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 - - 177.6 - 181.0 - - - - - - 182.0 - 34.5 - 2 GLY 2 - - - - - - - - - - - 179.4 - - - 3 HIS 3 ~l 58.9 - - - - - - - - - 180.7 - 28.5 - ** +* ** 4 HIS 4 B - 187.0 - - - - - - - - 175.8 - 34.4 - 5 HIS 5 S a - - -60.4 - - - - - - - 176.8 -.9 34.6 - +* +* 6 HIS 6 S B - - -85.4 - - - - - - - 185.9 - 32.4 - * * * 7 HIS 7 S l - - -59.2 - - - - - - - 181.3 - 32.0 - 8 HIS 8 B 66.6 - - - - - - - - - 178.9 - 31.4 - 9 LEU 9 b - - -57.2 178.1 - - - - - - 183.7 -.6 35.2 - +* +* 10 GLU 10 B - 186.8 - - - - - - - - 178.5 -.8 34.7 - +* +* 11 MET 11 l - 181.8 - 180.9 - - - - - - 179.1 - 32.4 - 12 ALA 12 b - - - - - - - - - - 179.9 - 33.1 - 13 SER 13 S B - - -57.6 - - - - - - - 178.9 -.6 35.2 - +* +* 14 GLU 14 B 56.0 - - - - - - - - - 183.4 - 31.9 - 15 GLU 15 B - 204.8 - - - - - - - - 189.9 -.6 35.3 - * +* +* +* 16 GLY 16 S - - - - - - - - - - - 187.0 -.6 - - * +* +* 17 GLN 17 e B 57.6 - - 173.3 - - - - - - 175.0 - 33.8 - 18 VAL 18 E B - 183.0 - - - - - - - - 180.2 - 35.4 - 19 ILE 19 E B - - -61.6 - - - - - - - 179.4 -3.2 33.3 - * * 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 ----------------------------------------------------------------------------------------------------------------------------------- 20 ALA 20 E B - - - - - - - - - - 181.9 -.9 33.8 - +* +* 21 CYS 21 E B - - -49.0 - - - - - - - 176.5 -2.7 36.1 - * * 22 HIS 22 a - - -64.0 - - - - - - - 182.8 -.5 34.2 - ** ** 23 THR 23 h B 49.4 - - - - - - - - - 180.3 - 33.7 - 24 VAL 24 H A 61.6 - - - - -71.4 -24.5 - - - 175.5 - 31.8 - * * 25 GLU 25 H A - 175.9 - - - -59.8 -52.0 - - - 179.9 - 35.8 - * * 26 THR 26 H A - - -55.7 - - -64.1 -44.1 - - - 177.5 - 33.8 - 27 TRP 27 H A - 170.2 - - - -55.4 -53.7 - - - 182.9 -2.2 35.0 - * * 28 ASN 28 H A - 187.6 - - - -63.5 -48.1 - - - 182.7 -3.3 35.1 - +* +* 29 GLU 29 H A - 183.9 - 179.8 - -61.9 -46.6 - - - 180.4 -2.8 33.5 - * * 30 GLN 30 H A - - -72.1 - - -61.1 -39.0 - - - 178.9 -2.9 33.2 - * * 31 LEU 31 H A - - -68.7 181.1 - -70.4 -43.3 - - - 178.3 -1.9 34.1 - 32 GLN 32 H A - 185.1 - 182.1 - -59.9 -43.8 - - - 179.4 -2.7 34.6 - 33 LYS 33 H A - 182.3 - 178.6 - -64.2 -44.7 - - - 181.2 -3.2 34.3 - +* +* 34 ALA 34 H A - - - - - -68.5 -39.4 - - - 180.6 -2.7 33.6 - 35 ASN 35 H A - 189.1 - - - -62.0 -53.2 - - - 181.0 -3.0 36.7 - * * * 36 GLU 36 H A - 177.9 - 176.7 - -63.4 -43.1 - - - 183.5 -2.7 34.0 - 37 SER 37 H A - - -55.8 - - -85.9 .3 - - - 181.0 -2.5 34.3 - +* +*** +*** 38 LYS 38 h l - - -69.9 181.9 - - - - - - 180.6 -.7 32.9 - +* +* 39 THR 39 t B - - -46.5 - - - - - - - 181.1 -1.7 35.2 - * * 40 LEU 40 e B - 184.9 - 168.8 - - - - - - 187.0 - 33.7 - * * 41 VAL 41 E B 57.8 - - - - - - - - - 178.4 - 33.9 - 42 VAL 42 E B 62.7 - - - - - - - - - 183.8 -2.0 33.3 - 43 VAL 43 E B - 180.5 - - - - - - - - 173.0 -3.0 34.8 - * * * 44 ASP 44 E B - 167.8 - - - - - - - - 176.3 -2.2 34.7 - 45 PHE 45 E B - - -65.3 - - - - - - - 184.7 -3.0 35.5 - * * 46 THR 46 E B - 181.7 - - - - - - - - 177.5 -2.7 35.5 - 47 ALA 47 t B - - - - - - - - - - 182.0 - 34.0 - 48 SER 48 T A - 181.8 - - - - - - - - 