Residue-by-residue listing for refined_6 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 - - - -58.5 - - - - - - - 178.7 - 35.2 - 2 ALA 2 b - - - - - - - - - - 178.0 - 32.3 - 3 ASP 3 XX - 176.6 - - - - - - - - 179.8 -1.3 31.2 - **** **** 4 THR 4 A - - -55.1 - - - - - - - 181.3 - 35.0 - 5 GLY 5 S - - - - - - - - - - - 179.9 - - - 6 GLU 6 B 63.9 - - - - - - - - - 175.9 - 34.5 - 7 VAL 7 E B - - -68.1 - - - - - - - 182.4 -3.0 32.2 - * * 8 GLN 8 E B - - -57.6 - - - - - - - 174.5 - 35.8 - 9 PHE 9 E B 61.9 - - - - - - - - - 183.6 -1.9 32.4 - 10 MET 10 E B 63.6 - - - - - - - - - 178.7 - 33.7 - 11 LYS 11 E B - - -68.9 183.7 - - - - - - 168.6 -2.1 34.5 - +* +* 12 PRO 12 E - - - - - -84.9 - - - - - 183.9 - 39.0 - +* * +* 13 PHE 13 e B 69.1 - - - - - - - - - 176.8 -.7 33.6 - +* +* 14 ILE 14 h B - - -64.8 176.0 - - - - - - 186.0 - 35.8 - * * 15 SER 15 H A - 185.1 - - - -53.7 -34.2 - - - 182.6 -.8 34.2 - +* +* 16 GLU 16 H A - 183.2 - 178.8 - -60.5 -39.9 - - - 182.8 - 34.6 - 17 LYS 17 H A 65.5 - - 186.0 - -104.8 -26.9 - - - 180.9 -1.2 33.2 - *** * * *** 18 SER 18 H A - - -63.9 - - -92.6 14.4 - - - 166.1 -3.5 31.0 - ** *4.8* ** +* *4.8* Residue-by-residue listing for refined_6 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 ----------------------------------------------------------------------------------------------------------------------------------- 19 SER 19 h A - - -67.9 - - - - - - - 181.9 -.6 32.6 - +* +* 20 LYS 20 T a 60.8 - - 180.3 - - - - - - 187.2 -1.0 33.6 - * * * 21 SER 21 t B - - -59.3 - - - - - - - 182.2 -1.4 36.7 - 22 LEU 22 E B - 181.6 - - - - - - - - 176.8 -2.5 35.6 - 23 GLU 23 E B - - -61.1 185.5 - - - - - - 177.8 - 34.5 - 24 ILE 24 E B - - -68.7 - - - - - - - 181.9 -2.6 33.0 - 25 PRO 25 h - - - - - -47.5 - - - - - 178.3 - 39.1 - +* * +* 26 LEU 26 H A - 184.6 - 169.8 - -62.6 -41.1 - - - 179.1 - 34.5 - 27 GLY 27 H - - - - - - -62.1 -36.1 - - - 179.1 - - - 28 PHE 28 H A - 184.9 - - - -73.8 -34.2 - - - 176.3 - 33.6 - 29 ASN 29 H A - 177.3 - - - -63.5 -46.5 - - - 180.9 -2.0 35.2 - 30 GLU 30 h A - 183.7 - 176.7 - - - - - - 179.6 -2.8 33.9 - * * 31 TYR 31 T A - 178.4 - - - - - - - - 180.4 - 34.0 - 32 PHE 32 t B 65.8 - - - - - - - - - 172.9 -1.1 33.1 - * * * 33 PRO 33 - - - - - -76.7 - - - - - 185.1 - 38.4 - * * * 34 ALA 34 B - - - - - - - - - - 167.9 - 34.6 - ** ** 35 PRO 35 - - - - - -61.7 - - - - - 184.9 - 39.3 - +* +* 36 PHE 36 B 59.2 - - - - - - - - - 178.0 - 32.7 - 37 PRO 37 - - - - - -71.2 - - - - - 177.6 - 38.9 - * * 38 ILE 38 S A - - -58.0 - - - - - - - 177.1 - 33.2 - 39 THR 39 B 49.3 - - - - - - - - - 173.5 - 34.7 - * * 40 VAL 40 E B - - -64.2 - - - - - - - 184.3 -3.1 33.1 - * * 41 