Residue-by-residue listing for refined_6 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 - - - -65.0 - - - - - - - 181.1 - 33.5 - 2 GLY 2 - - - - - - - - - - - 178.2 - - - 3 HIS 3 B - - -61.5 - - - - - - - 183.5 - 33.1 - 4 HIS 4 B - 181.3 - - - - - - - - 178.9 -.6 34.8 - +* +* 5 HIS 5 b - 182.6 - - - - - - - - 183.5 - 34.2 - 6 HIS 6 B - 184.6 - - - - - - - - 178.9 - 35.6 - 7 HIS 7 B 73.4 - - - - - - - - - 178.3 - 32.3 - 8 HIS 8 B - 177.4 - - - - - - - - 177.1 - 34.9 - 9 LEU 9 b - 186.2 - 168.1 - - - - - - 188.8 - 33.6 - +* +* 10 GLU 10 a - 213.7 - - - - - - - - 185.3 -.6 34.8 - +* +* +* 11 MET 11 ~l - - -71.4 182.0 - - - - - - 179.3 - 29.7 - ** * ** 12 ALA 12 b - - - - - - - - - - 174.8 - 36.1 - 13 SER 13 S XX - - -54.3 - - - - - - - 180.6 - 31.6 - **** **** 14 GLU 14 S A - 180.6 - 178.7 - - - - - - 182.3 - 36.9 - 15 GLU 15 b - - -73.6 - - - - - - - 188.9 - 32.3 - +* +* 16 GLY 16 S - - - - - - - - - - - 177.5 -.8 - - +* +* 17 GLN 17 B 49.5 - - 177.0 - - - - - - 179.6 - 33.0 - 18 VAL 18 B 61.7 - - - - - - - - - 180.3 - 35.1 - 19 ILE 19 E B - - -65.0 - - - - - - - 178.6 -2.6 30.8 - 20 ALA 20 E B - - - - - - - - - - 179.3 -.8 34.0 - +* +* Residue-by-residue listing for refined_6 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 - - -56.4 - - - - - - - 180.6 -1.7 35.4 - 22 HIS 22 S A - - -63.1 - - - - - - - 181.1 - 32.8 - 23 THR 23 h B 57.2 - - - - - - - - - 173.6 - 36.6 - * * 24 VAL 24 H A 64.2 - - - - -75.5 -22.1 - - - 177.4 - 32.5 - +* +* 25 GLU 25 H A - 181.0 - 179.4 - -55.4 -52.0 - - - 178.4 - 36.6 - * * 26 THR 26 H A - - -54.5 - - -73.5 -37.7 - - - 180.0 - 34.3 - 27 TRP 27 H A - 170.4 - - - -53.4 -55.4 - - - 181.4 -1.5 35.2 - * * * 28 ASN 28 H A - 182.5 - - - -62.9 -39.5 - - - 181.7 -3.1 35.0 - * * 29 GLU 29 H A - 179.9 - 172.5 - -62.6 -44.3 - - - 179.9 -1.3 33.6 - * * 30 GLN 30 H A - - -66.0 - - -64.1 -40.4 - - - 178.0 -2.7 34.0 - 31 LEU 31 H A - - -65.9 179.3 - -68.1 -45.4 - - - 177.6 -1.8 34.9 - 32 GLN 32 H A - 182.0 - 179.6 - -58.1 -40.6 - - - 179.5 -2.9 34.4 - * * 33 LYS 33 H A - 188.7 - - - -70.3 -39.8 - - - 179.2 -2.6 33.6 - 34 ALA 34 H A - - - - - -63.4 -40.2 - - - 178.5 -2.4 33.8 - 35 ASN 35 H A - 188.5 - - - -62.9 -49.9 - - - 180.8 -2.8 37.0 - * * 36 GLU 36 H A - 180.8 - 181.6 - -59.0 -40.4 - - - 182.1 -2.4 35.9 - 37 SER 37 h A - - -54.1 - - - - - - - 182.0 -2.5 35.1 - 38 LYS 38 T l - - -66.1 185.5 - - - - - - 184.6 -1.2 32.6 - * * 39 THR 39 e B - - -45.0 - - - - - - - 181.7 -2.1 35.0 - * * 40 LEU 40 E B - 181.8 - 167.9 - - - - - - 182.7 - 33.1 - 41 VAL 41 E B 60.7 - - - - - - - - - 180.9 -1.0 33.8 - * * 42 VAL 42 E B 63.8 - - - - - - - - - 184.4 -3.2 33.4 - +* +* 43 VAL 43 E B - 180.8 - - - - - - - - 174.6 -2.6 34.2 - 44 ASP 44 E B - 161.8 - - - - - - - - 172.6 -2.5 35.3 - * * * 45 PHE 45 E B - - -57.9 - - - - - - - 182.1 -2.7 36.8 - 46 THR 46 E B - 189.5 - - - - - - - - 180.5 -2.0 33.8 - 47 ALA 47 t B - - - - - - - - - - 183.1 - 34.7 - 48 SER 48 T A - 183.1 - - - - - - - - 179.9 - 34.1 - 49 TRP 49 T A 53.5 - - - - - - - - - 178.2 - 32.0 - 50 CYS 50 h B - 171.6 - 225.2 - - - 48.8 - 2.0 184.7 -1.3 