Residue-by-residue listing for refined_7 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 - 55.7 - - - - - - - - - 179.6 - 31.8 - 2 GLY 2 - - - - - - - - - - - 183.0 - - - 3 HIS 3 S B - 180.5 - - - - - - - - 175.5 - 32.4 - 4 HIS 4 B - - -74.9 - - - - - - - 184.9 -1.1 32.0 - * * 5 HIS 5 B - 176.7 - - - - - - - - 174.5 - 32.9 - 6 HIS 6 B - - -61.7 - - - - - - - 174.8 - 35.0 - 7 HIS 7 B - - -64.2 - - - - - - - 179.4 - 32.6 - 8 HIS 8 b - 182.9 - - - - - - - - 182.0 -1.1 33.7 - * * 9 LEU 9 B - - -59.8 178.4 - - - - - - 181.1 -1.4 34.1 - 10 GLU 10 B - - -65.4 178.7 - - - - - - 172.4 - 34.5 - * * 11 MET 11 B - - -73.5 - - - - - - - 183.6 - 32.3 - 12 ALA 12 b - - - - - - - - - - 177.3 -1.0 33.1 - * * 13 SER 13 B - - -61.0 - - - - - - - 181.8 -1.1 33.6 - * * 14 GLU 14 A - 183.5 - 182.3 - - - - - - 177.7 - 35.3 - 15 GLU 15 p - - -61.0 - - - - - - - 182.6 - 31.7 - 16 GLY 16 - - - - - - - - - - - 181.1 -1.7 - - 17 GLN 17 B 49.5 - - - - - - - - - 178.9 - 29.0 - * * 18 VAL 18 B - 183.1 - - - - - - - - 181.9 - 35.3 - 19 ILE 19 E B - - -60.2 178.8 - - - - - - 180.1 -3.1 34.7 - * * 20 ALA 20 E B - - - - - - - - - - 181.5 -.8 33.7 - +* +* Residue-by-residue listing for refined_7 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 - - -52.7 - - - - - - - 180.6 -2.3 35.4 - 22 HIS 22 S A - - -56.2 - - - - - - - 182.8 -.6 34.8 - +* +* 23 THR 23 h B 58.6 - - - - - - - - - 175.4 - 36.0 - 24 VAL 24 H A 64.8 - - - - -76.1 -22.0 - - - 177.8 - 32.1 - +* +* 25 GLU 25 H A - 183.1 - - - -56.5 -51.8 - - - 178.2 - 35.9 - * * 26 THR 26 H A - - -57.0 - - -67.4 -45.8 - - - 180.3 - 34.4 - 27 TRP 27 H A - 168.7 - - - -52.8 -51.3 - - - 184.0 -1.6 35.0 - * * * 28 ASN 28 H A - 188.7 - - - -61.5 -46.0 - - - 180.1 -3.3 33.9 - +* +* 29 GLU 29 H A - 178.9 - 183.6 - -60.6 -45.9 - - - 184.1 -1.5 34.4 - 30 GLN 30 H A - - -69.2 - - -60.1 -35.1 - - - 180.7 -2.3 33.6 - 31 LEU 31 H A - - -63.8 179.2 - -65.3 -50.4 - - - 177.3 -1.5 33.6 - 32 GLN 32 H A - - -65.7 - - -65.2 -32.7 - - - 179.2 -1.3 31.8 - * * 33 LYS 33 H A - 186.4 - 181.7 - -64.5 -44.0 - - - 180.9 -2.2 34.2 - 34 ALA 34 H A - - - - - -69.4 -36.4 - - - 181.2 -2.8 34.2 - * * 35 ASN 35 H A - 191.6 - - - -69.6 -53.6 - - - 182.0 -2.4 36.1 - * * 36 GLU 36 H A - 189.5 - - - -59.5 -43.6 - - - 181.7 -3.2 35.0 - +* +* 37 SER 37 h A - - -59.1 - - - - - - - 176.9 -2.4 33.8 - 38 LYS 38 T L - 189.0 - 184.3 - - - - - - 179.2 -1.1 33.5 - * * 39 THR 39 t B - - -46.8 - - - - - - - 177.9 -2.2 35.6 - * * 40 LEU 40 e B - 189.2 - 170.9 - - - - - - 186.1 - 33.8 - * * 41 VAL 41 E B 59.5 - - - - - - - - - 179.4 - 33.4 - 42 VAL 42 E B 62.4 - - - - - - - - - 180.8 -2.5 33.8 - 43 VAL 43 E B - 183.0 - - - - - - - - 177.5 -3.3 33.6 - +* +* 44 ASP 44 E B - 171.5 - - - - - - - - 175.6 -3.1 35.8 - * * 45 PHE 45 E B - - -64.3 - - - - - - - 182.9 -2.8 36.2 - 46 THR 46 E B - 188.2 - - - - - - - - 177.7 -2.2 35.4 - 47 ALA 47 t B - - - - - - - - - - 182.6 - 34.0 - 48 SER 48 T A - - -58.1 - - - - - - - 180.5 - 32.3 - 49 TRP 49 T A 56.8 - - - - - - - - - 178.6 - 31.6 - 50 CYS 50 h B 47.9 - - - - - - - -104.7 2.0 183.7 -1.5 28.2 - * +* +* +* 