ASP 41 E B - 187.5 - - - - - - - - 181.9 -2.9 33.1 - * * 42 LEU 42 E B - - -56.4 180.9 - - - - - - 182.9 -3.2 36.2 - +* +* 43 LEU 43 E B - - -67.7 - - - - - - - 173.7 -3.2 33.7 - * +* +* 44 ASP 44 e B - 159.3 - - - - - - - - 183.4 -2.5 34.4 - * * 45 TYR 45 S A 48.6 - - - - - - - - - 175.6 - 31.8 - 46 SER 46 S A - 185.0 - - - - - - - - 176.4 - 33.2 - 47 GLY 47 S - - - - - - - - - - - 181.0 - - - 48 ARG 48 e B - - -57.5 - - - - - - - 178.0 - 33.1 - 49 SER 49 E B 57.8 - - - - - - - - - 180.8 - 33.7 - 50 TRP 50 E B - - -60.4 - - - - - - - 177.9 -2.6 34.8 - 51 THR 51 E B - - -53.6 - - - - - - - 187.1 - 33.8 - * * 52 VAL 52 E B - - -57.1 - - - - - - - 177.9 -2.9 34.9 - * * 53 ARG 53 e B - - -64.0 186.0 - - - - - - 180.7 -3.0 32.3 - * * 54 MET 54 E B - 184.1 - 190.2 - - - - - - 181.1 -.6 36.1 - +* +* 55 LYS 55 E B 53.7 - - - - - - - - - 177.3 -2.7 31.9 - Residue-by-residue listing for refined_6 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 - - -59.6 196.9 - - - - - - 178.1 - 34.5 - * * 57 ARG 57 E B 57.1 - - 169.3 - - - - - - 175.3 -3.3 31.9 - +* +* 58 GLY 58 T - - - - - - - - - - - 184.2 - - - 59 GLU 59 T A - - -60.3 171.7 - - - - - - 189.9 -.9 37.1 - +* +* +* 60 LYS 60 E B - - -62.1 176.6 - - - - - - 170.1 -2.1 37.0 - +* +* 61 VAL 61 E B - 177.9 - - - - - - - - 184.2 -.8 33.9 - +* +* 62 PHE 62 E B - 190.8 - - - - - - - - 178.6 -3.4 34.9 - +* +* 63 LEU 63 E B - 190.3 - 178.6 - - - - - - 185.5 -2.7 35.7 - 64 THR 64 e a 54.3 - - - - - - - - - 183.2 -2.0 33.3 - 65 VAL 65 S B - - -62.9 - - - - - - - 177.2 - 31.3 - 66 GLY 66 h - - - - - - - - - - - 178.7 - - - 67 TRP 67 H A - 174.1 - - - -58.7 -26.2 - - - 182.8 - 35.2 - * * 68 GLU 68 H A 60.5 - - 187.7 - -72.4 -26.2 - - - 177.4 -.7 32.2 - * +* +* 69 ASN 69 H A - - -59.4 - - -72.0 -37.9 - - - 182.3 -1.5 34.9 - 70 PHE 70 H A - 170.0 - - - -72.8 -51.3 - - - 185.1 -1.3 35.0 - * * * 71 VAL 71 H A 71.9 - - - - -62.7 -44.6 - - - 178.7 -3.3 33.0 - +* +* 72 LYS 72 H A - - -58.1 - - -73.4 -43.8 - - - 185.3 -1.7 30.3 - * * 73 ASP 73 H A - 180.4 - - - -69.1 -40.0 - - - 177.3 -2.3 31.8 - 74 ASN 74 h A - 181.1 - - - - - - - - 176.5 -2.4 33.0 - 75 ASN 75 T l - 185.6 - - - - - - - - 178.7 - 31.8 - 76 LEU 76 t B - - -55.6 - - - - - - - 180.8 -2.1 33.9 - 77 GLU 77 t B - 181.7 - 180.4 - - - - - - 176.3 - 35.3 - 78 ASP 78 T B - 176.6 - - - - - - - - 183.3 - 34.8 - 79 GLY 79 T - - - - - - - - - - - 176.0 - - - 80 LYS 80 e B - - -79.0 - - - - - - - 183.8 -2.2 32.8 - 81 TYR 81 E B - - -61.2 - - - - - - - 182.1 -.8 34.3 - +* +* 82 LEU 82 E B - - -68.9 - - - - - - - 178.9 -1.5 32.7 - 83 GLN 83 E B - 187.7 - - - - - - - - 187.0 -3.1 34.9 - * * * 84 PHE 84 E B - - -51.9 - - - - - - - 