Residue-by-residue listing for refined_13 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 - - 180.5 - 180.2 - - - - - - 180.4 - 34.5 - 2 GLY 2 - - - - - - - - - - - 182.6 - - - 3 HIS 3 l - - -58.7 - - - - - - - 185.7 - 32.4 - 4 HIS 4 a - 183.9 - - - - - - - - 179.8 - 34.4 - 5 HIS 5 b - 178.8 - - - - - - - - 176.6 - 32.7 - 6 HIS 6 b - - -68.7 - - - - - - - 182.4 -.6 33.6 - +* +* 7 HIS 7 B - 180.8 - - - - - - - - 176.9 - 33.7 - 8 HIS 8 B - - -69.8 - - - - - - - 176.2 -.5 34.5 - ** ** 9 LEU 9 S B 55.7 - - - - - - - - - 185.9 - 28.4 - * +* +* 10 GLU 10 B 58.9 - - 184.5 - - - - - - 174.5 -.8 36.5 - +* +* 11 MET 11 b - - -79.2 - - - - - - - 183.1 - 32.7 - 12 ALA 12 B - - - - - - - - - - 179.6 -1.3 33.6 - 13 SER 13 b - 182.9 - - - - - - - - 182.3 -1.0 33.9 - * * 14 GLU 14 b - 194.4 - - - - - - - - 181.2 -1.7 34.3 - 15 GLU 15 S b 55.1 - - 181.2 - - - - - - 182.9 -1.7 34.3 - 16 GLY 16 S - - - - - - - - - - - 180.7 -2.2 - - 17 GLN 17 B 43.6 - - 179.2 - - - - - - 182.1 - 31.9 - * * 18 VAL 18 B - 180.9 - - - - - - - - 178.0 - 35.8 - 19 ILE 19 E B - - -60.1 - - - - - - - 179.8 -3.2 33.6 - +* +* 20 ALA 20 E B - - - - - - - - - - 181.1 -.8 33.8 - +* +* Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 21 CYS 21 E B - - -51.2 - - - - - - - 178.1 -2.0 35.3 - * * 22 HIS 22 A - - -60.6 - - - - - - - 183.7 -.7 34.8 - +* +* 23 THR 23 h B - - -36.9 - - - - - - - 180.9 - 36.8 - +* +* 24 VAL 24 H A 64.2 - - - - -76.4 -24.3 - - - 176.2 - 32.0 - * * 25 GLU 25 H A - 178.9 - 188.8 - -57.7 -52.3 - - - 181.2 - 36.4 - * * 26 THR 26 H A - - -51.2 - - -65.3 -41.3 - - - 178.5 - 35.4 - * * 27 TRP 27 H A - 172.1 - - - -53.5 -54.1 - - - 180.4 -1.8 34.0 - * * 28 ASN 28 H A - 183.3 - - - -68.2 -44.6 - - - 182.9 -2.7 34.5 - 29 GLU 29 H A - 180.4 - 176.1 - -58.6 -46.4 - - - 180.1 -2.7 33.2 - 30 GLN 30 H A - - -71.9 - - -65.3 -39.2 - - - 178.1 -3.2 33.1 - +* +* 31 LEU 31 H A - - -69.0 180.1 - -68.9 -41.1 - - - 177.2 -1.5 34.6 - 32 GLN 32 H A - 182.8 - - - -59.3 -46.4 - - - 178.3 -2.9 34.7 - * * 33 LYS 33 H A - 176.8 - 179.4 - -61.2 -45.3 - - - 181.4 -2.8 34.4 - * * 34 ALA 34 H A - - - - - -66.7 -32.6 - - - 181.5 -2.7 34.0 - 35 ASN 35 H A - 194.0 - - - -70.8 -54.5 - - - 182.7 -2.3 37.0 - * * 36 GLU 36 H A - - -59.3 181.6 - -62.8 -35.6 - - - 182.5 -2.7 33.6 - 37 SER 37 H A - - -53.2 - - -87.3 -10.2 - - - 183.9 -2.2 35.1 - +* +** +** 38 LYS 38 h l - - -62.4 182.0 - - - - - - 180.1 -.8 31.8 - +* +* 39 THR 39 t B - - -46.2 - - - - - - - 177.6 -2.4 35.7 - * * 40 LEU 40 E B - 179.4 - - - - - - - - 185.6 -.6 34.5 - +* +* 41 VAL 41 E B 59.5 - - - - - - - - - 178.3 -.5 33.0 - ** ** 42 VAL 42 E B - 181.1 - - - - - - - - 181.4 -3.2 34.4 - * * 43 VAL 43 E B - 180.3 - - - - - - - - 178.8 -3.1 34.4 - * * 44 ASP 44 E B - 178.8 - - - - - - - - 177.6 -3.1 36.2 - * * 45 PHE 45 E B - - -62.5 - - - - - - - 182.3 -2.9 35.1 - * * 46 THR 46 E B - - -63.7 - - - - - - - 173.5 -2.7 35.3 - * * 47 ALA 47 t B - - - - - - - - - - 180.8 - 35.1 - 48 SER 48 T A - - -61.0 - - - - - - - 181.9 - 34.3 - 49 TRP 49 T A 56.7 - - - - - - - - - 181.3 - 33.7 - 50 CYS 50 h B - 177.5 - 216.2 - - - 60.8 - 2.0 181.9 -2.5 34.0 - ** ** ** 51 GLY 51 H - - - - - - -65.4 -66.4 - - - 180.4 -.6 - - ** +* ** 52 PRO 52 H - - - - - -56.2 -56.2 -30.7 - - - 179.2 - 38.2 - * * Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 53 CYS 53 H A - - -54.5 - - -66.6 -38.0 60.8 - 2.0 178.0 - 35.2 - ** ** 54 ARG 54 H A - 183.5 - 181.7 - -78.4 -33.6 - - - 179.9 -1.3 33.6 - * * 55 PHE 55 H A - 180.5 - - - -63.6 -29.0 - - - 182.0 -2.5 33.7 - 56 ILE 56 h A - 194.9 - - - - - - - - 182.0 -1.5 34.2 - 57 ALA 57 H A - - - - - -59.3 -47.4 - - - 178.2 -.8 30.8 - +* +* 58 PRO 58 H - - - - - -57.6 -57.6 -32.0 - - - 180.6 - 38.7 - * * 59 PHE 59 H A - 190.2 - - - -73.7 -40.7 - - - 179.0 - 34.6 - 60 PHE 60 H A - 185.2 - - - -70.3 -34.5 - - - 176.6 -2.0 34.1 - 61 ALA 61 H A - - - - - -68.4 -28.3 - - - 177.4 -2.8 34.0 - * * 62 ASP 62 H A - 184.4 - - - -72.6 -43.6 - - - 176.1 -1.1 35.6 - * * 63 LEU 63 H A - - -66.1 181.6 - -53.4 -40.6 - - - 179.8 -2.1 35.2 - 64 ALA 64 H A - - - - - -63.9 -34.6 - - - 177.8 -1.7 33.5 - 65 LYS 65 H A - 187.4 - 181.8 - -80.7 -31.0 - - - 184.7 -.9 33.7 - * +* +* 66 LYS 66 H A - 191.9 - 184.1 - -70.9 -40.5 - - - 178.5 -2.4 35.5 - 67 LEU 67 h b - - -65.8 - - - - - - - 184.5 -2.6 33.2 - 68 PRO 68 T - - - - - -85.9 - - - - - 179.5 - 39.5 - +* +* +* 69 ASN 69 e a - 184.2 - - - - - - - - 183.8 - 34.8 - 70 VAL 70 E B - 181.6 - - - - - - - - 178.4 -1.1 34.2 - * * 71 LEU 71 E B - - -62.9 178.7 - - - - - - 177.9 -2.9 35.6 - * * 72 PHE 72 E B - - -60.5 - - - - - - - 182.7 -.7 34.3 - +* +* 73 LEU 73 E B - - -69.2 - - - - - - - 172.9 -2.5 34.2 - * * 74 LYS 74 E B - - -87.9 - - - - - - - 179.1 -2.3 34.7 - * * 75 VAL 75 E B - 179.9 - - - - - - - - 178.4 -3.0 34.9 - * * 76 ASP 76 E B - 181.2 - - - - - - - - 183.8 -1.1 32.7 - * * 77 THR 77 e A 57.5 - - - - - - - - - 179.2 -2.6 34.2 - 78 ASP 78 T A - 180.3 - - - - - - - - 174.0 - 34.2 - * * 79 GLU 79 T a - - -67.6 182.2 - - - - - - 180.1 - 34.2 - 80 LEU 80 h b - - -68.6 178.1 - - - - - - 180.0 -3.1 32.9 - * * 81 LYS 81 H A - - -59.1 180.3 - -68.7 -35.2 - - - 182.7 -1.8 34.6 - 82 SER 82 H A 51.9 - - - - -65.9 -28.9 - - - 178.6 - 33.3 - 83 VAL 83 H A - 178.8 - - - -72.9 -51.9 - - - 179.3 - 33.7 - * * 84 ALA 84 H A - - - - - -58.8 -42.2 - - - 182.2 -1.4 34.5 - 85 SER 85 H A - 184.7 - - - -69.9 -30.5 - - - 182.8 -2.7 33.9 - 86 ASP 86 H A - 187.0 - - - -74.2 -37.2 - - - 181.2 -1.3 36.0 - 87 TRP 87 h A - - -65.0 - - - - - - - 176.9 -2.1 32.7 - 88 ALA 88 T l - - - - - - - - - - 181.6 -.8 32.8 - +* +* 89 ILE 89 t B - - -57.5 179.2 - - - - - - 178.6 -2.6 34.2 - Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 90 GLN 90 A 53.3 - - 177.2 - - - - - - 179.6 -.7 34.0 - +* +* 91 ALA 91 S B - - - - - - - - - - 183.8 - 33.5 - 92 MET 92 S B - - -59.7 175.6 - - - - - - .7 - 35.5 - 93 PRO 93 e cis - - - - - -83.7 - - - - - 177.4 - 39.0 - +* * +* 94 THR 94 E B - - -55.0 - - - - - - - 178.3 -1.1 35.1 - * * 95 PHE 95 E B - - -50.8 - - - - - - - 181.7 -3.1 36.8 - * * * 96 MET 96 E B - 177.1 - 181.0 - - - - - - 183.4 -3.7 