Residue-by-residue listing for refined_9 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 - - 188.5 - - - - - - - - 181.5 - 34.4 - 2 GLY 2 - - - - - - - - - - - 182.5 - - - 3 HIS 3 XX - - -65.9 - - - - - - - 184.2 - 30.1 - **** * **** 4 HIS 4 B - 189.2 - - - - - - - - 176.4 - 33.8 - 5 HIS 5 B - - -65.2 - - - - - - - 177.8 -1.0 33.6 - * * 6 HIS 6 b - 184.4 - - - - - - - - 175.5 - 33.9 - 7 HIS 7 B 47.6 - - - - - - - - - 184.8 - 31.2 - * * 8 HIS 8 b 59.5 - - - - - - - - - 179.8 -.6 30.7 - +* +* 9 LEU 9 b - - -63.1 175.9 - - - - - - 177.5 - 34.8 - 10 GLU 10 b - 191.5 - - - - - - - - 182.5 -1.1 33.7 - * * 11 MET 11 B - - -61.0 180.5 - - - - - - 184.5 -1.5 33.7 - 12 ALA 12 l - - - - - - - - - - 182.7 - 31.2 - 13 SER 13 B - 179.4 - - - - - - - - 175.2 - 35.4 - 14 GLU 14 a - 179.5 - 180.3 - - - - - - 175.6 - 33.9 - 15 GLU 15 ~p - - -61.0 - - - - - - - 171.6 - 33.3 - ** * ** 16 GLY 16 - - - - - - - - - - - 182.3 -1.9 - - 17 GLN 17 e B 50.0 - - - - - - - - - 180.5 - 26.5 - ** ** 18 VAL 18 E B - 185.5 - - - - - - - - 179.0 -.5 36.3 - ** ** 19 ILE 19 E B - - -60.8 178.8 - - - - - - 178.6 -3.1 32.0 - * * Residue-by-residue listing for refined_9 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 20 ALA 20 E B - - - - - - - - - - 179.8 -.5 34.2 - +* +* 21 CYS 21 E B - - -51.4 - - - - - - - 181.0 -1.7 36.1 - * * 22 HIS 22 A - - -63.8 - - - - - - - 180.8 -.6 33.2 - +* +* 23 THR 23 h B 58.6 - - - - - - - - - 177.7 - 34.8 - 24 VAL 24 H A 59.3 - - - - -66.6 -29.3 - - - 180.2 - 33.2 - 25 GLU 25 H A - 183.3 - 179.3 - -63.0 -50.1 - - - 178.6 - 33.9 - 26 THR 26 H A - - -54.6 - - -60.3 -42.9 - - - 179.4 - 34.5 - 27 TRP 27 H A - 175.1 - - - -57.5 -53.2 - - - 179.8 -1.9 33.8 - * * 28 ASN 28 H A - 183.4 - - - -60.1 -42.0 - - - 179.4 -3.0 34.7 - * * 29 GLU 29 H A - 182.4 - - - -60.2 -47.1 - - - 180.9 -2.6 34.7 - 30 GLN 30 H A - - -65.6 - - -62.5 -42.4 - - - 179.6 -2.9 34.3 - * * 31 LEU 31 H A - - -67.1 178.9 - -66.7 -44.4 - - - 178.6 -2.2 35.2 - 32 GLN 32 H A - 193.8 - - - -62.9 -40.0 - - - 177.6 -2.5 34.0 - 33 LYS 33 H A - 184.9 - 180.9 - -64.3 -37.2 - - - 179.7 -2.8 34.7 - 34 ALA 34 H A - - - - - -73.6 -37.1 - - - 181.7 -2.1 33.7 - 35 ASN 35 H A - 193.0 - - - -74.3 -53.9 - - - 183.6 -2.7 36.4 - * * 36 GLU 36 H A - 181.5 - 180.2 - -59.0 -42.9 - - - 181.1 -3.2 34.2 - +* +* 37 SER 37 h A - - -55.3 - - - - - - - 177.7 -1.6 34.2 - 38 LYS 38 T l - 193.9 - 184.4 - - - - - - 184.5 -1.6 31.7 - 39 THR 39 t B - - -46.6 - - - - - - - 179.2 -3.0 36.0 - * * * 40 LEU 40 e B - 187.9 - 174.0 - - - - - - 182.1 - 34.8 - 41 VAL 41 E B 60.8 - - - - - - - - - 176.6 -.7 33.3 - +* +* 42 VAL 42 E B - 181.0 - - - - - - - - 184.9 -2.9 34.0 - * * 43 VAL 43 E B - 185.1 - - - - - - - - 173.6 -3.0 36.0 - * * * 44 ASP 44 E B - 173.4 - - - - - - - - 177.4 -2.7 32.9 - 45 PHE 45 E B - - -62.7 - - - - - - - 187.9 -3.3 36.0 - * +* +* 46 THR 46 E B - 188.6 - - - - - - - - 175.4 -2.8 35.7 - * * 47 ALA 47 t B - - - - - - - - - - 181.8 - 33.4 - 48 SER 48 T A - - -55.4 - - - - - - - 181.0 - 34.0 - 49 TRP 49 T A 56.4 - - - - - - - - - 178.8 - 30.6 - 50 CYS 50 h B 46.6 - - - - - - - -119.2 2.8 185.7 -1.2 30.0 - * *** *7.8* * * *7.8* 51 GLY 51 H - - - - - - -58.3 -62.2 - - - 181.7 -.6 - - ** +* ** 52 PRO 52 H - - - - - -58.2 -58.2 -30.6 - - - 180.1 - 38.3 - * * 53 CYS 53 H A - - -47.7 153.1 - -69.5 -39.5 - -119.2 2.8 179.6 - 36.5 - * * *** *7.8* *7.8* 54 ARG 54 H A - 183.5 - 186.0 - -69.8 -30.3 - - - 182.3 -1.7 36.0 - 55 PHE 55 H A - 183.3 - - - -79.4 -27.3 - - - 182.9 -1.7 34.2 - * * * 56 ILE 56 H A - 190.8 - - - -87.0 -22.8 - - - 181.4 -1.5 34.2 - +* * +* Residue-by-residue listing for refined_9 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 - - - - - -56.2 -43.4 - - - 178.6 -1.3 32.1 - 58 PRO 58 H - - - - - -57.1 -57.1 -30.0 - - - 179.5 - 38.4 - * * 59 PHE 59 H A - 187.4 - - - -76.4 -29.8 - - - 177.3 -1.0 33.2 - * * 60 PHE 60 H A - 183.6 - - - -69.9 -35.1 - - - 177.1 -1.0 34.6 - * * 61 ALA 61 H A - - - - - -70.6 -35.5 - - - 176.6 -1.9 34.1 - 62 ASP 62 H A - 179.6 - - - -64.4 -44.0 - - - 177.2 -1.6 36.0 - 63 LEU 63 H A - 215.8 - 179.5 - -55.7 -43.2 - - - 177.4 -2.3 36.2 - +* +* 64 ALA 64 H A - - - - - -60.9 -32.0 - - - 179.4 -1.6 33.8 - 65 LYS 65 H A - - -60.2 179.1 - -71.9 -25.6 - - - 184.5 -1.0 34.7 - * * * 66 LYS 66 H A - - -61.5 178.1 - -91.2 -25.8 - - - 178.2 -1.0 31.5 - ** * * ** 67 LEU 67 h b - - -71.8 - - - - - - - 185.0 -1.6 32.5 - 68 PRO 68 T - - - - - -68.6 - - - - - 185.6 - 38.3 - * * 69 ASN 69 T A - - -62.6 - - - - - - - 179.4 - 33.5 - 70 VAL 70 t B - 177.5 - - - - - - - - 179.8 -.6 33.2 - +* +* 71 LEU 71 E B - - -71.3 - - - - - - - 180.1 -1.6 33.7 - 72 PHE 72 E B - - -62.3 - - - - - - - 183.0 -.7 33.4 - +* +* 73 LEU 73 E B - - -70.0 165.0 - - - - - - 176.8 -2.4 35.3 - 74 LYS 74 E B - - -65.6 - - - - - - - 178.4 -2.3 35.9 - 75 VAL 75 E B - 176.5 - - - - - - - - 175.6 -3.0 34.9 - * * 76 ASP 76 E B - 189.2 - - - - - - - - 186.5 -.6 33.8 - * +* +* 77 THR 77 e A 55.2 - - - - - - - - - 176.1 -3.5 33.4 - +* +* 78 ASP 78 T A - 187.2 - - - - - - - - 179.0 - 34.8 - 79 GLU 79 T a - 192.2 - 169.3 - - - - - - 176.2 - 36.3 - 80 LEU 80 h b - - -69.9 - - - - - - - 186.3 -3.5 33.3 - * ** ** 81 LYS 81 H A - 190.8 - 175.1 - -68.8 -36.2 - - - 179.9 -1.5 33.0 - 82 SER 82 H A - - -55.5 - - -74.5 -33.9 - - - 175.1 - 33.1 - 83 VAL 83 H A - 176.0 - - - -63.1 -45.7 - - - 177.6 - 34.3 - 84 ALA 84 H A - - - - - -57.2 -47.8 - - - 179.6 -2.3 34.5 - 85 SER 85 H A - - -54.8 - - -62.8 -40.1 - - - 181.1 -2.3 34.7 - 86 ASP 86 H A - 182.2 - - - -65.2 -37.0 - - - 179.9 -2.6 35.1 - 87 TRP 87 h A - - -68.7 - - - - - - - 177.3 -2.3 32.4 - 88 ALA 88 T l - - - - - - - - - - 180.1 -1.1 32.9 - * * 89 ILE 89 t b - - -53.6 - - - - - - - 180.0 -3.0 34.3 - * * 90 GLN 90 A - 178.8 - 178.9 - - - - - - 178.8 -1.2 33.8 - * * 91 ALA 91 S B - - - - - - - - - - 184.0 - 33.3 - 92 MET 92 S B - - -59.7 174.5 - - - - - - -2.2 - 36.3 - 93 PRO 93 e cis - - - - - -91.6 - - - - - 177.0 - 39.4 - ** +* ** 94 THR 94 E B - - -56.7 - - - - - - - 180.8 -2.7 34.5 - 95 PHE 95 E B - - -63.1 - - - - - - - 183.3 -2.7 36.7 - Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 96 MET 96 E B - 177.4 - 183.1 - - - - - - 181.0 -3.8 35.1 - ** ** 97 PHE 97 E B - - -66.1 - - - - - - - 177.8 -2.9 36.6 - * * 98 LEU 98 E B 58.4 - - 166.8 - - - - - - 184.0 -1.8 31.6 - 99 LYS 99 E B - 175.4 - 179.6 - - - - - - 175.3 -3.5 34.1 - +* +* 100 GLU 100 T l - - -59.8 181.7 - - - - - - 180.7 - 32.9 - 101 GLY 101 T - - - - - - - - - - - 176.3 - - - 102 LYS 102 E B - - -62.6 187.4 - - - - - - 179.9 -2.2 33.9 - 103 ILE 103 E B - - -59.6 176.4 - - - - - - 177.1 - 34.3 - 104 LEU 104 E a - - -64.3 181.9 - - - - - - 184.5 -2.1 34.9 - 105 ASP 105 E B 48.8 - - - - - - - - - 179.6 -1.8 32.4 - 106 LYS 106 E B 51.4 - - - - - - - - - 180.3 - 31.0 - 107 VAL 107 E B - 180.9 - - - - - - - - 178.4 -2.9 35.6 - * * 108 VAL 108 E B 56.2 - - - - - - - - - 181.1 -.5 31.8 - ** ** 109 GLY 109 e - - - - - - - - - - - 180.4 -2.5 - - 110 ALA 110 B - - - - - - - - - - 172.2 - 34.2 - * * 111 LYS 111 h B - - -69.6 - - - - - - - 185.3 -.9 35.2 - * * 112 LYS 112 H A - 182.9 - 177.9 - -68.1 -51.2 - - - 181.3 -.6 33.0 - * +* +* 113 ASP 113 H A - 177.1 - - - -72.2 -36.7 - - - 178.3 - 32.7 - 114 GLU 114 H A - 183.8 - - - -62.2 -29.0 - - - 179.3 - 34.1 - 115 LEU 115 H A - 188.2 - - - -61.2 -53.4 - - - 177.7 -1.2 34.6 - * * * 116 GLN 116 H A - - -60.5 - - -63.3 -32.1 - - - 179.0 -1.1 31.7 - * * 117 SER 117 H A - - -55.6 - - -66.3 -45.2 - - - 177.1 -2.0 34.0 - 118 THR 118 H A - - -56.8 - - -62.2 -35.5 - - - 175.1 -3.3 34.0 - +* +* 119 ILE 119 H A - - -60.7 178.2 - -62.7 -46.0 - - - 179.2 -2.2 33.3 - 120 ALA 120 H A - - - - - -65.4 -31.9 - - - 176.9 -2.5 33.2 - 121 LYS 121 H A - - -73.2 173.9 - -67.6 -30.2 - - - 174.1 -2.2 35.3 - * * 122 HIS 122 H A - - -77.0 - - -89.5 -25.0 - - - 182.8 -1.3 34.8 - ** * ** 123 LEU 123 h B - 194.0 - 167.3 - - - - - - 179.5 -1.9 34.6 - 124 ALA 124 - - - - - - - - - - - - - 34.4 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +* * * ** ** ** *** *7.8* * ** ** *7.8* ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 54.5 184.9 -61.8 177.0 -68.9 -66.5 -38.6 - -119.2 2.8 179.8 -2.0 34.1 *** *7.8* *7.8* Standard deviations: 5.0 7.3 6.6 6.9 16.0 8.3 9.0 - .0 .0 3.1 .9 1.8 Numbers of values: 13 45 44 31 4 46 46 0 2 2 122 84 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_9 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_9 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 - 1.235 1.521 1.551 1.452 - 116.09 120.87 111.82 108.06 109.66 123.01 * * * 2 GLY 2 1.303 1.242 1.504 - 1.430 121.98 116.19 119.69 - 110.58 - 124.11 +* * +* 3 HIS 3 1.332 1.226 1.521 1.548 1.477 124.63 116.32 121.45 112.05 111.76 113.83 122.23 +* * +* +* 4 HIS 4 1.305 1.231 1.525 1.541 1.444 120.52 116.27 120.93 110.66 110.80 110.74 122.78 +* +* 5 HIS 5 1.304 1.236 1.495 1.544 1.454 122.12 116.25 120.41 109.19 109.17 113.09 123.33 +* * +* +* 6 HIS 6 1.299 1.235 1.501 1.537 1.429 121.73 115.28 121.14 109.84 109.60 112.03 123.57 ** * +* ** 7 HIS 7 1.283 1.230 1.518 1.556 1.439 122.16 115.81 120.68 113.61 109.49 112.16 123.46 *** * +* *** 8 HIS 8 