178.8 -3.6 36.0 - ** ** 85 ILE 85 E B - - -56.4 177.3 - - - - - - 174.8 -3.1 35.0 - * * 86 TYR 86 E B - 169.8 - - - - - - - - 179.7 -3.3 35.7 - +* +* 87 ASP 87 e a - 186.8 - - - - - - - - 173.7 -.9 33.2 - * +* +* 88 ARG 88 S ~a - 187.9 - - - - - - - - 182.1 - 33.4 - ** ** 89 ASP 89 S b - 181.5 - - - - - - - - 180.3 - 36.0 - 90 ARG 90 e a - - -70.2 - - - - - - - 179.8 - 33.6 - 91 THR 91 E B 47.2 - - - - - - - - - 178.2 - 33.7 - * * 92 PHE 92 E B - - -65.1 - - - - - - - 177.3 -2.6 34.9 - Residue-by-residue listing for refined_6 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 ----------------------------------------------------------------------------------------------------------------------------------- 93 TYR 93 E B - - -52.4 - - - - - - - 185.5 -2.9 34.6 - * * 94 VAL 94 E B - 186.0 - - - - - - - - 176.2 -1.7 34.5 - 95 ILE 95 E B - - -58.0 - - - - - - - 181.3 -3.5 34.8 - +* +* 96 ILE 96 E B - - -55.8 - - - - - - - 175.2 -.6 35.3 - +* +* 97 TYR 97 E B - - -64.4 - - - - - - - 184.7 -3.3 32.8 - +* +* 98 GLY 98 S - - - - - - - - - - - 174.7 -.8 - - +* +* 99 HIS 99 XX - 176.8 - - - - - - - - 175.1 - 32.2 - **** **** 100 ASN 100 B - 182.1 - - - - - - - - 183.2 - 34.0 - 101 MET 101 B - 189.1 - - - - - - - - 180.1 - 33.8 - 102 CYS 102 - - 182.9 - - - - - - - - - -.7 34.4 - +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * * +* *** *4.8* ** ** +* *4.8* ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.4 181.5 -61.4 180.7 -68.4 -70.3 -34.3 - - - 179.6 -2.1 34.2 Standard deviations: 7.1 6.6 5.8 7.1 14.4 13.3 15.4 - - - 4.2 1.0 1.8 Numbers of values: 17 33 38 19 5 15 15 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_6 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 - 1.233 1.504 1.535 1.461 - 117.37 120.18 109.05 109.02 110.84 122.45 * * 2 ALA 2 1.311 1.236 1.512 1.524 1.437 120.38 115.20 120.70 111.52 110.21 112.05 123.97 * * * * 3 ASP 3 1.336 1.231 1.548 1.544 1.473 123.78 116.14 121.41 112.54 113.28 111.20 122.41 * * * * 4 THR 4 1.322 1.233 1.545 1.554 1.454 122.53 115.64 121.53 110.27 109.89 109.74 122.80 * * 5 GLY 5 1.309 1.239 1.481 - 1.437 121.93 113.65 121.76 - 110.07 - 124.59 * +* * +* 6 GLU 6 1.291 1.248 1.522 1.560 1.436 124.26 116.30 120.51 109.60 109.07 111.66 123.19 +** +* * * +** 7 VAL 7 1.306 1.235 1.513 1.560 1.445 122.56 115.86 121.09 110.37 109.72 113.93 123.03 +* * +* 8 GLN 8 1.297 1.237 1.509 1.545 1.406 122.35 116.83 120.31 108.35 109.23 111.01 122.85 ** +** +** 9 PHE 9 1.297 1.219 1.507 1.558 1.444 121.71 117.27 120.12 112.15 108.62 112.31 122.61 ** * * * ** 10 MET 10 1.299 1.239 1.508 1.556 1.444 120.90 116.12 120.66 110.64 110.59 111.28 123.20 ** * ** 11 LYS 