Residue-by-residue listing for refined_3 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 - - - -69.2 - - - - - - - 183.4 - 31.7 - 2 GLY 2 - - - - - - - - - - - 182.6 - - - 3 HIS 3 B 61.5 - - - - - - - - - 173.9 - 33.8 - * * 4 HIS 4 b 55.9 - - - - - - - - - 185.2 - 29.9 - * * 5 HIS 5 A - - -61.6 - - - - - - - 180.2 - 34.2 - 6 HIS 6 S B 55.3 - - - - - - - - - 187.1 - 31.8 - * * 7 HIS 7 S b - 187.9 - - - - - - - - 178.1 - 32.6 - 8 HIS 8 S B - - -88.5 - - - - - - - 175.5 -.5 34.4 - * ** ** 9 LEU 9 t A - - -67.5 - - - - - - - 175.1 - 33.4 - 10 GLU 10 T l - 192.1 - 186.4 - - - - - - 182.1 - 34.0 - 11 MET 11 T l - 185.7 - 176.7 - - - - - - 181.0 - 32.8 - 12 ALA 12 t B - - - - - - - - - - 178.7 -2.0 33.7 - 13 SER 13 B - - -55.5 - - - - - - - 172.9 -.6 36.0 - * +* +* 14 GLU 14 S b - 183.3 - 176.7 - - - - - - 189.1 - 33.4 - +* +* 15 GLU 15 B 61.6 - - 187.7 - - - - - - 176.8 -1.5 36.5 - 16 GLY 16 S - - - - - - - - - - - 180.8 - - - 17 GLN 17 B 49.1 - - 182.1 - - - - - - 184.0 - 30.8 - 18 VAL 18 B - 180.4 - - - - - - - - 180.4 - 36.0 - 19 ILE 19 E B - - -59.5 178.6 - - - - - - 179.6 -2.5 34.1 - 20 ALA 20 E B - - - - - - - - - - 179.3 -.8 34.1 - +* +* 21 CYS 21 E B - - -58.7 - - - - - - - 181.4 -1.4 34.8 - Residue-by-residue listing for refined_3 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 HIS 22 a - - -58.2 - - - - - - - 179.3 - 34.1 - 23 THR 23 h B 53.3 - - - - - - - - - 178.1 - 34.9 - 24 VAL 24 H A 62.8 - - - - -71.9 -23.4 - - - 178.4 - 32.7 - * * 25 GLU 25 H A - 189.2 - - - -63.1 -50.9 - - - 177.3 - 35.0 - * * 26 THR 26 H A - - -58.7 - - -67.9 -40.5 - - - 179.6 - 34.3 - 27 TRP 27 H A - 169.3 - - - -53.2 -53.2 - - - 181.2 -2.2 34.5 - * * * 28 ASN 28 H A - 186.1 - - - -61.0 -38.3 - - - 179.8 -2.8 34.9 - * * 29 GLU 29 H A - 178.5 - 177.6 - -63.6 -46.6 - - - 180.1 -1.4 34.5 - 30 GLN 30 H A - - -60.3 - - -60.5 -43.5 - - - 179.4 -2.7 35.3 - 31 LEU 31 H A - - -67.8 180.5 - -66.3 -44.9 - - - 177.1 -2.2 34.2 - 32 GLN 32 H A - 176.6 - 183.6 - -54.7 -46.7 - - - 180.0 -2.6 35.0 - 33 LYS 33 H A - 180.8 - 176.1 - -62.4 -43.2 - - - 180.3 -2.6 33.7 - 34 ALA 34 H A - - - - - -70.5 -37.9 - - - 181.6 -2.4 33.9 - 35 ASN 35 H A - 187.0 - - - -65.3 -53.8 - - - 181.7 -3.3 37.1 - * +* +* 36 GLU 36 H A - 180.5 - 178.1 - -64.3 -36.9 - - - 180.4 -3.1 32.9 - * * 37 SER 37 H A - - -52.8 - - -83.7 -10.1 - - - 179.7 -1.8 34.7 - +* +** +** 38 LYS 38 h L - - -62.9 182.7 - - - - - - 178.7 -.7 32.0 - +* +* 39 THR 39 t B - - -47.8 - - - - - - - 181.7 -1.8 34.8 - * * 40 LEU 40 e B - 190.4 - 173.7 - - - - - - 182.8 - 34.8 - 41 VAL 41 E B 59.5 - - - - - - - - - 177.9 - 33.5 - 42 VAL 42 E B - 179.8 - - - - - - - - 183.2 -2.9 34.0 - * * 43 VAL 43 E B - 182.9 - - - - - - - - 176.8 -2.9 35.5 - * * 44 ASP 44 E B 71.2 - - - - - - - - - 176.2 -2.1 34.3 - 45 PHE 45 E B - - -62.9 - - - - - - - 186.6 -3.3 35.4 - * +* +* 46 THR 46 E B - 184.3 - - - - - - - - 176.1 -2.7 36.3 - 47 ALA 47 t B - - - - - - - - - - 182.4 - 33.4 - 48 SER 48 T A - - -53.1 - - - - - - - 178.7 - 34.3 - 49 TRP 49 T A 53.7 - - - - - - - - - 