34.6 - ** ** 97 PHE 97 E B - - -70.2 - - - - - - - 177.4 -3.5 36.1 - +* +* 98 LEU 98 E B - - -54.3 - - - - - - - 175.7 -2.5 35.0 - 99 LYS 99 E B - 180.1 - 187.6 - - - - - - 176.3 -3.3 34.8 - +* +* 100 GLU 100 T l - - -60.1 179.0 - - - - - - 180.8 - 33.5 - 101 GLY 101 T - - - - - - - - - - - 175.2 - - - 102 LYS 102 E B - - -66.9 - - - - - - - 181.1 -2.2 34.3 - 103 ILE 103 E B - - -61.4 172.5 - - - - - - 177.8 - 34.7 - 104 LEU 104 E a - - -67.9 188.5 - - - - - - 185.9 -2.0 32.6 - * * 105 ASP 105 E B 59.3 - - - - - - - - - 177.0 -2.1 33.1 - 106 LYS 106 E B 57.8 - - - - - - - - - 178.6 - 31.3 - 107 VAL 107 E B - 181.6 - - - - - - - - 180.1 -2.8 34.9 - 108 VAL 108 E B - 180.0 - - - - - - - - 181.1 - 34.0 - 109 GLY 109 e - - - - - - - - - - - 187.3 -3.3 - - * +* +* 110 ALA 110 B - - - - - - - - - - 166.9 - 34.2 - ** ** 111 LYS 111 h B - - -70.3 188.4 - - - - - - 187.1 -.8 31.3 - * +* +* 112 LYS 112 H A - 185.6 - 180.2 - -67.8 -34.7 - - - 185.7 - 34.9 - 113 ASP 113 H A - 186.7 - - - -72.1 -47.0 - - - 180.6 - 30.8 - 114 GLU 114 H A - - -61.8 - - -61.9 -38.7 - - - 180.8 - 32.4 - 115 LEU 115 H A - 186.9 - - - -57.7 -52.9 - - - 177.3 -1.2 34.8 - * * * 116 GLN 116 H A - - -62.3 183.6 - -60.4 -37.7 - - - 180.9 -1.8 33.6 - 117 SER 117 H A - - -55.5 - - -67.5 -30.7 - - - 178.1 -2.5 33.9 - 118 THR 118 H A - - -58.0 - - -75.1 -30.0 - - - 176.2 -2.2 33.9 - 119 ILE 119 H A - - -56.0 176.6 - -64.6 -46.4 - - - 178.3 -1.5 34.3 - 120 ALA 120 H A - - - - - -66.6 -31.1 - - - 175.7 -2.1 32.9 - 121 LYS 121 H A - 188.5 - 186.8 - -60.8 -44.0 - - - 179.8 -1.5 36.7 - 122 HIS 122 h A - - -73.9 - - - - - - - 175.8 -2.1 32.5 - 123 LEU 123 t A - 198.6 - - - - - - - - 179.7 -.7 34.7 - +* +* 124 ALA 124 t - - - - - - - - - - - - -1.0 33.9 - * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * +* ** +* +* +** ** ** ** +* +** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_13 Page 5 ---------------------------------------- ................................................................................................................................... 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 ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.1 183.4 -62.1 182.3 -70.8 -66.4 -39.1 60.8 - 2.0 179.9 -2.0 34.3 ** ** Standard deviations: 5.1 5.4 8.6 7.3 16.1 7.3 9.8 .0 - .0 3.1 .9 1.6 Numbers of values: 12 44 46 32 4 45 45 2 0 2 122 85 119 0 Number of cis-peptides (labelled cis): 1 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_13 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 1.538 1.453 - 116.05 120.68 110.27 109.19 110.61 123.27 2 GLY 2 1.303 1.228 1.487 - 1.423 121.72 116.70 119.22 - 109.97 - 124.08 +* +* +* +* 3 HIS 3 1.331 1.236 1.520 1.539 1.477 123.50 116.00 121.63 111.04 110.05 112.36 122.35 * * * 4 HIS 4 1.288 1.228 1.532 1.546 1.433 121.18 116.37 120.66 112.74 110.80 107.94 122.94 +** * * +* +** 5 HIS 5 1.325 1.233 1.538 1.545 1.464 121.76 115.53 121.23 110.69 111.97 111.73 123.22 6 HIS 6 1.311 1.234 1.513 1.548 1.456 123.91 116.73 120.57 109.53 109.14 112.69 122.69 * * * * 7 HIS 7 1.311 1.226 1.512 1.546 1.449 121.38 115.56 121.04 110.74 110.55 110.96 123.39 * * 8 HIS 8 1.294 1.241 1.504 1.554 1.451 123.50 117.56 119.65 109.58 107.91 111.93 122.77 ** * * * ** 9 LEU 9 1.313 1.236 1.521 1.570 1.430 119.61 115.04 122.18 116.30 109.69 113.31 122.64 * +* * * *** +* *** 10 GLU 10 1.291 1.237 1.494 1.535 1.421 122.00 116.33 120.21 109.72 109.02 108.60 123.43 +** * +* * +** 11 MET 11 1.300 1.233 1.493 1.525 1.432 120.98 115.04 121.65 111.02 108.63 112.72 123.24 ** +* * * ** 12 ALA 12 1.285 1.235 1.494 1.519 1.424 121.67 115.58 121.10 111.06 109.87 110.97 123.29 *** * +* *** Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 13 SER 13 1.295 1.239 1.523 1.546 1.418 121.73 115.48 121.54 112.01 108.32 110.23 122.83 ** ** * * ** 14 GLU 14 1.317 1.240 1.527 1.536 1.438 121.44 114.99 121.41 110.99 108.50 110.41 123.30 * * 15 GLU 15 1.304 1.235 1.502 1.535 1.441 123.85 116.78 120.09 110.89 108.28 110.59 123.09 +* * * * +* 16 GLY 16 1.316 1.229 1.508 - 1.452 120.12 114.86 121.62 - 110.67 - 123.52 17 GLN 17 1.306 1.231 1.491 1.539 1.424 123.82 114.25 121.44 112.10 110.79 112.23 124.28 +* +* +* * * * +* 18 VAL 18 1.286 1.231 1.515 1.560 1.440 123.86 118.07 119.46 109.21 107.71 110.41 122.43 *** * * *** 19 ILE 19 1.312 1.239 1.517 1.565 1.432 119.90 116.53 120.77 109.18 108.35 113.70 122.70 * * * * * 20 ALA 20 1.296 1.234 1.510 1.518 1.434 120.99 116.62 120.72 111.06 109.61 110.55 122.65 ** * ** 21 CYS 21 1.303 1.233 1.504 1.503 1.413 121.09 115.81 121.08 109.43 109.05 110.14 123.09 +* * * ** ** 22 HIS 22 1.292 1.229 1.501 1.535 1.445 121.83 115.39 121.58 109.73 108.37 110.96 123.01 +** * * +** 23 THR 23 1.319 1.242 1.519 1.531 1.433 121.12 116.62 120.23 107.17 107.78 110.58 123.14 * * * 24 VAL 24 1.305 1.236 1.534 1.568 1.456 121.41 115.61 121.13 111.66 109.78 112.73 123.23 +* * * +* 25 GLU 25 1.345 1.230 1.520 1.530 1.459 122.14 115.04 120.81 107.92 109.28 109.95 124.09 * * * 26 THR 26 1.330 1.222 1.519 1.535 1.444 123.19 115.71 120.58 109.91 110.14 109.36 123.68 * * 27 TRP 27 1.326 1.236 1.533 1.537 1.450 122.83 116.51 120.65 111.44 111.49 109.35 122.82 28 ASN 28 1.318 1.237 1.524 1.529 1.458 120.85 115.51 120.87 109.14 110.56 111.11 123.61 29 GLU 29 1.324 1.234 1.531 1.530 1.461 123.18 117.01 120.07 111.16 112.40 110.26 122.90 30 GLN 30 1.323 1.226 1.506 1.492 1.426 122.29 117.05 120.19 111.12 112.72 110.29 122.75 +* +* +* 31 LEU 31 1.321 1.224 1.502 1.487 1.412 121.52 115.79 120.60 110.52 110.82 109.50 123.60 * ** ** ** 32 GLN 32 1.318 1.232 1.530 1.538 1.444 122.03 115.09 121.22 110.62 108.88 110.07 123.63 33 LYS 33 1.325 1.238 1.532 1.535 1.448 123.26 116.92 120.23 110.46 111.38 109.77 122.84 34 ALA 34 1.333 1.234 1.519 1.520 1.457 121.73 115.69 120.75 110.22 111.17 110.50 123.55 35 ASN 35 1.321 1.234 1.513 1.527 1.457 122.58 115.24 121.26 107.98 109.41 108.98 123.45 * * 36 GLU 36 1.319 1.232 1.523 1.527 1.470 122.29 116.59 120.73 109.54 112.12 111.46 122.67 37 SER 37 1.311 1.237 1.536 1.515 1.438 121.19 116.21 120.29 110.22 111.75 108.74 123.48 * * * * 38 LYS 38 1.342 1.238 1.514 1.521 1.469 123.16 114.89 121.98 111.15 110.50 112.83 123.12 * * 39 THR 39 1.295 1.242 1.516 1.532 1.413 121.66 115.69 121.01 108.49 108.23 110.95 123.27 ** ** * ** 40 LEU 40 1.281 1.233 1.532 1.552 1.431 122.50 116.82 120.37 112.33 106.93 109.40 122.76 *** * * * +* *** 41 VAL 41 1.310 1.240 1.533 1.567 1.439 121.22 115.65 121.21 111.68 111.87 110.66 123.13 * * * * 42 VAL 42 1.310 1.239 1.518 1.539 1.436 122.72 116.17 120.90 109.25 108.92 111.98 122.92 * * * 43 VAL 43 1.298 1.224 1.515 1.547 1.436 121.72 115.92 120.84 109.02 110.04 111.89 123.24 ** * ** Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 44 ASP 44 1.287 1.243 1.520 1.524 1.440 122.90 116.60 120.68 109.70 108.75 108.70 122.70 *** * *** 45 PHE 45 1.303 1.237 1.526 1.523 1.420 121.67 115.93 120.85 110.28 109.73 109.49 123.18 +* ** ** 46 THR 46 1.310 1.216 1.522 1.561 1.442 123.17 115.87 121.12 109.48 110.09 110.22 122.97 * * 47 ALA 47 1.292 1.232 1.504 1.513 1.421 122.66 117.24 119.31 110.41 106.56 110.23 123.43 +** +* +* +** 48 SER 48 1.322 1.237 1.542 1.527 1.474 122.85 116.05 121.08 109.79 112.66 109.88 122.83 49 TRP 49 1.315 1.222 1.535 1.539 1.451 122.55 117.12 120.69 111.15 112.27 109.76 122.20 * * 50 CYS 50 1.311 1.238 1.528 1.530 1.446 121.23 115.52 120.89 110.79 111.09 110.13 123.57 * * 51 GLY 51 1.324 1.232 1.526 - 1.460 122.59 118.87 119.71 - 113.84 - 121.41 * * * 52 PRO 52 1.361 1.231 1.531 1.539 1.478 122.87 115.76 121.12 110.49 112.08 103.98 123.11 * * 53 CYS 53 1.318 1.227 1.531 1.522 1.454 122.35 116.50 121.17 109.43 110.24 109.89 122.33 54 ARG 54 1.316 1.222 1.525 1.526 1.442 120.70 115.91 121.12 110.41 109.74 111.46 122.95 55 PHE 55 1.322 1.231 1.535 1.543 1.459 122.45 116.83 120.76 110.75 111.52 110.42 122.38 56 ILE 56 1.318 1.238 1.551 1.571 1.453 120.77 115.86 121.47 110.14 109.89 111.08 122.62 * * * 57 ALA 57 1.329 1.217 1.552 1.528 1.457 122.23 120.57 118.84 111.97 113.80 111.99 120.59 * ** * * +* ** 58 PRO 58 1.382 1.236 1.534 1.534 1.483 122.03 116.18 120.93 109.81 112.38 103.78 122.87 +** * +** 59 PHE 59 1.324 1.225 1.535 1.543 1.447 121.76 115.79 121.15 110.97 108.63 109.95 123.03 60 PHE 60 1.325 1.231 1.540 1.539 1.465 122.74 116.23 121.14 111.52 110.41 109.36 122.62 61 ALA 61 1.319 1.235 1.526 1.524 1.460 121.84 115.36 121.51 110.58 109.81 110.55 123.12 62 ASP 62 1.320 1.222 1.494 1.508 1.458 122.64 114.65 121.21 109.25 108.72 109.79 124.13 * * * 63 LEU 63 1.320 1.229 1.532 1.532 1.437 123.74 115.95 120.68 110.11 110.89 109.13 123.34 * * * 64 ALA 64 1.323 1.230 1.525 1.516 1.454 122.52 117.03 120.74 110.50 112.13 110.47 122.19 65 LYS 65 1.316 1.233 1.527 1.534 1.446 120.31 115.18 121.35 110.23 110.01 111.43 123.47 66 LYS 66 1.318 1.244 1.535 1.532 1.445 123.07 116.54 120.68 110.30 110.75 108.59 122.77 * * 67 LEU 67 1.327 1.227 1.536 1.545 1.434 122.00 117.33 120.91 110.36 110.15 112.14 121.76 * * 68 PRO 68 1.338 1.238 1.538 1.524 1.466 123.26 116.59 120.98 110.18 113.56 102.01 122.43 69 ASN 69 1.304 1.228 1.527 1.541 1.463 121.76 115.38 121.98 110.77 