9 - 70 THR 70 B B - - -46.6 - - - - - - - 180.4 - 37.0 - * * 71 VAL 71 G A - 176.6 - - - - - - - - 178.4 -2.9 33.0 - * * 72 LYS 72 G A - 178.6 - 183.9 - - - - - - 180.6 -2.6 35.5 - 73 ASP 73 G A - - -73.8 - - - - - - - 180.3 -.6 33.7 - +* +* 74 TYR 74 G A - - -69.4 - - - - - - - 176.2 -2.0 32.2 - 75 ARG 75 g b - - -62.5 - - - - - - - 180.7 -1.2 35.6 - * * 76 SER 76 B - 185.7 - - - - - - - - 182.8 - 33.9 - 77 PRO 77 S - - - - - -52.1 - - - - - 185.5 - 37.7 - * * * 78 VAL 78 S a 60.8 - - - - - - - - - 178.8 - 31.0 - 79 SER 79 S b - 182.1 - - - - - - - - 184.0 - 32.4 - 80 ASN 80 B - 192.0 - - - - - - - - 186.4 -1.1 35.0 - * * * 81 LEU 81 B - - -55.9 178.8 - - - - - - 180.8 -.6 36.5 - +* +* 82 ALA 82 b - - - - - - - - - - 180.9 - 33.6 - 83 GLY 83 S - - - - - - - - - - - 182.8 -.6 - - +* +* 84 ALA 84 e B - - - - - - - - - - 177.3 - 34.4 - 85 VAL 85 E B - 182.4 - - - - - - - - 185.1 -.5 34.1 - ** ** 86 THR 86 E B - - -58.2 - - - - - - - 174.3 -3.6 34.5 - ** ** 87 THR 87 E B - - -59.7 - - - - - - - 185.1 - 34.7 - 88 MET 88 E B - 178.6 - - - - - - - - 185.7 -2.1 33.9 - 89 HIS 89 E B - - -61.2 - - - - - - - 177.7 -2.0 35.1 - 90 VAL 90 E B - 185.5 - - - - - - - - 179.3 -2.8 33.5 - * * 91 ILE 91 E B - - -76.1 - - - - - - - 182.7 -2.8 33.2 - 92 ILE 92 E B - - -59.6 - - - - - - - 175.9 -.5 35.6 - ** ** 93 GLN 93 e B - 177.9 - 179.8 - - - - - - 178.3 -2.0 33.8 - 94 ALA 94 B - - - - - - - - - - 174.4 -.8 34.5 - +* +* 95 PRO 95 - - - - - -68.1 - - - - - 181.3 - 39.1 - * * 96 VAL 96 b 58.2 - - - - - - - - - 177.7 - 30.2 - * * 97 THR 97 S B - - -51.0 - - - - - - - 185.8 -1.4 35.8 - * * * Residue-by-residue listing for refined_11 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 ----------------------------------------------------------------------------------------------------------------------------------- 98 GLU 98 S XX - 179.7 - 176.9 - - - - - - 177.6 -.8 32.2 - **** +* **** 99 LYS 99 ~a - - -70.3 - - - - - - - 177.5 -2.0 32.9 - ** ** 100 GLU 100 l - - -60.3 182.0 - - - - - - 182.0 - 32.5 - 101 LYS 101 - - 184.9 - 183.8 - - - - - - - - 34.9 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * * +* ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.4 183.6 -61.6 178.3 -62.4 -65.2 -39.5 - - - 179.7 -1.8 34.3 Standard deviations: 3.4 5.8 7.4 5.2 8.6 6.7 9.1 - - - 3.4 .9 1.8 Numbers of values: 11 29 42 23 6 10 10 0 0 0 100 60 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_11 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 - 1.234 1.508 1.531 1.456 - 115.00 121.30 110.45 110.43 111.20 123.70 2 ALA 2 1.300 1.238 1.505 1.520 1.428 123.22 117.43 119.91 110.52 107.64 110.30 122.64 ** +* * ** 3 GLU 3 1.298 1.235 1.516 1.541 1.429 120.71 114.93 121.30 111.44 110.36 113.33 123.72 ** +* +* ** 4 VAL 4 1.298 1.240 1.518 1.567 1.435 123.91 117.81 119.85 110.04 107.41 109.62 122.32 ** * * * * * ** 5 HIS 5 1.312 1.235 1.513 1.552 1.436 120.10 115.64 121.14 111.28 109.77 112.52 123.11 * * * * * 6 ASN 6 1.302 1.237 1.488 1.543 1.435 121.01 115.43 120.13 110.11 107.25 112.71 124.39 +* +* * * * +* 7 GLN 7 1.322 1.239 1.495 1.547 1.442 124.14 116.03 121.06 110.54 110.38 112.10 122.85 * * * 8 LEU 8 1.271 1.217 1.506 1.510 1.432 120.39 117.43 120.37 110.81 110.58 111.57 122.19 **** * **** 9 GLU 9 1.292 1.231 1.491 