Residue-by-residue listing for refined_4 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 - - - -66.1 - - - - - - - 181.8 - 33.3 - 2 GLY 2 - - - - - - - - - - - 178.3 - - - 3 HIS 3 l - - -63.6 - - - - - - - 177.1 - 31.6 - 4 HIS 4 B 64.0 - - - - - - - - - 180.2 - 31.8 - 5 HIS 5 B 65.8 - - - - - - - - - 179.7 -.5 32.3 - ** ** 6 HIS 6 b - - -62.3 - - - - - - - 177.4 - 34.0 - 7 HIS 7 B - 190.9 - - - - - - - - 183.1 - 33.8 - 8 HIS 8 B 53.9 - - - - - - - - - 173.6 - 34.3 - * * 9 LEU 9 B - - -69.4 - - - - - - - 188.4 - 32.9 - * * 10 GLU 10 B - 186.2 - 172.9 - - - - - - 175.6 -.9 34.5 - +* +* 11 MET 11 b - 178.0 - - - - - - - - 181.3 -.6 33.8 - +* +* 12 ALA 12 b - - - - - - - - - - 182.5 -1.5 32.5 - 13 SER 13 B 51.0 - - - - - - - - - 182.1 -1.7 34.8 - 14 GLU 14 S A - 193.5 - - - - - - - - 178.3 - 34.6 - 15 GLU 15 B 47.5 - - - - - - - - - 175.4 - 32.3 - * * 16 GLY 16 S - - - - - - - - - - - 182.1 -2.4 - - 17 GLN 17 e B 58.9 - - 180.9 - - - - - - 173.7 -.6 31.9 - * +* +* 18 VAL 18 E B - 179.8 - - - - - - - - 179.0 -.5 35.4 - ** ** 19 ILE 19 E B - - -61.8 - - - - - - - 180.5 -2.9 34.0 - * * Residue-by-residue listing for refined_4 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 - - - - - - - - - - 182.0 -.8 33.9 - +* +* 21 CYS 21 E B - - -51.3 - - - - - - - 176.5 -1.5 35.8 - * * 22 HIS 22 S A - - -66.3 - - - - - - - 181.8 -.6 33.5 - +* +* 23 THR 23 h B 58.8 - - - - - - - - - 175.6 - 36.4 - 24 VAL 24 H A 65.8 - - - - -75.6 -22.5 - - - 177.6 - 32.2 - * * 25 GLU 25 H A - 176.4 - - - -58.0 -52.5 - - - 178.5 - 35.4 - * * 26 THR 26 H A - - -58.6 - - -62.7 -46.7 - - - 179.6 - 34.1 - 27 TRP 27 H A - 170.7 - - - -55.6 -52.3 - - - 183.2 -1.5 35.0 - * * 28 ASN 28 H A - 189.2 - - - -65.6 -43.3 - - - 181.1 -3.5 35.2 - +* +* 29 GLU 29 H A - 181.7 - 179.7 - -62.9 -47.5 - - - 182.3 -2.5 33.3 - 30 GLN 30 H A - - -67.5 - - -61.9 -36.0 - - - 178.5 -2.7 33.6 - 31 LEU 31 H A - - -67.2 180.5 - -68.1 -47.6 - - - 177.0 -1.7 33.6 - 32 GLN 32 H A - 184.2 - 181.7 - -64.5 -36.2 - - - 177.3 -2.2 33.2 - 33 LYS 33 H A - 181.5 - 180.6 - -60.4 -45.6 - - - 179.8 -3.0 33.9 - * * 34 ALA 34 H A - - - - - -69.6 -34.8 - - - 180.3 -2.6 33.6 - 35 ASN 35 H A - 194.8 - - - -67.9 -53.8 - - - 179.9 -2.5 36.6 - * * 36 GLU 36 H A - 180.5 - - - -63.6 -43.2 - - - 182.1 -3.6 34.1 - ** ** 37 SER 37 h A - - -54.8 - - - - - - - 176.7 -2.7 33.8 - 38 LYS 38 T L - 189.3 - 181.2 - - - - - - 184.1 -.9 34.5 - +* +* 39 THR 39 t B - - -50.8 - - - - - - - 180.7 -2.3 34.9 - * * 40 LEU 40 E B - 177.4 - - - - - - - - 185.7 -.8 35.5 - +* +* 41 VAL 41 E B 59.7 - - - - - - - - - 176.5 - 33.4 - 42 VAL 42 E B - 178.4 - - - - - - - - 183.9 -2.7 33.5 - 43 VAL 43 E B - 181.8 - - - - - - - - 176.8 -3.0 34.3 - * * 44 ASP 44 E B - 172.8 - - - - - - - - 174.4 -2.8 36.3 - * * 45 PHE 45 E B - - -63.6 - - - - - - - 184.4 -2.6 35.4 - 46 THR 46 E B - - -65.3 - - - - - - - 176.4 -2.5 36.1 - 47 ALA 47 t B - - - - - - - - - - 182.4 - 34.1 - 48 SER 48 T A - - -57.5 - - - - - - - 181.9 - 33.4 - 49 TRP 49 T A 57.3 - - - - - - - - - 178.9 - 31.1 - 50 CYS 50 h B 47.3 - - - - - - - -119.5 2.8 186.1 -1.6 29.1 - * *** *7.9* * * *7.9* 51 GLY 51 H - - - - - - -57.5 -68.1 - - - 180.6 -.6 - - +** +* +** 52 PRO 52 H - - - - - -54.8 -54.8 -30.2 - - - 181.2 - 38.2 - * * 53 CYS 53 H A - - -46.6 152.6 - -71.1 -38.5 - -119.5 2.8 176.6 - 35.9 - * * *** *7.9* *7.9* 54 ARG 54 H A - 180.6 - 181.0 - -74.7 -28.9 - - - 179.8 -1.7 33.4 - 55 PHE 55 H A - 183.1 - - - -68.5 -32.7 - - - 183.1 -2.1 35.3 - 56 ILE 56 H A - 189.2 - - - -87.2 -13.6 - - - 180.7 -1.6 33.9 - +* ** ** Residue-by-residue listing for refined_4 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 - - - - - -55.9 -47.4 - - - 178.0 -.6 31.5 - +* +* 58 PRO 58 H - - - - - -59.3 -59.3 -30.6 - - - 180.0 - 38.9 - * * 59 PHE 59 H A - 181.9 - - - -69.5 -38.0 - - - 178.6 -.5 34.3 - ** ** 60 PHE 60 H A - 183.4 - - - -72.9 -33.8 - - - 176.9 -1.5 34.0 - 61 ALA 61 H A - - - - - -63.6 -35.3 - - - 176.3 -2.2 33.8 - 62 ASP 62 H A - 178.6 - - - -66.4 -47.6 - - - 178.1 -1.6 35.5 - 63 LEU 63 H A - - -64.8 181.2 - -52.3 -39.9 - - - 178.5 -1.9 35.4 - * * 64 ALA 64 H A - - - - - -59.7 -43.6 - - - 179.4 -1.9 33.0 - 65 LYS 65 H A 69.8 - - 176.1 - -80.5 -19.4 - - - 183.5 -1.2 31.0 - * +* * +* 66 LYS 66 H A - 185.0 - 173.9 - -80.5 -33.9 - - - 180.7 -2.0 33.5 - * * 67 LEU 67 h B - - -67.7 170.8 - - - - - - 183.6 -2.4 32.4 - 68 PRO 68 T - - - - - -77.3 - - - - - 181.6 - 39.3 - * +* +* 69 ASN 69 e A - 192.9 - - - - - - - - 184.4 - 34.4 - 70 VAL 70 E B - 184.2 - - - - - - - - 174.9 -.9 34.1 - * * 71 LEU 71 E B - 179.4 - - - - - - - - 180.5 -3.1 35.4 - * * 72 PHE 72 E B - - -62.4 - - - - - - - 179.6 -.6 33.9 - +* +* 73 LEU 73 E B - - -71.1 - - - - - - - 177.7 -2.2 33.5 - 74 LYS 74 E B - 195.6 - 182.5 - - - - - - 180.5 -2.8 35.3 - * * 75 VAL 75 E B - 180.7 - - - - - - - - 176.8 -3.4 34.8 - +* +* 76 ASP 76 E B - 185.2 - - - - - - - - 185.1 -.7 33.2 - +* +* 77 THR 77 e A 49.3 - - - - - - - - - 177.4 -1.1 32.8 - * * 78 ASP 78 T A - 175.6 - - - - - - - - 174.3 - 34.5 - 79 GLU 79 T A - - -74.5 - - - - - - - 179.3 - 34.2 - 80 LEU 80 h b - - -69.5 - - - - - - - 181.7 -3.6 33.3 - ** ** 81 LYS 81 H A - - -57.4 179.7 - -68.5 -39.5 - - - 180.8 -1.8 34.5 - 82 SER 82 H A - - -55.5 - - -66.2 -40.8 - - - 179.7 - 33.6 - 83 VAL 83 H A - 180.3 - - - -68.3 -41.5 - - - 178.2 - 33.7 - 84 ALA 84 H A - - - - - -60.8 -43.2 - - - 178.8 -2.1 34.0 - 85 SER 85 H A - 179.4 - - - -64.6 -51.0 - - - 183.4 -2.5 34.8 - * * 86 ASP 86 H A - 181.5 - - - -62.0 -34.6 - - - 180.1 -3.0 34.0 - * * 87 TRP 87 h A - - -70.2 - - - - - - - 175.3 -2.3 31.4 - 88 ALA 88 T L - - - - - - - - - - 179.8 -1.6 33.7 - 89 ILE 89 t B - - -54.1 - - - - - - - 182.2 -2.6 33.6 - 90 GLN 90 A - 180.8 - 181.6 - - - - - - 182.5 -1.1 35.0 - * * 91 ALA 91 S B - - - - - - - - - - 182.0 - 34.2 - 92 MET 92 S B - - -59.4 177.7 - - - - - - -1.2 -.6 35.0 - +* +* 93 PRO 93 e cis - - - - - -91.2 - - - - - 176.1 - 39.5 - ** +* ** Residue-by-residue listing for refined_4 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 ----------------------------------------------------------------------------------------------------------------------------------- 94 THR 94 E B - - -56.9 - - - - - - - 178.0 -1.7 