109.16 109.50 122.62 +* +* 70 VAL 70 1.308 1.233 1.515 1.551 1.442 122.11 116.40 120.56 110.30 109.87 110.94 122.96 +* +* 71 LEU 71 1.307 1.230 1.514 1.526 1.421 121.78 116.51 120.61 109.59 109.24 109.72 122.86 +* +* +* 72 PHE 72 1.303 1.235 1.499 1.515 1.442 121.52 116.06 120.68 109.43 109.00 111.62 123.26 +* * +* 73 LEU 73 1.289 1.217 1.510 1.549 1.437 122.18 115.48 120.82 108.45 111.82 112.20 123.69 +** * +** 74 LYS 74 1.307 1.235 1.506 1.528 1.426 124.06 116.19 120.70 109.95 108.41 110.93 123.06 +* +* * +* 75 VAL 75 1.291 1.235 1.512 1.559 1.438 121.94 116.61 120.12 109.50 108.82 111.20 123.25 +** * +** Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 76 ASP 76 1.321 1.239 1.510 1.516 1.452 120.92 115.28 121.10 110.69 109.89 112.28 123.61 * * 77 THR 77 1.304 1.236 1.533 1.529 1.447 123.55 116.97 120.52 109.70 112.98 110.19 122.50 +* * +* 78 ASP 78 1.324 1.235 1.496 1.524 1.456 121.10 114.56 121.68 110.51 108.18 111.02 123.76 * * * 79 GLU 79 1.302 1.233 1.527 1.506 1.408 122.87 116.87 120.70 111.55 110.70 109.14 122.42 +* * +** +** 80 LEU 80 1.311 1.245 1.523 1.508 1.419 122.21 114.99 121.69 111.51 112.45 110.38 123.30 * * ** ** 81 LYS 81 1.314 1.235 1.519 1.530 1.454 122.60 115.52 121.20 109.71 110.72 110.43 123.27 * * 82 SER 82 1.318 1.227 1.523 1.526 1.447 122.64 116.69 120.41 111.82 112.35 109.62 122.89 83 VAL 83 1.319 1.226 1.525 1.554 1.446 121.40 116.14 120.97 110.53 109.50 111.62 122.83 84 ALA 84 1.322 1.227 1.522 1.518 1.461 122.06 116.24 120.71 109.96 110.82 110.08 123.01 85 SER 85 1.317 1.230 1.538 1.535 1.436 121.54 116.70 120.36 111.52 110.91 109.59 122.91 * * 86 ASP 86 1.328 1.227 1.513 1.528 1.471 121.98 115.72 121.29 108.37 110.52 109.64 122.97 87 TRP 87 1.312 1.232 1.521 1.523 1.441 122.25 115.65 120.53 111.55 111.95 110.76 123.82 * * 88 ALA 88 1.342 1.236 1.524 1.532 1.474 123.97 115.97 120.89 111.11 112.30 110.95 123.04 * * 89 ILE 89 1.310 1.239 1.526 1.553 1.443 122.73 115.51 121.04 109.97 110.41 111.09 123.42 * * 90 GLN 90 1.311 1.227 1.528 1.531 1.442 123.01 116.25 121.13 110.81 110.64 110.31 122.61 * * 91 ALA 91 1.312 1.234 1.505 1.519 1.437 121.64 115.96 120.76 111.34 109.02 111.04 123.28 * * * 92 MET 92 1.302 1.227 1.515 1.527 1.435 122.41 118.88 119.50 111.00 108.96 108.45 121.62 +* * * * +* 93 PRO 93 1.342 1.240 1.516 1.523 1.456 123.99 115.87 121.22 110.39 111.94 103.03 122.87 94 THR 94 1.280 1.228 1.507 1.520 1.408 121.26 116.49 120.34 109.92 108.41 110.36 123.16 +*** +** +*** 95 PHE 95 1.297 1.224 1.497 1.533 1.402 121.78 116.84 120.18 109.15 105.61 109.52 122.96 ** * +** +* +** 96 MET 96 1.281 1.230 1.503 1.528 1.430 121.79 114.82 121.48 111.81 108.92 109.16 123.70 *** * * *** 97 PHE 97 1.276 1.246 1.499 1.508 1.398 123.95 115.59 121.52 109.53 110.77 108.74 122.89 +*** * * *** * * +*** 98 LEU 98 1.283 1.221 1.511 1.556 1.417 121.10 117.15 120.08 107.75 106.96 113.48 122.77 *** * ** * +* +* *** 99 LYS 99 1.287 1.228 1.483 1.520 1.429 121.57 115.33 120.36 108.61 108.59 112.10 124.24 +** ** +* +** 100 GLU 100 1.322 1.227 1.541 1.523 1.450 