11 1.314 1.235 1.512 1.548 1.452 122.48 117.47 120.55 107.43 111.12 112.90 121.93 * * * * Residue-by-residue listing for refined_6 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 ----------------------------------------------------------------------------------------------------------------------------------- 12 PRO 12 1.336 1.235 1.535 1.541 1.441 121.99 117.09 120.53 110.20 108.10 104.15 122.37 +* * * +* 13 PHE 13 1.295 1.242 1.520 1.542 1.453 121.53 116.73 120.48 110.29 110.64 111.40 122.77 ** ** 14 ILE 14 1.312 1.230 1.501 1.554 1.422 121.36 116.49 119.87 109.83 105.46 110.51 123.63 * * +* ** ** 15 SER 15 1.325 1.213 1.528 1.538 1.456 122.80 115.81 120.86 110.35 111.09 110.27 123.20 16 GLU 16 1.311 1.230 1.525 1.526 1.444 123.12 117.39 120.39 110.16 111.67 109.68 122.20 * * 17 LYS 17 1.320 1.225 1.510 1.531 1.446 118.99 116.05 121.22 111.38 110.80 110.87 122.72 +* +* 18 SER 18 1.299 1.209 1.523 1.518 1.424 121.48 117.38 120.59 113.14 113.24 111.00 122.03 ** * +* +* ** 19 SER 19 1.322 1.220 1.537 1.538 1.459 118.86 116.46 120.60 110.14 109.91 112.99 122.94 +* * +* 20 LYS 20 1.340 1.227 1.551 1.550 1.457 121.44 117.11 120.19 110.36 112.93 110.49 122.69 * * 21 SER 21 1.332 1.240 1.555 1.527 1.462 122.97 117.41 120.04 109.36 110.38 107.46 122.53 * +* +* 22 LEU 22 1.331 1.244 1.543 1.541 1.475 122.33 116.88 120.30 108.83 110.75 109.67 122.82 23 GLU 23 1.337 1.243 1.526 1.533 1.462 121.70 116.10 120.63 108.01 110.68 112.15 123.26 * * 24 ILE 24 1.308 1.237 1.548 1.581 1.454 123.26 117.88 119.80 111.01 109.11 112.29 122.20 * * +* +* 25 PRO 25 1.367 1.241 1.541 1.528 1.487 123.90 115.46 121.15 109.40 114.79 102.98 123.37 +* * * +* 26 LEU 26 1.329 1.232 1.527 1.569 1.459 123.57 115.90 120.87 112.00 109.17 109.09 123.22 +* * +* 27 GLY 27 1.327 1.226 1.511 - 1.447 121.53 116.00 120.75 - 111.57 - 123.23 28 PHE 28 1.322 1.217 1.532 1.539 1.450 122.02 116.33 120.87 111.78 109.64 110.25 122.77 29 ASN 29 1.324 1.236 1.525 1.537 1.472 121.98 115.07 121.84 108.89 110.01 110.44 123.07 30 GLU 30 1.309 1.242 1.549 1.534 1.445 123.16 115.88 121.47 112.12 110.86 108.87 122.65 * * * * 31 TYR 31 1.321 1.238 1.536 1.544 1.446 122.31 117.61 120.39 110.70 111.40 110.18 121.99 32 PHE 32 1.321 1.234 1.533 1.566 1.455 120.00 118.31 120.73 110.66 111.86 111.51 120.93 +* * * +* 33 PRO 33 1.339 1.243 1.500 1.518 1.440 121.77 115.70 121.25 109.77 108.88 105.18 123.04 * +* * +* +* 34 ALA 34 1.272 1.244 1.492 1.529 1.424 121.12 118.05 119.57 110.00 110.93 110.36 122.37 **** +* +* **** 35 PRO 35 1.334 1.249 1.520 1.538 1.446 121.40 117.96 119.38 110.21 106.54 103.78 122.65 * ** ** 36 PHE 36 1.310 1.240 1.528 1.542 1.410 120.62 