Residue-by-residue listing for refined_3 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 - - 180.6 - 181.7 - - - - - - 179.6 - 33.9 - 2 ALA 2 B - - - - - - - - - - 180.9 - 34.3 - 3 ASP 3 B - - -69.6 - - - - - - - 174.7 - 32.8 - 4 THR 4 S A - - -54.9 - - - - - - - 180.4 -1.0 35.0 - * * 5 GLY 5 S - - - - - - - - - - - 177.9 - - - 6 GLU 6 l - 180.4 - 185.9 - - - - - - 171.9 -.9 30.8 - * +* +* 7 VAL 7 E B - - -62.4 - - - - - - - 185.7 -3.1 32.3 - * * 8 GLN 8 E B - - -57.0 182.5 - - - - - - 175.3 - 35.0 - 9 PHE 9 E B - 181.8 - - - - - - - - 181.2 -2.4 34.9 - 10 MET 10 E B 58.0 - - 183.1 - - - - - - 178.2 - 33.9 - 11 LYS 11 E B - 191.7 - 184.9 - - - - - - 174.3 -1.2 35.1 - * * 12 PRO 12 - - - - - -65.2 - - - - - 175.8 - 38.6 - * * 13 PHE 13 B 58.5 - - - - - - - - - 180.9 - 32.9 - 14 ILE 14 t B - - -60.4 - - - - - - - 191.0 - 34.4 - +* +* 15 SER 15 T A - 190.2 - - - - - - - - 180.4 -.6 31.0 - +* +* 16 GLU 16 T A - 182.4 - 184.1 - - - - - - 184.5 - 35.4 - 17 LYS 17 T A - 181.3 - - - - - - - - 179.6 -.9 35.2 - * * 18 SER 18 T A - - -58.1 - - - - - - - 175.1 -3.2 33.9 - +* +* 19 SER 19 T A - - -62.3 - - - - - - - 177.3 - 33.4 - Residue-by-residue listing for refined_3 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 LYS 20 T a - - -72.9 182.7 - - - - - - 183.9 -.8 33.0 - +* +* 21 SER 21 t B 55.3 - - - - - - - - - 172.5 -1.0 35.2 - * * * 22 LEU 22 E B - 186.4 - - - - - - - - 180.0 -3.3 32.5 - +* +* 23 GLU 23 E B 48.1 - - 175.3 - - - - - - 179.1 -.6 33.9 - * +* +* 24 ILE 24 e B - - -61.9 180.5 - - - - - - 179.7 -1.1 33.7 - * * 25 PRO 25 h - - - - - -55.6 - - - - - 181.5 - 39.2 - +* +* 26 LEU 26 H A - - -57.1 182.6 - -65.2 -25.6 - - - 176.6 - 33.6 - * * 27 GLY 27 H - - - - - - -72.9 -35.6 - - - 180.7 - - - 28 PHE 28 H A - 184.1 - - - -76.0 -27.6 - - - 176.9 - 34.0 - * * 29 ASN 29 H A - 175.4 - - - -56.2 -31.4 - - - 180.4 -1.9 35.0 - 30 GLU 30 h A - - -61.9 187.5 - - - - - - 175.6 -.6 31.0 - +* +* 31 TYR 31 T A - - -67.1 - - - - - - - 179.8 -2.0 33.7 - 32 PHE 32 t B - 211.2 - - - - - - - - 190.0 -1.9 35.3 - +* +* +* 33 PRO 33 - - - - - -54.7 - - - - - 183.5 - 38.1 - * * 34 ALA 34 b - - - - - - - - - - 178.6 - 34.3 - 35 PRO 35 S - - - - - -58.2 - - - - - 174.8 - 38.5 - * * 36 PHE 36 S b - 182.6 - - - - - - - - 179.3 - 32.8 - 37 PRO 37 - - - - - -83.6 - - - - - 178.5 - 38.8 - +* * +* 38 ILE 38 S A - - -57.4 - - - - - - - 178.7 - 33.9 - 39 THR 39 B 52.2 - - - - - - - - - 179.4 - 33.5 - 40 VAL 40 E B - 180.6 - - - - - - - - 181.8 -3.1 35.4 - * * 41 ASP 41 E B - - -66.2 - - - - - - - 182.2 -2.7 33.7 - 42 LEU 42 E B - 198.1 - 174.9 - - - - - - 176.1 -1.3 35.8 - 43 LEU 43 E B - - -69.0 - - - - - - - 180.1 -3.0 34.5 - * * 44 ASP 44 E