184.0 - 31.7 - 50 CYS 50 h B - 173.5 - 222.3 - - - 50.5 - 2.0 183.2 -1.9 33.7 - ** *** *** 51 GLY 51 H - - - - - - -55.0 -69.7 - - - 180.7 -.5 - - +** ** +** 52 PRO 52 H - - - - - -59.7 -59.7 -30.6 - - - 180.8 - 38.3 - * * 53 CYS 53 H A - - -53.0 - - -69.5 -39.4 50.5 - 2.0 178.5 - 35.7 - *** *** 54 ARG 54 H A - 186.7 - 179.4 - -78.5 -29.5 - - - 178.1 -2.4 32.9 - * * 55 PHE 55 H A - 179.5 - - - -68.3 -30.6 - - - 181.6 -2.3 34.5 - 56 ILE 56 H A - 192.5 - - - -87.7 -14.8 - - - 180.9 -1.6 33.6 - +* ** ** 57 ALA 57 H A - - - - - -58.2 -48.5 - - - 177.2 -.6 31.4 - +* +* 58 PRO 58 H - - - - - -59.1 -59.1 -33.1 - - - 179.8 - 38.5 - * * Residue-by-residue listing for refined_3 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 PHE 59 H A - 185.7 - - - -69.2 -35.8 - - - 177.4 - 33.9 - 60 PHE 60 H A - 187.7 - - - -73.2 -33.3 - - - 175.3 -1.7 33.4 - 61 ALA 61 H A - - - - - -67.8 -36.7 - - - 174.7 -2.2 33.7 - 62 ASP 62 H A - 176.5 - - - -62.0 -46.7 - - - 176.3 -2.3 35.9 - 63 LEU 63 H A - 208.1 - 182.7 - -53.2 -47.4 - - - 177.4 -2.2 37.0 - * * * 64 ALA 64 H A - - - - - -60.4 -31.2 - - - 178.7 -2.1 33.7 - 65 LYS 65 H A - 184.6 - 187.2 - -77.8 -40.5 - - - 184.0 -1.2 34.7 - * * * 66 LYS 66 H A - 190.5 - 178.0 - -70.5 -39.9 - - - 175.5 -2.9 34.3 - * * 67 LEU 67 h b - - -69.4 - - - - - - - 181.8 -3.1 33.6 - * * 68 PRO 68 T - - - - - -85.5 - - - - - 181.2 - 39.2 - +* +* +* 69 ASN 69 T A - 185.9 - - - - - - - - 180.1 - 35.0 - 70 VAL 70 t B - 176.9 - - - - - - - - 181.4 -.8 33.7 - +* +* 71 LEU 71 E B - 180.8 - - - - - - - - 180.0 -2.3 35.4 - 72 PHE 72 E B - - -58.7 - - - - - - - 178.0 -.7 34.8 - +* +* 73 LEU 73 E B - - -68.7 - - - - - - - 180.0 -2.3 32.6 - 74 LYS 74 E B - 175.7 - 164.7 - - - - - - 178.4 -2.4 34.4 - 75 VAL 75 E B - 176.2 - - - - - - - - 176.9 -2.9 34.4 - * * 76 ASP 76 E B - 187.9 - - - - - - - - 186.6 -.6 34.0 - * +* +* 77 THR 77 e A 54.2 - - - - - - - - - 176.3 -2.8 33.2 - * * 78 ASP 78 T A - 182.2 - - - - - - - - 176.0 - 34.7 - 79 GLU 79 T A - - -69.6 180.7 - - - - - - 182.6 - 35.4 - 80 LEU 80 h b - - -64.6 179.1 - - - - - - 179.3 -3.6 33.9 - ** ** 81 LYS 81 H A - - -60.3 185.9 - -69.9 -40.8 - - - 182.7 -1.2 32.6 - * * 82 SER 82 H A - - -48.4 - - -63.4 -44.6 - - - 179.0 - 34.8 - * * 83 VAL 83 H A - 177.7 - - - -60.0 -43.7 - - - 179.1 - 33.7 - 84 ALA 84 H A - - - - - -62.0 -44.2 - - - 180.1 -1.5 33.9 - 85 SER 85 H A 55.4 - - - - -68.5 -29.7 - - - 180.9 -2.5 31.6 - 86 ASP 86 H A - 184.3 - - - -63.6 -37.1 - - - 178.7 -2.2 34.4 - 87 TRP 87 h A - - -61.4 - - - - - - - 178.3 -1.4 33.4 - 88 ALA 88 T l - - - - - - - - - - 180.4 -1.0 33.2 - * * 89 ILE 89 t B - - -58.1 - - - - - - - 182.0 -2.6 34.0 - 90 GLN 90 A - - -56.9 181.5 - - - - - - 181.6 -1.0 35.5 - * * 91 ALA 91 S B - - - - - - - - - - 180.7 - 33.8 - 92 MET 92 S B - - -64.8 166.7 - - - - - - -3.2 - 36.5 - 93 PRO 93 e cis - - - - - -89.5 - - - - - 178.6 - 39.3 - ** +* ** 94 THR 94 E B - - -60.1 - - - - - - - 181.9 -2.3 33.5 - 95 PHE 95 E B - - -60.4 - - - - - - - 183.5 -2.6 36.4 - 96 MET 96 E B - 183.2 - 180.7 - - - - - - 