182.3 - 35.1 - 49 TRP 49 T A 55.7 - - - - - - - - - 180.3 - 32.9 - 50 CYS 50 h B - 177.9 - 214.8 - - - 59.8 - 2.0 180.8 -1.9 34.4 - ** ** ** 51 GLY 51 H - - - - - - -67.9 -62.2 - - - 178.7 -.6 - - ** +* ** 52 PRO 52 H - - - - - -51.5 -51.5 -38.6 - - - 181.0 - 39.7 - * * +* +* 53 CYS 53 H A - - -51.5 - - -66.8 -43.0 59.8 - 2.0 179.4 - 36.0 - * ** ** 54 ARG 54 H A - 178.2 - 179.6 - -67.0 -32.6 - - - 180.1 -1.8 35.4 - 55 PHE 55 H A - 175.4 - - - -77.2 -32.8 - - - 182.7 -2.2 34.2 - 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 ----------------------------------------------------------------------------------------------------------------------------------- 56 ILE 56 H A - 191.7 - - - -87.4 -16.3 - - - 180.9 -2.0 34.1 - +* ** ** 57 ALA 57 H A - - - - - -52.3 -51.0 - - - 179.0 -1.4 32.0 - * * * 58 PRO 58 H - - - - - -61.0 -61.0 -30.1 - - - 180.8 - 38.5 - * * 59 PHE 59 H A - 187.5 - - - -71.7 -39.7 - - - 177.7 - 34.1 - 60 PHE 60 H A - 182.3 - - - -70.7 -33.7 - - - 176.5 -2.0 34.1 - 61 ALA 61 H A - - - - - -68.6 -34.8 - - - 177.9 -2.3 33.9 - 62 ASP 62 H A - 186.8 - - - -67.6 -33.3 - - - 174.2 -1.8 35.8 - 63 LEU 63 H A - - -70.2 181.6 - -63.0 -46.7 - - - 177.7 -1.3 33.6 - 64 ALA 64 H A - - - - - -63.5 -32.9 - - - 177.3 -1.8 34.3 - 65 LYS 65 H A - 169.6 - 191.4 - -64.9 -29.5 - - - 181.5 -1.8 37.1 - 66 LYS 66 H A - - -64.9 180.4 - -96.7 -32.2 - - - 179.7 -.9 31.9 - +** +* +** 67 LEU 67 h b - - -66.7 - - - - - - - 182.5 -2.5 33.6 - 68 PRO 68 S - - - - - -86.1 - - - - - 181.2 - 39.4 - +* +* +* 69 ASN 69 S A - 188.1 - - - - - - - - 177.7 - 33.6 - 70 VAL 70 S B - 176.7 - - - - - - - - 181.1 - 34.4 - 71 LEU 71 E B - 199.8 - - - - - - - - 182.2 -1.8 34.6 - 72 PHE 72 E B - - -62.8 - - - - - - - 178.3 -.7 35.5 - +* +* 73 LEU 73 E B - - -65.7 - - - - - - - 178.3 -2.3 33.5 - 74 LYS 74 E B - 193.4 - 175.6 - - - - - - 186.1 -3.1 36.0 - * * * 75 VAL 75 E B - 179.8 - - - - - - - - 176.4 -3.5 34.4 - +* +* 76 ASP 76 E b - 186.3 - - - - - - - - 184.3 -1.8 34.0 - 77 THR 77 e A - 185.2 - - - - - - - - 178.6 -2.7 32.4 - 78 ASP 78 T A - 183.2 - - - - - - - - 174.8 -.6 34.3 - +* +* 79 GLU 79 T A - - -69.9 183.9 - - - - - - 179.9 - 34.7 - 80 LEU 80 h a - - -71.2 - - - - - - - 181.9 -2.5 33.6 - 81 LYS 81 H A 52.0 - - - - -65.6 -28.6 - - - 179.0 -1.6 30.1 - * * 82 SER 82 H A - - -58.0 - - -74.1 -30.3 - - - 176.2 - 33.7 - 83 VAL 83 H A - 178.6 - - - -71.2 -42.7 - - - 178.9 - 34.7 - 84 ALA 84 H A - - - - - -55.2 -50.4 - - - 180.7 -2.2 34.5 - 85 SER 85 H A - - -57.1 - - -59.6 -36.5 - - - 182.9 -2.2 34.9 - 86 ASP 86 H A - 187.8 - - - -73.8 -36.6 - - - 179.4 -1.2 34.0 - * * 87 TRP 87 h A - - -66.8 - - - - - - - 176.0 -2.3 32.0 - 88 ALA 88 T l - - - - - - - - - - 179.6 -.9 33.2 - +* +* 89 ILE 89 t b - - -54.3 - - - - - - - 180.6 -3.0 34.5 - * * 90 GLN 90 A 52.8 - - - - - - - - - 179.4 -1.1 31.9 - * * 91 ALA 91 S B - - - - - - - - - - 183.0 - 33.7 - 92 MET 92 S B - - -60.8 177.0 - - - - - - -3.1 - 35.8 - 93 PRO 93 e cis - - - - - -90.3 - - - - - 175.5 - 39.6 - ** +* ** 94 THR 94 E B - - -57.6 - - - - - - - 178.7 -1.6 33.5 - 95 PHE 95 E