117.31 120.88 112.48 111.15 110.54 121.72 * +** * +** 37 PRO 37 1.336 1.233 1.507 1.542 1.443 121.95 116.75 120.69 109.90 110.04 104.45 122.55 +* * +* 38 ILE 38 1.294 1.222 1.506 1.549 1.426 119.99 116.13 120.63 111.05 107.86 112.47 123.18 ** +* * ** 39 THR 39 1.302 1.237 1.522 1.547 1.428 121.80 115.31 120.98 109.47 110.72 110.91 123.68 +* +* +* 40 VAL 40 1.296 1.231 1.513 1.577 1.436 124.41 118.37 119.55 110.65 106.07 113.86 122.07 ** * * +* * +* * ** 41 ASP 41 1.283 1.239 1.515 1.545 1.445 119.51 115.94 120.91 112.75 110.08 109.92 123.13 *** * * *** Residue-by-residue listing for refined_6 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 1.300 1.230 1.493 1.541 1.437 122.49 116.32 120.43 108.23 107.62 110.85 123.25 ** +* * * ** 43 LEU 43 1.293 1.247 1.493 1.551 1.430 121.03 113.68 121.76 108.85 111.84 112.71 124.56 +** +* * * * * +** 44 ASP 44 1.285 1.237 1.508 1.526 1.431 124.27 114.82 121.21 110.46 109.52 110.45 123.97 *** * * *** 45 TYR 45 1.304 1.229 1.529 1.539 1.450 124.03 117.68 120.13 112.34 114.04 110.54 122.19 +* * * * +* 46 SER 46 1.312 1.231 1.535 1.537 1.433 120.18 116.57 120.77 112.04 108.55 111.01 122.64 * * * * 47 GLY 47 1.330 1.227 1.521 - 1.452 120.09 117.58 120.27 - 114.13 - 122.15 48 ARG 48 1.313 1.228 1.525 1.531 1.466 121.17 117.00 120.58 111.13 110.76 110.98 122.32 * * 49 SER 49 1.303 1.233 1.515 1.526 1.437 120.98 116.57 120.50 111.32 110.13 110.46 122.91 +* * +* 50 TRP 50 1.300 1.223 1.509 1.536 1.457 121.74 116.74 120.50 109.01 110.47 110.98 122.76 ** ** 51 THR 51 1.299 1.243 1.533 1.533 1.428 121.18 115.38 121.35 111.57 108.50 110.62 123.25 ** +* * ** 52 VAL 52 1.306 1.232 1.533 1.556 1.442 123.34 117.04 120.61 109.38 110.69 110.60 122.33 +* +* 53 ARG 53 1.307 1.234 1.522 1.526 1.447 120.76 115.56 121.26 111.28 111.54 111.71 123.18 +* +* 54 MET 54 1.315 1.226 1.515 1.528 1.449 122.83 117.49 119.90 108.38 108.68 110.06 122.60 55 LYS 55 1.313 1.232 1.522 1.546 1.433 121.42 117.10 120.23 112.47 111.94 111.24 122.66 * * * * 56 LYS 56 1.320 1.240 1.503 1.513 1.433 120.59 115.92 120.54 106.97 109.18 113.63 123.53 * * +* +* +* 57 ARG 57 1.293 1.244 1.522 1.543 1.433 122.18 115.25 121.44 110.90 110.97 113.12 123.25 +** * +* +** 58 GLY 58 1.301 1.232 1.501 - 1.431 121.96 115.39 121.15 - 114.57 - 123.46 +* * +* 59 GLU 59 1.297 1.236 1.508 1.516 1.440 122.66 116.47 120.85 107.92 111.08 108.51 122.67 ** * * ** 60 LYS 60 1.307 1.231 1.510 1.526 1.439 120.59 115.08 121.51 107.62 112.64 108.65 123.41 +* * * * +* 61 VAL 61 1.305 1.237 1.510 1.559 1.431 122.13 117.48 120.20 110.28 105.49 112.93 122.28 +* * ** ** 62 PHE 62 1.281 1.241 1.505 1.532 1.415 119.88 115.49 120.87 111.86 109.10 