51 GLY 51 H - - - - - - -49.6 -61.2 - - - 179.3 -.6 - - * +* +* +* 52 PRO 52 H - - - - - -57.2 -57.2 -30.5 - - - 180.2 - 38.5 - * * 53 CYS 53 H A - - -46.3 150.6 - -72.6 -47.5 - -104.7 2.0 181.1 - 36.7 - * * +* +* 54 ARG 54 H A - 189.6 - - - -66.5 -31.3 - - - 180.5 -2.9 34.7 - * * 55 PHE 55 H A - 182.6 - - - -64.7 -23.5 - - - 183.5 -2.5 34.5 - * * 56 ILE 56 H A - 199.4 - - - -93.3 -12.6 - - - 183.1 -1.0 33.8 - ** ** * ** Residue-by-residue listing for refined_7 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 - - - - - -56.4 -54.0 - - - 179.3 -.9 30.9 - * +* +* 58 PRO 58 H - - - - - -64.0 -64.0 -24.2 - - - 181.1 - 38.7 - * * * 59 PHE 59 H A - 189.6 - - - -76.9 -47.5 - - - 179.4 - 34.2 - 60 PHE 60 H A - 188.3 - - - -63.9 -33.2 - - - 177.0 -3.0 34.1 - * * 61 ALA 61 H A - - - - - -65.6 -28.2 - - - 177.5 -2.1 33.8 - 62 ASP 62 H A - 184.9 - - - -73.7 -44.0 - - - 174.6 -.8 34.9 - +* +* 63 LEU 63 H A - - -85.0 - - -53.8 -44.6 - - - 177.5 -1.9 33.6 - * * 64 ALA 64 H A - - - - - -61.6 -31.7 - - - 179.1 -2.2 33.2 - 65 LYS 65 H A - 174.5 - 186.2 - -79.1 -22.4 - - - 186.6 -.9 37.0 - * +* * +* +* 66 LYS 66 H A - 198.6 - - - -84.2 -40.6 - - - 182.8 -1.3 34.9 - +* * +* 67 LEU 67 h B - - -73.8 - - - - - - - 181.0 -2.0 31.5 - 68 PRO 68 S - - - - - -66.2 - - - - - 177.8 - 38.5 - * * 69 ASN 69 S b - 181.0 - - - - - - - - 176.9 - 32.1 - 70 VAL 70 B - 173.3 - - - - - - - - 182.2 - 33.2 - 71 LEU 71 E B - 189.0 - - - - - - - - 180.8 -2.9 34.2 - * * 72 PHE 72 E B - - -57.1 - - - - - - - 177.3 -.8 36.7 - +* +* 73 LEU 73 E B - - -72.1 - - - - - - - 181.0 -3.0 32.4 - * * 74 LYS 74 E B - 192.4 - 181.9 - - - - - - 177.7 -3.2 36.4 - +* +* 75 VAL 75 E B - 179.5 - - - - - - - - 177.3 -3.4 34.9 - +* +* 76 ASP 76 E B - 188.1 - - - - - - - - 187.0 -.5 33.6 - * ** ** 77 THR 77 e A 49.8 - - - - - - - - - 175.5 -2.7 32.8 - 78 ASP 78 T A - 185.9 - - - - - - - - 178.2 - 34.0 - 79 GLU 79 T a - - -63.3 - - - - - - - 179.3 - 36.7 - 80 LEU 80 h b - - -70.8 - - - - - - - 186.8 -3.2 34.8 - * +* +* 81 LYS 81 H A - 190.3 - 186.9 - -68.0 -35.3 - - - 178.2 -1.5 33.8 - 82 SER 82 H A 55.8 - - - - -68.9 -34.9 - - - 177.4 - 33.0 - 83 VAL 83 H A - 181.8 - - - -70.0 -40.1 - - - 176.4 - 34.3 - 84 ALA 84 H A - - - - - -60.0 -43.5 - - - 177.8 -2.6 34.4 - 85 SER 85 H A - 180.8 - - - -64.0 -42.2 - - - 180.5 -2.6 34.3 - 86 ASP 86 H A - 179.2 - - - -63.4 -37.0 - - - 177.0 -2.4 33.7 - 87 TRP 87 h A - - -70.4 - - - - - - - 177.7 -2.3 32.6 - 88 ALA 88 T L - - - - - - - - - - 179.6 -1.0 33.2 - * * 89 ILE 89 t b - - -54.4 - - - - - - - 177.7 -3.0 33.3 - * * 90 GLN 90 A - 177.7 - - - - - - - - 178.5 -1.9 34.8 - 91 ALA 91 S B - - - - - - - - - - 183.4 - 34.0 - 92 MET 92 S B - - -57.0 177.6 - - - - - - -2.1 -.6 35.7 - +* +* 93 PRO 93 e cis - - - - - -92.1 - - - - - 176.9 - 39.7 - ** +* ** 94 THR 94 E B - - -57.0 - - - - - - - 179.5 -2.3 34.6 - Residue-by-residue listing for refined_7 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 ----------------------------------------------------------------------------------------------------------------------------------- 95 PHE 95 E B - - -50.0 - - - - - - - 180.2 -3.4 36.9 - * +* +* 96 MET 96 E B - 178.8 - 177.6 - - - - - - 183.1 -3.2 32.8 - +* +* 97 PHE 97 E B - - -69.4 - - - - - - - 178.7 -3.4 36.3 - +* +* 98 LEU 98 E B - - -54.3 - - - - - - - 175.4 -2.5 35.4 - 99 LYS 99 E B - 176.1 - 174.5 - - - - - - 174.8 -3.4 33.3 - +* +* 100 GLU 100 T L - - -56.3 180.2 - - - - - - 178.8 - 34.0 - 101 GLY 101 T - - - - - - - - - - - 174.4 - - - 102 LYS 102 E B - 180.0 - 188.0 - - - - - - 178.2 -1.8 34.9 - 103 ILE 103 E B - - -58.0 177.2 - - - - - - 178.6 - 33.9 - 104 LEU 104 E a - - -69.5 187.6 - - - - - - 186.3 -2.4 34.0 - * * 105 ASP 105 E B 54.0 - - - - - - - - - 179.6 -2.1 32.5 - 106 LYS 106 E B 51.9 - - 180.4 - - - - - - 181.7 - 32.0 - 107 VAL 107 E B - 180.6 - - - - - - - - 177.4 -3.0 35.6 - * * 108 VAL 108 E B 61.8 - - - - - - - - - 183.0 - 32.5 - 109 GLY 109 e - - - - - - - - - - - 184.9 -3.3 - - +* +* 110 ALA 110 B - - - - - - - - - - 172.9 - 34.1 - * * 111 LYS 111 h B - - -64.0 - - - - - - - 179.7 -.9 35.9 - * * 112 LYS 112 H A - - -65.8 181.1 - -61.6 -44.9 - - - 181.0 - 36.0 - 113 ASP 113 H A 55.5 - - - - -60.3 -46.2 - - - 181.2 - 34.7 - 114 GLU 114 H A - 182.6 - - - -72.3 -33.9 - - - 178.9 - 33.7 - 115 LEU 115 H A - 190.5 - - - -64.9 -51.0 - - - 176.9 -2.3 34.5 - * * 116 GLN 116 H A - - -74.5 - - -57.0 -35.9 - - - 179.3 -3.0 32.6 - * * 117 SER 117 H A - - -56.6 - - -70.1 -36.1 - - - 177.2 -1.8 33.6 - 118 THR 118 H A - - -56.1 - - -70.9 -34.8 - - - 175.3 -2.2 34.1 - 119 ILE 119 H A - - -62.1 - - -63.0 -48.3 - - - 179.4 -2.5 33.7 - 120 ALA 120 H A - - - - - -63.9 -31.4 - - - 175.9 -2.8 33.1 - 121 LYS 121 H A - 185.2 - 181.2 - -58.2 -44.1 - - - 178.7 -1.7 36.9 - 122 HIS 122 H A - - -73.3 - - -78.6 -40.5 - - - 181.5 -1.6 33.4 - * * 123 LEU 123 h a - - -82.0 - - - - - - - 174.1 -3.2 32.6 - * * * * 124 ALA 124 - - - - - - - - - - - - - 34.2 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * * * ** ** ** +* * ** +* ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.0 184.0 -63.0 179.5 -69.9 -65.8 -39.5 - -104.7 2.0 179.6 -2.1 34.1 +* +* Standard deviations: 5.1 6.5 8.6 7.5 15.3 8.3 9.9 - .0 .0 3.0 .9 1.7 Numbers of values: 14 44 44 23 4 46 46 0 2 2 122 80 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_7 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_7 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 - 1.244 1.528 1.557 1.470 - 116.83 120.61 111.92 112.19 111.77 122.56 * * 2 GLY 2 1.319 1.236 1.504 - 1.434 121.00 117.10 120.26 - 110.97 - 122.64 * * 3 HIS 3 1.305 1.226 1.526 1.537 1.446 121.28 115.38 121.23 111.76 112.33 110.97 123.35 +* +* 4 HIS 4 1.311 1.230 1.503 1.545 1.457 123.62 116.28 120.22 111.46 109.13 113.16 123.50 * * * +* +* 5 HIS 5 1.307 1.237 1.525 1.540 1.454 122.35 115.44 120.93 111.10 113.45 110.48 123.63 +* +* 6 HIS 6 1.318 1.229 1.505 1.551 1.462 123.37 117.39 119.89 107.54 107.86 113.04 122.72 * * * * * 7 HIS 7 1.307 1.235 1.498 1.534 1.446 120.43 115.77 121.29 110.02 109.12 113.64 122.83 +* * +* +* 8 HIS 8 1.290 1.229 1.515 1.536 1.425 121.34 115.18 120.75 112.30 108.14 110.25 123.92 +** +* * * +** 9 LEU 9 1.318 