B 82.7 - - - - - - - - - 179.8 -1.0 33.9 - * * * 45 TYR 45 e A - 190.9 - - - - - - - - 176.1 -.9 34.2 - +* +* 46 SER 46 S A - 181.4 - - - - - - - - 176.6 - 34.1 - 47 GLY 47 - - - - - - - - - - - 177.8 - - - 48 ARG 48 e B - 192.2 - 188.4 - - - - - - 175.9 - 35.0 - 49 SER 49 E B 55.9 - - - - - - - - - 173.3 - 33.6 - * * 50 TRP 50 E B - - -59.4 - - - - - - - 174.1 -1.5 37.4 - * * * 51 THR 51 E B - - -53.9 - - - - - - - 184.6 - 35.6 - 52 VAL 52 E B - - -57.0 - - - - - - - 182.1 -1.9 32.5 - 53 ARG 53 e B - 183.1 - 171.8 - - - - - - 175.4 -3.0 33.8 - * * 54 MET 54 E B - 184.8 - 188.1 - - - - - - 181.5 -.5 34.7 - ** ** 55 LYS 55 E B - 184.2 - 180.7 - - - - - - 176.5 -1.9 35.6 - Residue-by-residue listing for refined_3 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 LYS 56 E B - - -54.5 200.6 - - - - - - 176.9 - 33.8 - * * 57 ARG 57 E b - - -60.9 188.1 - - - - - - 184.4 -3.0 32.6 - * * 58 GLY 58 T - - - - - - - - - - - 181.0 -.9 - - * * 59 GLU 59 T A - - -58.0 - - - - - - - 183.8 -.8 34.6 - +* +* 60 LYS 60 E B - - -56.2 - - - - - - - 179.3 -2.5 35.4 - 61 VAL 61 E B - - -60.5 - - - - - - - 170.1 - 32.7 - +* +* 62 PHE 62 E B - - -67.3 - - - - - - - 179.2 -1.4 32.0 - 63 LEU 63 E B - 187.4 - 170.5 - - - - - - 190.0 -2.6 34.7 - +* +* 64 THR 64 e a 53.5 - - - - - - - - - 186.7 -2.1 33.2 - * * 65 VAL 65 T B - 185.7 - - - - - - - - 182.0 - 33.3 - 66 GLY 66 h - - - - - - - - - - - 178.0 - - - 67 TRP 67 H A - 174.3 - - - -64.7 -29.7 - - - 180.9 -1.0 35.1 - * * 68 GLU 68 H A 56.8 - - 182.5 - -70.1 -25.8 - - - 172.8 -.6 26.7 - * * +* ** ** 69 ASN 69 H A - - -68.0 - - -71.8 -30.5 - - - 178.9 -.7 33.5 - +* +* 70 PHE 70 H A - 176.6 - - - -74.4 -48.5 - - - 180.6 -1.1 32.5 - * * 71 VAL 71 H A 68.3 - - - - -60.0 -42.5 - - - 177.8 -3.2 32.9 - +* +* 72 LYS 72 H A - - -64.6 - - -70.9 -33.7 - - - 182.6 -1.8 32.2 - 73 ASP 73 H A - 181.7 - - - -77.1 -39.7 - - - 187.1 -1.5 33.5 - * * 74 ASN 74 h A - 187.7 - - - - - - - - 178.0 -3.1 33.3 - * * 75 ASN 75 XX - 174.4 - - - - - - - - 176.7 - 31.6 - **** **** 76 LEU 76 l - - -78.3 - - - - - - - 173.9 -2.0 27.0 - * +* +* 77 GLU 77 t B 58.0 - - 176.1 - - - - - - 181.1 - 30.0 - * * 78 ASP 78 T B - - -58.2 - - - - - - - 183.6 - 35.3 - 79 GLY 79 T - - - - - - - - - - - 175.2 - - - 80 LYS 80 t B - - -54.4 - - - - - - - 182.1 -2.5 35.7 - 81 TYR 81 E B - - -59.6 - - - - - - - 186.2 -2.9 33.7 - * * * 82 LEU 82 E B - 191.3 - - - - - - - - 173.8 -.6 36.5 - * +* +* 83 GLN 83 E B 61.3 - - 181.3 - - - - - - 182.9 -2.3 33.0 - 84 PHE 84 E B - - -56.6 - - - - - - - 173.9 -3.5 36.3 - * +* +* 85 ILE 85 E B - - -57.7 178.7 - - - - - - 182.3 -2.4 34.0 - 86 TYR 86 E B - 177.3 - - - - - - - - 180.5 -3.6 36.5 - ** ** 87 ASP 87 e