34.5 - 95 PHE 95 E B - - -52.3 - - - - - - - 178.7 -3.3 36.9 - +* +* 96 MET 96 E B - 181.5 - 177.1 - - - - - - 180.1 -3.1 32.4 - * * 97 PHE 97 E B - - -69.6 - - - - - - - 179.1 -3.5 36.4 - +* +* 98 LEU 98 E B - - -53.4 - - - - - - - 176.1 -2.3 35.0 - 99 LYS 99 E B - 177.1 - 176.1 - - - - - - 176.6 -3.5 33.2 - ** ** 100 GLU 100 T l - - -55.8 169.4 - - - - - - 181.5 - 33.9 - 101 GLY 101 T - - - - - - - - - - - 177.1 - - - 102 LYS 102 E B - 177.9 - 180.6 - - - - - - 180.4 -1.8 35.4 - 103 ILE 103 E B - - -59.1 176.4 - - - - - - 176.2 - 35.1 - 104 LEU 104 E a - - -69.4 186.2 - - - - - - 183.6 -2.1 33.0 - 105 ASP 105 E B 54.3 - - - - - - - - - 183.4 -2.1 30.8 - 106 LYS 106 E B 53.0 - - - - - - - - - 178.5 - 32.1 - 107 VAL 107 E B - 176.1 - - - - - - - - 178.2 -3.2 35.1 - +* +* 108 VAL 108 E B 61.0 - - - - - - - - - 180.9 - 32.8 - 109 GLY 109 e - - - - - - - - - - - 181.2 -3.0 - - * * 110 ALA 110 B - - - - - - - - - - 172.1 - 34.0 - * * 111 LYS 111 h B - - -65.6 183.3 - - - - - - 182.7 -.8 34.7 - +* +* 112 LYS 112 H A - - -69.6 - - -50.1 -49.1 - - - 183.7 - 34.8 - * * 113 ASP 113 H A 61.3 - - - - -67.5 -42.5 - - - 184.8 - 34.0 - 114 GLU 114 H A - 187.1 - - - -76.9 -38.5 - - - 177.6 - 33.0 - 115 LEU 115 H A - 183.8 - - - -61.2 -52.8 - - - 181.3 -3.0 35.4 - * * * 116 GLN 116 H A 69.1 - - 179.1 - -64.7 -27.1 - - - 176.9 -2.2 31.4 - * * 117 SER 117 H A - 184.3 - - - -67.4 -36.8 - - - 177.2 -1.3 33.7 - 118 THR 118 H A - - -54.4 - - -74.3 -29.4 - - - 176.0 -1.8 33.9 - 119 ILE 119 H A - - -57.6 176.3 - -70.2 -42.6 - - - 177.2 -1.8 33.8 - 120 ALA 120 H A - - - - - -64.4 -31.1 - - - 175.8 -2.8 33.7 - * * 121 LYS 121 H A - 182.9 - 183.5 - -57.6 -44.2 - - - 178.3 -1.4 37.2 - 122 HIS 122 H A - - -73.5 - - -84.6 -11.3 - - - 181.9 -1.3 34.2 - +* ** * ** 123 LEU 123 h B - 179.7 - - - - - - - - 179.0 -.8 33.9 - +* +* 124 ALA 124 - - - - - - - - - - - - -1.0 34.2 - * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * * * ** +* +** *** *7.9* * ** +* *7.9* ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.2 182.6 -62.0 177.9 -70.7 -66.1 -39.1 - -119.5 2.8 179.6 -2.0 34.1 *** *7.9* *7.9* Standard deviations: 7.1 5.6 7.1 6.4 16.8 8.1 10.7 - .0 .0 3.0 .9 1.6 Numbers of values: 18 45 39 27 4 46 46 0 2 2 122 86 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_4 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_4 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 - 1.224 1.505 1.538 1.453 - 116.71 120.21 110.87 109.54 111.74 123.07 2 GLY 2 1.308 1.227 1.501 - 1.441 120.97 115.08 120.83 - 110.78 - 124.08 * * 3 HIS 3 1.330 1.236 1.518 1.542 1.464 124.37 116.32 121.09 110.52 112.75 113.00 122.58 * * * 4 HIS 4 1.308 1.230 1.517 1.566 1.439 120.34 116.71 120.69 111.95 109.37 113.12 122.58 * +* +* +* 5 HIS 5 1.306 1.236 1.515 1.565 1.450 120.76 116.09 120.90 111.82 110.21 112.08 122.95 +* +* +* 6 HIS 6 1.307 1.231 1.504 1.544 1.446 121.87 116.40 120.81 109.06 110.09 112.45 122.71 +* * +* 7 HIS 7 1.299 1.229 1.513 1.534 1.429 120.54 116.07 120.81 111.32 107.95 111.15 123.09 ** * * ** 8 HIS 8 1.293 1.225 1.512 1.566 1.448 122.74 117.31 119.84 111.08 