1.246 1.514 1.533 1.451 122.91 115.64 120.88 110.53 110.81 110.40 123.48 10 GLU 10 1.306 1.233 1.499 1.522 1.436 122.25 116.11 120.76 108.79 111.82 111.33 123.10 +* * * +* 11 MET 11 1.295 1.230 1.491 1.535 1.430 121.03 115.26 121.09 111.26 107.82 113.46 123.56 ** +* * * +* ** Residue-by-residue listing for refined_7 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 1.298 1.232 1.508 1.523 1.434 122.00 115.61 121.29 111.32 110.72 111.00 122.99 ** * ** 13 SER 13 1.288 1.233 1.521 1.538 1.428 123.08 116.57 120.30 112.12 108.56 110.34 123.05 +** +* * +** 14 GLU 14 1.315 1.241 1.523 1.518 1.456 122.18 114.72 120.93 110.36 109.69 108.84 124.35 * * 15 GLU 15 1.327 1.238 1.519 1.531 1.455 124.44 115.37 121.44 112.41 113.09 110.91 123.08 +* * +* 16 GLY 16 1.299 1.228 1.497 - 1.438 121.16 115.67 120.97 - 110.84 - 123.33 ** * ** 17 GLN 17 1.313 1.226 1.497 1.546 1.431 121.58 114.49 121.76 113.34 113.71 113.32 123.69 * * * +* +* +* 18 VAL 18 1.286 1.238 1.521 1.552 1.440 123.10 118.43 119.33 109.70 107.59 110.66 122.24 *** * * *** 19 ILE 19 1.323 1.228 1.515 1.547 1.445 119.85 116.33 120.72 109.48 109.58 111.12 122.94 * * 20 ALA 20 1.302 1.231 1.500 1.522 1.431 121.26 116.19 120.72 111.33 108.96 110.89 123.07 +* * * +* 21 CYS 21 1.301 1.220 1.501 1.509 1.413 121.27 116.04 120.77 109.93 108.55 109.83 123.18 ** * * ** ** 22 HIS 22 1.295 1.234 1.508 1.537 1.441 121.49 115.44 121.09 109.62 109.14 110.93 123.47 ** ** 23 THR 23 1.324 1.247 1.513 1.556 1.439 122.47 116.85 120.27 107.81 108.94 111.18 122.88 * * 24 VAL 24 1.319 1.225 1.542 1.572 1.444 120.67 115.31 121.37 111.89 108.78 112.89 123.30 * * * 25 GLU 25 1.341 1.241 1.533 1.537 1.462 123.78 115.99 121.09 109.49 110.35 108.85 122.92 * * 26 THR 26 1.319 1.232 1.535 1.545 1.447 121.75 115.45 120.72 110.52 110.07 110.20 123.77 27 TRP 27 1.327 1.234 1.538 1.540 1.465 123.88 116.15 120.64 110.68 112.78 108.21 123.19 * * * 28 ASN 28 1.317 1.228 1.534 1.552 1.457 122.68 116.82 120.36 111.90 110.82 109.30 122.79 * * 29 GLU 29 1.332 1.248 1.526 1.534 1.474 121.41 115.33 120.93 108.52 111.18 111.59 123.74 30 GLN 30 1.324 1.224 1.513 1.500 1.421 123.42 117.52 120.04 110.82 114.10 109.54 122.44 +* +* * +* 31 LEU 31 1.311 1.239 1.522 1.489 1.416 121.25 117.36 120.03 111.26 112.44 109.49 122.61 * ** ** ** 32 GLN 32 1.324 1.211 1.494 1.543 1.450 120.05 115.97 120.43 109.90 109.99 114.76 123.57 * +** +** 33 LYS 33 1.318 1.234 1.529 1.531 1.438 121.86 116.75 120.40 110.55 110.07 110.34 122.81 * * 34 ALA 34 1.340 1.239 1.517 1.518 1.455 121.26 115.34 121.12 110.24 110.78 110.36 123.53 35 ASN 35 1.319 1.231 1.512 1.533 1.457 122.63 114.79 121.41 109.32 109.64 108.94 123.76 36 GLU 36 1.306 1.240 1.543 1.553 1.472 123.23 116.78 120.62 111.48 110.39 108.27 122.52 +* * * +* 37 SER 37 1.327 1.239 1.533 1.518 1.449 121.53 115.99 120.56 110.83 111.57 109.92 123.44 38 LYS 38 1.346 1.227 1.558 1.519 1.422 124.18 115.62 122.36 113.41 110.78 108.15 121.98 * +* +* * +* * +* 39 THR 39 1.311 1.242 1.535 1.536 1.445 121.80 116.59 120.62 108.26 108.55 111.03 122.74 * * 40 LEU 40 1.304 1.237 1.526 1.566 1.449 