a - 178.7 - - - - - - - - 178.4 -1.6 33.5 - 88 ARG 88 S ~a - 189.4 - - - - - - - - 191.3 - 36.3 - ** +* ** 89 ASP 89 S b - 186.1 - - - - - - - - 180.1 - 37.8 - * * Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 90 ARG 90 e A 68.4 - - 179.4 - - - - - - 182.4 - 36.1 - 91 THR 91 E B - - -54.8 - - - - - - - 178.0 - 35.7 - 92 PHE 92 E B - - -67.9 - - - - - - - 174.1 -3.0 35.1 - * * * 93 TYR 93 E B - - -54.5 - - - - - - - 184.1 -2.8 35.2 - * * 94 VAL 94 E B - - -60.5 - - - - - - - 177.4 -3.5 32.7 - +* +* 95 ILE 95 E B - - -58.8 179.0 - - - - - - 179.4 -2.1 33.9 - 96 ILE 96 E B - 178.9 - 177.8 - - - - - - 177.0 - 33.1 - 97 TYR 97 E B 48.8 - - - - - - - - - 194.9 -2.4 28.0 - +** +* +** 98 GLY 98 S - - - - - - - - - - - 189.0 - - - +* +* 99 HIS 99 b - 183.9 - - - - - - - - 173.6 - 33.4 - * * 100 ASN 100 b - 187.2 - - - - - - - - 184.1 - 34.0 - 101 MET 101 a - 179.1 - 180.6 - - - - - - 176.9 - 33.5 - 102 CYS 102 - - - -55.9 - - - - - - - - - 34.3 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +* * +* * +** ** ** **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.0 184.5 -60.9 181.8 -63.5 -69.0 -33.7 - - - 179.7 -1.9 34.1 Standard deviations: 9.1 7.1 5.8 6.0 12.0 6.7 7.3 - - - 4.5 1.0 2.1 Numbers of values: 14 36 38 27 5 11 11 0 0 0 101 57 95 0 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_3 Page 5 ---------------------------------------- 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 - 1.226 1.517 1.539 1.464 - 116.68 120.57 110.55 109.77 110.97 122.74 2 ALA 2 1.316 1.238 1.513 1.518 1.444 121.66 116.54 120.36 110.62 109.46 110.34 123.09 3 ASP 3 1.310 1.236 1.498 1.535 1.450 121.44 115.62 121.22 109.57 112.17 112.71 123.14 * * * * 4 THR 4 1.287 1.234 1.526 1.543 1.428 121.86 115.69 121.53 109.93 108.07 110.67 122.73 +** +* * +** 5 GLY 5 1.311 1.242 1.499 - 1.416 120.66 114.98 120.53 - 111.97 - 124.47 * ** ** 6 GLU 6 1.312 1.248 1.531 1.545 1.447 124.51 114.96 121.81 111.78 112.60 113.00 123.09 * +* * +* 7 VAL 7 1.304 1.230 1.520 1.569 1.443 122.79 117.30 120.36 111.32 107.29 113.78 122.30 +* * * * * +* 8 GLN 8 1.294 1.233 1.502 1.517 1.434 120.54 115.50 121.08 109.40 111.64 109.98 123.41 ** * * ** 9 PHE 9 1.299 1.221 1.522 1.539 1.429 122.65 117.37 120.20 111.13 107.65 109.69 122.43 ** +* * ** 10 MET 10 1.300 1.226 1.510 1.540 1.458 121.40 117.21 120.15 110.96 110.07 110.52 122.61 ** ** 11 LYS 11 1.311 1.234 1.508 1.545 1.448 120.50 118.74 119.31 109.15 108.38 111.25 121.91 * * * * 12 PRO 12 1.334 1.252 1.536 1.538 1.450 121.49 115.79 121.16 110.10 110.58 104.32 122.94 * * * * Residue-by-residue listing for refined_3 Page 6 ---------------------------------------- ................................................................................................................................... 