B - - -60.6 - - - - - - - 182.1 -3.4 36.6 - +* +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 96 MET 96 E B - 181.3 - 179.2 - - - - - - 182.8 -3.2 34.2 - +* +* 97 PHE 97 E B - - -64.3 - - - - - - - 177.7 -3.3 36.9 - +* +* 98 LEU 98 E B - - -52.8 - - - - - - - 174.1 -2.6 35.6 - * * 99 LYS 99 E B - 182.6 - 179.4 - - - - - - 183.1 -2.9 32.7 - * * 100 GLU 100 T l - - -56.5 177.4 - - - - - - 185.5 - 33.9 - 101 GLY 101 T - - - - - - - - - - - 176.2 - - - 102 LYS 102 E B - - -59.5 178.5 - - - - - - 181.7 -2.1 36.4 - 103 ILE 103 E B - - -62.2 172.5 - - - - - - 175.0 - 34.9 - 104 LEU 104 E a - - -64.3 184.3 - - - - - - 183.7 -2.0 33.5 - 105 ASP 105 E B 60.7 - - - - - - - - - 179.9 -2.0 32.6 - 106 LYS 106 E B 49.8 - - - - - - - - - 178.9 - 31.0 - 107 VAL 107 E B - 181.3 - - - - - - - - 180.0 -3.0 35.2 - * * 108 VAL 108 E B 61.4 - - - - - - - - - 180.4 - 33.1 - 109 GLY 109 e - - - - - - - - - - - 180.1 -3.2 - - * * 110 ALA 110 B - - - - - - - - - - 180.1 - 33.9 - 111 LYS 111 h B - - -54.0 - - - - - - - 184.8 -1.0 37.1 - * * 112 LYS 112 H A - 187.7 - - - -69.3 -51.7 - - - 182.9 -.5 34.1 - * ** ** 113 ASP 113 H A - 181.0 - - - -73.2 -44.3 - - - 181.9 - 32.8 - 114 GLU 114 H A - 177.5 - 173.1 - -64.7 -33.2 - - - 177.7 - 32.1 - 115 LEU 115 H A - 185.2 - - - -61.6 -42.9 - - - 179.1 -1.4 35.8 - 116 GLN 116 H A - - -59.7 185.4 - -61.4 -32.5 - - - 176.7 -1.2 32.0 - * * 117 SER 117 H A - - -57.2 - - -69.4 -30.6 - - - 175.6 -1.2 33.7 - * * 118 THR 118 H A - - -59.0 - - -74.9 -31.2 - - - 173.8 -1.4 33.3 - * * 119 ILE 119 H A - - -57.9 177.7 - -63.1 -49.3 - - - 177.7 -1.8 34.3 - 120 ALA 120 H A - - - - - -59.9 -31.8 - - - 176.2 -2.7 33.9 - 121 LYS 121 H A - 188.4 - 190.2 - -58.8 -37.5 - - - 180.1 -1.3 37.2 - 122 HIS 122 h A - - -73.6 - - - - - - - 174.1 -1.2 32.2 - * * * 123 LEU 123 t b - - -94.4 - - - - - - - 180.0 -.9 33.1 - +* * +* 124 ALA 124 - - - - - - - - - - - - -1.6 34.6 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * +* ** ** +** +*** ** +* ** +* +*** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.3 183.2 -62.4 180.8 -72.2 -66.6 -38.6 59.8 - 2.0 179.9 -1.9 34.2 ** ** Standard deviations: 5.1 6.9 8.8 8.1 18.9 8.6 10.7 .0 - .0 3.0 .9 1.7 Numbers of values: 14 45 43 29 4 46 46 2 0 2 122 82 119 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 - 1.233 1.523 1.535 1.461 - 116.36 120.84 110.00 110.54 110.40 122.80 2 GLY 2 1.313 1.227 1.501 - 1.424 120.84 115.96 120.04 - 110.95 - 123.99 * +* +* 3 HIS 3 1.338 1.236 1.543 1.568 1.490 124.72 115.95 121.71 112.62 114.86 113.87 122.34 +* +* +* * * +* +* 4 HIS 4 1.318 1.236 1.531 1.552 1.456 121.54 116.15 120.65 110.43 109.72 110.46 123.12 * * 5 HIS 5 1.311 1.228 1.505 1.549 1.467 122.98 114.13 121.61 108.20 107.38 113.04 124.25 * * * * * * 6 HIS 6 1.316 1.233 1.487 1.535 1.448 125.76 116.32 119.49 110.84 108.45 113.42 124.19 +* ** +* ** 7 HIS 7 1.317 1.243 1.503 1.544 1.462 123.92 115.58 121.34 110.81 108.94 113.82 122.97 * * +* +* 8 HIS 8 1.300 1.234 1.508 1.561 1.429 120.63 115.09 121.22 112.06 110.44 113.11 123.65 ** +* * * +* ** 9 LEU 9 1.304 1.242 