181.9 -3.4 35.0 - +* +* 97 PHE 97 E B - - -70.4 - - - - - - - 178.8 -3.3 36.7 - +* +* Residue-by-residue listing for refined_3 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 LEU 98 E B - - -53.6 - - - - - - - 174.1 -2.4 35.1 - * * 99 LYS 99 E B - 184.2 - 182.5 - - - - - - 181.4 -3.1 33.7 - * * 100 GLU 100 T l - - -56.3 174.3 - - - - - - 182.9 - 33.7 - 101 GLY 101 T - - - - - - - - - - - 179.6 - - - 102 LYS 102 E B - - -65.7 - - - - - - - 183.0 -2.1 33.4 - 103 ILE 103 E B - - -55.6 176.7 - - - - - - 175.4 - 36.3 - 104 LEU 104 E a - - -72.0 187.3 - - - - - - 184.8 -2.4 33.5 - 105 ASP 105 E B - - -61.5 - - - - - - - 175.0 -2.3 34.7 - 106 LYS 106 E B 59.7 - - 176.4 - - - - - - 180.3 - 32.1 - 107 VAL 107 E B - 181.1 - - - - - - - - 181.0 -2.9 35.0 - * * 108 VAL 108 E B 58.0 - - - - - - - - - 180.7 -.5 32.4 - +* +* 109 GLY 109 e - - - - - - - - - - - 179.5 -2.7 - - 110 ALA 110 B - - - - - - - - - - 182.0 - 34.1 - 111 LYS 111 h B - - -67.9 179.8 - - - - - - 179.8 -.9 35.8 - * * 112 LYS 112 H A - 181.2 - 181.1 - -69.7 -51.0 - - - 186.6 -.5 36.0 - * * ** ** 113 ASP 113 H A - - -59.0 - - -74.2 -49.1 - - - 183.1 - 33.6 - 114 GLU 114 H A - 186.4 - 185.0 - -66.2 -32.8 - - - 179.0 - 33.8 - 115 LEU 115 H A - 186.1 - - - -59.0 -50.5 - - - 178.6 -.8 35.2 - +* +* 116 GLN 116 H A - - -64.5 178.5 - -57.0 -38.0 - - - 179.8 -1.3 33.5 - 117 SER 117 H A - - -56.6 - - -69.1 -31.3 - - - 176.8 -1.6 33.5 - 118 THR 118 H A - - -55.1 - - -74.8 -37.7 - - - 178.1 -1.9 34.7 - 119 ILE 119 H A - - -57.0 175.1 - -62.7 -49.2 - - - 181.1 -2.6 34.8 - 120 ALA 120 H A - - - - - -63.3 -31.0 - - - 176.0 -3.1 32.7 - * * 121 LYS 121 H A - 183.1 - 177.1 - -61.7 -43.9 - - - 179.6 -1.2 36.3 - * * 122 HIS 122 H A - - -73.3 - - -78.0 -37.7 - - - 180.8 -1.6 33.0 - * * 123 LEU 123 h b - 189.1 - - - - - - - - 179.8 -3.1 34.3 - * * 124 ALA 124 - - - - - - - - - - - - -1.2 34.4 - * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * * ** ** +* +** *** +* ** +* *** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.9 183.7 -61.5 180.6 -73.5 -66.0 -39.8 50.5 - 2.0 179.9 -2.0 34.3 *** *** Standard deviations: 5.4 6.3 7.4 8.8 16.3 7.6 10.2 .0 - .0 2.9 .8 1.5 Numbers of values: 14 44 44 36 4 47 47 2 0 2 122 80 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_3 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_3 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 - 1.229 1.504 1.536 1.454 - 115.28 120.83 112.13 110.49 112.25 123.87 * * * * 2 GLY 2 1.306 1.248 1.500 - 1.435 122.55 118.03 119.38 - 108.44 - 122.57 +* * * * +* 3 HIS 3 1.312 1.231 1.518 1.548 1.452 120.31 114.59 120.88 109.72 112.60 111.06 124.51 * * 4 HIS 4 1.314 1.230 1.523 1.574 1.462 125.54 115.60 121.71 113.13 108.97 114.56 122.62 * ** ** +* ** ** 5 HIS 5 1.310 1.233 1.513 1.536 1.467 121.69 115.38 121.23 109.78 110.91 110.91 123.39 * * 6 HIS 6 1.302 1.240 1.521 1.556 1.442 122.79 116.84 119.35 113.24 109.43 111.63 123.81 +* * +* +* 7 HIS 7 1.328 1.218 1.542 1.547 1.478 123.20 114.76 121.01 111.02 113.52 110.87 124.23 * * 8 HIS 8 1.314 