108.73 123.62 *** ** * * *** 63 LEU 63 1.290 1.227 1.510 1.546 1.426 122.49 116.89 119.84 111.80 105.36 108.52 123.27 +** +* ** * +** 64 THR 64 1.301 1.229 1.548 1.560 1.433 121.25 114.83 121.76 110.63 113.23 110.79 123.41 ** * * ** 65 VAL 65 1.289 1.240 1.519 1.553 1.451 124.98 115.88 121.00 111.09 113.20 112.83 123.09 +** +* +** 66 GLY 66 1.318 1.228 1.477 - 1.436 120.62 115.35 120.96 - 112.55 - 123.69 ** ** 67 TRP 67 1.316 1.229 1.510 1.528 1.453 122.86 114.83 121.66 110.36 109.89 109.25 123.40 68 GLU 68 1.299 1.226 1.537 1.527 1.436 121.57 115.96 121.40 112.96 110.56 110.67 122.60 ** * +* ** 69 ASN 69 1.325 1.200 1.501 1.556 1.458 122.25 114.64 121.62 108.67 108.15 112.13 123.67 +* * * * +* 70 PHE 70 1.297 1.244 1.507 1.543 1.436 124.22 115.43 120.76 110.32 111.09 109.46 123.80 ** * * ** Residue-by-residue listing for refined_6 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 ----------------------------------------------------------------------------------------------------------------------------------- 71 VAL 71 1.323 1.228 1.514 1.579 1.439 121.74 115.46 121.11 111.27 109.68 112.08 123.43 * * 72 LYS 72 1.312 1.226 1.527 1.527 1.435 121.74 118.14 119.62 112.21 113.69 112.67 122.23 * * * * * 73 ASP 73 1.347 1.231 1.521 1.530 1.489 119.53 117.27 120.40 110.55 112.88 112.48 122.31 * +* * * +* 74 ASN 74 1.319 1.229 1.535 1.548 1.465 120.36 114.43 121.82 112.44 108.73 110.75 123.73 * * 75 ASN 75 1.330 1.244 1.521 1.549 1.467 125.16 115.75 121.52 112.03 112.17 111.65 122.62 +* * +* 76 LEU 76 1.316 1.241 1.513 1.544 1.433 121.53 115.82 120.76 109.38 109.36 112.54 123.42 * * * 77 GLU 77 1.306 1.242 1.513 1.531 1.443 122.65 115.64 120.30 110.71 109.11 109.00 124.05 +* +* 78 ASP 78 1.311 1.234 1.516 1.537 1.476 123.17 116.36 120.40 109.35 109.40 110.79 123.22 * * 79 GLY 79 1.302 1.223 1.500 - 1.440 120.89 115.67 121.17 - 110.27 - 123.15 +* +* 80 LYS 80 1.319 1.243 1.522 1.551 1.453 121.91 116.36 120.61 111.23 109.92 112.01 123.03 * * 81 TYR 81 1.311 1.233 1.491 1.533 1.438 121.55 116.62 120.26 110.43 108.88 110.93 123.08 * +* * +* 82 LEU 82 1.298 1.240 1.504 1.546 1.431 121.10 114.94 121.15 110.67 111.21 112.33 123.90 ** * * * ** 83 GLN 83 1.297 1.232 1.530 1.556 1.427 123.23 116.33 120.68 113.94 106.04 107.52 122.97 ** * +* ** +* +* ** 84 PHE 84 1.304 1.241 1.515 1.534 1.446 122.35 116.28 120.51 108.85 110.32 109.50 123.21 +* +* 85 ILE 85 1.308 1.237 1.523 1.554 1.439 121.69 116.03 120.77 108.46 109.95 111.72 123.20 * * 86 TYR 86 1.300 1.224 1.500 1.552 1.440 122.50 117.18 119.88 110.12 107.32 109.80 122.94 ** * * * ** 87 ASP 87 1.315 1.232 1.519 1.543 1.455 119.74 115.70 120.66 111.80 108.34 111.29 