1.516 1.529 1.437 122.51 116.35 120.82 110.48 108.81 109.49 122.80 +* * +* 10 GLU 10 1.307 1.234 1.512 1.532 1.433 121.05 115.51 120.12 110.15 110.76 110.01 124.37 +* * +* 11 MET 11 1.331 1.235 1.533 1.548 1.462 124.16 116.02 121.65 111.68 111.88 111.22 122.28 * * 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 1.305 1.236 1.504 1.519 1.440 121.41 115.25 121.22 111.22 109.87 111.40 123.43 +* +* 13 SER 13 1.303 1.242 1.527 1.545 1.446 123.97 118.08 119.27 110.65 107.14 109.87 122.65 +* * * +* 14 GLU 14 1.318 1.230 1.528 1.554 1.422 121.66 116.04 121.31 112.40 110.37 112.08 122.63 * +* * +* 15 GLU 15 1.297 1.242 1.549 1.553 1.442 122.18 119.35 118.98 113.90 105.75 106.69 121.67 ** * * +* * ** +* ** ** 16 GLY 16 1.328 1.238 1.503 - 1.440 119.26 115.97 120.83 - 111.16 - 123.19 17 GLN 17 1.319 1.229 1.494 1.513 1.441 121.34 112.73 122.69 107.95 113.80 112.34 124.57 * +* * * * +* 18 VAL 18 1.278 1.241 1.527 1.550 1.432 124.18 118.88 119.21 109.30 106.66 111.11 121.90 +*** * * * +* +*** 19 ILE 19 1.318 1.230 1.516 1.552 1.445 119.19 115.89 121.03 110.19 110.52 112.10 123.08 * * 20 ALA 20 1.307 1.237 1.507 1.520 1.438 122.02 116.11 120.61 110.78 109.45 110.90 123.26 +* * +* 21 CYS 21 1.302 1.238 1.515 1.503 1.405 121.81 115.81 121.01 109.09 109.65 109.20 123.16 +* * +** +** 22 HIS 22 1.298 1.219 1.500 1.534 1.449 122.02 115.73 121.34 109.73 108.96 111.67 122.91 ** * ** 23 THR 23 1.310 1.244 1.512 1.556 1.441 121.52 116.56 120.37 110.48 110.55 111.37 123.06 * * 24 VAL 24 1.330 1.216 1.534 1.574 1.449 121.21 115.94 120.89 112.07 109.75 112.72 123.13 * * * 25 GLU 25 1.334 1.226 1.521 1.535 1.459 122.72 115.69 120.93 109.21 109.69 109.50 123.34 26 THR 26 1.320 1.223 1.535 1.546 1.445 121.79 115.92 120.60 111.04 110.08 110.57 123.44 27 TRP 27 1.327 1.239 1.537 1.540 1.461 122.95 115.42 121.18 110.54 111.52 108.79 123.38 * * 28 ASN 28 1.312 1.244 1.521 1.545 1.451 123.12 115.86 120.45 110.65 110.15 109.12 123.65 * * 29 GLU 29 1.324 1.229 1.524 1.525 1.449 122.39 117.22 119.92 110.57 111.67 110.81 122.85 30 GLN 30 1.333 1.226 1.506 1.498 1.426 121.97 117.33 120.34 110.97 112.36 110.40 122.32 +* +* +* 31 LEU 31 1.322 1.223 1.503 1.485 1.404 120.72 116.31 120.33 110.47 111.25 110.12 123.37 * ** +** +** 32 GLN 32 1.316 1.234 1.531 1.530 1.446 121.77 115.31 121.05 110.18 109.42 110.38 123.61 33 LYS 33 1.323 1.237 1.528 1.536 1.443 123.11 116.97 120.14 110.53 110.97 109.97 122.88 34 ALA 34 1.339 1.224 1.517 1.523 1.454 121.07 115.69 120.76 110.56 110.74 110.89 123.53 35 ASN 35 1.318 1.233 1.507 1.525 1.463 123.26 114.21 122.00 108.18 109.87 109.09 123.80 * * 36 GLU 36 1.302 1.238 1.538 1.531 1.451 123.28 117.04 120.36 110.85 112.66 109.45 122.57 +* +* 37 SER 37 1.317 1.230 1.535 1.518 1.447 121.52 116.77 120.08 110.48 112.58 109.29 123.15 38 LYS 38 1.342 1.237 1.513 1.513 1.476 123.01 115.93 121.11 109.95 112.33 111.72 122.86 39 THR 39 1.296 1.244 1.522 1.520 1.417 121.42 115.87 121.32 109.37 108.52 110.60 122.80 ** ** ** 40 LEU 40 1.279 1.241 1.532 1.564 1.430 121.83 116.37 120.54 113.41 106.88 109.75 123.09 +*** +* * +* +* +*** 