1.240 1.498 1.560 1.470 127.30 117.37 119.56 107.98 107.14 113.86 123.08 * * +* *** * * +* *** 9 LEU 9 1.314 1.234 1.511 1.555 1.456 121.02 114.85 121.11 110.24 108.01 112.74 124.04 * * * * * 10 GLU 10 1.338 1.235 1.556 1.550 1.475 124.61 116.07 121.13 111.17 111.08 109.65 122.79 * +* +* 11 MET 11 1.341 1.231 1.545 1.558 1.476 123.59 115.18 122.39 112.67 109.27 110.51 122.36 * * * * Residue-by-residue listing for refined_3 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 1.314 1.229 1.510 1.519 1.441 121.98 116.00 121.10 110.77 110.37 110.75 122.88 * * 13 SER 13 1.287 1.242 1.521 1.529 1.430 121.93 117.99 119.53 110.43 108.22 108.43 122.44 *** * * * *** 14 GLU 14 1.321 1.235 1.517 1.534 1.446 120.25 115.03 121.64 112.16 106.03 111.28 123.17 * +* +* 15 GLU 15 1.295 1.233 1.517 1.547 1.427 122.14 116.41 120.61 110.57 109.79 107.57 122.96 ** +* +* ** 16 GLY 16 1.307 1.225 1.498 - 1.446 120.63 115.92 120.82 - 112.73 - 123.26 +* * +* 17 GLN 17 1.301 1.234 1.494 1.516 1.425 121.64 113.35 122.07 112.67 112.31 112.27 124.56 +* * +* * * * +* 18 VAL 18 1.285 1.237 1.533 1.555 1.448 124.55 118.15 119.44 109.95 109.07 108.81 122.40 *** +* +* *** 19 ILE 19 1.329 1.229 1.527 1.553 1.451 120.30 116.57 121.00 109.71 109.97 111.55 122.42 20 ALA 20 1.302 1.228 1.511 1.524 1.437 121.15 116.57 120.57 110.70 109.67 110.58 122.83 +* * +* 21 CYS 21 1.310 1.229 1.508 1.515 1.425 121.35 116.87 120.44 110.47 108.98 109.89 122.67 * +* +* 22 HIS 22 1.307 1.224 1.512 1.537 1.452 120.75 116.25 120.64 110.11 110.43 110.92 123.11 +* +* 23 THR 23 1.327 1.247 1.525 1.558 1.459 122.35 117.13 119.95 108.77 109.96 111.45 122.92 24 VAL 24 1.334 1.241 1.541 1.576 1.460 121.36 115.35 121.43 110.91 109.65 112.60 123.20 * * 25 GLU 25 1.333 1.239 1.538 1.532 1.450 122.99 116.26 120.74 110.67 109.54 109.25 122.99 26 THR 26 1.335 1.219 1.536 1.551 1.454 121.62 115.77 120.77 110.02 109.95 110.96 123.42 27 TRP 27 1.322 1.237 1.539 1.530 1.460 123.73 116.50 120.38 111.13 112.45 108.41 123.11 * * * 28 ASN 28 1.328 1.235 1.528 1.530 1.469 121.88 115.03 121.17 109.47 110.15 110.22 123.78 29 GLU 29 1.322 1.236 1.530 1.527 1.452 123.48 116.42 120.53 110.69 111.19 109.39 123.04 30 GLN 30 1.331 1.235 1.517 1.498 1.425 122.58 116.05 120.78 109.36 111.07 109.55 123.17 +* +* +* 31 LEU 31 1.323 1.217 1.501 1.486 1.410 122.42 116.67 119.73 110.46 111.68 109.76 123.60 * ** +** +** 32 GLN 32 1.322 1.235 1.518 1.523 1.455 122.00 115.25 121.13 109.33 109.85 110.37 123.59 33 LYS 33 1.316 1.233 1.530 1.528 1.436 122.46 117.10 120.14 111.56 111.24 109.77 122.73 * * 34 ALA 34 1.329 1.231 1.528 1.521 1.459 121.07 115.50 121.07 110.43 110.83 110.43 123.42 35 ASN 35 1.318 1.231 1.505 1.525 1.462 123.84 114.78 121.47 107.71 110.39 108.84 123.75 * * * 36 GLU 36 1.308 1.243 1.537 1.536 1.461 122.56 116.88 120.62 111.07 112.16 110.90 122.50 * * 37 SER 37 1.316 1.227 1.535 1.515 1.444 121.22 116.01 120.52 110.49 110.91 109.23 123.47 38 LYS 38 1.343 1.236 1.525 1.518 1.467 123.90 115.56 121.46 111.78 112.26 111.15 122.89 * * 39 THR 39 1.308 