33.7 - +** *** *** 51 GLY 51 H - - - - - - -54.7 -71.6 - - - 180.2 -.6 - - +** +* +** 52 PRO 52 H - - - - - -57.1 -57.1 -30.6 - - - 181.2 - 39.1 - * * 53 CYS 53 H A - - -54.6 - - -68.8 -38.1 48.8 - 2.0 179.5 - 36.1 - *** *** 54 ARG 54 H A - 182.8 - 179.4 - -78.5 -38.2 - - - 181.0 -2.1 35.3 - * * 55 PHE 55 H A - 181.8 - - - -66.7 -26.6 - - - 183.4 -2.7 34.6 - * * 56 ILE 56 H A - 193.6 - - - -87.8 -22.9 - - - 185.1 -1.4 34.4 - +* * +* Residue-by-residue listing for refined_6 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 ----------------------------------------------------------------------------------------------------------------------------------- 57 ALA 57 H A - - - - - -57.2 -47.3 - - - 179.7 -.7 31.2 - +* +* 58 PRO 58 H - - - - - -57.5 -57.5 -28.1 - - - 178.8 - 38.4 - * * * 59 PHE 59 H A - 173.9 - - - -69.5 -38.8 - - - 180.3 -.9 33.8 - +* +* 60 PHE 60 H A - 186.2 - - - -68.1 -33.5 - - - 176.4 -1.1 34.0 - * * 61 ALA 61 H A - - - - - -67.6 -30.4 - - - 178.6 -1.6 33.8 - 62 ASP 62 H A - 181.6 - - - -74.2 -43.2 - - - 176.6 -1.1 35.2 - * * 63 LEU 63 H A - - -69.8 181.7 - -52.6 -36.8 - - - 178.8 -2.4 35.0 - * * 64 ALA 64 H A - - - - - -60.0 -32.8 - - - 179.2 -1.3 33.8 - 65 LYS 65 H A - 180.2 - 182.9 - -80.3 -30.7 - - - 183.9 -1.4 35.0 - * * 66 LYS 66 H A - 186.7 - 175.5 - -75.9 -30.6 - - - 178.9 -1.5 33.8 - 67 LEU 67 h b - - -63.1 171.5 - - - - - - 178.9 -2.0 33.8 - 68 PRO 68 T - - - - - -65.3 - - - - - 182.1 - 39.1 - * * 69 ASN 69 T A - 190.2 - - - - - - - - 179.9 - 34.3 - 70 VAL 70 t B - 177.9 - - - - - - - - 176.9 -1.3 34.1 - 71 LEU 71 E B - - -72.6 - - - - - - - 178.4 -2.3 34.3 - 72 PHE 72 E B - - -64.5 - - - - - - - 181.7 -.7 35.2 - +* +* 73 LEU 73 E B - - -71.1 162.4 - - - - - - 184.8 -2.6 34.0 - 74 LYS 74 E B - 197.0 - - - - - - - - 178.6 -2.2 35.6 - 75 VAL 75 E B - 177.1 - - - - - - - - 175.5 -3.2 34.5 - +* +* 76 ASP 76 E B - 178.3 - - - - - - - - 183.4 - 33.5 - 77 THR 77 e A - 179.6 - - - - - - - - 176.1 -2.1 30.6 - 78 ASP 78 T A - 179.5 - - - - - - - - 176.0 - 33.5 - 79 GLU 79 T A - - -72.8 179.5 - - - - - - 181.6 - 34.2 - 80 LEU 80 h a - - -75.4 - - - - - - - 181.3 -3.2 34.0 - +* +* 81 LYS 81 H A - 208.9 - - - -58.2 -43.1 - - - 179.7 -.7 36.5 - +* +* +* 82 SER 82 H A 51.9 - - - - -62.9 -42.9 - - - 180.2 - 33.6 - 83 VAL 83 H A - 180.9 - - - -70.2 -40.2 - - - 178.0 - 33.6 - 84 ALA 84 H A - - - - - -65.3 -32.2 - - - 177.5 -3.0 33.8 - * * 85 SER 85 H A - 185.8 - - - -75.0 -35.8 - - - 180.4 -2.0 34.5 - 86 ASP 86 H A - 179.4 - - - -66.4 -37.2 - - - 175.9 -2.1 34.1 - 87 TRP 87 h A - - -71.4 - - - - - - - 178.8 -2.3 32.7 - 88 ALA 88 T l - - - - - - - - - - 177.2 - 30.7 - 89 ILE 89 t B - - -57.3 - - - - - - - 181.6 -2.5 34.7 - 90 GLN 90 A - - -59.1 - - - - - - - 184.1 -.7 34.8 - +* +* 91 ALA 91 S B - - - - - - - - - - 179.7 - 33.8 - 92 MET 92 S B - - -66.0 - - - - - - - -5.0 - 34.2 - 93 PRO 93 e cis - - - - - -93.5 - - - - - 175.6 - 39.8 - +** +* +** 94 THR 94 E B - - -61.4 - - - - - - - 177.1 -2.6 34.0 - 95 PHE 95 E B - - -63.2 - - - - - - - 182.2 -2.5 36.1 - 96 MET 96 E B - 180.6 - 178.6 - - - - - - 178.9 -3.3 33.6 - +* +* Residue-by-residue listing for refined_6 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 - - -67.1 - - - - - - - 182.4 -3.0 35.8 - * * 98 LEU 98 E B 60.1 - - 172.9 - - - - - - 181.3 -1.6 32.8 - 99 LYS 99 E B - 176.7 - 179.6 - - - - - - 183.8 -3.1 32.7 - * * 100 GLU 100 e l - - -57.3 176.6 - - - - - - 186.6 -.9 33.4 - * +* +* 101 GLY 101 T - - - - - - - - - - - 175.9 - - - 102 LYS 102 E B - - -55.0 170.3 - - - - - - 187.2 -1.7 36.5 - * * 103 ILE 103 E B - - -56.3 177.3 - - - - - - 177.2 - 33.8 - 104 LEU 104 E a - - -65.1 183.1 - - - - - - 182.2 -1.7 34.0 - 105 ASP 105 E B 49.8 - - - - - - - - - 183.9 -2.5 32.1 - 106 LYS 106 E B 54.3 - - - - - - - - - 177.4 - 31.0 - 107 VAL 107 E B - 183.3 - - - - - - - - 178.3 -3.1 35.9 - * * 108 VAL 108 E B 58.2 - - - - - - - - - 181.4 -.5 32.4 - ** ** 109 GLY 109 e - - - - - - - - - - - 181.1 -2.8 - - 110 ALA 110 B - - - - - - - - - - 174.6 - 34.2 - 111 LYS 111 h B - - -65.1 - - - - - - - 182.1 -.9 35.3 - +* +* 112 LYS 112 H A - 185.4 - 175.9 - -69.3 -49.8 - - - 181.5 - 34.3 - 113 ASP 113 H A - 178.3 - - - -73.1 -48.8 - - - 182.2 - 34.0 - 114 GLU 114 H A - 180.1 - 176.9 - -62.6 -29.7 - - - 176.8 - 32.8 - 115 LEU 115 H A - 184.8 - - - -65.2 -50.2 - - - 178.1 -1.1 34.9 - * * 116 GLN 116 H A - - -62.1 - - -53.9 -40.2 - - - 180.2 -1.4 34.2 - 117 SER 117 H A - - -55.2 - - -64.1 -38.6 - - - 179.9 -2.0 34.4 - 118 THR 118 H A - - -52.8 - - -74.7 -31.7 - - - 176.9 -1.8 34.5 - 119 ILE 119 H A - - -59.0 176.4 - -70.8 -42.8 - - - 178.5 -2.3 33.3 - 120 ALA 120 H A - - - - - -62.7 -31.0 - - - 177.8 -3.2 33.4 - * * 121 LYS 121 H A - 187.6 - 178.7 - -59.5 -41.8 - - - 180.0 -1.4 36.6 - 122 HIS 122 h A - - -67.4 - - - - - - - 182.2 -1.1 35.1 - * * 123 LEU 123 B - 188.3 - - - - - - - - 178.3 - 34.9 - 124 ALA 124 - - - - - - - - - - - - - 34.1 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** +* * +** +** +* +** *** +* ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.3 183.2 -62.6 178.5 -68.3 -65.8 -39.2 48.8 - 2.0 180.1 -1.9 34.3 *** *** Standard deviations: 6.7 8.3 6.9 10.2 17.2 7.9 9.1 .0 - .0 3.0 .8 1.6 Numbers of values: 13 49 40 30 4 45 45 2 0 2 122 77 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_6 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_6 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 - 1.230 1.500 1.544 1.463 - 116.45 120.20 110.49 109.33 111.83 123.34 * * 2 GLY 2 1.315 1.237 1.507 - 1.433 120.58 116.76 120.63 - 111.12 - 122.60 * * 3 HIS 3 1.298 1.233 1.502 1.533 1.439 121.58 115.68 121.20 110.79 109.24 112.20 123.09 ** * ** 4 HIS 4 1.295 1.230 1.526 1.538 1.438 122.14 116.01 120.72 111.21 110.08 108.98 123.25 ** * ** 5 HIS 5 1.309 1.237 1.525 1.550 1.452 122.66 115.94 120.78 110.85 108.37 110.87 123.23 * * * 6 HIS 6 1.307 1.235 1.530 1.552 1.453 122.55 117.63 120.13 110.39 109.43 108.86 122.24 +* * +* 7 HIS 7 1.321 1.237 1.526 1.562 1.463 119.94 116.19 120.77 110.54 110.22 113.19 123.03 +* +* +* 8 HIS 8 1.295 1.227 1.512 1.553 1.444 122.67 117.14 119.23 110.94 107.69 110.03 123.55 ** * * ** 9 LEU 9 1.326 1.245 1.529 1.559 1.451 122.35 115.45 