1.321 1.225 1.515 1.564 1.460 122.74 115.29 121.43 112.31 112.70 112.72 123.26 +* * * +* 9 LEU 9 1.301 1.236 1.506 1.536 1.433 122.39 116.54 120.66 109.67 109.65 110.74 122.75 ** * ** 10 GLU 10 1.307 1.236 1.523 1.558 1.435 120.78 115.49 121.28 112.84 106.47 110.39 123.02 +* * * * +* +* 11 MET 11 1.311 1.249 1.511 1.534 1.445 122.42 115.69 120.12 110.83 110.24 110.90 124.18 * * Residue-by-residue listing for refined_9 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 1.330 1.247 1.523 1.529 1.462 124.09 115.09 121.71 112.06 110.59 112.78 123.15 * * +* +* 13 SER 13 1.300 1.245 1.508 1.542 1.423 122.89 115.12 121.19 110.20 109.52 109.59 123.66 ** +* ** 14 GLU 14 1.288 1.245 1.505 1.533 1.423 123.12 115.13 120.32 111.68 106.71 110.98 124.40 +** +* +* +** 15 GLU 15 1.337 1.248 1.538 1.554 1.450 124.67 115.37 121.70 110.01 112.79 111.42 122.84 * +* +* 16 GLY 16 1.311 1.238 1.505 - 1.447 122.10 117.89 119.86 - 115.31 - 122.25 * * 17 GLN 17 1.303 1.236 1.480 1.539 1.418 119.26 112.39 122.79 115.02 114.01 114.56 124.69 +* ** ** * +* * +** * ** * +** 18 VAL 18 1.281 1.236 1.518 1.555 1.426 124.28 119.00 119.03 109.26 106.90 109.93 121.96 *** +* * * * +* *** 19 ILE 19 1.313 1.226 1.528 1.555 1.444 118.87 116.55 121.13 111.58 110.30 112.63 122.26 * +* * +* 20 ALA 20 1.301 1.232 1.513 1.522 1.438 121.51 116.87 120.61 110.72 109.38 110.42 122.50 +* * +* 21 CYS 21 1.310 1.221 1.507 1.511 1.430 121.35 117.11 120.10 109.12 108.17 109.54 122.78 * * * * 22 HIS 22 1.306 1.236 1.503 1.533 1.455 121.17 115.88 121.01 110.41 110.94 111.74 123.10 +* * +* 23 THR 23 1.311 1.251 1.509 1.558 1.440 121.92 116.28 120.29 108.53 109.12 112.21 123.43 * * * 24 VAL 24 1.314 1.235 1.539 1.565 1.451 121.84 116.08 120.90 110.93 110.48 111.63 122.96 * * 25 GLU 25 1.338 1.234 1.511 1.523 1.449 121.77 115.87 120.57 109.96 110.23 111.34 123.56 26 THR 26 1.327 1.220 1.533 1.541 1.446 121.58 116.36 120.29 109.62 109.96 110.95 123.30 27 TRP 27 1.332 1.242 1.531 1.539 1.463 122.42 115.86 120.82 111.11 111.28 109.98 123.30 28 ASN 28 1.322 1.239 1.527 1.536 1.462 122.37 115.26 120.98 110.07 110.24 110.08 123.75 29 GLU 29 1.325 1.222 1.533 1.543 1.459 123.65 116.73 120.34 110.48 110.82 109.48 122.92 * * 30 GLN 30 1.333 1.224 1.519 1.499 1.427 122.92 116.93 120.37 110.05 112.36 109.81 122.69 +* +* +* 31 LEU 31 1.321 1.230 1.509 1.486 1.420 122.19 115.71 120.87 109.74 111.43 109.03 123.42 ** ** ** 32 GLN 32 1.313 1.216 1.530 1.557 1.441 122.23 116.12 120.56 113.21 108.01 108.94 123.23 * * +* * +* 33 LYS 33 1.325 1.238 1.539 1.539 1.457 122.86 116.79 120.94 110.01 110.54 109.99 122.27 34 ALA 34 1.323 1.230 1.521 1.517 1.445 121.24 116.28 120.76 110.63 110.97 110.60 122.94 35 ASN 35 1.314 1.231 1.508 1.525 1.457 121.80 115.05 121.13 107.86 109.66 109.94 123.78 * * * 36 GLU 36 1.315 1.228 1.521 1.531 1.468 122.94 116.93 120.33 109.88 112.02 110.26 122.72 37 SER 37 1.308 1.240 1.548 1.514 1.434 121.06 115.91 120.64 111.43 111.28 108.84 123.44 +* * * +* 38 LYS 38 1.352 1.238 1.553 1.515 1.443 125.30 114.84 122.40 