1.523 1.435 119.26 115.50 121.11 110.62 109.69 115.15 123.39 +** +* * * +** +** 10 ILE 10 1.283 1.228 1.508 1.569 1.425 122.38 116.37 120.55 109.03 109.43 110.47 123.07 *** * +* *** 11 LYS 11 1.297 1.247 1.504 1.553 1.428 121.14 116.52 120.44 110.71 106.89 112.85 123.04 ** * +* +* * ** Residue-by-residue listing for refined_11 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 1.290 1.215 1.497 1.538 1.432 120.69 117.14 120.27 109.29 108.73 110.14 122.56 +** * * +** 13 ARG 13 1.296 1.230 1.507 1.532 1.427 120.18 115.57 120.96 112.87 109.05 110.75 123.45 ** +* * ** 14 LEU 14 1.304 1.235 1.502 1.529 1.435 122.54 115.06 121.18 108.24 111.39 110.72 123.73 +* * * +* 15 THR 15 1.307 1.229 1.551 1.554 1.447 123.20 114.85 122.02 110.81 109.41 109.40 123.11 +* * * +* 16 ASP 16 1.326 1.222 1.540 1.540 1.462 123.24 116.11 121.26 110.21 110.12 109.32 122.60 17 GLY 17 1.324 1.237 1.521 - 1.452 121.29 117.58 120.28 - 114.39 - 122.13 18 SER 18 1.307 1.235 1.524 1.532 1.444 120.73 117.77 120.13 112.20 108.89 110.58 122.07 +* * +* 19 ASP 19 1.310 1.224 1.514 1.528 1.433 120.46 114.33 121.70 109.15 112.22 110.78 123.97 * * * 20 ILE 20 1.293 1.259 1.527 1.566 1.437 125.34 116.97 119.59 109.70 107.08 110.66 123.29 +** * * ** * +** 21 GLY 21 1.324 1.237 1.531 - 1.452 122.05 117.83 120.61 - 112.77 - 121.56 22 PRO 22 1.337 1.244 1.518 1.539 1.450 122.86 115.42 121.39 110.50 112.59 104.38 123.19 * * * 23 LYS 23 1.294 1.230 1.465 1.528 1.437 123.06 115.69 120.44 109.37 108.37 111.25 123.87 ** +** * * +** 24 ALA 24 1.263 1.242 1.505 1.522 1.432 120.73 115.61 120.89 110.57 109.52 110.75 123.49 *4.7* * *4.7* 25 PHE 25 1.298 1.238 1.499 1.524 1.429 122.74 116.80 120.72 109.21 108.18 111.23 122.37 ** * +* * ** 26 PRO 26 1.300 1.236 1.528 1.527 1.445 122.66 115.72 121.11 110.85 112.28 103.97 123.16 +** * +** 27 ASP 27 1.323 1.231 1.513 1.533 1.461 122.98 115.81 120.97 108.69 110.29 110.82 123.20 28 ALA 28 1.323 1.226 1.531 1.521 1.447 122.03 117.13 120.44 110.59 111.92 110.38 122.43 29 THR 29 1.312 1.234 1.538 1.542 1.441 121.44 116.64 120.87 110.64 109.63 110.10 122.47 * * 30 THR 30 1.306 1.247 1.533 1.539 1.440 121.86 116.07 120.96 110.57 111.94 110.55 122.97 +* +* 31 VAL 31 1.333 1.234 1.534 1.561 1.458 122.63 116.17 121.00 111.31 110.48 112.26 122.83 * * 32 SER 32 1.327 1.219 1.533 1.521 1.447 122.05 116.63 120.40 109.95 110.14 109.61 122.88 33 ALA 33 1.334 1.238 1.527 1.517 1.459 122.00 115.76 121.04 110.96 110.82 110.49 123.19 34 LEU 34 1.322 1.231 1.536 1.529 1.419 123.27 116.48 120.92 112.73 109.15 107.29 122.56 ** * +* ** 35 LYS 35 1.323 1.210 1.516 1.513 1.450 121.05 117.44 119.71 111.49 111.60 112.62 122.85 * * * 36 GLU 36 1.340 1.234 1.510 1.523 1.475 121.79 115.87 120.74 109.17 110.86 111.61 123.39 37 THR 37 1.317 1.224 1.533 1.543 1.428 121.73 115.62 120.80 110.80 109.34 110.98 123.51 +* +* 38 VAL 38 1.321 1.210 1.528 1.558 1.459 123.38 115.19 121.06 108.33 109.36 110.37 123.74 * * 39 ILE 39 1.320 1.232 1.534 1.558 1.464 123.92 116.61 120.79 109.03 111.32 109.67 122.59 * * * 40 SER 40 1.319 1.236 1.535 1.521 1.447 121.16 116.72 120.68 110.42 112.12 109.17 122.53 41 GLU 41 1.327 1.237 1.518 1.509 1.442 121.94 115.86 120.57 109.48 111.95 109.82 123.58 * * 42 TRP 42 1.311 1.246 1.512 1.548 1.448 122.57 117.76 119.81 