121.26 113.53 107.77 109.30 123.26 * +* * +* 10 GLU 10 1.306 1.231 1.530 1.544 1.427 121.59 116.02 120.27 111.14 110.45 109.05 123.65 +* +* +* 11 MET 11 1.334 1.241 1.511 1.541 1.472 123.81 114.75 121.89 111.24 112.46 114.85 123.37 * +** +** Residue-by-residue listing for refined_6 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 1.301 1.243 1.525 1.525 1.438 122.94 116.15 119.94 110.28 108.59 108.30 123.88 +* * * +* 13 SER 13 1.325 1.238 1.535 1.545 1.454 124.09 114.24 122.03 111.88 113.50 111.41 123.72 * * 14 GLU 14 1.308 1.244 1.536 1.527 1.449 125.09 113.93 122.58 111.33 108.09 105.91 123.49 +* +* * * * +** +** 15 GLU 15 1.304 1.231 1.521 1.543 1.440 124.75 116.60 120.75 113.63 111.78 109.49 122.65 +* +* +* +* 16 GLY 16 1.302 1.223 1.496 - 1.437 120.70 114.98 121.33 - 110.74 - 123.69 +* * +* 17 GLN 17 1.308 1.235 1.485 1.523 1.428 123.13 114.64 121.11 110.34 110.44 112.47 124.25 * +* +* * +* 18 VAL 18 1.277 1.246 1.532 1.554 1.424 123.06 118.33 120.00 111.09 108.96 109.32 121.64 +*** +* * * +*** 19 ILE 19 1.326 1.230 1.519 1.574 1.435 118.02 115.92 121.45 111.50 110.60 114.46 122.60 * * ** * +* ** 20 ALA 20 1.297 1.236 1.511 1.525 1.429 121.71 116.33 120.84 110.85 109.43 110.76 122.80 ** * ** 21 CYS 21 1.302 1.229 1.505 1.512 1.417 121.48 116.83 120.46 110.23 108.44 109.56 122.69 +* ** ** 22 HIS 22 1.305 1.227 1.507 1.538 1.446 120.29 115.34 121.42 111.37 110.19 111.73 123.22 +* +* 23 THR 23 1.314 1.246 1.513 1.551 1.438 122.66 117.04 120.12 107.50 108.72 110.69 122.84 * * * 24 VAL 24 1.322 1.232 1.547 1.570 1.449 120.48 114.44 121.86 111.63 108.09 112.69 123.68 * * * * * 25 GLU 25 1.336 1.239 1.538 1.531 1.462 124.88 116.15 120.90 109.98 110.63 107.16 122.94 +* +* +* 26 THR 26 1.322 1.230 1.537 1.547 1.449 121.43 115.55 120.95 110.38 110.00 110.46 123.46 27 TRP 27 1.324 1.237 1.536 1.533 1.465 123.59 116.20 120.68 110.46 112.33 108.25 123.10 * * * 28 ASN 28 1.325 1.231 1.514 1.534 1.463 122.30 114.95 121.19 109.45 110.22 110.31 123.83 29 GLU 29 1.311 1.230 1.534 1.523 1.442 123.10 116.82 120.28 111.63 111.90 109.41 122.88 * * 30 GLN 30 1.324 1.228 1.518 1.497 1.424 122.34 116.43 120.77 110.98 111.90 109.43 122.79 +* +* +* 31 LEU 31 1.319 1.233 1.514 1.495 1.415 122.30 115.99 120.59 110.67 111.01 108.87 123.42 +* ** ** 32 GLN 32 1.319 1.240 1.524 1.531 1.449 122.23 115.95 120.84 110.23 109.91 110.51 123.19 33 LYS 33 1.322 1.234 1.529 1.534 1.438 121.65 116.94 120.21 110.35 110.56 111.34 122.85 * * 34 ALA 34 1.337 1.229 1.516 1.524 1.459 121.63 115.54 120.89 110.53 110.30 110.77 123.57 35 ASN 35 1.323 1.231 1.503 1.516 1.466 123.44 113.96 121.65 107.27 109.64 109.50 124.39 * * * * 36 GLU 36 1.310 1.234 1.524 1.529 1.463 123.99 115.70 121.36 109.13 110.91 109.03 122.93 * * * 37 SER 37 1.301 1.230 1.533 1.515 1.426 121.77 116.50 120.36 110.48 111.34 108.69 123.13 +* +* * +* 38 LYS 38 1.347 1.232 1.524 1.519 1.474 123.64 115.33 121.50 110.97 111.62 111.44 123.06 * * * 39 THR 39 1.307 1.240 1.523 1.524 1.429 122.52 115.60 121.32 109.34 109.66 110.62 123.06 +* +* +* 40 LEU 40 1.289 1.243 1.543 1.573 1.440 122.44 115.50 