109.85 110.31 122.83 +** +* +** 9 LEU 9 1.315 1.237 1.506 1.551 1.456 120.71 116.17 120.75 110.92 107.22 113.07 123.04 * * +* +* 10 GLU 10 1.301 1.238 1.503 1.533 1.432 120.97 115.67 121.00 110.91 111.61 109.41 123.33 ** * * ** 11 MET 11 1.307 1.237 1.517 1.541 1.433 121.61 115.71 121.32 111.22 108.42 111.06 122.83 +* * +* Residue-by-residue listing for refined_4 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 1.310 1.238 1.509 1.523 1.431 121.27 114.53 121.79 112.14 109.88 111.45 123.57 * * * * 13 SER 13 1.296 1.236 1.520 1.521 1.423 123.25 116.84 120.59 111.87 110.57 108.10 122.57 ** +* * ** 14 GLU 14 1.313 1.237 1.542 1.534 1.450 120.93 115.19 121.83 111.35 109.22 109.14 122.98 * * 15 GLU 15 1.318 1.241 1.515 1.564 1.447 122.84 115.56 120.87 112.34 111.50 111.21 123.52 +* * +* 16 GLY 16 1.308 1.218 1.500 - 1.436 121.63 117.77 120.14 - 113.43 - 122.09 * * 17 GLN 17 1.307 1.232 1.475 1.497 1.436 119.60 112.95 122.38 109.80 113.83 112.88 124.65 +* ** +* * * +* * * ** 18 VAL 18 1.266 1.237 1.512 1.558 1.432 123.30 118.21 119.54 108.97 106.58 111.69 122.25 *4.5* * * +* *4.5* 19 ILE 19 1.302 1.226 1.506 1.544 1.427 119.54 116.25 121.08 110.46 109.21 111.41 122.67 +* +* * +* 20 ALA 20 1.290 1.236 1.496 1.507 1.429 121.06 116.14 121.00 110.73 109.20 110.93 122.85 +** * +* +** 21 CYS 21 1.288 1.220 1.503 1.505 1.410 121.13 116.30 120.66 109.86 109.16 109.08 123.00 +** * * +** +** 22 HIS 22 1.296 1.228 1.499 1.535 1.448 121.80 114.81 121.65 110.86 109.01 111.57 123.53 ** * ** 23 THR 23 1.311 1.252 1.511 1.554 1.434 123.12 117.40 119.90 108.08 108.03 110.55 122.69 * * * * * 24 VAL 24 1.319 1.213 1.539 1.572 1.445 120.01 115.69 121.11 111.45 108.68 113.22 123.18 * * * * 25 GLU 25 1.339 1.234 1.531 1.534 1.464 123.41 116.20 120.64 110.29 110.85 108.53 123.13 * * 26 THR 26 1.325 1.226 1.525 1.548 1.460 121.54 115.18 120.99 110.07 110.20 111.05 123.79 27 TRP 27 1.311 1.234 1.537 1.538 1.449 123.56 115.44 121.14 111.42 111.72 107.82 123.38 * * +* +* 28 ASN 28 1.308 1.244 1.529 1.531 1.450 122.99 116.10 120.65 109.77 110.95 109.48 123.24 +* +* 29 GLU 29 1.331 1.228 1.513 1.533 1.455 121.53 116.57 120.11 109.68 111.41 112.13 123.31 30 GLN 30 1.325 1.227 1.513 1.493 1.421 122.31 116.91 120.53 110.79 112.75 109.92 122.56 +* +* +* 31 LEU 31 1.316 1.228 1.509 1.484 1.409 121.56 117.14 119.96 111.03 111.88 109.91 122.90 ** +** +** 32 GLN 32 1.326 1.214 1.509 1.522 1.446 120.36 116.02 120.49 110.21 109.39 112.40 123.47 * * 33 LYS 33 1.321 1.216 1.522 1.528 1.439 122.05 117.14 120.07 110.42 110.07 110.93 122.77 * * 34 ALA 34 1.334 1.221 1.521 1.521 1.453 121.15 115.86 120.79 110.64 110.89 110.70 123.34 35 ASN 35 1.314 1.226 1.517 1.534 1.463 123.09 115.08 121.22 109.30 108.97 108.34 123.70 * * * 36 GLU 36 1.310 1.225 1.527 1.540 1.467 123.18 116.90 120.84 110.59 111.64 109.99 122.23 * * 37 SER 37 1.317 1.233 1.530 1.518 1.438 120.94 116.81 119.98 110.72 111.81 110.13 123.21 * * 38 LYS 38 1.357 1.234 1.554 1.507 1.434 123.83 114.66 122.74 113.46 110.03 106.62 122.50 ** * * * * * +* ** ** 39 THR 39 1.312 1.235 1.526 1.525 1.431 122.87 114.25 121.93 