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 ----------------------------------------------------------------------------------------------------------------------------------- 13 PHE 13 1.300 1.242 1.531 1.543 1.438 122.52 116.70 120.50 111.74 109.54 111.35 122.77 ** * ** 14 ILE 14 1.312 1.220 1.491 1.586 1.462 121.67 118.00 119.15 109.14 105.15 113.68 122.85 * +* +* ** * ** 15 SER 15 1.306 1.216 1.522 1.510 1.445 120.13 117.27 119.77 112.01 113.74 111.75 122.84 +* * +* 16 GLU 16 1.313 1.224 1.520 1.521 1.457 122.32 115.66 121.72 109.33 110.20 109.64 122.54 * * 17 LYS 17 1.299 1.233 1.491 1.535 1.457 121.29 113.86 122.02 110.71 108.10 109.46 124.08 ** +* * * ** 18 SER 18 1.285 1.207 1.534 1.527 1.399 123.33 117.09 120.33 112.99 111.15 108.28 122.58 *** * *** +* * *** 19 SER 19 1.344 1.236 1.531 1.538 1.461 120.88 116.55 120.75 110.14 110.45 111.77 122.68 * * 20 LYS 20 1.332 1.227 1.508 1.526 1.459 120.78 118.18 119.63 108.62 113.87 112.59 122.19 * * 21 SER 21 1.307 1.229 1.513 1.522 1.443 119.14 115.39 121.45 109.39 113.72 109.01 123.16 +* * +* 22 LEU 22 1.292 1.243 1.509 1.552 1.417 121.66 114.56 121.43 112.92 107.39 111.92 123.96 +** * ** * * +** 23 GLU 23 1.293 1.242 1.528 1.534 1.428 123.34 115.71 121.25 111.84 111.00 109.39 123.01 +** +* +** 24 ILE 24 1.306 1.230 1.526 1.565 1.437 121.97 117.52 120.23 110.69 109.08 111.68 122.21 +* * +* 25 PRO 25 1.347 1.242 1.521 1.526 1.466 122.98 116.00 120.81 109.56 112.22 103.42 123.16 26 LEU 26 1.317 1.234 1.528 1.534 1.456 122.18 116.04 120.97 110.69 110.74 110.80 122.99 27 GLY 27 1.324 1.228 1.516 - 1.442 121.21 116.09 120.87 - 111.37 - 123.01 28 PHE 28 1.326 1.228 1.530 1.542 1.460 122.04 115.06 121.40 111.23 109.37 110.19 123.53 29 ASN 29 1.326 1.233 1.529 1.537 1.474 124.00 116.11 121.32 110.00 111.18 109.27 122.53 * * 30 GLU 30 1.318 1.232 1.531 1.517 1.451 121.87 115.93 121.14 112.23 112.61 111.91 122.91 * * 31 TYR 31 1.309 1.235 1.515 1.530 1.453 122.20 116.44 120.75 109.58 110.40 112.01 122.81 * * 32 PHE 32 1.315 1.236 1.536 1.532 1.439 121.25 117.52 119.90 110.36 106.68 109.90 122.58 * * +* +* 33 PRO 33 1.347 1.244 1.519 1.532 1.479 123.92 115.16 120.37 110.41 115.60 103.46 124.46 * +* +* +* 34 ALA 34 1.319 1.234 1.528 1.522 1.464 124.16 117.41 120.31 110.01 112.41 109.85 122.27 * * 35 PRO 35 1.360 1.229 1.521 1.536 1.468 122.96 116.09 121.07 110.63 110.96 103.72 122.84 * * 36 PHE 36 1.305 1.230 1.521 1.537 1.429 121.62 117.30 120.77 111.63 109.21 111.73 121.82 +* +* +* 37 PRO 37 1.329 1.238 1.523 1.528 1.446 122.12 116.45 120.97 110.63 111.47 103.26 122.57 * * 38 ILE 