123.58 * * * * 88 ARG 88 1.322 1.225 1.531 1.548 1.464 123.47 114.39 122.67 112.00 107.63 110.92 122.81 * * * 89 ASP 89 1.310 1.217 1.522 1.557 1.423 124.06 118.04 119.67 111.70 105.56 108.22 122.25 * * +* * ** * ** 90 ARG 90 1.276 1.230 1.518 1.559 1.461 121.98 115.37 121.64 110.27 109.09 112.09 122.97 +*** * +*** 91 THR 91 1.304 1.241 1.520 1.534 1.420 122.57 115.69 120.95 110.78 111.10 110.74 123.33 +* ** ** 92 PHE 92 1.309 1.236 1.499 1.534 1.441 122.31 116.37 120.63 108.77 109.36 111.59 123.00 * * * 93 TYR 93 1.292 1.230 1.504 1.531 1.433 121.44 116.54 120.63 111.06 106.53 110.57 122.79 +** * * +* +** 94 VAL 94 1.294 1.235 1.514 1.552 1.436 120.43 115.93 120.90 109.34 110.69 111.38 123.15 ** * ** 95 ILE 95 1.302 1.230 1.520 1.561 1.434 122.05 116.29 120.75 109.62 107.78 111.57 122.94 +* * * +* 96 ILE 96 1.302 1.230 1.504 1.582 1.444 121.82 116.89 120.01 107.37 108.27 113.09 123.10 +* * +* * +* 97 TYR 97 1.304 1.236 1.505 1.527 1.434 120.81 114.44 121.27 111.67 108.62 111.84 124.26 +* * +* Residue-by-residue listing for refined_6 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 1.299 1.224 1.495 - 1.424 122.91 115.77 120.07 - 108.26 - 124.14 ** * +* * * ** 99 HIS 99 1.333 1.229 1.525 1.545 1.477 124.21 115.78 121.61 110.93 113.73 111.36 122.61 * * * 100 ASN 100 1.301 1.233 1.525 1.529 1.440 120.82 117.05 120.44 110.85 108.55 110.78 122.49 ** ** 101 MET 101 1.304 1.237 1.528 1.550 1.454 121.60 115.84 120.92 112.10 109.55 109.70 123.21 +* * * +* 102 CYS 102 1.312 - 1.521 1.539 1.440 122.50 - - 110.83 108.67 110.40 - * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** +* ** +* +** +* * * ** ** +* * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_6 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 1.272 1.347 1.309 .014 **** * * C-N (Pro) 1.341 .016 5 1.334 1.367 1.342 .012 +* C-O C-O 1.231 .020 101 1.200 1.249 1.233 .008 +* CA-C CH1E-C (except Gly) 1.525 .021 95 1.491 1.555 1.520 .014 +* * CH2G*-C (Gly) 1.516 .018 7 1.477 1.521 1.498 .015 ** CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.524 1.529 1.526 .002 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.533 1.582 1.558 .014 +* CH1E-CH2E (the rest) 1.530 .020 75 1.513 1.569 1.539 .012 +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.406 1.489 1.444 .015 +** +* NH1-CH2G* (Gly) 1.451 .016 7 1.424 1.452 1.438 .009 +* N-CH1E (Pro) 1.466 .015 5 1.440 1.487 1.451 .018 +* * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_6 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 89 113.68 118.37 116.28 .98 * * CH2G*-C-NH1 (Gly) 116.4 2.1 7 113.65 117.58 115.63 1.07 * CH1E-C-N (Pro) 116.9 1.5 5 115.46 117.96 116.59 .92 O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.93 124.59 122.99 .62 * O-C-N (Pro) 122.0 1.4 5 122.37 123.37 122.80 .36 C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.86 125.16 121.96 1.33 +* +* C-NH1-CH2G* (Gly) 120.6 1.7 7 120.09 122.91 121.42 .88 * C-N-CH1E (Pro) 122.6 5.0 5 121.40 123.90 122.20 .88 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 119.38 122.67 120.73 .60 * CH2G*-C-O (Gly) 120.8 2.1 7 120.07 121.76 120.88 .53 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.00 111.52 110.76 .76 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 107.37 111.57 110.14 1.04 * CH2E-CH1E-C (the rest) 110.1 1.9 75 106.97 113.94 110.55 1.50 +* ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 105.36 114.04 109.93 1.93 ** * NH1-CH2G*-C (Gly) 112.5 2.9 7 108.26 114.57 111.63 2.12 * N-CH1E-C (Pro) 111.8 2.5 5 106.54 114.79 109.67 2.80 ** * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 110.36 112.05 111.21 .84 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 109.74 113.93 111.78 1.19 * * N-CH1E-CH2E (Pro) 103.0 1.1 5 102.98 105.18 104.11 .73 +* * NH1-CH1E-CH2E (the rest) 110.5 1.7 70 107.46 113.63 110.75 1.33 +* +* ------------------------------------------------------------------------------------------------------------- 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_6 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] 78 88.6% Residues in additional allowed regions [a,b,l,p] 7 8.0% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.1% Residues in disallowed regions [XX] 2 2.3% ---- ------ 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 88.6 83.8 10.0 .5 Inside b. Omega angle st dev 101 4.2 6.0 3.0 -.6 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 1.8 3.1 1.6 -.8 Inside e. H-bond energy st dev 57 1.0 .8 .2 .8 Inside f. Overall G-factor 102 -.1 -.4 .3 1.0 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 17 7.1 18.1 6.5 -1.7 BETTER b. Chi-1 trans st dev 33 6.6 19.0 5.3 -2.3 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 7.7 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 19 7.1 20.4 5.0 -2.7 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 88.6 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 7.9 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .98 3 Residue-by-residue listing for refined_6 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.61 Chi1-chi2 distribution -.38 Chi1 only -.20 Chi3 & chi4 .60 Omega -.17 ------ -.26 ===== Main-chain covalent forces:- Main-chain bond lengths -.09 Main-chain bond angles .40 ------ .19 ===== OVERALL AVERAGE -.10 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.