41 VAL 41 1.306 1.237 1.535 1.571 1.439 121.82 116.22 120.87 111.35 111.41 110.04 122.88 +* * * +* 42 VAL 42 1.311 1.233 1.528 1.555 1.440 122.00 116.60 120.95 111.11 109.65 111.51 122.42 * * 43 VAL 43 1.303 1.233 1.523 1.551 1.444 121.22 115.33 120.65 108.61 111.93 111.15 124.00 +* +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 44 ASP 44 1.312 1.236 1.520 1.538 1.455 123.97 116.67 120.63 109.97 109.62 110.46 122.60 * * * 45 PHE 45 1.313 1.238 1.510 1.527 1.430 121.56 116.50 120.24 109.26 108.43 110.42 123.23 * * * 46 THR 46 1.306 1.236 1.532 1.556 1.434 121.09 115.93 120.70 109.85 110.61 109.41 123.37 +* * * +* 47 ALA 47 1.314 1.238 1.514 1.517 1.437 123.25 115.93 120.39 110.39 108.83 111.10 123.66 * * * 48 SER 48 1.311 1.230 1.535 1.548 1.455 123.93 116.36 120.88 110.66 111.08 108.77 122.75 * * * * 49 TRP 49 1.318 1.238 1.533 1.543 1.452 121.99 116.90 120.43 111.39 112.61 110.49 122.66 50 CYS 50 1.319 1.228 1.526 1.534 1.447 121.23 115.99 120.66 110.23 110.53 110.30 123.33 51 GLY 51 1.325 1.229 1.523 - 1.458 122.56 118.74 119.63 - 113.25 - 121.63 * * * 52 PRO 52 1.364 1.224 1.523 1.527 1.479 123.02 115.32 121.33 109.30 112.00 102.89 123.34 * * * 53 CYS 53 1.310 1.225 1.538 1.515 1.450 123.18 115.59 121.37 109.78 110.10 108.25 123.01 * * * 54 ARG 54 1.319 1.236 1.535 1.532 1.455 123.17 115.15 121.33 111.15 110.01 107.91 123.51 +* +* 55 PHE 55 1.318 1.237 1.542 1.540 1.454 123.33 117.15 120.69 110.68 112.56 109.41 122.16 56 ILE 56 1.318 1.238 1.541 1.571 1.462 120.83 115.05 121.56 110.31 109.80 111.07 123.36 * * 57 ALA 57 1.322 1.239 1.562 1.522 1.452 123.64 120.27 119.09 111.78 113.95 110.44 120.64 +* * ** * * ** 58 PRO 58 1.376 1.227 1.530 1.536 1.476 121.89 116.11 121.03 110.04 112.24 103.95 122.84 ** ** 59 PHE 59 1.317 1.232 1.539 1.540 1.453 121.94 115.85 120.96 111.31 109.47 109.94 123.18 60 PHE 60 1.330 1.231 1.534 1.541 1.470 122.81 116.16 121.18 111.45 109.90 109.64 122.66 61 ALA 61 1.320 1.229 1.530 1.522 1.459 121.40 115.50 121.43 110.77 109.71 110.46 123.05 62 ASP 62 1.325 1.225 1.508 1.508 1.471 123.35 114.63 121.96 109.46 109.28 109.03 123.41 * * 63 LEU 63 1.296 1.228 1.532 1.518 1.425 123.11 116.86 120.23 111.76 111.16 109.59 122.89 ** +* ** 64 ALA 64 1.328 1.218 1.522 1.514 1.476 122.05 114.37 121.80 110.16 110.34 110.11 123.83 65 LYS 65 1.303 1.232 1.534 1.521 1.453 125.13 116.69 120.71 110.36 111.13 105.92 122.60 +* +* +** +** 66 LYS 66 1.311 1.237 1.525 1.527 1.449 121.19 117.24 120.20 111.80 113.10 111.19 122.55 * * 67 LEU 67 1.317 1.222 1.530 1.548 1.439 121.69 117.94 120.48 110.06 110.57 111.73 121.58 68 PRO 68 1.342 1.233 1.529 1.524 1.458 122.33 117.12 120.81 110.10 112.79 102.46 122.06 69 ASN 69 1.323 1.234 1.523 1.533 1.461 120.57 115.70 121.58 110.80 109.62 111.07 122.71 70 VAL 70 1.307 1.229 1.514 1.557 1.440 122.11 117.00 120.21 110.15 108.40 111.45 122.77 +* * +* 71 LEU 71 1.308 1.240 1.534 1.557 1.435 120.43 115.97 120.85 112.22 107.38 109.31 123.15 +* * * * * +* 72 PHE 72 1.315 1.237 1.516 1.538 1.455 122.20 116.02 120.93 107.87 110.24 111.11 123.04 * * 73 