Residue-by-residue listing for refined_2 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 - - - -63.1 - - - - - - - 182.5 - 33.7 - 2 GLY 2 - - - - - - - - - - - 180.4 - - - 3 HIS 3 S B - - -66.3 - - - - - - - 179.4 - 33.6 - 4 HIS 4 B - - -64.8 - - - - - - - 180.4 -.6 32.7 - +* +* 5 HIS 5 b - - -60.2 - - - - - - - 174.9 - 36.1 - 6 HIS 6 B - 181.9 - - - - - - - - 184.8 - 34.8 - 7 HIS 7 B 60.8 - - - - - - - - - 174.5 -.6 31.0 - +* +* 8 HIS 8 a - 188.9 - - - - - - - - 172.2 -.9 31.8 - * +* +* 9 LEU 9 B - - -62.1 179.4 - - - - - - 182.1 - 33.7 - 10 GLU 10 B - - -69.6 - - - - - - - 174.5 -.8 33.6 - +* +* 11 MET 11 B - - -65.9 - - - - - - - 184.3 -1.0 33.7 - * * 12 ALA 12 B - - - - - - - - - - 178.2 - 33.8 - 13 SER 13 b - 185.1 - - - - - - - - 181.6 - 34.9 - 14 GLU 14 B - 182.0 - 172.8 - - - - - - 181.4 - 32.3 - 15 GLU 15 B 60.2 - - 184.1 - - - - - - 177.3 -1.1 35.8 - * * 16 GLY 16 S - - - - - - - - - - - 183.2 -2.0 - - 17 GLN 17 e B 48.4 - - 177.1 - - - - - - 176.4 -.5 31.1 - * ** ** 18 VAL 18 E B - 181.7 - - - - - - - - 178.5 -.6 35.4 - +* +* 19 ILE 19 E B - - -63.0 - - - - - - - 179.3 -3.3 30.6 - +* +* Residue-by-residue listing for refined_2 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 ALA 20 E B - - - - - - - - - - 181.6 -.8 34.2 - +* +* 21 CYS 21 e B - - -56.1 - - - - - - - 177.7 -1.3 35.4 - * * 22 HIS 22 S A - - -58.5 - - - - - - - 180.5 - 33.4 - 23 THR 23 h B 52.3 - - - - - - - - - 180.0 - 35.1 - 24 VAL 24 H A 66.3 - - - - -69.9 -25.6 - - - 178.6 - 32.5 - * * 25 GLU 25 H A - 181.5 - - - -58.5 -51.9 - - - 181.0 - 35.5 - * * 26 THR 26 H A - - -55.2 - - -69.6 -35.3 - - - 174.1 - 33.5 - * * 27 TRP 27 H A - 169.8 - - - -57.4 -46.2 - - - 177.5 -1.6 34.8 - 28 ASN 28 H A - 182.5 - - - -61.5 -45.6 - - - 183.3 -3.0 35.6 - * * 29 GLU 29 H A - 197.9 - - - -57.2 -48.4 - - - 182.2 -2.5 35.7 - 30 GLN 30 H A - - -63.1 - - -68.3 -43.5 - - - 179.1 -2.5 34.4 - 31 LEU 31 H A - - -67.8 182.1 - -65.7 -44.4 - - - 177.6 -2.2 34.6 - 32 GLN 32 H A - 180.9 - 182.8 - -57.9 -45.0 - - - 177.7 -3.1 35.4 - * * 33 LYS 33 H A - 180.3 - 181.6 - -56.6 -49.0 - - - 181.9 -2.3 35.5 - 34 ALA 34 H A - - - - - -70.1 -39.2 - - - 181.2 -2.6 33.6 - 35 ASN 35 H A - 185.1 - - - -62.8 -54.5 - - - 182.1 -3.3 37.1 - * +* +* 36 GLU 36 H A - 182.1 - 179.7 - -63.7 -40.3 - - - 182.0 -3.0 34.6 - * * 37 SER 37 h A - - -58.1 - - - - - - - 178.7 -2.1 34.1 - 38 LYS 38 T L - - -60.3 180.2 - - - - - - 182.1 -1.1 33.1 - * * 39 THR 39 t B - - -48.3 - - - - - - - 181.0 -2.4 36.1 - * * 40 LEU 40 e B - 185.7 - 169.7 - - - - - - 182.3 - 34.1 - 41 VAL 41 E B 57.8 - - - - - - - - - 177.0 -1.0 33.4 - * * 42 VAL 42 E B - 185.5 - - - - - - - - 183.6 -2.6 33.9 - 43 VAL 43 E B - 184.5 - - - - - - - - 175.6 -2.8 34.7 - * * 44 ASP 44 E B - 168.8 - - - - - - - - 175.4 -2.7 34.0 - 45 PHE 45 E B - - -61.5 - - - - - - - 187.0 -3.0 36.6 - * * * 46 THR 46 E B - 188.1 - - - - - - - - 177.4 -3.0 35.6 - * * 47 ALA 47 t B - - - - - - - - - - 182.6 - 34.4 - 48 SER 48 T A - - -52.0 - - - - - - - 176.8 - 33.7 - 49 TRP 49 T A 56.2 - - - - - - - - - 183.9 - 33.0 - 50 CYS 50 h B - 173.1 - 218.5 - - - 59.2 - 2.0 181.8 -1.4 34.5 - ** +** +** 51 GLY 51 H - - - - - - -61.3 -63.2 - - - 179.9 -.5 - - ** +* ** 52 PRO 52 H - - - - - -56.9 -56.9 -34.7 - - - 179.8 - 38.8 - * * 53 CYS 53 H A - - -53.1 - - -66.5 -41.6 59.2 - 2.0 179.3 - 35.2 - +** +** 54 ARG 54 H A - 177.9 - - - -71.5 -29.6 - - - 180.1 -2.1 33.1 - 55 PHE 55 H A - 181.5 - - - -80.2 -29.5 - - - 183.6 -2.0 33.8 - * * Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 56 ILE 56 H A - 190.0 - - - -87.4 -25.8 - - - 182.7 -2.0 34.0 - +* * +* 57 ALA 57 h A - - - - - - - - - - 180.8 -1.8 32.1 - 58 PRO 58 H - - - - - -45.9 -45.9 -37.2 - - - 181.2 - 39.0 - +* +* * +* 59 PHE 59 H A - 182.8 - - - -63.5 -33.9 - - - 178.4 -.8 33.0 - +* +* 60 PHE 60 H A - 177.6 - - - -65.6 -33.5 - - - 178.5 -1.7 34.3 - 61 ALA 61 H A - - - - - -70.5 -31.4 - - - 178.4 -1.0 33.6 - * * 62 ASP 62 H A - 187.3 - - - -71.8 -43.4 - - - 175.7 -1.4 35.0 - 63 LEU 63 H A - - -69.2 181.0 - -54.2 -42.2 - - - 179.6 -2.4 35.6 - 64 ALA 64 H A - - - - - -58.9 -35.4 - - - 180.9 -1.8 33.6 - 65 LYS 65 H A - 191.2 - 184.3 - -79.5 -31.0 - - - 181.9 -.9 33.8 - * * * 66 LYS 66 H A - - -61.9 176.1 - -69.5 -40.1 - - - 182.0 -1.8 34.7 - 67 LEU 67 h b - - -64.6 169.4 - - - - - - 181.6 -2.4 33.3 - 68 PRO 68 S - - - - - -73.6 - - - - - 182.9 - 39.1 - * * 69 ASN 69 S A - 183.3 - - - - - - - - 176.0 - 32.6 - 70 VAL 70 S B - 175.3 - - - - - - - - 182.3 - 33.1 - 71 LEU 71 E B - 195.3 - - - - - - - - 179.3 -2.4 35.2 - 72 PHE 72 E B - - -63.4 - - - - - - - 182.9 -.7 33.3 - +* +* 73 LEU 73 E B - - -74.0 163.5 - - - - - - 181.4 -2.2 33.6 - 74 LYS 74 E B - 188.7 - - - - - - - - 179.9 -2.4 36.1 - 75 VAL 75 E B - 177.8 - - - - - - - - 174.8 -3.1 34.5 - * * 76 ASP 76 E B - 183.7 - - - - - - - - 185.5 -.6 33.0 - +* +* 77 THR 77 e A 51.3 - - - - - - - - - 176.7 -3.4 32.4 - +* +* 78 ASP 78 T A - 186.2 - - - - - - - - 175.4 - 34.5 - 79 GLU 79 T a - - -59.9 187.7 - - - - - - 183.4 -.7 36.2 - +* +* 80 LEU 80 h b - - -67.9 181.4 - - - - - - 180.9 -2.7 34.4 - 81 LYS 81 H A 57.2 - - 184.3 - -65.7 -28.7 - - - 178.9 -1.5 32.3 - 82 SER 82 H A - - -53.1 - - -72.3 -40.2 - - - 177.2 - 34.1 - 83 VAL 83 H A - 180.6 - - - -65.0 -43.3 - - - 177.7 - 34.5 - 84 ALA 84 H A - - - - - -56.9 -50.4 - - - 179.4 -2.6 34.3 - 85 SER 85 H A - - -57.8 - - -60.5 -40.9 - - - 181.3 -2.6 35.2 - 86 ASP 86 H A - 181.2 - - - -63.7 -37.3 - - - 178.4 -2.3 34.9 - 87 TRP 87 h A - - -71.4 - - - - - - - 176.8 -2.2 32.4 - 88 ALA 88 T l - - - - - - - - - - 179.5 -1.5 33.0 - 89 ILE 89 t b - - -53.3 - - - - - - - 180.3 -3.2 34.7 - +* +* 90 GLN 90 A - 186.5 - 181.1 - - - - - - 177.2 -1.5 34.0 - 91 ALA 91 S B - - - - - - - - - - 184.1 - 33.5 - 92 MET 92 S B - - -50.9 163.0 - - - - - - .9 -.7 36.8 - * +* +* 93 PRO 93 e cis - - - - - -94.3 - - - - - 175.1 - 40.2 - +** +* +** 94 THR 94 E B - - -62.1 - - - - - - - 176.9 -2.4 33.6 - 95 PHE 95 E B - - -68.3 - - - - - - - 182.1 -2.3 36.5 - 96 MET 96 E B - 183.2 - 178.4 - - - - - - 178.9 -3.2 33.1 - +* +* Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 97 PHE 97 E B - - -68.1 - - - - - - - 180.4 -3.0 36.4 - * * 98 LEU 98 E B 59.2 - - 168.7 - - - - - - 185.7 -1.8 31.2 - 99 LYS 99 E B - 183.3 - 174.4 - - - - - - 179.4 -3.4 34.5 - +* +* 100 GLU 100 