121.26 113.65 109.14 109.64 123.23 +** ** +* +** Residue-by-residue listing for refined_6 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 1.307 1.221 1.534 1.565 1.434 122.82 117.41 120.21 111.74 108.98 110.61 122.32 +* * * +* 42 VAL 42 1.296 1.235 1.525 1.546 1.439 121.70 116.72 120.88 111.35 109.92 111.05 122.37 ** * ** 43 VAL 43 1.306 1.233 1.526 1.548 1.445 120.65 115.07 120.82 109.22 112.27 111.23 124.10 +* +* 44 ASP 44 1.310 1.230 1.520 1.538 1.459 124.50 117.00 120.41 108.99 110.60 110.17 122.54 * +* +* 45 PHE 45 1.311 1.237 1.511 1.525 1.419 121.61 117.55 119.99 107.50 106.85 110.54 122.42 * ** * +* ** 46 THR 46 1.302 1.251 1.534 1.570 1.435 119.98 115.92 120.63 111.01 110.12 110.92 123.44 +* * * * +* 47 ALA 47 1.318 1.238 1.516 1.517 1.443 123.22 116.54 120.12 110.23 109.19 110.14 123.33 48 SER 48 1.318 1.231 1.532 1.541 1.456 122.77 116.69 120.41 110.60 111.65 110.01 122.90 49 TRP 49 1.323 1.229 1.522 1.541 1.458 121.45 115.92 121.15 111.88 112.09 111.45 122.92 50 CYS 50 1.303 1.223 1.515 1.531 1.436 121.77 116.24 120.05 111.55 109.14 110.48 123.71 +* * +* 51 GLY 51 1.324 1.234 1.526 - 1.468 122.62 118.60 119.84 - 114.66 - 121.56 * * * * 52 PRO 52 1.357 1.228 1.521 1.533 1.477 122.86 115.00 121.46 109.79 111.47 103.44 123.53 * * * 53 CYS 53 1.307 1.223 1.536 1.513 1.443 123.42 116.13 121.03 109.23 110.80 108.54 122.84 +* * +* 54 ARG 54 1.311 1.224 1.524 1.529 1.446 122.54 115.30 121.34 110.94 109.39 108.60 123.33 * * * 55 PHE 55 1.317 1.242 1.545 1.541 1.459 123.41 116.97 120.85 110.78 112.19 108.90 122.17 56 ILE 56 1.319 1.234 1.553 1.571 1.460 121.16 115.79 121.01 109.89 110.66 110.80 123.12 * * * 57 ALA 57 1.329 1.237 1.565 1.527 1.471 123.22 120.28 119.39 111.73 115.15 111.00 120.32 +* ** * +* ** 58 PRO 58 1.380 1.244 1.542 1.529 1.484 122.13 115.78 121.04 110.42 112.81 103.41 123.16 ** * ** 59 PHE 59 1.326 1.227 1.532 1.541 1.454 122.63 116.09 121.04 111.23 110.69 110.11 122.84 60 PHE 60 1.318 1.232 1.534 1.539 1.462 122.33 115.92 121.06 111.87 109.48 109.49 123.01 61 ALA 61 1.325 1.231 1.539 1.524 1.457 121.70 116.17 120.97 110.74 110.44 110.45 122.85 62 ASP 62 1.327 1.235 1.484 1.508 1.479 122.46 114.34 121.30 108.79 109.79 110.57 124.36 +* * * +* 63 LEU 63 1.304 1.232 1.524 1.516 1.427 123.64 115.99 120.47 110.31 111.42 109.03 123.52 +* +* * +* 64 ALA 64 1.330 1.227 1.528 1.520 1.459 122.88 116.17 121.05 110.55 111.64 110.20 122.76 65 LYS 65 1.314 1.228 1.527 1.526 1.454 121.99 115.72 121.10 110.60 110.58 109.00 123.18 * * 66 LYS 66 1.313 1.247 1.532 1.535 1.444 121.91 116.38 120.86 111.65 110.98 109.56 122.76 * * 67 LEU 67 1.328 1.225 1.534 1.511 1.432 122.18 117.17 121.03 111.00 111.98 109.70 121.74 * * 68 PRO 68 1.345 1.232 1.542 1.539 1.481 123.40 117.18 120.63 109.71 113.54 103.15 122.18 69 ASN 69 1.326 1.226 1.540 1.543 1.470 120.91 116.49 121.62 110.11 110.30 110.49 121.89 70 VAL 70 1.310 1.227 1.521 1.563 1.447 121.77 116.85 120.50 109.88 109.66 111.72 122.60 * * 71 LEU 71 1.314 1.224 1.515 1.542 1.424 121.15 116.26 120.82 109.86 109.36 111.46 122.91 * +* +* 72 PHE 72 1.300 1.243 1.515 1.533 