1.240 1.531 1.528 1.434 121.79 115.88 121.07 109.48 108.61 111.02 123.00 +* * +* 40 LEU 40 1.291 1.240 1.549 1.560 1.449 122.74 116.55 120.62 112.20 108.29 108.59 122.83 +** * * * * * +** 41 VAL 41 1.318 1.233 1.544 1.569 1.444 121.99 116.42 120.87 111.30 111.12 110.69 122.68 * * * 42 VAL 42 1.314 1.231 1.522 1.547 1.454 122.88 116.72 120.46 109.65 108.75 112.11 122.81 * * 43 VAL 43 1.309 1.234 1.518 1.553 1.451 121.62 117.32 120.11 108.21 110.14 111.01 122.55 * * Residue-by-residue listing for refined_3 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 1.313 1.244 1.528 1.518 1.390 121.66 115.58 121.49 110.92 110.08 110.15 122.81 * +*** +*** 45 PHE 45 1.302 1.242 1.513 1.526 1.421 122.36 116.45 120.53 110.37 107.67 109.59 123.01 +* +* * +* 46 THR 46 1.300 1.213 1.531 1.570 1.436 121.61 117.23 120.27 110.10 109.22 108.60 122.49 ** * * +* ** 47 ALA 47 1.306 1.239 1.495 1.512 1.443 121.92 115.76 120.39 110.37 108.87 112.08 123.84 +* * * +* 48 SER 48 1.299 1.234 1.553 1.523 1.447 123.45 117.34 120.50 111.08 112.56 108.72 122.15 ** * * ** 49 TRP 49 1.337 1.233 1.527 1.551 1.465 121.19 117.03 120.62 110.68 113.09 112.69 122.32 * * * 50 CYS 50 1.301 1.228 1.523 1.538 1.450 121.04 115.81 120.49 111.71 110.54 109.88 123.70 ** ** 51 GLY 51 1.337 1.237 1.523 - 1.467 122.87 118.77 119.58 - 114.24 - 121.65 * * * 52 PRO 52 1.355 1.229 1.526 1.541 1.473 122.66 115.34 121.32 110.48 111.70 103.95 123.32 * * 53 CYS 53 1.310 1.225 1.535 1.512 1.444 122.94 116.86 120.94 109.35 110.57 109.03 122.20 * * 54 ARG 54 1.320 1.222 1.523 1.536 1.446 120.65 115.94 120.93 111.17 109.65 111.82 123.13 55 PHE 55 1.326 1.229 1.532 1.543 1.461 122.69 116.65 120.98 110.03 111.00 110.13 122.37 56 ILE 56 1.316 1.235 1.551 1.574 1.450 120.81 115.71 121.33 111.16 109.85 110.98 122.92 * * * 57 ALA 57 1.334 1.227 1.555 1.527 1.462 122.58 120.33 118.99 111.69 113.49 111.59 120.68 * ** * * ** 58 PRO 58 1.384 1.219 1.526 1.537 1.468 121.92 116.52 120.76 109.96 111.73 104.27 122.69 +** * +** 59 PHE 59 1.321 1.234 1.531 1.536 1.452 121.38 115.70 121.30 110.90 109.51 110.69 123.00 60 PHE 60 1.318 1.228 1.543 1.539 1.450 122.00 116.09 121.31 111.90 109.29 110.38 122.60 61 ALA 61 1.326 1.227 1.531 1.522 1.462 121.77 115.55 121.29 110.82 109.58 110.72 123.16 62 ASP 62 1.324 1.215 1.498 1.511 1.467 123.08 114.61 121.28 108.38 109.55 110.02 124.11 * * 63 LEU 63 1.307 1.229 1.547 1.530 1.448 124.33 115.69 120.88 110.11 108.95 106.89 123.42 +* * * ** ** 64 ALA 64 1.328 1.227 1.527 1.521 1.463 123.33 116.11 121.35 110.49 111.24 110.55 122.48 65 LYS 65 1.316 1.231 1.515 1.534 1.440 121.32 115.53 120.93 109.04 110.18 111.21 123.52 66 LYS 66 1.312 1.238 1.527 1.528 1.442 122.41 116.04 120.94 111.67 109.88 109.22 123.01 * * 67 LEU 67 1.321 1.213 1.535 1.544 1.431 122.70 118.20 120.62 109.65 110.18 112.34 121.18 * * * * 68 PRO 68 1.342 1.236 1.535 1.526 1.466 122.36 115.60 121.26 110.42 112.11 102.43 123.14 69 ASN 69 1.318 1.231 1.537 1.541 1.464 123.24 114.65 122.44 110.99 108.68 109.04 122.91 70 VAL 70 1.305 1.227 1.514 