38 1.304 1.226 1.518 1.553 1.442 121.00 116.10 121.19 110.25 109.31 111.69 122.71 +* +* 39 THR 39 1.308 1.234 1.516 1.552 1.435 121.70 115.35 120.95 110.03 110.35 112.14 123.68 +* * +* 40 VAL 40 1.299 1.254 1.539 1.575 1.436 124.06 117.55 120.08 110.87 106.94 109.75 122.36 ** * * * * +* * ** 41 ASP 41 1.311 1.232 1.501 1.538 1.450 121.41 115.99 120.88 110.23 110.35 111.56 123.12 * * * Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 42 LEU 42 1.309 1.237 1.518 1.553 1.436 121.36 115.78 120.45 110.65 108.13 108.92 123.74 * * * * * 43 LEU 43 1.307 1.220 1.504 1.557 1.444 123.34 116.92 120.20 109.20 108.12 112.26 122.88 +* * * * +* 44 ASP 44 1.290 1.237 1.509 1.538 1.449 121.90 115.40 120.68 108.97 108.70 113.00 123.87 +** * +** 45 TYR 45 1.305 1.230 1.569 1.537 1.455 124.52 118.01 120.11 111.82 112.47 108.13 121.88 +* ** +* * ** 46 SER 46 1.339 1.236 1.521 1.547 1.449 121.31 116.23 120.93 110.95 108.15 110.96 122.83 * * 47 GLY 47 1.319 1.233 1.503 - 1.435 120.45 117.06 120.25 - 113.26 - 122.68 48 ARG 48 1.312 1.233 1.517 1.533 1.451 120.31 117.95 119.70 108.98 107.87 111.39 122.35 * * * 49 SER 49 1.310 1.236 1.517 1.532 1.428 119.41 115.02 121.61 110.68 111.63 110.76 123.35 * +* * +* 50 TRP 50 1.293 1.243 1.496 1.523 1.396 124.24 117.10 120.08 108.86 107.65 108.35 122.80 +** * *** * * * *** 51 THR 51 1.292 1.230 1.516 1.542 1.414 119.27 116.87 120.50 110.09 105.57 110.45 122.61 +** ** * ** +** 52 VAL 52 1.300 1.232 1.499 1.559 1.436 120.11 116.41 120.54 111.07 110.51 112.64 123.03 ** * * ** 53 ARG 53 1.292 1.237 1.512 1.526 1.420 120.85 115.37 121.37 111.47 111.43 109.81 123.24 +** +* +** 54 MET 54 1.304 1.227 1.492 1.533 1.438 121.71 117.06 120.08 108.95 107.05 112.41 122.86 +* +* * * * +* 55 LYS 55 1.283 1.239 1.489 1.522 1.426 120.46 116.97 120.16 110.27 108.57 109.24 122.85 *** +* +* *** 56 LYS 56 1.302 1.226 1.487 1.522 1.415 119.14 115.91 120.86 108.33 108.04 114.06 123.17 +* +* ** * * ** ** 57 ARG 57 1.271 1.242 1.486 1.525 1.427 120.79 115.10 121.12 111.17 107.90 113.03 123.71 **** +* +* * * **** 58 GLY 58 1.303 1.239 1.503 - 1.415 120.90 115.41 121.10 - 110.59 - 123.46 +* ** ** 59 GLU 59 1.300 1.227 1.529 1.525 1.436 122.21 117.46 120.29 110.08 111.05 109.95 122.24 ** * ** 60 LYS 60 1.336 1.237 1.482 1.545 1.454 120.38 116.16 120.78 106.28 109.46 113.39 123.06 ** ** +* ** 61 VAL 61 1.298 1.234 1.503 1.555 1.413 120.08 114.59 122.38 110.08 111.58 112.94 122.94 ** * ** ** 62 PHE 62 1.272 1.250 1.506 1.538 1.427 120.62 115.35 120.88 111.90 109.71 112.50 123.74 **** +* * **** 63 LEU 63 1.302 1.218 1.516 1.558 1.437 122.94 117.06 120.19 113.69 105.95 108.16 122.73 +* * * +* +* * +* 64 THR 64 1.305 1.239 1.538 1.542 1.444 