LEU 73 1.293 1.225 1.500 1.541 1.439 122.73 115.09 121.06 108.38 110.64 113.64 123.85 +** * * +* +** 74 LYS 74 1.291 1.227 1.500 1.492 1.416 123.50 116.66 120.78 110.07 107.06 108.89 122.53 +** * +* ** * * +** 75 VAL 75 1.287 1.241 1.507 1.556 1.433 121.28 115.76 120.76 109.89 111.05 110.93 123.47 +** * +** 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 ----------------------------------------------------------------------------------------------------------------------------------- 76 ASP 76 1.319 1.240 1.515 1.518 1.441 121.20 115.32 121.45 110.37 107.83 111.45 123.15 * * 77 THR 77 1.304 1.238 1.533 1.559 1.439 122.76 116.58 120.62 111.34 111.69 111.85 122.79 +* * +* 78 ASP 78 1.319 1.227 1.508 1.518 1.447 121.46 115.43 121.10 110.64 108.58 110.58 123.46 79 GLU 79 1.319 1.233 1.515 1.507 1.428 122.83 116.41 120.82 109.73 111.12 110.04 122.76 * +* +* 80 LEU 80 1.317 1.235 1.540 1.534 1.433 123.03 115.39 121.64 111.18 111.30 110.24 122.91 * * 81 LYS 81 1.315 1.234 1.545 1.556 1.451 123.19 117.54 120.19 113.63 114.03 111.37 122.26 * +* * +* 82 SER 82 1.331 1.239 1.522 1.521 1.451 120.67 115.20 121.57 111.14 109.29 110.63 123.22 83 VAL 83 1.322 1.232 1.527 1.558 1.445 122.21 115.20 121.30 110.22 108.35 110.80 123.45 * * 84 ALA 84 1.328 1.230 1.524 1.514 1.460 123.38 116.45 120.55 109.72 111.44 110.03 122.99 85 SER 85 1.324 1.243 1.535 1.526 1.454 122.35 116.19 121.08 110.16 111.61 109.19 122.69 86 ASP 86 1.320 1.232 1.527 1.528 1.452 121.16 116.14 121.08 110.68 110.64 110.27 122.70 87 TRP 87 1.319 1.228 1.533 1.527 1.449 122.04 116.40 120.26 111.46 112.60 111.49 123.34 88 ALA 88 1.345 1.245 1.531 1.535 1.484 123.89 115.99 121.18 110.99 112.02 110.54 122.78 * * * * 89 ILE 89 1.312 1.235 1.526 1.559 1.444 121.93 116.37 120.81 109.24 108.81 111.89 122.73 * * 90 GLN 90 1.310 1.242 1.521 1.545 1.435 121.67 115.90 121.07 113.21 112.20 110.37 123.03 * * +* +* 91 ALA 91 1.314 1.235 1.510 1.515 1.444 122.09 116.56 120.64 111.06 109.38 110.71 122.79 * * 92 MET 92 1.302 1.236 1.516 1.520 1.434 121.72 117.98 120.30 109.01 110.24 109.58 121.72 +* * +* 93 PRO 93 1.333 1.236 1.525 1.527 1.458 123.55 117.08 120.77 110.06 111.07 102.60 122.09 94 THR 94 1.290 1.231 1.512 1.531 1.422 119.89 116.09 120.46 110.10 109.11 112.39 123.44 +** +* * +** 95 PHE 95 1.304 1.224 1.492 1.521 1.410 122.55 116.60 120.45 108.91 107.07 109.58 122.94 +* +* +** * +** 96 MET 96 1.278 1.231 1.502 1.519 1.428 121.00 114.98 121.15 111.92 109.68 109.27 123.87 +*** * +* +*** 97 PHE 97 1.290 1.249 1.512 1.521 1.407 124.17 116.59 120.92 108.99 109.65 108.37 122.48 +** +** * * +** 98 LEU 98 1.294 1.215 1.522 1.561 1.427 120.58 117.47 120.13 107.07 107.57 112.91 122.39 ** +* +* +* * * ** 99 LYS 99 1.296 1.219 1.490 1.526 1.444 121.22 115.37 120.46 111.22 107.96 112.78 124.07 ** +* * * ** 100 GLU 100 1.321 1.224 1.534 1.525 1.470 124.94 116.47 120.85 107.69 110.72 113.17 122.68 +* * +* +* 101 GLY 101 1.306 1.235 1.529 - 1.447 120.87 116.04 120.87 - 111.80 - 123.09 +* +* 102 LYS 102 1.329 1.232 1.515 1.537 1.454 122.37 117.19 119.70 107.62 107.52 