110.60 107.66 110.02 122.34 * * * 43 PRO 43 1.337 1.220 1.516 1.533 1.452 122.40 116.01 121.07 110.60 111.09 103.96 122.92 Residue-by-residue listing for refined_11 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 1.297 1.231 1.516 1.527 1.453 122.30 114.93 121.33 113.25 110.38 110.42 123.74 ** +* ** 45 GLU 45 1.325 1.241 1.539 1.550 1.451 123.39 115.40 121.24 108.79 109.15 111.46 123.35 * * 46 LYS 46 1.330 1.236 1.499 1.535 1.435 123.72 115.99 120.29 108.91 110.08 109.60 123.71 * * * * 47 GLU 47 1.315 1.263 1.503 1.526 1.432 121.90 115.60 121.23 109.77 110.09 111.32 123.17 +* * * +* 48 ASN 48 1.288 1.233 1.515 1.541 1.412 120.68 113.81 122.28 112.39 108.54 112.99 123.62 +** ** * * * +** 49 GLY 49 1.301 1.225 1.496 - 1.421 122.46 117.19 120.22 - 109.98 - 122.58 +* * +* * +* 50 PRO 50 1.348 1.237 1.523 1.533 1.466 123.42 116.96 120.39 108.92 111.29 102.15 122.57 51 LYS 51 1.310 1.225 1.508 1.513 1.434 120.69 116.44 120.53 109.53 110.55 111.10 123.04 * * * 52 THR 52 1.328 1.241 1.543 1.533 1.445 120.93 114.51 121.49 109.19 113.39 112.55 124.00 53 VAL 53 1.342 1.233 1.555 1.576 1.484 126.66 115.92 121.43 110.14 112.60 109.37 122.65 * * * +** * +** 54 LYS 54 1.305 1.239 1.537 1.532 1.455 123.73 115.99 121.21 109.63 111.70 107.77 122.75 +* * +* +* 55 GLU 55 1.305 1.242 1.518 1.505 1.455 121.62 115.73 121.22 112.02 112.18 107.64 123.03 +* * * +* +* 56 VAL 56 1.308 1.233 1.515 1.554 1.434 121.37 116.81 120.66 109.16 108.40 111.66 122.51 +* * +* 57 LYS 57 1.299 1.231 1.506 1.533 1.430 120.81 114.91 121.19 111.84 109.05 111.39 123.89 ** * ** 58 LEU 58 1.298 1.221 1.525 1.562 1.435 122.86 118.41 119.19 110.83 104.88 105.71 122.40 ** +* * * ** +** +** 59 ILE 59 1.316 1.242 1.512 1.569 1.461 120.32 114.86 121.57 110.08 112.10 111.95 123.56 * * 60 SER 60 1.304 1.242 1.521 1.546 1.424 122.80 116.11 120.08 111.08 107.44 110.66 123.66 +* +* * +* 61 ALA 61 1.338 1.238 1.531 1.532 1.475 124.06 115.87 121.16 111.22 111.75 111.37 122.93 * * 62 GLY 62 1.312 1.229 1.511 - 1.436 121.19 116.91 120.42 - 112.53 - 122.67 * * 63 LYS 63 1.322 1.234 1.502 1.534 1.419 121.88 115.88 120.57 109.24 110.14 111.95 123.54 * ** ** 64 VAL 64 1.302 1.237 1.520 1.557 1.434 122.04 116.14 120.73 109.18 108.72 111.94 123.10 +* * +* 65 LEU 65 1.301 1.246 1.513 1.549 1.434 122.39 116.52 120.70 110.02 109.08 112.21 122.77 ** * * ** 66 GLU 66 1.300 1.230 1.540 1.541 1.429 121.42 115.83 120.48 113.47 110.18 109.81 123.69 ** +* +* ** 67 ASN 67 1.325 1.225 1.545 1.544 1.482 125.10 118.35 119.99 109.49 115.02 110.46 121.65 * +* * * +* 68 SER 68 1.317 1.229 1.541 1.530 1.455 120.18 116.60 120.82 111.23 112.20 110.51 122.57 69 LYS 69 1.317 1.239 1.513 1.525 1.440 122.06 114.84 121.51 111.09 113.62 111.76 123.65 70 THR 70 1.310 1.236 1.541 1.542 1.431 123.41 118.00 119.44 109.75 106.46 108.09 122.55 * * +* ** ** 71 VAL 71 1.325 1.235 1.531 1.565 1.474 121.54 115.23 120.96 110.53 110.19 112.24 123.75 72 LYS 72 1.327 1.238 1.537 1.526 1.471 124.59 116.37 120.87 109.44 111.86 108.82 122.76 +* +* 73 ASP 73 1.323 1.227 1.511 1.519 1.447 122.91 116.51 120.54 110.33 112.47 110.49 122.95 Residue-by-residue listing for refined_11 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 1.306 1.232 1.523 1.526 1.432 122.05 116.09 121.13 112.83 111.80 110.33 