120.40 116.01 121.21 110.36 115.29 110.22 122.77 +* * +* 65 VAL 65 1.308 1.236 1.519 1.562 1.451 122.34 115.66 121.05 111.23 110.52 111.24 123.25 * * 66 GLY 66 1.312 1.235 1.479 - 1.426 121.40 114.76 121.35 - 110.93 - 123.89 * ** +* ** 67 TRP 67 1.312 1.229 1.489 1.531 1.424 123.02 116.03 121.10 109.78 108.81 110.63 122.84 * +* +* +* 68 GLU 68 1.311 1.219 1.526 1.513 1.429 118.53 116.02 121.20 115.21 112.37 114.65 122.75 * +* +* +** ** +** 69 ASN 69 1.318 1.211 1.510 1.539 1.454 121.60 115.98 121.08 110.59 109.35 111.73 122.93 * * Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 70 PHE 70 1.320 1.233 1.519 1.541 1.452 122.36 116.18 120.43 111.41 111.16 111.57 123.38 71 VAL 71 1.332 1.210 1.524 1.577 1.456 121.68 115.84 121.28 111.19 109.63 112.16 122.84 * * * 72 LYS 72 1.304 1.233 1.535 1.532 1.448 121.25 117.40 120.38 111.43 112.25 111.43 122.21 +* +* 73 ASP 73 1.332 1.237 1.529 1.540 1.479 120.28 117.22 120.61 109.30 112.84 111.62 122.12 * * 74 ASN 74 1.311 1.231 1.542 1.548 1.448 121.25 115.73 121.20 112.97 110.43 109.25 123.07 * +* +* 75 ASN 75 1.350 1.229 1.502 1.552 1.493 124.07 115.14 120.75 112.12 112.03 111.82 124.10 * * * +* * * +* 76 LEU 76 1.297 1.251 1.517 1.511 1.479 123.45 118.02 120.37 110.40 117.46 116.10 121.51 ** * ** *** *** 77 GLU 77 1.272 1.237 1.512 1.517 1.423 117.77 116.15 120.09 112.92 111.00 113.57 123.75 **** +* ** * +* **** 78 ASP 78 1.331 1.239 1.512 1.531 1.476 122.80 116.22 120.65 108.14 109.73 111.12 123.11 * * 79 GLY 79 1.299 1.225 1.500 - 1.439 121.06 115.49 121.22 - 109.82 - 123.29 ** ** 80 LYS 80 1.313 1.235 1.521 1.546 1.445 122.17 118.53 119.42 110.08 105.96 109.95 122.03 * * +* +* 81 TYR 81 1.306 1.233 1.509 1.521 1.458 120.46 117.30 120.18 110.50 110.15 111.07 122.49 +* +* 82 LEU 82 1.322 1.241 1.518 1.527 1.422 120.00 116.12 120.64 109.35 110.28 108.42 123.21 +* * +* 83 GLN 83 1.307 1.242 1.514 1.542 1.441 121.76 115.94 120.72 111.10 108.32 112.44 123.33 +* * * +* 84 PHE 84 1.293 1.233 1.504 1.540 1.431 122.44 116.82 120.32 108.35 109.10 110.10 122.82 +** * +** 85 ILE 85 1.292 1.234 1.512 1.552 1.426 120.79 115.61 120.93 110.12 107.20 112.50 123.46 +** +* * +** 86 TYR 86 1.286 1.227 1.504 1.545 1.431 123.04 116.28 120.46 110.56 107.61 108.03 123.24 *** * * * * *** 87 ASP 87 1.309 1.227 1.527 1.539 1.455 121.18 115.52 120.94 111.12 110.86 110.64 123.53 * * 88 ARG 88 1.301 1.230 1.521 1.552 1.449 124.59 113.52 122.80 110.13 104.46 109.37 123.52 ** * +* * * ** ** 89 ASP 89 1.310 1.226 1.531 1.554 1.418 124.11 117.55 119.71 111.21 105.98 105.79 122.65 * * ** * +* +** +** 90 ARG 90 1.298 1.224 1.526 1.545 1.459 123.06 115.18 121.76 108.67 107.63 110.20 123.05 ** * ** 91 THR 91 1.299 