121.72 116.51 120.39 112.86 106.53 110.11 123.09 +* +* * +* +* 41 VAL 41 1.308 1.237 1.531 1.568 1.434 121.50 115.69 121.11 111.61 111.17 110.50 123.17 +* * * * +* Residue-by-residue listing for refined_7 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 ----------------------------------------------------------------------------------------------------------------------------------- 42 VAL 42 1.303 1.234 1.522 1.551 1.433 122.74 116.71 120.78 110.55 109.57 111.37 122.47 +* * +* 43 VAL 43 1.300 1.236 1.520 1.540 1.436 120.88 114.95 121.02 109.49 111.05 112.15 124.02 ** * ** 44 ASP 44 1.295 1.233 1.531 1.547 1.450 124.30 116.91 120.49 110.44 109.90 108.45 122.49 ** * * ** 45 PHE 45 1.324 1.236 1.509 1.528 1.435 121.80 117.57 119.85 107.79 107.83 110.87 122.55 * * * * 46 THR 46 1.299 1.223 1.523 1.561 1.436 120.06 116.47 120.46 109.90 109.83 109.82 123.06 ** * ** 47 ALA 47 1.303 1.234 1.505 1.517 1.433 122.28 116.36 120.69 110.69 108.42 111.06 122.95 +* * +* 48 SER 48 1.297 1.231 1.554 1.522 1.449 122.03 117.37 120.30 112.21 113.59 109.82 122.33 ** * * ** 49 TRP 49 1.333 1.231 1.538 1.546 1.460 121.16 118.03 120.30 111.31 113.45 111.95 121.67 50 CYS 50 1.317 1.233 1.527 1.556 1.451 119.44 114.99 121.24 114.41 112.87 113.57 123.76 * * ** +* ** 51 GLY 51 1.333 1.235 1.523 - 1.465 123.99 119.14 119.36 - 115.03 - 121.50 +* * +* 52 PRO 52 1.359 1.235 1.534 1.544 1.475 122.85 115.72 121.14 110.23 112.26 103.87 123.14 * * 53 CYS 53 1.312 1.217 1.525 1.513 1.449 122.90 115.68 121.41 108.03 109.43 109.15 122.90 * * * 54 ARG 54 1.316 1.229 1.540 1.561 1.454 123.02 115.28 121.35 112.84 108.79 107.94 123.31 +* * +* +* 55 PHE 55 1.318 1.238 1.544 1.548 1.457 123.77 117.27 120.79 110.88 112.07 109.12 121.93 * * 56 ILE 56 1.321 1.233 1.541 1.566 1.452 119.94 116.38 120.77 109.98 110.57 111.68 122.83 57 ALA 57 1.331 1.232 1.550 1.527 1.467 122.19 119.84 119.25 112.10 113.54 111.75 120.90 * +* * * +* 58 PRO 58 1.371 1.236 1.530 1.534 1.478 121.76 115.48 121.50 110.05 112.00 103.67 123.00 +* +* 59 PHE 59 1.311 1.215 1.522 1.537 1.442 121.78 116.28 120.69 111.06 109.38 110.22 122.98 * * 60 PHE 60 1.321 1.237 1.538 1.542 1.465 122.49 115.85 121.18 111.72 109.40 109.50 122.96 61 ALA 61 1.329 1.241 1.539 1.520 1.458 122.34 116.42 120.73 110.44 111.02 110.50 122.85 62 ASP 62 1.332 1.219 1.495 1.519 1.468 121.90 115.13 121.19 108.76 108.62 111.48 123.68 * * 63 LEU 63 1.310 1.228 1.528 1.515 1.434 123.21 116.51 120.62 111.45 112.19 109.58 122.84 * * * 64 ALA 64 1.318 1.223 1.528 1.517 1.467 122.16 114.97 121.64 111.13 111.22 110.59 123.38 65 LYS 65 1.302 1.231 1.545 1.531 1.449 124.28 116.27 121.16 110.00 110.71 106.52 122.55 +* * ** ** 66 LYS 66 1.317 1.247 1.537 1.560 1.454 121.86 116.64 120.75 111.28 110.26 108.78 122.60 * * * 67 LEU 67 1.316 1.224 1.525 1.533 1.443 120.92 117.30 120.18 111.66 112.53 112.20 122.50 68 PRO 68 1.360 1.225 1.531 1.539 1.475 123.11 116.82 120.34 109.79 113.09 104.13 122.79 * * * 69 ASN 69 1.326 1.233 1.513 1.537 1.453 121.34 115.01 121.83 110.86 111.42 112.68 123.02 * * 70 VAL 70 1.288 1.224 1.501 1.566 1.443 