109.42 110.91 110.29 123.82 * * * 40 LEU 40 1.278 1.229 1.544 1.541 1.440 124.63 117.10 120.26 112.10 108.39 107.46 122.60 +*** +* * * +* +*** Residue-by-residue listing for refined_4 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 1.321 1.233 1.546 1.571 1.453 121.45 116.35 120.86 111.39 112.36 110.24 122.78 * * * * 42 VAL 42 1.321 1.238 1.522 1.549 1.456 122.74 116.66 120.61 110.02 108.84 112.49 122.72 43 VAL 43 1.309 1.237 1.527 1.550 1.444 121.41 115.15 120.78 109.17 111.64 111.34 124.06 * * 44 ASP 44 1.308 1.238 1.527 1.532 1.453 124.43 117.16 120.34 108.91 109.85 109.02 122.45 +* +* +* 45 PHE 45 1.315 1.240 1.525 1.527 1.428 121.46 116.28 120.42 109.46 108.52 110.22 123.25 +* +* 46 THR 46 1.310 1.212 1.516 1.551 1.450 122.85 116.68 120.42 109.18 110.11 109.33 122.91 * * * 47 ALA 47 1.300 1.231 1.515 1.517 1.440 122.25 116.62 120.57 110.45 108.54 111.00 122.81 ** ** 48 SER 48 1.301 1.236 1.553 1.529 1.454 122.53 117.83 120.29 111.00 113.59 109.62 121.86 +* * +* 49 TRP 49 1.322 1.221 1.536 1.540 1.452 120.44 118.40 119.96 111.83 114.03 111.88 121.64 * * * 50 CYS 50 1.321 1.242 1.541 1.548 1.453 119.13 114.80 121.41 114.46 112.47 112.54 123.79 * ** * ** 51 GLY 51 1.339 1.238 1.527 - 1.471 123.80 118.85 119.53 - 115.26 - 121.62 * +* * +* 52 PRO 52 1.357 1.226 1.528 1.539 1.480 123.36 115.77 121.21 110.43 112.46 103.90 123.01 * * 53 CYS 53 1.311 1.219 1.535 1.498 1.447 122.47 116.49 121.29 109.10 109.87 108.91 122.22 * +* +* 54 ARG 54 1.317 1.234 1.535 1.533 1.454 121.09 115.10 121.58 110.85 109.45 111.35 123.32 55 PHE 55 1.320 1.225 1.528 1.540 1.455 123.32 116.66 120.79 109.97 110.55 109.30 122.53 56 ILE 56 1.316 1.236 1.549 1.575 1.456 121.29 115.59 121.25 111.18 110.05 110.54 123.09 * * * 57 ALA 57 1.326 1.236 1.563 1.527 1.462 123.03 120.34 119.08 111.90 113.98 111.05 120.58 +* ** * +* ** 58 PRO 58 1.385 1.236 1.537 1.534 1.481 122.05 115.87 121.16 109.77 111.98 103.57 122.95 +** +** 59 PHE 59 1.322 1.229 1.529 1.546 1.453 122.27 115.75 121.02 111.66 109.22 109.50 123.20 60 PHE 60 1.324 1.230 1.533 1.544 1.461 122.71 116.14 120.99 111.61 109.89 109.75 122.86 61 ALA 61 1.326 1.241 1.530 1.523 1.461 121.74 115.43 121.29 110.78 109.85 110.59 123.28 62 ASP 62 1.326 1.222 1.486 1.509 1.467 122.73 114.84 120.83 108.14 110.03 110.80 124.34 +* * * +* 63 LEU 63 1.313 1.230 1.518 1.518 1.437 123.70 115.76 120.81 109.99 110.74 109.01 123.41 * * * * 64 ALA 64 1.322 1.225 1.524 1.518 1.441 122.09 117.79 120.25 111.04 111.78 110.93 121.95 65 LYS 65 1.333 1.219 1.525 1.539 1.455 119.32 115.85 121.39 111.41 111.22 113.63 122.75 * +* +* 66 LYS 66 1.312 1.232 1.534 1.535 1.438 122.13 117.33 120.29 111.86 111.85 109.52 122.38 * * * 67 LEU 67 1.323 1.225 1.533 1.506 1.437 121.13 116.20 121.43 112.37 112.56 109.91 122.37 * * * * 68 PRO 68 1.340 1.232 1.518 1.524 1.481 123.86 117.46 120.47 109.81 114.72 102.45 122.07 * * * 69 ASN 69 1.301 1.232 1.522 1.532 1.444 119.47 115.72 121.69 110.25 109.39 110.59 122.55 +* * +* 70 VAL 70 1.316 1.233 1.519 1.550 1.436 121.36 115.46 121.08 109.46 110.90 111.69 123.39 * * 71 LEU 71 1.298 1.230 1.526 