1.247 1.534 1.549 1.416 122.41 115.59 120.90 109.98 109.46 109.37 123.49 ** ** * ** 92 PHE 92 1.314 1.227 1.503 1.537 1.446 122.71 115.97 120.58 108.25 110.22 111.46 123.43 * * * 93 TYR 93 1.294 1.224 1.511 1.542 1.439 122.31 117.85 120.15 109.51 105.73 111.32 121.95 ** +* ** 94 VAL 94 1.292 1.236 1.514 1.546 1.432 119.77 115.46 121.46 110.23 112.20 112.38 123.07 +** * * +** 95 ILE 95 1.300 1.242 1.513 1.562 1.435 122.02 116.01 120.56 109.90 108.47 112.51 123.40 ** * ** 96 ILE 96 1.303 1.244 1.525 1.569 1.434 121.78 115.58 121.28 110.94 110.43 111.95 123.10 +* * * +* 97 TYR 97 1.297 1.242 1.508 1.557 1.433 122.07 115.93 120.64 115.81 110.23 113.87 123.43 ** * * *** +* *** Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 98 GLY 98 1.301 1.230 1.506 - 1.438 120.64 113.08 122.22 - 105.50 - 124.67 ** +* ** * ** 99 HIS 99 1.327 1.228 1.523 1.534 1.451 125.40 114.52 121.43 110.57 114.62 109.96 124.04 ** * ** 100 ASN 100 1.305 1.235 1.509 1.553 1.449 124.65 116.92 119.18 111.12 105.65 111.81 123.84 +* * +* +* +* 101 MET 101 1.336 1.232 1.520 1.540 1.477 123.11 116.49 120.84 110.72 111.39 110.76 122.65 * * 102 CYS 102 1.289 - 1.509 1.529 1.419 121.00 - - 111.75 107.28 110.11 - +** ** * +** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * ** +* *** ** +* * *** ** *** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 Page 10 ---------------------------------------- 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 96 1.271 1.350 1.307 .015 **** * +* C-N (Pro) 1.341 .016 5 1.329 1.360 1.343 .011 * C-O C-O 1.231 .020 101 1.207 1.254 1.233 .008 * * CA-C CH1E-C (except Gly) 1.525 .021 95 1.482 1.569 1.516 .014 ** ** CH2G*-C (Gly) 1.516 .018 7 1.479 1.516 1.501 .011 ** CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.518 1.522 1.520 .002 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.542 1.586 1.559 .012 +* CH1E-CH2E (the rest) 1.530 .020 75 1.510 1.558 1.536 .011 * N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.396 1.493 1.442 .017 *** +* NH1-CH2G* (Gly) 1.451 .016 7 1.415 1.442 1.430 .010 ** * N-CH1E (Pro) 1.466 .015 5 1.446 1.479 1.462 .012 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 Page 11 ---------------------------------------- +-----------------+ | 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 89 113.52 118.74 116.31 1.03 * * CH2G*-C-NH1 (Gly) 116.4 2.1 7 113.08 117.06 115.27 1.14 +* CH1E-C-N (Pro) 116.9 1.5 5 115.16 116.45 115.90 .43 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 121.51 124.67 122.99 .59 * O-C-N (Pro) 122.0 1.4 5 122.57 124.46 123.19 .66 +* C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 117.77 125.40 121.80 1.48 ** ** C-NH1-CH2G* (Gly) 120.6 