123.92 118.13 119.75 111.17 107.33 112.61 122.04 +** * * * +** 71 LEU 71 1.296 1.231 1.531 1.534 1.425 118.99 116.00 121.06 111.45 108.92 110.01 122.93 ** +* +* ** Residue-by-residue listing for refined_7 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 ----------------------------------------------------------------------------------------------------------------------------------- 72 PHE 72 1.312 1.241 1.514 1.539 1.453 122.17 116.40 120.62 106.48 108.38 111.22 122.98 * +* * +* 73 LEU 73 1.284 1.224 1.497 1.541 1.441 122.80 115.33 120.95 109.60 110.59 113.98 123.72 *** * ** *** 74 LYS 74 1.294 1.237 1.498 1.496 1.415 123.32 116.12 120.53 108.64 108.85 109.25 123.33 ** * +* ** ** 75 VAL 75 1.296 1.241 1.507 1.562 1.432 122.28 116.41 120.53 109.09 108.13 111.93 123.05 ** * * ** 76 ASP 76 1.308 1.236 1.510 1.515 1.436 120.48 115.73 121.02 111.16 107.40 111.50 123.23 +* * * +* 77 THR 77 1.294 1.235 1.525 1.532 1.437 123.37 117.21 120.47 111.50 114.06 110.04 122.29 +** * * * +** 78 ASP 78 1.311 1.245 1.508 1.507 1.447 119.95 113.79 121.95 110.13 108.49 111.32 124.26 * * * * 79 GLU 79 1.316 1.232 1.515 1.514 1.427 124.54 115.55 121.38 108.54 109.82 108.77 123.07 +* +* * +* 80 LEU 80 1.318 1.234 1.502 1.532 1.415 123.28 114.60 121.72 110.50 108.34 110.41 123.68 * ** * ** 81 LYS 81 1.301 1.232 1.534 1.520 1.433 122.85 116.89 120.62 111.25 111.36 109.73 122.48 ** * ** 82 SER 82 1.324 1.230 1.532 1.531 1.449 120.80 115.91 121.06 111.87 110.18 110.66 122.98 83 VAL 83 1.332 1.227 1.523 1.558 1.456 121.96 115.47 121.33 109.85 108.31 111.65 123.17 * * 84 ALA 84 1.329 1.217 1.513 1.517 1.450 122.38 115.97 120.67 109.98 109.90 110.55 123.35 85 SER 85 1.318 1.235 1.533 1.541 1.445 122.57 116.47 120.59 110.74 110.45 110.03 122.91 86 ASP 86 1.329 1.239 1.529 1.534 1.468 122.39 116.11 121.01 110.66 111.58 110.35 122.84 87 TRP 87 1.316 1.231 1.526 1.526 1.448 122.14 115.88 120.49 111.02 111.80 111.50 123.63 88 ALA 88 1.340 1.240 1.533 1.522 1.472 124.26 116.31 120.94 111.17 111.91 110.30 122.68 * * 89 ILE 89 1.321 1.241 1.538 1.567 1.443 121.25 115.27 121.52 109.88 109.20 112.97 123.00 * * 90 GLN 90 1.310 1.237 1.511 1.538 1.441 122.42 115.50 121.22 110.62 108.69 110.07 123.28 * * 91 ALA 91 1.312 1.235 1.511 1.516 1.434 121.76 116.07 121.06 111.17 109.06 110.28 122.87 * * * 92 MET 92 1.294 1.235 1.515 1.528 1.434 121.89 118.55 120.08 110.00 109.36 109.12 121.35 ** * * * ** 93 PRO 93 1.338 1.236 1.543 1.523 1.463 124.22 116.76 120.85 110.08 112.26 102.06 122.36 94 THR 94 1.305 1.229 1.525 1.532 1.439 121.65 116.83 120.40 109.28 109.11 111.42 122.76 +* * +* 95 PHE 95 1.305 1.229 1.503 1.531 1.415 122.02 117.13 120.20 108.82 107.09 109.23 122.66 +* * ** * ** 96 MET 96 1.289 1.230 1.508 1.532 1.438 120.68 115.06 121.19 111.93 110.04 111.18 123.75 +** * +** 97 PHE 97 1.293 1.245 1.501 1.506 1.409 124.46 115.79 121.42 109.27 110.75 108.55 122.79 +** * * +** +* * +** 98 LEU 98 1.285 1.224 1.519 1.559 1.417 121.09 116.85 120.61 107.77 107.72 112.64 122.54 *** * ** * * * *** 99 LYS 99 1.288 1.228 1.482 1.525 1.429 121.42 114.75 120.60 110.68 