T l - - -57.4 175.6 - - - - - - 182.2 - 33.5 - 101 GLY 101 T - - - - - - - - - - - 177.9 - - - 102 LYS 102 E B - - -62.8 174.3 - - - - - - 186.6 -1.7 34.8 - * * 103 ILE 103 E B - - -57.5 177.9 - - - - - - 176.4 - 33.9 - 104 LEU 104 E a - - -64.8 182.6 - - - - - - 184.1 -1.7 33.9 - 105 ASP 105 E B 53.4 - - - - - - - - - 182.1 -1.9 32.8 - 106 LYS 106 E B 56.4 - - 180.6 - - - - - - 178.1 - 34.4 - 107 VAL 107 E B - 183.0 - - - - - - - - 183.6 -3.1 36.2 - * * 108 VAL 108 E B 60.6 - - - - - - - - - 183.0 -.6 31.9 - +* +* 109 GLY 109 e - - - - - - - - - - - 180.4 -2.5 - - 110 ALA 110 B - - - - - - - - - - 178.5 - 34.0 - 111 LYS 111 h B - - -62.6 - - - - - - - 182.0 -1.0 36.2 - * * 112 LYS 112 H A - 199.7 - - - -69.8 -48.2 - - - 181.6 - 34.5 - 113 ASP 113 H A - 180.3 - - - -68.6 -43.1 - - - 180.2 - 32.6 - 114 GLU 114 H A - 183.6 - - - -65.7 -33.0 - - - 176.6 - 33.1 - 115 LEU 115 H A - 183.4 - - - -60.2 -53.1 - - - 179.4 -1.6 35.4 - * * 116 GLN 116 H A - - -59.2 - - -60.6 -39.3 - - - 177.1 -1.9 33.8 - 117 SER 117 H A - 179.7 - - - -60.1 -46.9 - - - 179.4 -2.6 34.8 - 118 THR 118 H A - - -58.0 - - -61.6 -31.5 - - - 177.2 -3.0 33.5 - * * 119 ILE 119 H A - - -55.4 - - -67.7 -44.7 - - - 179.3 -1.7 33.7 - 120 ALA 120 H A - - - - - -66.6 -31.5 - - - 176.3 -2.1 32.7 - 121 LYS 121 H A - - -73.9 176.1 - -65.2 -35.1 - - - 177.7 -2.2 35.4 - 122 HIS 122 H A - - -75.2 - - -90.0 -21.4 - - - 181.6 -1.5 33.8 - ** +* ** 123 LEU 123 h B - 197.7 - 172.3 - - - - - - 178.9 -2.0 34.6 - 124 ALA 124 - - - - - - - - - - - - - 34.3 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * * ** +** ** ** +** * ** +* +** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.9 183.7 -61.8 178.7 -67.7 -65.4 -39.8 59.2 - 2.0 179.9 -2.0 34.3 +** +** Standard deviations: 4.8 6.4 6.4 9.5 21.1 8.2 8.6 .0 - .0 2.9 .8 1.6 Numbers of values: 13 45 44 31 4 45 45 2 0 2 122 86 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_2 Page 5 ---------------------------------------- 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_2 Page 6 ---------------------------------------- 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 - 1.238 1.510 1.544 1.461 - 116.88 120.39 110.43 109.24 111.64 122.74 2 GLY 2 1.315 1.239 1.504 - 1.437 120.45 116.91 120.33 - 110.44 - 122.76 * * 3 HIS 3 1.298 1.226 1.504 1.529 1.452 121.36 116.34 120.83 110.17 110.49 111.61 122.82 ** * ** 4 HIS 4 1.307 1.236 1.510 1.548 1.446 121.47 115.64 120.90 110.63 110.17 112.68 123.46 +* * +* 5 HIS 5 1.301 1.240 1.510 1.549 1.451 123.68 116.87 119.78 108.67 107.41 110.47 123.34 +* * * +* 6 HIS 6 1.321 1.230 1.528 1.546 1.452 121.94 116.56 120.64 110.53 108.19 110.16 122.80 * * 7 HIS 7 1.300 1.230 1.520 1.562 1.444 121.09 115.88 121.23 111.99 112.61 112.73 122.85 ** +* * ** 8 HIS 8 1.323 1.234 1.529 1.545 1.459 120.92 114.73 122.70 112.10 108.86 112.81 122.57 * * * * 9 LEU 9 1.291 1.229 1.500 1.530 1.421 121.77 115.74 120.94 111.41 106.77 111.65 123.09 +** * +* +* +** 10 GLU 10 1.294 1.231 1.509 1.554 1.435 121.71 116.42 120.38 110.13 110.79 111.84 123.12 ** * * ** 11 MET 11 1.328 1.229 1.510 1.547 1.454 121.47 116.45 120.30 109.95 108.44 112.41 123.24 * * Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 12 ALA 12 1.306 1.241 1.517 1.507 1.449 121.89 115.42 121.14 110.29 112.02 110.30 123.43 +* +* 13 SER 13 1.300 1.243 1.532 1.547 1.425 122.89 117.49 120.17 111.52 107.31 109.47 122.33 ** +* * ** 14 GLU 14 1.297 1.237 1.534 1.530 1.430 121.18 114.85 121.65 113.19 110.45 110.33 123.43 ** * +* ** 15 GLU 15 1.314 1.239 1.522 1.544 1.450 123.49 117.11 119.99 109.86 109.09 109.16 122.89 * * 16 GLY 16 1.317 1.235 1.502 - 1.447 120.08 116.63 120.72 - 112.31 - 122.64 17 GLN 17 1.308 1.234 1.486 1.500 1.431 120.00 112.59 122.73 110.91 114.21 112.57 124.67 +* +* * * +* * * * * +* 18 VAL 18 1.274 1.242 1.522 1.551 1.434 124.27 119.15 119.31 109.17 107.51 111.10 121.54 +*** * * * * +*** 19 ILE 19 1.313 1.234 1.522 1.567 1.429 117.99 116.26 121.06 111.51 110.16 114.83 122.64 * * +* ** * +* ** 20 ALA 20 1.307 1.232 1.504 1.525 1.435 121.42 116.14 120.92 110.79 109.03 110.60 122.93 +* * +* 21 CYS 21 1.298 1.221 1.503 1.512 1.411 121.35 116.62 120.85 110.01 109.33 109.49 122.50 ** * ** ** 22 HIS 22 1.294 1.223 1.510 1.540 1.444 120.70 115.18 121.26 111.05 108.90 111.64 123.56 +** +** 23 THR 23 1.328 1.249 1.529 1.556 1.448 123.65 117.22 119.86 109.05 108.84 111.15 122.92 * * 24 VAL 24 1.327 1.217 1.541 1.573 1.459 121.44 116.09 121.01 110.91 110.38 112.56 122.88 * * 25 GLU 25 1.330 1.237 1.529 1.548 1.466 122.96 115.94 121.07 111.24 110.22 107.81 122.97 +* +* 26 THR 26 1.311 1.230 1.535 1.528 1.444 121.57 115.52 121.06 112.04 110.35 109.81 123.38 * * * 27 TRP 27 1.319 1.236 1.546 1.536 1.457 122.86 115.31 121.34 112.11 109.90 107.83 123.33 * +* +* 28 ASN 28 1.320 1.230 1.531 1.549 1.458 123.72 115.79 120.52 110.49 109.91 108.56 123.65 * * * 29 GLU 29 1.336 1.232 1.538 1.561 1.473 123.68 115.93 120.78 110.99 109.39 108.05 123.18 +* * * +* 30 GLN 30 1.325 1.232 1.525 1.487 1.424 123.02 117.45 120.29 110.69 113.05 108.72 122.26 ** +* * ** 31 LEU 31 1.327 1.220 1.498 1.485 1.420 121.38 116.02 120.33 109.48 111.50 110.23 123.65 * ** ** ** 32 GLN 32 1.316 1.227 1.517 1.518 1.444 122.44 114.91 121.08 109.85 109.01 109.58 124.00 33 LYS 33 1.319 1.237 1.535 1.531 1.445 123.57 116.71 120.34 110.25 110.65 108.66 122.92 * * * 34 ALA 34 1.335 1.230 1.527 1.522 1.456 121.42 115.97 120.62 110.73 111.44 110.46 123.41 35 ASN 35 1.321 1.236 1.503 1.534 1.472 123.49 114.10 121.57 108.07 109.94 108.63 124.30 * * * * * 36 GLU 36 1.305 1.226 1.529 1.526 1.455 123.56 116.80 120.88 110.17 111.97 109.52 122.32 +* * +* 37 SER 37 1.312 1.242 1.532 1.513 1.441 121.11 116.11 120.38 111.06 111.93 109.23 123.51 * * 38 LYS 38 1.352 1.240 1.526 1.511 1.470 123.57 114.15 122.08 112.22 110.91 109.70 123.70 +* * * * +* 39 THR 39 1.305 1.240 1.517 1.520 1.424 124.12 115.80 121.15 109.11 109.03 109.45 123.03 +* +* * * +* 40 LEU 40 1.278 1.240 1.542 1.563 1.431 121.92 116.59 120.61 113.26 107.58 108.98 122.77 +*** +* * +* * +*** Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 41 VAL 41 1.309 1.227 1.535 1.567 1.435 121.96 116.89 120.62 111.80 110.78 110.49 122.45 * * * * * 42 VAL 42 1.310 1.241 1.515 1.542 1.449 121.50 116.83 120.48 109.39 108.31 112.73 122.68 * * * 43 VAL 43 