1.556 1.439 123.64 116.68 120.40 110.36 108.77 112.15 122.88 +* * * +* 71 LEU 71 1.303 1.230 1.525 1.537 1.434 121.27 116.30 120.80 110.50 109.17 109.07 122.88 +* * +* 72 PHE 72 1.316 1.247 1.502 1.521 1.450 121.43 115.42 121.08 107.78 110.39 112.14 123.49 * * * 73 LEU 73 1.294 1.221 1.503 1.534 1.430 123.02 115.37 120.86 109.46 110.52 113.81 123.76 ** * * +* ** 74 LYS 74 1.299 1.243 1.500 1.507 1.427 122.88 115.79 120.75 110.54 110.60 109.93 123.45 ** * * +* ** 75 VAL 75 1.305 1.236 1.511 1.559 1.437 122.18 116.04 120.63 109.58 109.48 111.75 123.32 +* * +* Residue-by-residue listing for refined_3 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 1.312 1.225 1.513 1.523 1.439 120.81 116.24 120.53 111.01 107.05 111.19 123.20 * * * 77 THR 77 1.306 1.242 1.526 1.537 1.451 123.20 116.65 120.71 110.71 113.30 110.59 122.64 +* +* 78 ASP 78 1.317 1.233 1.498 1.516 1.443 120.85 114.61 121.39 109.99 107.64 110.95 124.00 * * * 79 GLU 79 1.315 1.233 1.519 1.508 1.422 123.35 116.26 120.83 109.45 111.43 109.30 122.91 * * +* +* 80 LEU 80 1.309 1.239 1.519 1.513 1.402 122.37 115.60 121.36 111.30 111.87 109.61 122.95 * +** +** 81 LYS 81 1.312 1.244 1.521 1.532 1.445 121.59 116.06 120.46 110.73 111.14 112.07 123.46 * * 82 SER 82 1.334 1.235 1.524 1.519 1.450 122.39 116.21 120.37 109.86 110.38 109.93 123.36 83 VAL 83 1.330 1.233 1.527 1.556 1.463 122.05 115.90 121.12 110.11 110.25 111.69 122.94 84 ALA 84 1.322 1.231 1.528 1.515 1.448 121.64 116.35 120.76 110.62 110.79 110.32 122.87 85 SER 85 1.327 1.233 1.533 1.541 1.447 121.49 116.62 120.65 112.45 112.22 111.35 122.72 * * 86 ASP 86 1.331 1.236 1.525 1.535 1.467 121.82 116.21 120.96 109.94 110.34 110.55 122.78 87 TRP 87 1.321 1.230 1.520 1.517 1.450 121.81 115.74 120.56 110.41 111.43 111.13 123.70 88 ALA 88 1.342 1.226 1.528 1.531 1.471 124.03 116.52 120.76 110.91 111.89 110.61 122.67 * * 89 ILE 89 1.319 1.240 1.521 1.557 1.451 121.95 115.66 121.18 110.13 109.14 111.65 123.07 90 GLN 90 1.304 1.232 1.508 1.524 1.434 122.28 115.56 121.23 109.35 109.79 109.81 123.21 +* * +* 91 ALA 91 1.305 1.237 1.511 1.504 1.431 121.41 115.57 121.27 110.76 110.82 110.35 123.16 +* * +* 92 MET 92 1.298 1.231 1.521 1.509 1.431 122.91 118.31 119.97 108.37 109.66 109.09 121.71 ** * * * ** 93 PRO 93 1.326 1.226 1.536 1.527 1.447 123.18 116.98 120.67 110.45 110.76 102.69 122.34 * * 94 THR 94 1.288 1.230 1.515 1.531 1.431 121.09 116.57 120.39 110.72 109.45 111.53 123.04 +** * +** 95 PHE 95 1.305 1.221 1.496 1.516 1.420 122.26 116.40 120.62 109.22 108.51 109.00 122.98 +* * +* +* 96 MET 96 1.286 1.228 1.513 1.515 1.428 121.55 115.07 121.40 111.42 109.84 108.36 123.53 *** +* * *** 97 PHE 97 1.295 1.250 1.501 1.516 1.415 124.26 116.24 121.03 108.64 110.02 108.91 122.73 ** * ** * ** 98 LEU 98 1.287 1.218 1.515 1.561 1.417 120.48 116.74 120.67 108.04 107.87 112.75 122.59 +** +* ** * * * +** 99 LYS 99 1.286 1.238 1.492 1.515 1.428 121.50 115.46 120.34 110.62 107.63 111.86 124.13 *** +* +* * *** 100 GLU 100 1.324 1.240 1.542 1.529 1.465 124.05 115.48 121.43 110.25 110.25 