109.71 111.99 124.55 +** ** +* +** 100 GLU 100 1.322 1.228 1.538 1.512 1.446 124.02 116.10 121.08 111.51 112.07 108.86 122.78 * * 101 GLY 101 1.317 1.226 1.517 - 1.444 120.93 117.67 119.92 - 114.32 - 122.39 102 LYS 102 1.312 1.223 1.513 1.531 1.457 120.77 117.55 119.70 108.29 108.95 111.90 122.75 * * Residue-by-residue listing for refined_7 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 1.317 1.243 1.528 1.561 1.455 121.00 116.41 120.47 109.76 109.11 112.13 123.06 104 LEU 104 1.317 1.230 1.498 1.527 1.429 121.51 116.14 120.72 109.00 111.33 112.04 123.14 * +* +* 105 ASP 105 1.304 1.216 1.500 1.527 1.439 121.17 115.56 121.14 110.54 112.56 111.97 123.24 +* * * +* 106 LYS 106 1.304 1.240 1.520 1.542 1.447 122.10 115.48 121.07 112.13 111.47 111.57 123.45 +* * +* 107 VAL 107 1.310 1.226 1.522 1.560 1.453 123.46 117.12 120.25 108.49 109.59 110.80 122.62 * * 108 VAL 108 1.308 1.242 1.539 1.561 1.444 121.19 116.26 121.16 111.50 110.27 112.08 122.58 +* * +* 109 GLY 109 1.306 1.238 1.502 - 1.441 121.04 117.37 120.26 - 109.74 - 122.37 +* +* 110 ALA 110 1.308 1.242 1.506 1.508 1.428 119.52 114.36 121.76 110.12 112.30 110.19 123.87 * +* * +* 111 LYS 111 1.299 1.233 1.505 1.519 1.416 124.34 118.00 119.15 109.24 106.82 110.26 122.85 ** ** * +* ** 112 LYS 112 1.313 1.232 1.520 1.503 1.431 122.02 114.36 121.49 109.02 110.08 109.05 124.11 * * * * 113 ASP 113 1.311 1.229 1.528 1.538 1.452 124.43 116.64 120.78 110.54 111.96 109.12 122.57 * +* +* 114 GLU 114 1.314 1.237 1.516 1.537 1.452 121.83 116.36 120.61 111.67 110.10 110.07 122.99 * * 115 LEU 115 1.326 1.213 1.507 1.515 1.439 121.01 115.88 120.66 109.30 108.62 111.53 123.45 116 GLN 116 1.324 1.239 1.511 1.518 1.472 122.11 116.59 120.33 109.76 112.57 112.29 123.06 * * 117 SER 117 1.314 1.231 1.532 1.521 1.443 120.63 115.64 121.32 112.03 109.55 109.80 122.96 * * * 118 THR 118 1.321 1.237 1.541 1.541 1.441 122.17 116.07 121.35 110.68 109.75 110.51 122.58 119 ILE 119 1.317 1.216 1.523 1.561 1.448 121.78 116.39 120.56 110.31 109.20 111.96 122.98 120 ALA 120 1.322 1.221 1.528 1.518 1.462 122.18 115.89 120.66 111.15 111.07 110.79 123.45 121 LYS 121 1.321 1.240 1.530 1.507 1.462 123.67 114.93 121.79 109.17 109.76 107.37 123.28 * * +* +* 122 HIS 122 1.311 1.229 1.515 1.522 1.442 122.84 116.70 120.78 110.64 112.01 110.72 122.49 * * 123 LEU 123 1.316 1.230 1.516 1.508 1.421 122.76 115.30 121.49 112.32 112.70 109.86 123.18 * +* * +* 124 ALA 124 1.291 - 1.505 1.526 1.423 122.19 - - 110.92 106.97 111.17 - +** +* +* +** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *** ** ** +** +* +* ** +* +** * *** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_7 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 1.284 1.346 1.312 .013 *** * * C-N (Pro) 1.341 .016 4 1.338 1.371 1.357 .012 +* * C-O C-O 1.231 .020 123 1.211 1.248 1.232 .007 CA-C CH1E-C (except Gly) 1.525 .021 119 1.482 1.558 1.521 .015 ** +* CH2G*-C (Gly) 1.516 .018 5 1.497 1.523 1.509 .010 * CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.508 1.527 1.519 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.532 1.572 