1.539 1.432 122.70 117.27 120.18 110.61 107.65 109.50 122.52 ** * * ** Residue-by-residue listing for refined_4 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 1.309 1.234 1.497 1.515 1.452 120.83 115.22 121.30 108.97 110.93 112.07 123.47 * * * 73 LEU 73 1.290 1.225 1.500 1.544 1.437 122.98 115.61 120.89 108.67 110.88 113.31 123.49 +** * * +* +** 74 LYS 74 1.298 1.236 1.504 1.498 1.419 122.75 116.36 120.69 108.95 108.22 110.81 122.91 ** * +* ** * ** 75 VAL 75 1.292 1.238 1.510 1.556 1.435 122.02 116.59 120.38 109.43 109.30 111.26 123.02 +** * +** 76 ASP 76 1.316 1.217 1.505 1.519 1.441 120.72 116.49 120.44 110.77 108.46 112.18 123.05 77 THR 77 1.302 1.242 1.535 1.529 1.452 122.75 116.37 120.88 111.41 113.77 110.05 122.75 +* * +* 78 ASP 78 1.314 1.237 1.503 1.516 1.452 121.56 114.84 121.50 110.61 108.82 110.15 123.65 * * * 79 GLU 79 1.303 1.235 1.519 1.503 1.424 123.47 116.55 120.77 111.00 111.68 109.35 122.68 +* * +* +* 80 LEU 80 1.307 1.238 1.508 1.526 1.411 122.50 114.88 121.46 110.75 110.45 111.54 123.62 +* ** ** 81 LYS 81 1.307 1.231 1.514 1.528 1.444 122.76 115.64 121.11 110.67 110.20 109.84 123.22 +* +* 82 SER 82 1.317 1.229 1.530 1.516 1.441 121.96 116.55 120.56 111.57 111.51 109.53 122.84 83 VAL 83 1.327 1.233 1.526 1.556 1.458 121.26 115.83 121.02 110.21 109.59 111.81 123.12 84 ALA 84 1.330 1.234 1.524 1.518 1.454 122.01 115.81 120.69 110.45 110.34 110.44 123.48 85 SER 85 1.325 1.235 1.538 1.545 1.443 122.81 116.12 120.92 110.65 110.76 109.36 122.93 86 ASP 86 1.327 1.240 1.533 1.534 1.474 123.32 116.45 120.95 110.75 112.31 109.59 122.59 87 TRP 87 1.314 1.238 1.526 1.520 1.445 121.87 115.88 120.49 112.62 113.24 110.92 123.63 * * * 88 ALA 88 1.341 1.239 1.527 1.528 1.474 123.84 116.65 120.85 110.63 112.31 110.03 122.46 * * 89 ILE 89 1.314 1.234 1.519 1.556 1.441 121.01 115.52 121.14 110.15 108.43 112.49 123.25 * * 90 GLN 90 1.301 1.232 1.515 1.533 1.440 122.28 115.71 121.06 110.36 110.00 109.54 123.21 +* +* 91 ALA 91 1.309 1.225 1.507 1.510 1.437 121.71 116.03 121.04 110.77 109.76 110.19 122.92 * * * 92 MET 92 1.288 1.237 1.518 1.524 1.435 121.80 118.07 120.21 110.04 110.05 109.82 121.73 +** * +** 93 PRO 93 1.336 1.241 1.536 1.527 1.460 123.70 116.55 120.94 110.19 112.05 102.31 122.47 94 THR 94 1.304 1.225 1.516 1.532 1.431 120.97 116.42 120.64 109.08 108.75 111.97 122.94 +* * +* 95 PHE 95 1.294 1.232 1.502 1.518 1.413 122.38 117.85 119.74 108.51 106.70 109.36 122.40 +** * ** +* +** 96 MET 96 1.286 1.234 1.503 1.533 1.435 120.10 115.00 121.23 111.80 110.60 111.69 123.75 *** * * *** 97 PHE 97 1.296 1.246 1.500 1.520 1.405 124.15 116.17 121.07 109.57 109.23 108.65 122.75 ** * +** * * +** 98 LEU 98 1.290 1.222 1.513 1.558 1.416 120.68 116.97 120.31 107.97 107.13 113.14 122.73 +** * ** * * +* +** 99 LYS 99 1.286 1.232 1.487 1.519 1.426 121.62 115.36 120.38 110.93 109.79 111.68 124.21 *** +* +* *** 100 GLU 100 1.328 1.230 1.543 1.520 1.464 123.90 115.75 121.18 111.15 111.03 109.50 123.03 * * 101 GLY 101 1.328 1.230 1.519 - 1.455 121.69 116.38 120.78 - 112.55 - 122.84 102 LYS 102 1.312 1.221 1.517 1.523 1.445 122.04 116.97 