111.17 123.06 * * 101 GLY 101 1.325 1.222 1.526 - 1.442 121.97 117.09 120.16 - 112.65 - 122.75 102 LYS 102 1.327 1.228 1.511 1.559 1.468 122.07 116.21 120.28 109.71 109.85 112.70 123.51 * * * 103 ILE 103 1.314 1.225 1.523 1.554 1.463 123.23 117.16 120.17 107.53 110.54 110.40 122.67 * * 104 LEU 104 1.312 1.235 1.501 1.520 1.434 121.15 116.22 121.01 109.36 111.49 112.15 122.77 * * * * 105 ASP 105 1.303 1.224 1.483 1.529 1.443 120.80 115.59 120.96 107.95 110.59 112.26 123.44 +* +* * * +* 106 LYS 106 1.283 1.233 1.518 1.545 1.432 122.23 116.30 120.66 111.96 109.29 112.48 122.98 *** * * *** Residue-by-residue listing for refined_3 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 1.299 1.234 1.508 1.561 1.444 122.41 116.29 120.32 109.22 108.38 111.45 123.37 ** * ** 108 VAL 108 1.304 1.246 1.538 1.566 1.432 121.80 115.45 121.49 111.92 111.13 111.58 123.04 +* * * +* 109 GLY 109 1.311 1.238 1.503 - 1.435 121.51 117.60 119.95 - 110.19 - 122.46 * * * 110 ALA 110 1.322 1.232 1.508 1.526 1.441 119.34 115.27 120.91 110.70 108.61 110.90 123.81 * * 111 LYS 111 1.298 1.214 1.499 1.522 1.425 123.56 117.21 119.94 109.63 109.71 109.35 122.84 ** * +* * ** 112 LYS 112 1.306 1.233 1.538 1.526 1.439 121.22 115.08 121.69 109.04 111.00 108.92 123.23 +* * +* 113 ASP 113 1.307 1.239 1.518 1.526 1.456 123.12 116.55 120.54 110.90 113.31 109.78 122.88 +* +* 114 GLU 114 1.327 1.245 1.518 1.527 1.465 121.41 116.11 120.74 109.72 110.95 111.39 123.14 115 LEU 115 1.327 1.214 1.500 1.513 1.446 121.52 115.04 120.93 109.15 108.76 110.55 123.99 * * 116 GLN 116 1.316 1.226 1.514 1.515 1.469 122.97 116.56 120.57 110.13 112.11 110.90 122.84 117 SER 117 1.313 1.237 1.532 1.522 1.448 120.69 115.61 121.33 112.10 110.02 109.75 123.02 * * * 118 THR 118 1.315 1.236 1.546 1.547 1.434 121.99 116.03 121.05 110.20 109.19 110.42 122.91 * * * 119 ILE 119 1.333 1.219 1.519 1.555 1.456 122.30 116.13 120.60 108.31 109.41 112.22 123.24 120 ALA 120 1.327 1.232 1.523 1.514 1.459 122.57 116.04 120.58 111.26 111.81 110.95 123.37 121 LYS 121 1.320 1.228 1.514 1.499 1.452 122.84 114.74 121.72 109.07 109.54 108.54 123.54 +* * +* 122 HIS 122 1.306 1.227 1.522 1.525 1.432 122.51 117.44 119.93 110.75 112.71 110.94 122.63 +* * +* 123 LEU 123 1.325 1.240 1.528 1.522 1.417 122.14 114.83 121.08 113.32 110.22 107.49 124.01 ** +* +* ** 124 ALA 124 1.322 - 1.515 1.536 1.447 124.22 - - 110.22 108.14 111.11 - * * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *** +* ** +*** *** ** * +* +* ** * +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 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 1.283 1.343 1.314 .013 *** * C-N (Pro) 1.341 .016 4 1.326 1.384 1.352 .021 +** C-O C-O 1.231 .020 123 1.213 1.250 1.232 .008 CA-C CH1E-C (except Gly) 1.525 .021 119 1.483 1.556 1.522 .015 +* * CH2G*-C (Gly) 1.516 .018 5 1.498 1.526 1.510 .012 * CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.504 1.536 1.521 .008 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.528 1.576 1.555 .012 * CH1E-CH2E (the rest) 1.530 .020 84 1.486 