113.44 111.61 110.12 122.76 +* * ** +* ** 39 THR 39 1.308 1.236 1.536 1.519 1.441 123.45 115.86 121.02 108.71 110.22 109.35 123.08 +* * +* 40 LEU 40 1.297 1.239 1.547 1.564 1.443 122.78 116.77 120.41 112.11 107.52 108.96 122.80 ** * +* * * ** 41 VAL 41 1.314 1.233 1.544 1.566 1.444 121.59 116.74 120.54 111.63 110.88 110.63 122.67 * * * 42 VAL 42 1.315 1.229 1.527 1.542 1.452 122.33 117.07 120.51 109.74 108.76 112.03 122.41 * * Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 43 VAL 43 1.308 1.215 1.526 1.559 1.454 121.64 117.02 120.03 107.92 110.75 110.56 122.94 * * 44 ASP 44 1.314 1.246 1.517 1.527 1.456 122.27 115.57 121.13 110.20 110.56 112.33 123.26 * * * 45 PHE 45 1.303 1.232 1.510 1.523 1.420 122.85 116.41 120.56 109.54 107.51 109.67 122.96 +* ** * ** 46 THR 46 1.287 1.227 1.526 1.563 1.426 121.39 117.37 120.01 110.80 108.73 108.87 122.53 +** +* +* +** 47 ALA 47 1.299 1.236 1.505 1.520 1.437 121.93 116.58 120.68 110.90 108.45 111.70 122.73 ** * ** 48 SER 48 1.291 1.220 1.535 1.519 1.440 121.91 117.34 120.51 110.59 111.99 109.86 122.15 +** +** 49 TRP 49 1.320 1.222 1.533 1.537 1.442 120.56 118.58 119.78 111.91 114.15 112.31 121.64 * * * * 50 CYS 50 1.319 1.238 1.536 1.547 1.459 119.31 114.88 121.47 113.86 112.02 112.05 123.65 * +* +* 51 GLY 51 1.335 1.231 1.532 - 1.468 123.62 119.33 119.56 - 115.81 - 121.11 * +* * * * +* 52 PRO 52 1.361 1.235 1.524 1.536 1.478 122.75 115.39 121.25 110.38 112.18 103.95 123.35 * * * 53 CYS 53 1.308 1.223 1.527 1.505 1.443 123.08 115.42 121.59 109.30 109.37 108.17 122.97 +* * * +* 54 ARG 54 1.312 1.230 1.535 1.525 1.449 122.87 115.64 121.11 109.97 109.61 108.39 123.22 * * * 55 PHE 55 1.325 1.234 1.541 1.544 1.462 122.82 117.20 120.57 110.40 112.00 109.89 122.21 56 ILE 56 1.322 1.238 1.551 1.577 1.467 120.80 115.01 121.62 110.58 109.38 110.79 123.30 * * * 57 ALA 57 1.329 1.233 1.565 1.524 1.467 123.81 120.52 119.14 111.20 114.85 110.54 120.33 +* * ** * +* ** 58 PRO 58 1.376 1.230 1.535 1.523 1.477 122.13 117.28 120.71 110.00 113.34 103.75 122.00 ** ** 59 PHE 59 1.326 1.235 1.529 1.537 1.458 120.29 115.63 121.15 111.23 109.20 111.46 123.20 60 PHE 60 1.324 1.228 1.537 1.544 1.455 122.59 115.67 121.37 111.31 108.82 109.44 122.95 61 ALA 61 1.327 1.228 1.529 1.520 1.460 121.97 115.53 121.33 110.57 109.92 110.37 123.13 62 ASP 62 1.323 1.223 1.503 1.513 1.469 123.04 114.09 121.67 108.67 109.63 109.49 124.24 * * * 63 LEU 63 1.302 1.234 1.544 1.533 1.450 124.36 115.80 120.89 110.82 109.29 107.22 123.29 +* * +* +* 64 ALA 64 1.326 1.224 1.524 1.519 1.459 122.90 116.12 121.21 110.51 111.15 110.38 122.67 65 LYS 65 1.319 1.230 1.519 1.530 1.452 121.80 116.52 120.84 108.94 110.98 111.05 122.64 66 LYS 66 1.318 1.238 1.525 1.521 1.439 120.60 117.67 119.89 112.98 113.72 110.20 122.43 * +* +* 67 LEU 67 1.318 1.226 1.533 1.542 1.444 121.49 117.28 120.74 111.22 110.72 112.06 121.98 68 PRO 68 1.349 1.232 1.531 1.536 1.470 122.80 117.59 120.48 110.22 114.54 103.58 121.92 * * 69 ASN 69 1.312 1.233 1.514 1.518 1.437 120.66 116.76 120.53 110.62 112.56 