119.99 109.54 109.66 109.75 123.03 * * Residue-by-residue listing for refined_4 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 1.315 1.230 1.517 1.557 1.458 122.50 116.63 120.59 108.36 110.26 111.49 122.77 * * 104 LEU 104 1.305 1.237 1.501 1.523 1.421 120.89 116.60 120.54 110.60 110.97 111.98 122.84 +* * +* +* 105 ASP 105 1.308 1.220 1.502 1.536 1.443 120.63 115.44 121.30 112.06 113.44 112.46 123.26 * * * * * 106 LYS 106 1.307 1.232 1.524 1.565 1.447 122.60 115.79 120.74 112.43 112.26 110.99 123.46 +* +* * +* 107 VAL 107 1.309 1.229 1.521 1.559 1.450 123.52 116.80 120.36 108.90 109.05 111.39 122.81 * * * 108 VAL 108 1.307 1.241 1.539 1.564 1.441 121.21 116.39 120.89 111.52 110.23 111.65 122.70 +* * +* 109 GLY 109 1.317 1.239 1.508 - 1.448 120.99 117.96 119.85 - 110.53 - 122.18 110 ALA 110 1.317 1.247 1.517 1.521 1.439 118.94 114.63 121.71 110.19 111.98 110.41 123.66 * +* +* 111 LYS 111 1.307 1.230 1.505 1.519 1.421 124.58 117.66 119.18 110.29 107.53 110.84 123.16 +* +* +* * +* 112 LYS 112 1.331 1.230 1.531 1.507 1.438 122.75 115.98 120.46 109.91 112.89 109.12 123.50 * * * 113 ASP 113 1.317 1.229 1.536 1.545 1.463 123.46 116.78 120.67 110.20 112.77 110.14 122.52 114 GLU 114 1.312 1.241 1.519 1.549 1.458 121.75 116.17 120.77 114.09 110.23 108.71 123.01 * ** * ** 115 LEU 115 1.321 1.227 1.505 1.516 1.444 121.47 115.49 121.11 108.61 109.28 110.72 123.37 116 GLN 116 1.320 1.227 1.525 1.528 1.458 121.32 117.12 120.11 110.83 111.81 113.28 122.77 +* +* 117 SER 117 1.330 1.240 1.545 1.539 1.442 121.18 116.09 121.40 111.72 109.25 110.19 122.47 118 THR 118 1.322 1.236 1.548 1.541 1.447 122.27 116.18 121.57 111.10 109.82 110.31 122.25 * * 119 ILE 119 1.316 1.224 1.533 1.547 1.451 121.36 115.79 120.85 110.44 109.25 111.38 123.33 120 ALA 120 1.335 1.231 1.526 1.516 1.469 123.06 114.85 121.52 110.63 110.55 110.51 123.63 121 LYS 121 1.318 1.225 1.522 1.495 1.456 124.14 115.08 121.61 109.17 109.51 106.91 123.30 +* * ** ** 122 HIS 122 1.310 1.231 1.518 1.521 1.441 122.60 116.87 120.32 109.49 111.95 110.86 122.81 * * 123 LEU 123 1.311 1.246 1.511 1.508 1.412 122.04 114.78 121.43 111.29 110.97 109.82 123.75 * * ** ** 124 ALA 124 1.296 - 1.507 1.527 1.423 123.23 - - 111.27 107.76 110.61 - ** +* * ** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *4.5* * ** ** +** +* ** * ** +* ** +* *4.5* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_4 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 1.266 1.357 1.312 .014 *4.5* ** * C-N (Pro) 1.341 .016 4 1.336 1.385 1.355 .019 +** C-O C-O 1.231 .020 123 1.212 1.252 1.232 .007 * CA-C CH1E-C (except Gly) 1.525 .021 119 1.475 1.563 1.521 .015 ** +* CH2G*-C (Gly) 1.516 .018 5 1.500 1.527 1.511 .010 CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.507 1.528 1.520 .006 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.525 1.575 1.552 .013 * CH1E-CH2E (the rest) 1.530 .020 84 1.484 1.566 1.529 .017 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.405 1.474 1.443 .015 +** NH1-CH2G* (Gly) 1.451 .016 5 1.436 1.471 1.450 .012 * N-CH1E (Pro) 1.466 .015 4 1.460 1.481 1.476 .009 