1.445 121.73 115.72 121.00 108.51 108.62 111.38 123.28 ** ** Residue-by-residue listing for refined_6 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 1.278 1.230 1.496 1.512 1.441 123.39 115.50 120.89 111.33 110.63 109.72 123.62 +*** * +*** 74 LYS 74 1.293 1.240 1.529 1.555 1.426 121.81 116.15 120.77 111.78 108.23 108.00 123.06 +** * +* * * +** 75 VAL 75 1.309 1.242 1.528 1.563 1.441 123.01 116.31 121.34 109.60 109.81 111.30 122.30 * * 76 ASP 76 1.301 1.226 1.502 1.503 1.439 121.20 116.32 120.38 110.28 109.21 111.74 123.28 ** * * * ** 77 THR 77 1.309 1.229 1.544 1.562 1.455 121.95 117.59 121.02 112.68 113.33 112.06 121.38 * +* * +* 78 ASP 78 1.307 1.234 1.500 1.514 1.452 119.44 114.86 121.24 110.23 108.94 111.91 123.89 +* * * +* 79 GLU 79 1.308 1.237 1.530 1.514 1.424 123.46 116.67 120.63 110.95 111.89 109.33 122.68 * +* +* 80 LEU 80 1.321 1.234 1.512 1.531 1.436 123.23 114.48 121.45 110.62 110.65 110.51 123.99 * * 81 LYS 81 1.311 1.227 1.553 1.558 1.454 124.77 116.08 121.21 111.65 108.04 106.50 122.65 * * * +* * ** ** 82 SER 82 1.316 1.235 1.534 1.525 1.454 122.56 116.49 120.51 111.30 112.18 109.61 122.98 83 VAL 83 1.328 1.230 1.525 1.559 1.462 122.09 115.97 121.14 110.11 109.81 111.93 122.86 84 ALA 84 1.321 1.227 1.520 1.515 1.450 121.80 116.01 120.99 110.65 110.37 110.62 123.00 85 SER 85 1.318 1.228 1.533 1.534 1.437 121.66 115.92 120.92 110.83 109.56 109.81 123.13 * * 86 ASP 86 1.330 1.233 1.528 1.537 1.469 122.69 116.02 121.19 110.93 111.00 109.77 122.76 87 TRP 87 1.323 1.231 1.520 1.527 1.455 122.15 115.11 120.96 111.00 111.32 111.53 123.92 88 ALA 88 1.322 1.236 1.528 1.528 1.450 124.58 115.36 121.62 112.54 113.00 112.01 122.92 +* * * +* 89 ILE 89 1.308 1.241 1.523 1.561 1.445 122.53 116.24 120.72 109.68 108.30 111.46 122.99 +* * +* 90 GLN 90 1.316 1.238 1.516 1.538 1.450 121.71 116.01 120.91 108.19 111.20 111.66 123.08 * * 91 ALA 91 1.311 1.234 1.505 1.518 1.441 121.36 115.94 121.07 110.72 110.83 110.51 122.99 * * 92 MET 92 1.296 1.238 1.503 1.505 1.416 121.88 118.41 120.14 109.42 110.76 111.28 121.41 ** * * ** * ** 93 PRO 93 1.321 1.229 1.530 1.524 1.451 123.97 117.11 120.81 110.05 110.87 102.25 122.04 * * 94 THR 94 1.284 1.231 1.507 1.531 1.419 120.12 116.09 120.58 109.97 109.32 111.79 123.33 *** ** *** 95 PHE 95 1.300 1.228 1.489 1.518 1.406 121.93 116.69 120.39 109.32 107.26 109.84 122.92 ** +* +** * +** 96 MET 96 1.283 1.236 1.495 1.525 1.424 120.64 114.81 121.17 111.21 110.38 110.71 124.01 *** * +* *** 97 PHE 97 1.291 1.241 1.501 1.521 1.398 123.85 115.63 121.64 110.56 108.09 108.96 122.72 +** * *** * * *** 98 LEU 98 1.271 1.208 1.510 1.575 1.403 121.41 118.14 120.14 112.94 108.71 111.40 121.72 **** * ** +** * **** 99 LYS 99 1.284 1.221 1.476 1.538 1.436 119.95 114.31 121.00 110.92 109.26 112.85 124.63 *** ** * * * *** 100 GLU 100 1.320 1.215 1.529 1.528 1.461 125.40 116.29 121.09 108.32 110.25 113.46 122.60 ** +* ** 101 GLY 101 1.299 1.228 1.528 - 1.440 120.75 116.16 120.72 - 111.43 - 123.12 ** ** 102 LYS 102 1.332 1.235 1.522 1.531 1.465 122.83 117.24 119.45 109.02 106.85 109.08 123.28 +* +* Residue-by-residue listing for refined_6 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 ----------------------------------------------------------------------------------------------------------------------------------- 103 ILE 103 1.313 1.232 1.531 1.560 1.468 122.71 115.95 121.09 109.64 112.29 111.27 122.96 * * 104 LEU 104 1.321 1.226 1.520 1.525 1.429 122.05 116.36 120.72 110.30 110.80 110.69 122.92 +* +* 105 ASP 105 1.310 1.213 1.498 1.531 1.445 122.88 116.84 120.68 111.31 110.97 112.36 122.46 * * * * 106 LYS 106 1.296 1.228 1.521 1.567 1.443 120.76 115.68 121.15 113.16 113.10 111.36 123.15 ** +* +* ** 107 VAL 107 1.303 1.232 1.505 1.559 1.443 122.61 116.80 120.10 107.64 107.61 111.91 123.08 +* * +* 108 VAL 108 1.296 1.235 1.531 1.568 1.427 120.84 115.95 121.35 112.42 109.81 111.61 122.66 ** * +* +* ** 109 GLY 109 1.305 1.235 1.508 - 1.435 121.36 117.19 120.39 - 110.33 - 122.42 +* * +* 110 ALA 110 1.307 1.235 1.504 1.526 1.437 120.50 115.26 121.40 110.18 110.30 110.76 123.30 +* * * +* 111 LYS 111 1.297 1.222 1.484 1.520 1.415 123.13 117.36 119.50 108.21 106.93 112.17 123.14 ** +* ** +* ** 112 LYS 112 1.291 1.234 1.539 1.520 1.422 121.28 115.89 120.84 111.80 110.26 108.90 123.23 +** +* +** 113 ASP 113 1.326 1.234 1.531 1.533 1.469 122.62 116.12 120.84 109.98 112.36 110.43 123.03 114 GLU 114 1.329 1.250 1.531 1.533 1.472 122.53 116.53 120.87 111.90 111.79 110.26 122.59 115 LEU 115 1.326 1.222 1.500 1.508 1.444 120.69 115.23 120.76 109.15 108.46 111.07 123.99 * * * 116 GLN 116 1.322 1.221 1.518 1.533 1.474 122.77 116.37 120.60 108.56 111.05 111.89 123.03 117 SER 117 1.318 1.237 1.526 1.519 1.454 121.80 115.75 121.07 110.67 110.88 109.49 123.17 118 THR 118 1.312 1.243 1.542 1.536 1.433 121.94 116.12 121.38 110.60 109.64 110.02 122.48 * * * 119 ILE 119 1.321 1.215 1.526 1.546 1.436 121.08 116.69 120.27 110.42 109.70 112.13 123.00 * * 120 ALA 120 1.338 1.236 1.518 1.520 1.468 122.64 115.19 121.15 110.80 110.70 110.81 123.66 121 LYS 121 1.314 1.231 1.525 1.499 1.448 123.84 115.26 121.68 109.36 110.21 107.64 123.06 * +* * +* +* 122 HIS 122 1.312 1.224 1.532 1.523 1.441 122.61 117.67 120.16 108.74 112.33 110.14 122.17 * * 123 LEU 123 1.315 1.236 1.522 1.515 1.418 121.74 115.51 121.04 112.81 110.57 106.99 123.44 ** * ** ** 124 ALA 124 1.304 - 1.508 1.528 1.436 123.08 - - 111.07 108.08 110.76 - +* * * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * ** ** *** ** ** * +* +* +** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_6 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 1.271 1.347 1.312 .014 **** * * C-N (Pro) 1.341 .016 4 1.321 1.380 1.351 .021 * ** C-O C-O 1.231 .020 123 1.208 1.251 1.233 .007 * * CA-C CH1E-C (except Gly) 1.525 .021 119 1.476 1.565 1.522 .015 ** +* CH2G*-C (Gly) 1.516 .018 5 1.496 1.528 1.513 .012 * CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.515 1.528 1.523 .004 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.524 1.574 1.556 .013 * CH1E-CH2E (the rest) 1.530 .020 84 1.495 1.575 1.531 .016 +* ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.398 1.479 1.444 .017 *** * NH1-CH2G* (Gly) 1.451 .016 5 1.433 1.468 1.443 .013 * * N-CH1E (Pro) 1.466 .015 4 1.451 1.484 1.473 .013 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_6 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 2.0 114 113.93 120.28 116.11 .94 * ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 114.98 118.60 116.74 1.19 * CH1E-C-N (Pro) 116.9 1.5 4 115.00 117.18 116.27 .92 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.32 124.63 123.02 .64 +* * O-C-N (Pro) 122.0 1.4 4 122.04 123.53 122.73 .63 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 118.02 125.40 122.27 1.23 ** ** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.58 122.62 121.20 .76 * C-N-CH1E (Pro) 122.6 5.0 4 122.13 123.97 123.09 .68 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 119.23 122.58 120.85 .55 * CH2G*-C-O (Gly) 120.8 2.1 5 119.84 121.33 120.58 .48 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.18 112.54 110.84 .63 * CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 107.50 112.68 110.33 1.29 +* CH2E-CH1E-C (the rest) 110.1 1.9 84 107.27 113.65 110.56 1.28 * +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 106.85 115.15 110.21 1.52 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.33 114.66 111.66 1.55 N-CH1E-C (Pro) 111.8 2.5 4 110.87 113.54 112.17 1.06 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 108.30 112.01 110.55 .78 * * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.32 114.46 111.37 1.01 * +* N-CH1E-CH2E (Pro) 103.0 1.1 4 102.25 103.44 103.06 .48 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 105.91 114.85 110.17 1.57 +** +** ------------------------------------------------------------------------------------------------------------- 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_6 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] 100 88.5% Residues in additional allowed regions [a,b,l,p] 11 9.7% Residues in generously allowed regions [~a,~b,~l,~p] 1 .9% Residues in disallowed regions [XX] 1 .9% ---- ------ 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 88.5 83.8 10.0 .5 Inside b. Omega angle st dev 122 3.0 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 -.9 Inside e. H-bond energy st dev 77 .8 .8 .2 .0 Inside f. Overall G-factor 124 .1 -.4 .3 1.5 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 6.7 18.1 6.5 -1.8 BETTER b. Chi-1 trans st dev 49 8.3 19.0 5.3 -2.0 BETTER c. Chi-1 gauche plus st dev 40 6.9 17.5 4.9 -2.2 BETTER d. Chi-1 pooled st dev 102 8.3 18.2 4.8 -2.0 BETTER e. Chi-2 trans st dev 30 10.2 20.4 5.0 -2.0 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 88.5 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.0 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .83 2 Residue-by-residue listing for refined_6 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.20 Chi1-chi2 distribution -.20 Chi1 only -.11 Chi3 & chi4 .42 Omega .13 ------ -.02 ===== Main-chain covalent forces:- Main-chain bond lengths .01 Main-chain bond angles .44 ------ .26 ===== OVERALL AVERAGE .07 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.