123.64 116.15 120.91 111.20 112.07 109.94 122.88 * * 101 GLY 101 1.325 1.230 1.531 - 1.456 121.44 117.14 120.40 - 113.72 - 122.46 102 LYS 102 1.316 1.220 1.513 1.537 1.460 122.00 117.01 120.08 110.00 109.72 110.91 122.91 103 ILE 103 1.318 1.234 1.520 1.559 1.464 121.96 116.83 120.73 108.93 110.29 111.53 122.43 104 LEU 104 1.304 1.237 1.498 1.518 1.420 120.12 116.66 120.54 110.54 111.82 112.21 122.77 +* * +* * +* 105 ASP 105 1.298 1.218 1.490 1.521 1.439 120.67 115.29 121.21 109.81 112.68 111.86 123.44 ** +* ** 106 LYS 106 1.297 1.240 1.526 1.571 1.441 121.96 116.33 120.56 113.27 110.69 111.93 123.08 ** ** +* ** Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 107 VAL 107 1.304 1.230 1.524 1.564 1.452 122.92 117.15 120.09 109.17 108.48 111.52 122.75 +* +* 108 VAL 108 1.316 1.240 1.529 1.535 1.452 121.49 116.31 120.64 109.47 110.93 111.41 123.05 109 GLY 109 1.315 1.236 1.501 - 1.443 121.24 117.46 119.76 - 109.61 - 122.76 * * 110 ALA 110 1.310 1.241 1.506 1.517 1.441 120.33 114.62 121.53 109.25 113.68 110.54 123.83 * * 111 LYS 111 1.295 1.236 1.506 1.519 1.404 124.00 116.68 120.44 112.98 107.43 113.28 122.88 ** +** * +* * +* +** 112 LYS 112 1.289 1.241 1.539 1.519 1.430 122.42 116.63 120.67 110.97 112.46 108.14 122.69 +** * * +** 113 ASP 113 1.319 1.235 1.539 1.528 1.461 121.11 119.15 119.12 111.41 114.46 112.26 121.73 * * * * 114 GLU 114 1.354 1.227 1.491 1.541 1.495 119.61 116.00 120.35 107.04 110.96 116.06 123.65 +* +* +* * +* *** *** 115 LEU 115 1.313 1.228 1.516 1.512 1.441 122.08 115.50 120.92 110.21 109.74 109.86 123.55 * * 116 GLN 116 1.317 1.233 1.525 1.519 1.472 121.72 116.17 120.88 109.12 111.36 111.88 122.93 117 SER 117 1.319 1.235 1.530 1.532 1.455 121.38 115.43 121.40 111.12 109.89 110.23 123.14 118 THR 118 1.308 1.235 1.545 1.537 1.428 122.49 116.64 121.02 111.33 110.23 110.07 122.31 +* +* * +* 119 ILE 119 1.324 1.227 1.526 1.547 1.453 121.05 115.65 120.93 109.03 108.60 112.36 123.35 120 ALA 120 1.332 1.231 1.521 1.518 1.461 122.24 115.85 120.80 111.40 110.69 110.96 123.35 121 LYS 121 1.323 1.217 1.519 1.501 1.453 122.73 115.24 121.57 108.28 108.54 108.94 123.18 * * 122 HIS 122 1.319 1.224 1.517 1.520 1.442 122.88 117.44 120.16 110.93 113.23 111.19 122.39 123 LEU 123 1.329 1.226 1.545 1.519 1.432 121.74 113.93 123.28 114.26 107.95 106.42 122.74 * * * ** * ** ** 124 ALA 124 1.281 - 1.524 1.520 1.443 123.64 - - 110.96 109.68 110.49 - *** * *** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** ** ** *** * ** * *** +* *** +* +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_13 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 1.276 1.354 1.311 .015 +*** +* * C-N (Pro) 1.341 .016 4 1.338 1.382 1.356 .018 +** C-O C-O 1.231 .020 123 1.216 1.246 1.232 .006 CA-C CH1E-C (except Gly) 1.525 .021 119 1.483 1.552 1.520 .014 ** * CH2G*-C (Gly) 1.516 .018 5 1.487 1.531 1.511 .016 +* CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.513 1.532 1.520 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.520 1.571 1.549 .015 * CH1E-CH2E (the rest) 1.530 .020 