1.554 .012 * CH1E-CH2E (the rest) 1.530 .020 84 1.489 1.566 1.531 .015 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.409 1.474 1.444 .015 +** NH1-CH2G* (Gly) 1.451 .016 5 1.434 1.465 1.444 .011 * N-CH1E (Pro) 1.466 .015 4 1.463 1.478 1.473 .006 ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_7 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 2.0 114 113.79 119.84 116.13 .96 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.67 119.14 117.39 1.11 * CH1E-C-N (Pro) 116.9 1.5 4 115.48 116.82 116.20 .60 O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.90 124.55 123.00 .58 * O-C-N (Pro) 122.0 1.4 4 122.36 123.14 122.82 .29 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 118.99 124.54 122.11 1.21 +* +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.93 123.99 121.63 1.19 +* C-N-CH1E (Pro) 122.6 5.0 4 121.76 124.22 122.98 .87 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 119.15 122.36 120.82 .55 CH2G*-C-O (Gly) 120.8 2.1 5 119.36 120.97 120.15 .53 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 109.98 112.10 110.91 .57 * CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 107.81 111.89 110.03 1.07 * CH2E-CH1E-C (the rest) 110.1 1.9 84 106.48 114.41 110.55 1.44 +* ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 106.53 114.10 110.21 1.74 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 109.74 115.03 112.18 2.10 N-CH1E-C (Pro) 111.8 2.5 4 112.00 113.09 112.40 .41 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.19 111.75 110.73 .43 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.82 112.97 111.40 .88 N-CH1E-CH2E (Pro) 103.0 1.1 4 102.06 104.13 103.43 .81 * NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.52 114.76 110.50 1.63 ** +** ------------------------------------------------------------------------------------------------------------- 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_7 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] 104 92.0% Residues in additional allowed regions [a,b,l,p] 9 8.0% 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 92.0 83.8 10.0 .8 Inside b. Omega angle st dev 122 3.0 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 1.7 3.1 1.6 -.9 Inside e. H-bond energy st dev 80 .9 .8 .2 .2 Inside f. Overall G-factor 124 .1 -.4 .3 1.6 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 14 5.1 18.1 6.5 -2.0 BETTER b. Chi-1 trans st dev 44 6.5 19.0 5.3 -2.4 BETTER c. Chi-1 gauche plus st dev 44 8.6 17.5 4.9 -1.8 BETTER d. Chi-1 pooled st dev 102 8.2 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 23 7.5 20.4 5.0 -2.6 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 92.0 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.4 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .86 2 Residue-by-residue listing for refined_7 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 .19 Chi3 & chi4 .50 Omega .08 ------ .00 ===== Main-chain covalent forces:- Main-chain bond lengths .06 Main-chain bond angles .43 ------ .28 ===== OVERALL AVERAGE .10 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.