1.7 7 120.45 121.40 120.90 .32 C-N-CH1E (Pro) 122.6 5.0 5 121.49 123.92 122.69 .83 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 119.15 122.80 120.72 .65 * CH2G*-C-O (Gly) 120.8 2.1 7 120.25 122.22 121.08 .59 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.01 110.62 110.32 .30 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 109.14 111.32 110.41 .57 * CH2E-CH1E-C (the rest) 110.1 1.9 75 106.28 115.81 110.60 1.55 ** *** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.46 117.46 109.73 2.38 ** ** NH1-CH2G*-C (Gly) 112.5 2.9 7 105.50 113.26 110.49 2.27 ** N-CH1E-C (Pro) 111.8 2.5 5 110.58 115.60 112.17 1.81 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.85 110.34 110.09 .25 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.37 113.78 111.76 1.23 * * N-CH1E-CH2E (Pro) 103.0 1.1 5 103.26 104.32 103.64 .37 * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 105.79 116.10 110.94 1.75 +** *** ------------------------------------------------------------------------------------------------------------- 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_3 Page 12 ---------------------------------------- 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] 74 84.1% Residues in additional allowed regions [a,b,l,p] 12 13.6% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.1% Residues in disallowed regions [XX] 1 1.1% ---- ------ Number of non-glycine and non-proline residues 88 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 7 Number of proline residues 5 ---- Total number of residues 102 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 88 84.1 83.8 10.0 .0 Inside b. Omega angle st dev 101 4.5 6.0 3.0 -.5 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 2.1 3.1 1.6 -.6 Inside e. H-bond energy st dev 57 1.0 .8 .2 .7 Inside f. Overall G-factor 102 -.1 -.4 .3 .9 Inside 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 9.1 18.1 6.5 -1.4 BETTER b. Chi-1 trans st dev 36 7.1 19.0 5.3 -2.2 BETTER c. Chi-1 gauche plus st dev 38 5.8 17.5 4.9 -2.4 BETTER d. Chi-1 pooled st dev 88 8.2 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 27 6.0 20.4 5.0 -2.9 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% 84.1 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.2 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .97 3 Residue-by-residue listing for refined_3 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.57 Chi1-chi2 distribution -.24 Chi1 only -.05 Chi3 & chi4 .26 Omega -.16 ------ -.24 ===== Main-chain covalent forces:- Main-chain bond lengths -.18 Main-chain bond angles .32 ------ .11 ===== OVERALL AVERAGE -.12 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.