122.78 +* * * +* 75 ARG 75 1.318 1.240 1.523 1.507 1.418 122.50 117.02 120.54 109.21 109.04 109.85 122.44 * ** ** 76 SER 76 1.301 1.231 1.543 1.528 1.431 120.88 117.49 120.05 111.98 109.31 109.66 122.43 +* * +* 77 PRO 77 1.359 1.227 1.527 1.532 1.476 123.84 116.50 120.64 110.72 115.75 103.55 122.86 * +* +* 78 VAL 78 1.292 1.234 1.527 1.571 1.461 121.22 116.74 121.05 111.97 112.96 112.63 122.21 +** * * +** 79 SER 79 1.286 1.230 1.508 1.539 1.440 120.87 115.27 121.62 111.51 109.26 112.46 123.06 *** * *** 80 ASN 80 1.294 1.239 1.525 1.520 1.430 121.75 116.40 120.41 111.22 108.80 108.92 123.18 ** * ** 81 LEU 81 1.317 1.238 1.530 1.496 1.423 123.74 115.62 120.97 109.49 112.66 107.13 123.38 +* +* * +* +* 82 ALA 82 1.318 1.240 1.529 1.520 1.441 123.10 115.61 121.04 110.66 110.39 110.86 123.34 83 GLY 83 1.308 1.238 1.513 - 1.441 121.91 116.06 120.90 - 111.33 - 123.04 +* +* 84 ALA 84 1.318 1.242 1.520 1.522 1.443 122.46 116.51 120.65 110.27 111.02 110.07 122.84 85 VAL 85 1.314 1.230 1.514 1.547 1.446 120.99 116.12 121.28 109.58 107.87 112.37 122.60 * * * 86 THR 86 1.278 1.242 1.522 1.547 1.420 121.39 115.43 121.21 110.78 111.69 109.60 123.34 +*** +* * +*** 87 THR 87 1.303 1.242 1.510 1.538 1.413 121.92 115.40 121.38 110.16 106.96 111.41 123.19 +* ** +* ** 88 MET 88 1.283 1.239 1.523 1.546 1.418 122.16 116.32 120.32 114.91 108.99 107.15 123.35 *** ** +** +* *** 89 HIS 89 1.320 1.234 1.502 1.534 1.459 121.93 116.38 120.46 108.15 110.89 111.31 123.16 * * * 90 VAL 90 1.304 1.252 1.499 1.549 1.436 120.67 114.04 121.92 109.51 109.13 113.18 124.03 +* * * * * +* 91 ILE 91 1.277 1.236 1.501 1.561 1.412 123.45 115.24 121.41 111.88 108.81 111.56 123.33 +*** * ** * +*** 92 ILE 92 1.286 1.232 1.504 1.553 1.420 121.93 117.18 120.16 109.34 109.05 110.36 122.62 *** * ** *** 93 GLN 93 1.307 1.230 1.512 1.528 1.423 119.56 115.45 121.07 110.81 108.97 111.26 123.44 +* +* * +* 94 ALA 94 1.300 1.243 1.512 1.516 1.431 122.17 117.97 119.97 110.49 110.12 110.06 122.04 ** * ** 95 PRO 95 1.333 1.240 1.522 1.538 1.451 122.24 117.09 120.32 109.97 109.53 103.94 122.58 96 VAL 96 1.305 1.242 1.542 1.572 1.442 120.39 115.12 122.09 112.77 112.22 113.11 122.73 +* * +* +* 97 THR 97 1.307 1.226 1.520 1.542 1.428 122.24 116.49 119.95 109.76 106.89 109.91 123.54 +* +* +* +* 98 GLU 98 1.329 1.219 1.530 1.549 1.465 123.80 115.32 119.79 111.88 109.75 112.04 124.82 * * * 99 LYS 99 1.335 1.231 1.507 1.554 1.463 128.80 114.52 121.11 108.23 106.93 115.83 124.36 * +*** +* *** +*** 100 GLU 100 1.352 1.229 1.524 1.538 1.478 124.52 116.49 120.91 110.66 112.26 111.77 122.56 +* * +* +* 101 LYS 101 1.306 - 1.521 1.535 1.431 121.74 - - 110.94 108.46 109.64 - +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_11 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: *4.7* +* +** +* ** +*** * +** ** *** * *4.7* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_11 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 1.263 1.352 1.310 .016 *4.7* +* * C-N (Pro) 1.341 .016 6 1.300 1.359 1.336 .018 +** * C-O C-O 1.231 .020 100 1.210 1.263 1.234 .009 * +* CA-C CH1E-C (except Gly) 1.525 .021 96 1.465 1.555 1.519 .015 +** * CH2G*-C (Gly) 1.516 .018 5 1.496 1.531 1.514 .012 * CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.516 1.532 1.521 