1.308 1.236 1.518 1.547 1.444 120.94 115.69 120.65 108.38 111.24 111.64 123.66 +* +* 44 ASP 44 1.306 1.242 1.514 1.538 1.452 123.00 116.21 120.68 110.32 110.39 110.87 123.05 +* +* 45 PHE 45 1.316 1.229 1.512 1.532 1.426 121.93 117.27 120.20 108.64 106.69 109.85 122.48 +* +* +* 46 THR 46 1.294 1.225 1.527 1.562 1.439 120.72 116.79 120.35 110.34 109.64 109.05 122.81 ** * ** 47 ALA 47 1.307 1.232 1.504 1.509 1.444 122.57 116.48 120.22 110.03 108.73 110.85 123.31 +* * +* 48 SER 48 1.306 1.237 1.555 1.529 1.454 122.51 116.62 120.99 111.90 111.93 108.96 122.39 +* * +* 49 TRP 49 1.332 1.231 1.530 1.548 1.463 121.53 116.43 121.12 110.52 111.69 111.64 122.43 50 CYS 50 1.303 1.229 1.522 1.530 1.444 121.82 115.68 120.70 111.41 110.79 108.90 123.61 +* +* 51 GLY 51 1.327 1.234 1.523 - 1.460 122.60 118.75 119.68 - 113.62 - 121.57 * * * 52 PRO 52 1.364 1.226 1.516 1.534 1.471 122.72 115.57 121.08 110.09 111.38 103.65 123.33 * * 53 CYS 53 1.315 1.225 1.529 1.517 1.447 122.79 116.01 120.98 109.91 110.19 109.39 122.98 54 ARG 54 1.316 1.219 1.532 1.565 1.444 122.62 116.63 120.74 113.88 110.01 108.96 122.63 +* +* +* 55 PHE 55 1.316 1.238 1.545 1.541 1.450 121.78 117.11 120.83 110.85 111.66 110.17 122.05 56 ILE 56 1.317 1.237 1.553 1.577 1.458 120.63 115.62 120.98 110.62 110.80 110.70 123.25 * * * 57 ALA 57 1.325 1.227 1.574 1.520 1.473 123.85 120.86 118.53 110.78 116.25 110.26 120.60 ** * ** * +* +* ** 58 PRO 58 1.389 1.233 1.529 1.520 1.492 123.35 116.51 120.81 109.51 114.43 102.99 122.67 *** +* * *** 59 PHE 59 1.319 1.227 1.543 1.531 1.451 121.45 116.14 120.97 111.62 111.08 110.56 122.86 60 PHE 60 1.319 1.232 1.530 1.541 1.463 123.17 116.01 121.15 111.80 110.03 109.03 122.82 61 ALA 61 1.321 1.232 1.531 1.523 1.453 121.48 115.90 121.17 110.99 110.02 110.70 122.92 62 ASP 62 1.321 1.236 1.498 1.518 1.468 122.05 114.52 121.18 109.60 108.98 110.38 124.29 * * 63 LEU 63 1.319 1.234 1.516 1.521 1.439 123.99 115.61 120.68 109.50 111.05 109.19 123.71 * * * 64 ALA 64 1.321 1.228 1.516 1.515 1.448 122.54 117.02 120.54 110.48 111.85 110.56 122.43 65 LYS 65 1.324 1.223 1.531 1.531 1.447 119.92 116.02 121.11 110.43 109.79 111.16 122.85 66 LYS 66 1.323 1.237 1.515 1.522 1.458 122.20 116.35 120.66 109.41 111.60 110.27 122.98 67 LEU 67 1.314 1.225 1.527 1.509 1.425 121.61 116.44 121.41 112.41 111.77 109.14 122.12 * * +* * +* 68 PRO 68 1.338 1.228 1.534 1.533 1.467 123.22 116.97 120.64 109.96 113.20 102.95 122.38 69 ASN 69 1.323 1.220 1.531 1.549 1.460 121.36 116.09 121.72 112.65 110.71 110.37 122.19 * * 70 VAL 70 1.311 1.231 1.516 1.558 1.447 121.50 116.56 120.55 110.81 108.64 112.46 122.85 * * 71 LEU 71 1.300 1.230 1.536 1.562 1.436 121.46 116.93 120.64 112.14 107.51 108.43 122.39 ** +* * * * * ** 72 PHE 72 1.310 1.229 1.505 1.524 1.451 121.55 115.80 120.87 110.29 110.37 111.79 123.33 * * Residue-by-residue listing for refined_2 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 ----------------------------------------------------------------------------------------------------------------------------------- 73 LEU 73 1.293 1.234 1.501 1.516 1.448 122.97 115.14 121.09 111.08 112.20 109.91 123.77 +** * +** 