1.574 1.530 .016 ** ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.390 1.478 1.446 .016 +*** * NH1-CH2G* (Gly) 1.451 .016 5 1.435 1.467 1.445 .012 * N-CH1E (Pro) 1.466 .015 4 1.447 1.473 1.464 .010 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 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 2.0 114 113.35 120.33 116.09 .92 * ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.92 118.77 117.48 .96 * CH1E-C-N (Pro) 116.9 1.5 4 115.34 116.98 116.11 .67 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.68 124.56 123.06 .59 * O-C-N (Pro) 122.0 1.4 4 122.34 123.32 122.87 .38 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 119.34 127.30 122.25 1.18 * *** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.63 122.87 121.91 .79 * C-N-CH1E (Pro) 122.6 5.0 4 121.92 123.18 122.53 .46 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 118.99 122.44 120.81 .56 * CH2G*-C-O (Gly) 120.8 2.1 5 119.38 120.82 119.98 .50 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.22 111.69 110.75 .37 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 107.53 111.92 109.91 1.03 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.71 113.32 110.41 1.26 * +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 106.03 113.52 110.16 1.44 +* NH1-CH2G*-C (Gly) 112.5 2.9 5 108.44 114.24 111.65 2.07 * N-CH1E-C (Pro) 111.8 2.5 4 110.76 112.11 111.58 .50 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.32 112.08 110.84 .49 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 108.60 112.60 111.15 .96 +* N-CH1E-CH2E (Pro) 103.0 1.1 4 102.43 104.27 103.33 .79 * NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.89 114.56 110.43 1.51 ** ** ------------------------------------------------------------------------------------------------------------- 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_3 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] 101 89.4% Residues in additional allowed regions [a,b,l,p] 12 10.6% 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 89.4 83.8 10.0 .6 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 1.5 3.1 1.6 -1.0 Inside e. H-bond energy st dev 80 .8 .8 .2 .2 Inside f. Overall G-factor 124 .1 -.4 .3 1.8 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 14 5.4 18.1 6.5 -2.0 BETTER b. Chi-1 trans st dev 44 6.3 19.0 5.3 -2.4 BETTER c. Chi-1 gauche plus st dev 44 7.4 17.5 4.9 -2.1 BETTER d. Chi-1 pooled st dev 102 7.8 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 36 8.8 20.4 5.0 -2.3 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% 89.4 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.1 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .85 2 Residue-by-residue listing for refined_3 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.17 Chi1-chi2 distribution -.01 Chi1 only -.06 Chi3 & chi4 .51 Omega .14 ------ .05 ===== Main-chain covalent forces:- Main-chain bond lengths .10 Main-chain bond angles .46 ------ .31 ===== OVERALL AVERAGE .14 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.