110.44 122.70 * * * 70 VAL 70 1.307 1.225 1.517 1.553 1.441 121.29 116.01 120.83 110.79 110.01 111.87 123.12 +* +* 71 LEU 71 1.304 1.230 1.507 1.536 1.419 122.58 115.97 120.93 110.81 110.23 111.16 123.07 +* ** ** 72 PHE 72 1.297 1.234 1.509 1.525 1.436 122.17 115.98 120.70 110.95 109.58 111.33 123.31 ** * ** 73 LEU 73 1.293 1.225 1.512 1.523 1.447 123.15 115.93 120.83 109.70 111.45 109.25 123.22 +** +** Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 74 LYS 74 1.308 1.242 1.504 1.510 1.412 123.29 116.15 120.54 109.24 109.13 109.53 123.29 * * ** ** 75 VAL 75 1.297 1.238 1.507 1.558 1.436 121.72 116.51 120.31 109.09 109.61 111.51 123.18 ** * ** 76 ASP 76 1.316 1.222 1.500 1.512 1.439 120.53 115.66 121.01 110.29 107.32 112.08 123.29 * * * * 77 THR 77 1.288 1.229 1.523 1.529 1.444 123.37 117.00 120.41 110.38 113.67 110.50 122.55 +** +** 78 ASP 78 1.309 1.234 1.513 1.521 1.446 120.57 113.91 122.07 110.13 107.62 110.53 124.00 * * * * 79 GLU 79 1.317 1.236 1.509 1.520 1.448 124.12 115.41 121.78 109.95 108.21 108.33 122.79 * * * * 80 LEU 80 1.302 1.239 1.518 1.532 1.413 122.48 114.31 122.01 111.57 108.70 111.43 123.66 +* ** ** 81 LYS 81 1.313 1.243 1.523 1.529 1.439 123.33 116.62 120.77 112.20 112.28 109.78 122.59 * * * 82 SER 82 1.313 1.222 1.519 1.507 1.436 120.73 116.24 120.56 112.00 110.12 110.34 123.16 * * * * 83 VAL 83 1.333 1.225 1.520 1.549 1.459 121.76 115.78 121.04 109.53 109.24 111.61 123.16 84 ALA 84 1.325 1.221 1.519 1.511 1.450 122.06 115.76 120.82 110.05 110.25 110.14 123.40 85 SER 85 1.315 1.229 1.544 1.526 1.449 122.48 116.18 120.71 110.46 111.08 109.24 123.08 86 ASP 86 1.329 1.229 1.526 1.537 1.471 122.92 115.85 121.20 109.79 111.07 109.48 122.91 87 TRP 87 1.318 1.240 1.521 1.524 1.443 122.27 115.87 120.32 111.61 112.57 110.91 123.81 88 ALA 88 1.339 1.235 1.532 1.532 1.474 124.17 116.55 120.84 111.11 112.33 110.74 122.54 * * 89 ILE 89 1.314 1.235 1.526 1.561 1.446 121.73 116.00 121.04 109.38 108.90 112.09 122.88 * * 90 GLN 90 1.307 1.234 1.517 1.531 1.444 121.75 116.12 120.83 111.11 110.17 110.47 123.04 +* +* 91 ALA 91 1.312 1.236 1.514 1.515 1.445 121.13 116.25 120.82 111.23 109.45 111.14 122.93 * * 92 MET 92 1.302 1.242 1.517 1.523 1.432 122.43 118.41 120.03 109.02 109.50 108.99 121.56 +* * * +* 93 PRO 93 1.336 1.232 1.533 1.521 1.459 124.22 116.89 120.89 110.30 111.71 102.38 122.12 94 THR 94 1.289 1.225 1.511 1.519 1.422 120.72 116.39 120.34 109.56 109.41 111.19 123.21 +** +* +** 95 PHE 95 1.303 1.219 1.490 1.524 1.413 121.82 115.88 120.72 108.68 107.50 109.64 123.40 +* +* ** * ** 96 MET 96 1.279 1.233 1.505 1.518 1.425 122.74 115.00 121.43 110.83 109.99 108.89 123.57 +*** +* +*** 97 PHE 97 1.282 1.250 1.513 1.518 1.400 123.79 116.54 121.09 109.51 109.30 108.40 122.37 *** *** * * *** 98 LEU 98 1.291 1.232 1.516 1.562 1.417 120.32 116.81 120.79 111.83 109.75 113.42 122.40 +** +* ** +* +** 99 LYS 99 1.289 1.231 1.489 1.522 1.427 121.39 114.45 121.11 110.35 111.18 110.55 124.40 +** +* +* +** 100 GLU 100 1.321 1.232 1.534 1.522 1.444 124.28 115.47 121.32 