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.533 1.576 1.555 .012 * CH1E-CH2E (the rest) 1.530 .020 62 1.496 1.562 1.532 .013 +* +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.412 1.484 1.441 .017 ** * NH1-CH2G* (Gly) 1.451 .016 5 1.421 1.452 1.440 .012 +* N-CH1E (Pro) 1.466 .015 6 1.445 1.476 1.457 .011 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_11 Page 11 ---------------------------------------- +-----------------+ | BOND ANGLES | +-----------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Angle X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 89 113.81 118.41 116.09 .96 * * CH2G*-C-NH1 (Gly) 116.4 2.1 5 116.06 117.83 117.11 .61 CH1E-C-N (Pro) 116.9 1.5 6 115.42 117.09 116.28 .62 O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.56 124.82 123.06 .60 * O-C-N (Pro) 122.0 1.4 6 122.57 123.19 122.88 .24 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.26 128.80 122.21 1.52 * +*** C-NH1-CH2G* (Gly) 120.6 1.7 5 121.19 122.46 121.78 .48 * C-N-CH1E (Pro) 122.6 5.0 6 122.24 123.84 122.90 .56 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.19 122.28 120.79 .59 CH2G*-C-O (Gly) 120.8 2.1 5 120.22 120.90 120.49 .25 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 110.27 111.22 110.66 .28 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.33 112.77 110.16 1.02 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 108.15 114.91 110.56 1.38 * +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.88 115.02 109.98 1.84 ** * NH1-CH2G*-C (Gly) 112.5 2.9 5 109.98 114.39 112.20 1.48 N-CH1E-C (Pro) 111.8 2.5 6 109.53 115.75 112.09 1.91 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 110.06 111.37 110.53 .41 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 108.09 113.18 111.00 1.31 ** N-CH1E-CH2E (Pro) 103.0 1.1 6 102.15 104.38 103.66 .71 * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 105.71 115.83 110.72 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_11 Page 12 ---------------------------------------- R A M A C H A N D R A N P L O T S T A T I S T I C S Residues in most favoured regions [A,B,L] 75 85.2% Residues in additional allowed regions [a,b,l,p] 11 12.5% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.1% 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 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 85.2 83.8 10.0 .1 Inside b. Omega angle st dev 100 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 96 1.8 3.1 1.6 -.8 Inside e. H-bond energy st dev 60 .9 .8 .2 .7 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 11 3.4 18.1 6.5 -2.3 BETTER b. Chi-1 trans st dev 29 5.8 19.0 5.3 -2.5 BETTER c. Chi-1 gauche plus st dev 42 7.4 17.5 4.9 -2.1 BETTER d. Chi-1 pooled st dev 82 7.5 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 23 5.2 20.4 5.0 -3.0 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 9.0 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .96 3 Residue-by-residue listing for refined_11 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.54 Chi1-chi2 distribution -.01 Chi1 only .08 Chi3 & chi4 .22 Omega .02 ------ -.12 ===== Main-chain covalent forces:- Main-chain bond lengths -.11 Main-chain bond angles .38 ------ .17 ===== OVERALL AVERAGE -.02 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.