74 LYS 74 1.304 1.239 1.512 1.531 1.434 122.57 116.60 120.31 109.43 108.14 109.34 123.06 +* * * +* 75 VAL 75 1.303 1.242 1.511 1.559 1.437 121.22 116.00 121.02 109.35 110.48 111.53 122.98 +* * +* 76 ASP 76 1.305 1.236 1.500 1.519 1.429 120.99 114.58 121.70 111.38 107.33 112.35 123.67 +* * +* * * +* 77 THR 77 1.291 1.232 1.530 1.538 1.442 124.19 117.16 120.35 111.60 113.75 110.62 122.49 +** * * +** 78 ASP 78 1.320 1.238 1.511 1.521 1.451 120.71 114.82 121.41 110.31 107.84 110.75 123.77 * * 79 GLU 79 1.330 1.238 1.522 1.517 1.428 123.23 115.56 121.28 107.89 110.45 109.95 123.13 +* * +* 80 LEU 80 1.327 1.240 1.519 1.517 1.423 123.45 115.31 121.48 110.98 111.60 109.21 123.15 +* +* 81 LYS 81 1.308 1.238 1.529 1.531 1.445 122.69 117.08 120.24 112.00 112.30 110.84 122.66 * * * 82 SER 82 1.322 1.232 1.527 1.510 1.446 120.99 115.90 120.88 110.66 109.62 110.31 123.19 83 VAL 83 1.334 1.228 1.523 1.559 1.459 122.19 115.34 121.34 109.47 108.74 111.63 123.30 84 ALA 84 1.327 1.220 1.525 1.516 1.449 122.45 116.27 120.55 110.33 110.55 110.17 123.15 85 SER 85 1.324 1.236 1.529 1.519 1.458 122.48 115.79 120.98 109.38 111.34 109.59 123.22 86 ASP 86 1.322 1.234 1.530 1.530 1.460 122.82 116.04 121.17 110.55 110.77 109.08 122.73 87 TRP 87 1.316 1.241 1.528 1.528 1.453 122.69 115.62 120.66 111.63 112.19 110.97 123.72 88 ALA 88 1.344 1.241 1.531 1.530 1.471 124.02 115.98 121.07 111.43 111.84 110.41 122.91 * * * 89 ILE 89 1.317 1.236 1.520 1.564 1.442 121.96 116.13 120.87 108.79 108.25 112.40 122.89 * * 90 GLN 90 1.305 1.233 1.516 1.522 1.438 121.05 115.97 121.34 110.75 109.59 110.61 122.69 +* * +* 91 ALA 91 1.311 1.230 1.503 1.510 1.432 120.89 115.67 121.25 111.40 108.60 110.98 123.08 * * * * 92 MET 92 1.281 1.235 1.515 1.533 1.432 121.97 119.31 119.43 110.16 107.10 107.91 121.25 *** * +* * +* * *** 93 PRO 93 1.332 1.232 1.551 1.522 1.457 124.92 116.81 120.93 109.80 112.42 101.57 122.19 * * * 94 THR 94 1.299 1.229 1.528 1.541 1.436 121.34 116.53 120.67 109.52 109.93 112.52 122.80 ** * ** 95 PHE 95 1.308 1.226 1.493 1.527 1.426 122.09 117.11 120.32 108.21 106.89 110.38 122.56 +* +* +* +* +* 96 MET 96 1.289 1.237 1.497 1.523 1.429 119.98 114.75 121.32 111.10 110.67 111.40 123.93 +** * +* +** 97 PHE 97 1.289 1.243 1.505 1.521 1.396 123.52 116.36 121.18 110.31 108.49 108.18 122.46 +** *** * * *** 98 LEU 98 1.284 1.219 1.511 1.564 1.411 120.35 117.00 120.71 112.75 109.89 113.07 122.28 *** +* ** * +* *** 99 LYS 99 1.286 1.231 1.495 1.524 1.426 120.94 114.81 120.78 111.86 110.02 108.83 124.35 *** * +* *** 100 GLU 100 1.325 1.231 1.539 1.527 1.463 124.64 116.07 121.17 109.91 110.90 111.45 122.74 +* +* 101 GLY 101 1.322 1.230 1.522 - 1.452 121.26 116.02 121.00 - 111.95 - 122.98 102 LYS 102 1.315 1.228 1.519 1.523 1.451 122.65 116.81 120.19 111.20 108.90 109.12 122.99 103 ILE 103 1.314 1.235 1.523 1.561 1.461 122.50 116.30 120.76 109.58 111.96 111.38 122.94 * * Residue-by-residue listing for refined_2 Page 10 ---------------------------------------- ................................................................................................................................... 