112.13 112.06 109.87 123.10 * * * 101 GLY 101 1.318 1.227 1.519 - 1.445 121.58 117.19 120.25 - 113.23 - 122.56 102 LYS 102 1.325 1.226 1.517 1.535 1.455 121.35 116.84 120.19 109.25 110.05 112.10 122.96 103 ILE 103 1.315 1.235 1.519 1.561 1.463 122.12 116.41 120.41 109.13 110.47 111.73 123.16 104 LEU 104 1.315 1.240 1.504 1.526 1.432 121.56 115.30 121.60 109.36 110.07 110.68 123.05 * * 105 ASP 105 1.303 1.216 1.493 1.536 1.434 121.84 115.70 121.08 110.79 111.96 112.27 123.18 +* +* * * +* Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 106 LYS 106 1.298 1.237 1.525 1.567 1.432 122.14 115.83 120.85 113.84 111.59 111.40 123.29 ** +* * +* ** 107 VAL 107 1.303 1.226 1.511 1.562 1.443 122.57 116.89 120.20 108.72 108.45 111.12 122.89 +* +* 108 VAL 108 1.306 1.241 1.533 1.563 1.434 120.96 115.55 121.54 112.15 110.94 112.19 122.88 +* * * +* 109 GLY 109 1.309 1.237 1.504 - 1.435 121.71 117.58 120.08 - 109.85 - 122.34 * * * 110 ALA 110 1.308 1.233 1.503 1.527 1.433 119.68 115.14 121.41 110.12 110.25 110.86 123.43 +* * * * +* 111 LYS 111 1.293 1.233 1.491 1.523 1.417 122.96 116.99 119.84 108.40 106.01 112.49 123.16 +** +* ** +* * +** 112 LYS 112 1.301 1.209 1.525 1.520 1.422 120.91 117.46 119.67 112.01 111.83 110.09 122.77 +* * +* * +* 113 ASP 113 1.330 1.245 1.519 1.528 1.482 121.74 116.12 121.13 110.33 112.25 111.68 122.75 * * 114 GLU 114 1.322 1.216 1.519 1.523 1.461 121.65 116.63 120.54 109.82 109.80 111.18 122.83 115 LEU 115 1.322 1.227 1.515 1.513 1.443 121.60 116.59 120.35 109.92 109.72 110.40 123.03 116 GLN 116 1.332 1.233 1.513 1.547 1.483 120.25 116.04 120.78 108.95 110.62 115.21 123.16 * +** +** 117 SER 117 1.317 1.213 1.526 1.514 1.439 121.29 116.25 120.65 111.17 109.80 110.00 123.06 118 THR 118 1.324 1.234 1.535 1.554 1.452 123.20 116.40 120.80 111.34 109.62 110.16 122.76 * * 119 ILE 119 1.329 1.210 1.530 1.557 1.447 121.07 116.67 120.21 109.92 109.41 112.77 123.08 * * 120 ALA 120 1.332 1.233 1.536 1.523 1.469 122.55 116.24 120.80 110.88 111.60 110.63 122.96 121 LYS 121 1.326 1.235 1.544 1.503 1.414 124.32 115.76 121.29 112.43 111.24 106.39 122.95 * ** * * ** ** 122 HIS 122 1.321 1.227 1.529 1.526 1.453 123.00 116.09 120.95 108.56 111.47 110.92 122.94 123 LEU 123 1.311 1.238 1.531 1.535 1.429 123.66 115.47 121.34 112.74 110.51 107.61 123.19 * +* * * +* +* 124 ALA 124 1.304 - 1.514 1.529 1.433 122.99 - - 110.78 108.34 110.55 - +* * * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** * ** ** *** ** ** * +** +* +** +* +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 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 1.279 1.352 1.313 .014 +*** +* * C-N (Pro) 1.341 .016 4 1.336 1.376 1.356 .015 ** C-O C-O 1.231 .020 123 1.209 1.251 1.232 .008 * * CA-C CH1E-C (except Gly) 1.525 .021 119 1.480 1.565 1.521 .014 ** +* CH2G*-C (Gly) 1.516 .018 5 1.504 1.532 1.513 .011 CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.511 1.532 1.522 .006 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.519 1.577 1.553 .014 * CH1E-CH2E (the rest) 1.530 .020 84 