110.81 123.11 * * * 103 ILE 103 1.310 1.231 1.521 1.561 1.460 122.05 116.51 120.76 108.86 110.94 111.13 122.72 * * 104 LEU 104 1.311 1.235 1.500 1.524 1.419 120.66 116.15 120.67 109.99 109.56 112.27 123.11 * * ** * ** 105 ASP 105 1.314 1.218 1.494 1.520 1.437 121.17 115.32 121.31 110.01 112.39 112.39 123.34 * * * * * 106 LYS 106 1.297 1.239 1.527 1.564 1.442 122.35 115.86 120.89 113.16 112.31 111.63 123.23 ** +* +* ** 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 ----------------------------------------------------------------------------------------------------------------------------------- 107 VAL 107 1.310 1.227 1.513 1.560 1.455 123.28 116.91 120.21 108.69 108.35 111.63 122.86 * * * 108 VAL 108 1.302 1.240 1.530 1.552 1.432 121.17 115.89 121.06 111.32 110.58 111.26 123.01 +* * * +* 109 GLY 109 1.308 1.237 1.500 - 1.431 121.42 117.71 120.12 - 110.19 - 122.16 * * * 110 ALA 110 1.316 1.237 1.506 1.520 1.436 118.68 115.03 121.23 110.96 109.15 110.77 123.73 * +* +* 111 LYS 111 1.301 1.217 1.504 1.519 1.418 123.42 118.03 119.43 109.38 106.97 108.13 122.53 ** * ** +* * ** 112 LYS 112 1.306 1.230 1.533 1.531 1.434 120.89 116.81 120.43 112.74 111.70 107.90 122.73 +* * * +* +* 113 ASP 113 1.317 1.230 1.517 1.527 1.463 121.41 116.05 120.87 110.74 112.09 111.42 123.07 114 GLU 114 1.319 1.239 1.537 1.533 1.457 121.76 116.77 120.48 112.56 111.98 110.53 122.72 * * 115 LEU 115 1.332 1.223 1.503 1.513 1.463 121.58 114.88 121.51 108.15 109.23 110.39 123.61 * * * 116 GLN 116 1.306 1.232 1.524 1.518 1.459 122.18 116.51 120.71 111.45 111.81 111.75 122.74 +* +* 117 SER 117 1.313 1.235 1.536 1.519 1.444 121.57 115.76 121.33 111.94 109.53 109.70 122.89 * * 118 THR 118 1.321 1.236 1.540 1.535 1.437 121.97 116.39 121.07 111.47 109.94 110.77 122.53 * * * 119 ILE 119 1.321 1.222 1.525 1.553 1.449 121.13 115.49 120.85 109.90 107.76 111.86 123.55 * * 120 ALA 120 1.331 1.230 1.535 1.515 1.466 123.38 116.08 120.94 110.49 111.39 110.05 122.98 121 LYS 121 1.329 1.234 1.517 1.504 1.469 123.34 114.55 122.05 107.26 109.11 108.92 123.40 * * * 122 HIS 122 1.304 1.222 1.529 1.522 1.429 122.94 117.85 120.06 111.63 113.32 110.93 122.10 +* +* +* 123 LEU 123 1.327 1.241 1.514 1.517 1.418 121.40 114.88 121.36 111.31 110.53 111.15 123.65 ** ** 124 ALA 124 1.305 - 1.512 1.530 1.431 123.71 - - 110.65 108.05 110.52 - +* * * * +* ----------------------------------------------------------------------------------------------------------------------------------- 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 1.278 1.345 1.313 .013 +*** * * C-N (Pro) 1.341 .016 4 1.333 1.376 1.354 .017 ** C-O C-O 1.231 .020 123 1.215 1.249 1.233 .007 CA-C CH1E-C (except Gly) 1.525 .021 119 1.487 1.562 1.522 .014 +* +* CH2G*-C (Gly) 1.516 .018 5 1.500 1.529 1.511 .012 CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.514 1.535 1.521 .006 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.520 1.574 1.554 .012 * CH1E-CH2E (the rest) 1.530 .020 84 1.485 1.568 1.531 .016 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.404 1.490 1.445 .016 +** +* NH1-CH2G* (Gly) 1.451 .016 5 1.424 1.458 1.440 .012 +* N-CH1E (Pro) 1.466 .015 4 1.458 1.479 1.468 .010 ------------------------------------------------------------------------------------------------------------- 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 2.0 114 112.73 120.27 116.16 1.02 +* ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.96 118.74 116.89 1.14 * CH1E-C-N (Pro) 116.9 1.5 4 115.32 117.12 116.41 .75 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.64 124.57 123.01 .60 * O-C-N (Pro) 122.0 1.4 4 122.06 123.34 122.58 .54 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 118.68 125.76 122.21 1.20 +* ** C-NH1-CH2G* (Gly) 120.6 1.7 5 119.26 122.56 120.99 1.06 * C-N-CH1E (Pro) 122.6 5.0 4 121.89 123.55 122.70 .64 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 118.98 122.69 120.80 .61 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.63 120.87 120.30 .48 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 109.72 111.78 110.73 .49 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 108.61 112.07 110.22 .95 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.07 113.90 110.48 1.45 +* ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 105.75 114.86 110.19 1.75 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.19 113.25 111.47 1.03 N-CH1E-C (Pro) 111.8 2.5 4 111.07 112.79 112.03 .62 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.03 111.40 110.61 .39 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.41 112.72 111.26 .74 * N-CH1E-CH2E (Pro) 103.0 1.1 4 102.46 103.95 102.98 .58 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 105.92 113.87 110.44 1.57 +** +* ------------------------------------------------------------------------------------------------------------- The small molecule data used in the above analysis is from Engh & Huber (1991). The atom labelling follows that used in the X-PLOR dictionary, with some additional atoms (marked with an asterisk) as defined by Engh & Huber. Residue-by-residue listing for refined_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] 97 85.8% Residues in additional allowed regions [a,b,l,p] 15 13.3% Residues in generously allowed regions [~a,~b,~l,~p] 1 .9% 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 85.8 83.8 10.0 .2 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 82 .9 .8 .2 .3 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 14 5.1 18.1 6.5 -2.0 BETTER b. Chi-1 trans st dev 45 6.9 19.0 5.3 -2.3 BETTER c. Chi-1 gauche plus st dev 43 8.8 17.5 4.9 -1.8 BETTER d. Chi-1 pooled st dev 102 8.4 18.2 4.8 -2.0 BETTER e. Chi-2 trans st dev 29 8.1 20.4 5.0 -2.5 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 9.8 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .87 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 -.20 Chi1-chi2 distribution -.17 Chi1 only -.18 Chi3 & chi4 .63 Omega .15 ------ .01 ===== Main-chain covalent forces:- Main-chain bond lengths .09 Main-chain bond angles .43 ------ .29 ===== OVERALL AVERAGE .11 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.