84 1.487 1.571 1.530 .014 ** ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.398 1.495 1.443 .017 *** +* NH1-CH2G* (Gly) 1.451 .016 5 1.423 1.460 1.447 .013 +* N-CH1E (Pro) 1.466 .015 4 1.456 1.483 1.471 .011 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_13 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 2.0 114 113.93 120.57 116.13 .94 * ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 114.86 118.87 117.01 1.30 * CH1E-C-N (Pro) 116.9 1.5 4 115.76 116.59 116.10 .32 O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.59 124.28 123.01 .56 +* O-C-N (Pro) 122.0 1.4 4 122.43 123.11 122.82 .24 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 119.61 124.06 122.09 .99 * * C-NH1-CH2G* (Gly) 120.6 1.7 5 120.12 122.59 121.42 .80 * C-N-CH1E (Pro) 122.6 5.0 4 122.03 123.99 123.04 .71 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 118.84 123.28 120.83 .61 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.22 121.62 120.14 .83 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 109.25 111.97 110.76 .68 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 107.17 111.68 109.68 1.01 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.04 116.30 110.49 1.38 +* *** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 105.61 114.46 110.12 1.63 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 109.61 113.84 111.56 1.84 N-CH1E-C (Pro) 111.8 2.5 4 111.94 113.56 112.49 .64 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.08 111.99 110.72 .46 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.36 113.70 111.17 .96 * * N-CH1E-CH2E (Pro) 103.0 1.1 4 102.01 103.98 103.20 .77 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.42 116.06 110.54 1.52 ** *** ------------------------------------------------------------------------------------------------------------- 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_13 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] 97 85.8% Residues in additional allowed regions [a,b,l,p] 16 14.2% 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 85.8 83.8 10.0 .2 Inside b. Omega angle st dev 122 3.1 6.0 3.0 -1.0 Inside 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 85 .9 .8 .2 .4 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 12 5.1 18.1 6.5 -2.0 BETTER b. Chi-1 trans st dev 44 5.4 19.0 5.3 -2.6 BETTER c. Chi-1 gauche plus st dev 46 8.6 17.5 4.9 -1.8 BETTER d. Chi-1 pooled st dev 102 7.9 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 32 7.3 20.4 5.0 -2.6 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% 85.8 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.8 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .88 3 Residue-by-residue listing for refined_13 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.16 Chi1-chi2 distribution .00 Chi1 only -.01 Chi3 & chi4 .39 Omega .12 ------ .03 ===== Main-chain covalent forces:- Main-chain bond lengths -.03 Main-chain bond angles .46 ------ .26 ===== OVERALL AVERAGE .10 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.