1.486 1.567 1.530 .015 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.400 1.483 1.444 .016 *** * NH1-CH2G* (Gly) 1.451 .016 5 1.430 1.468 1.445 .013 * * N-CH1E (Pro) 1.466 .015 4 1.459 1.478 1.471 .008 ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 Page 12 ---------------------------------------- +-----------------+ | BOND ANGLES | +-----------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Angle X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 114 112.39 120.52 116.13 .98 +* ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 116.19 119.33 117.64 1.02 * CH1E-C-N (Pro) 116.9 1.5 4 115.39 117.59 116.79 .84 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.33 124.69 122.99 .61 +* * O-C-N (Pro) 122.0 1.4 4 121.92 123.35 122.35 .58 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 118.87 125.30 122.14 1.21 +* ** C-NH1-CH2G* (Gly) 120.6 1.7 5 121.58 123.62 122.20 .73 +* C-N-CH1E (Pro) 122.6 5.0 4 122.13 124.22 122.97 .77 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 119.03 122.79 120.82 .57 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.56 120.25 119.89 .25 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.05 112.06 110.83 .50 * CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 107.92 112.15 109.97 1.11 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.86 115.02 110.72 1.40 * +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 106.01 114.85 110.24 1.64 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 109.85 115.81 112.95 2.41 * N-CH1E-C (Pro) 111.8 2.5 4 111.71 114.54 112.94 1.10 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.14 112.78 110.83 .68 +* NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 108.87 112.77 111.20 1.00 +* N-CH1E-CH2E (Pro) 103.0 1.1 4 102.38 103.95 103.42 .62 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.39 115.21 110.51 1.56 ** +** ------------------------------------------------------------------------------------------------------------- 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_9 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] 14 12.4% 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 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 1.8 3.1 1.6 -.8 Inside e. H-bond energy st dev 84 .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 13 5.0 18.1 6.5 -2.0 BETTER b. Chi-1 trans st dev 45 7.3 19.0 5.3 -2.2 BETTER c. Chi-1 gauche plus st dev 44 6.6 17.5 4.9 -2.2 BETTER d. Chi-1 pooled st dev 102 8.2 18.2 4.8 -2.0 BETTER e. Chi-2 trans st dev 31 6.9 20.4 5.0 -2.7 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 8.2 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .89 3 Residue-by-residue listing for refined_9 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.17 Chi1-chi2 distribution -.19 Chi1 only -.02 Chi3 & chi4 .42 Omega .09 ------ -.01 ===== Main-chain covalent forces:- Main-chain bond lengths .03 Main-chain bond angles .43 ------ .27 ===== OVERALL AVERAGE .08 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.