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 ----------------------------------------------------------------------------------------------------------------------------------- 104 LEU 104 1.316 1.232 1.505 1.534 1.428 121.40 115.77 120.90 110.05 109.66 111.67 123.25 +* +* 105 ASP 105 1.302 1.220 1.488 1.525 1.436 122.33 115.67 121.20 110.66 111.10 112.11 123.11 +* +* * +* 106 LYS 106 1.286 1.230 1.507 1.539 1.434 121.65 115.77 120.65 110.53 110.56 110.19 123.58 *** * *** 107 VAL 107 1.300 1.232 1.496 1.560 1.436 122.62 116.47 120.21 108.13 106.12 111.52 123.30 ** * * +* ** 108 VAL 108 1.298 1.253 1.538 1.562 1.425 120.66 114.93 121.91 113.14 111.76 110.84 123.15 ** * +* +* ** 109 GLY 109 1.313 1.238 1.502 - 1.434 121.73 118.24 119.63 - 109.27 - 122.13 * * * * 110 ALA 110 1.316 1.226 1.505 1.524 1.436 118.31 115.26 121.26 110.68 109.24 110.88 123.48 * +* +* 111 LYS 111 1.303 1.230 1.503 1.508 1.419 123.29 117.46 119.79 109.23 108.65 109.10 122.74 +* * * ** ** 112 LYS 112 1.303 1.235 1.530 1.530 1.430 121.19 115.93 121.09 112.03 109.44 108.81 122.95 +* * * +* 113 ASP 113 1.322 1.228 1.524 1.528 1.460 121.45 116.84 120.47 110.94 112.17 111.38 122.67 114 GLU 114 1.325 1.227 1.529 1.525 1.460 121.15 117.14 120.22 110.96 111.02 111.10 122.64 115 LEU 115 1.333 1.226 1.509 1.520 1.459 121.11 114.81 121.29 108.32 108.97 111.04 123.88 116 GLN 116 1.317 1.233 1.523 1.528 1.466 122.31 115.71 120.93 110.11 110.74 111.11 123.36 117 SER 117 1.316 1.223 1.530 1.536 1.441 122.74 116.21 120.57 111.03 109.65 109.28 123.18 118 THR 118 1.322 1.238 1.533 1.543 1.450 122.83 116.57 120.99 111.52 110.93 110.20 122.39 * * 119 ILE 119 1.317 1.214 1.517 1.537 1.437 120.60 116.58 120.38 109.79 109.53 112.23 122.98 * * 120 ALA 120 1.324 1.230 1.526 1.519 1.459 121.80 116.06 120.91 111.44 110.96 111.12 123.03 121 LYS 121 1.319 1.220 1.535 1.497 1.404 123.80 116.70 120.90 111.67 111.40 106.98 122.40 +* +** * ** +** 122 HIS 122 1.320 1.237 1.518 1.519 1.446 121.76 116.46 120.09 109.44 112.30 111.23 123.44 123 LEU 123 1.328 1.240 1.523 1.532 1.431 122.96 115.25 121.53 111.72 109.70 108.93 123.18 * * 124 ALA 124 1.296 - 1.500 1.523 1.427 122.65 - - 110.96 108.34 110.60 - ** * +* * ** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** * ** ** *** ** ** * +* +* ** +* +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_2 Page 11 ---------------------------------------- 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 .014 119 1.274 1.352 1.313 .014 +*** +* * C-N (Pro) 1.341 .016 4 1.332 1.389 1.356 .023 *** C-O C-O 1.231 .020 123 1.214 1.253 1.232 .007 * CA-C CH1E-C (except Gly) 1.525 .021 119 1.486 1.574 1.521 .015 +* ** CH2G*-C (Gly) 1.516 .018 5 1.502 1.523 1.511 .010 CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.507 1.530 1.519 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.520 1.577 1.553 .014 * CH1E-CH2E (the rest) 1.530 .020 84 1.485 1.565 1.530 .016 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.396 1.473 1.444 .015 *** NH1-CH2G* (Gly) 1.451 .016 5 1.434 1.460 1.446 .009 * N-CH1E (Pro) 1.466 .015 4 1.457 1.492 1.472 .013 +* ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_2 Page 12 ---------------------------------------- +-----------------+ | 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 2.0 114 112.59 120.86 116.15 1.00 +* ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 116.02 118.75 117.31 1.02 * CH1E-C-N (Pro) 116.9 1.5 4 115.57 116.97 116.46 .54 O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.60 124.67 122.98 .60 +* * O-C-N (Pro) 122.0 1.4 4 122.19 123.33 122.64 .43 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 117.99 124.64 122.06 1.17 ** +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.08 122.60 121.22 .90 * C-N-CH1E (Pro) 122.6 5.0 4 122.72 124.92 123.55 .82 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 118.53 122.73 120.82 .57 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.63 121.00 120.27 .55 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.03 111.44 110.79 .43 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 108.13 113.14 110.18 1.30 +* CH2E-CH1E-C (the rest) 110.1 1.9 84 107.89 113.88 110.68 1.18 * +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 106.12 116.25 110.10 1.67 +* +* NH1-CH2G*-C (Gly) 112.5 2.9 5 109.27 113.62 111.52 1.51 * N-CH1E-C (Pro) 111.8 2.5 4 111.38 114.43 112.86 1.11 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.17 111.12 110.61 .28 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.05 114.83 111.40 1.26 * +* N-CH1E-CH2E (Pro) 103.0 1.1 4 101.57 103.65 102.79 .76 * NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.98 113.07 110.14 1.37 ** +* ------------------------------------------------------------------------------------------------------------- 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_2 Page 13 ---------------------------------------- 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] 103 91.2% Residues in additional allowed regions [a,b,l,p] 10 8.8% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 113 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 5 Number of proline residues 4 ---- Total number of residues 124 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 113 91.2 83.8 10.0 .7 Inside b. Omega angle st dev 122 2.9 6.0 3.0 -1.0 BETTER c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 119 1.6 3.1 1.6 -1.0 Inside e. H-bond energy st dev 86 .8 .8 .2 .2 Inside f. Overall G-factor 124 .1 -.4 .3 1.6 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 4.8 18.1 6.5 -2.1 BETTER b. Chi-1 trans st dev 45 6.4 19.0 5.3 -2.4 BETTER c. Chi-1 gauche plus st dev 44 6.4 17.5 4.9 -2.3 BETTER d. Chi-1 pooled st dev 102 7.4 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 31 9.5 20.4 5.0 -2.2 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% 91.2 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.1 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .85 2 Residue-by-residue listing for refined_2 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.11 Chi1-chi2 distribution -.14 Chi1 only -.08 Chi3 & chi4 .46 Omega .08 ------ .01 ===== Main-chain covalent forces:- Main-chain bond lengths .04 Main-chain bond angles .45 ------ .28 ===== OVERALL AVERAGE .10 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.