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_4 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 2.0 114 112.95 120.34 116.16 .98 +* ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.08 118.85 117.21 1.33 * CH1E-C-N (Pro) 116.9 1.5 4 115.77 117.46 116.41 .68 O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.58 124.65 122.98 .59 +* * O-C-N (Pro) 122.0 1.4 4 122.07 123.01 122.63 .38 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 118.94 124.63 122.01 1.23 +* +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.97 123.80 121.81 1.04 +* C-N-CH1E (Pro) 122.6 5.0 4 122.05 123.86 123.24 .71 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 119.08 122.74 120.82 .58 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.53 120.83 120.23 .51 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.19 112.14 110.89 .55 * CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 108.08 111.52 109.98 1.03 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.97 114.46 110.66 1.22 * ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 106.58 114.03 110.33 1.63 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.53 115.26 112.51 1.75 N-CH1E-C (Pro) 111.8 2.5 4 111.98 114.72 112.81 1.12 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.03 111.45 110.68 .37 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.33 113.22 111.26 .89 * * N-CH1E-CH2E (Pro) 103.0 1.1 4 102.31 103.90 103.06 .69 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.62 113.63 110.45 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_4 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] 106 93.8% Residues in additional allowed regions [a,b,l,p] 7 6.2% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 113 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 5 Number of proline residues 4 ---- Total number of residues 124 Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good quality model would be expected to have over 90% in the most favoured regions [E,H,L]. S T E R E O C H E M I S T R Y O F M A I N - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. %-tage residues in A, B, L 113 93.8 83.8 10.0 1.0 BETTER 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 86 .9 .8 .2 .5 Inside f. Overall G-factor 124 .1 -.4 .3 1.7 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 18 7.1 18.1 6.5 -1.7 BETTER b. Chi-1 trans st dev 45 5.6 19.0 5.3 -2.5 BETTER c. Chi-1 gauche plus st dev 39 7.1 17.5 4.9 -2.1 BETTER d. Chi-1 pooled st dev 102 7.4 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 27 6.4 20.4 5.0 -2.8 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% 93.8 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.5 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .91 3 Residue-by-residue listing for refined_4 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.12 Chi1-chi2 distribution -.10 Chi1 only -.03 Chi3 & chi4 .46 Omega .08 ------ .02 ===== Main-chain covalent forces:- Main-chain bond lengths .03 Main-chain bond angles .45 ------ .28 ===== OVERALL AVERAGE .11 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.