
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   39 (  156),  selected   39 , name T0339TS474_1-D1
# Molecule2: number of CA atoms  136 ( 1077),  selected  136 , name T0339_D1.pdb
# PARAMETERS: T0339TS474_1-D1.T0339_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    K       3      E       1           -
LGA    V       4      R       2           -
LGA    Y       5      K       3           -
LGA    M       6      V       4           -
LGA    D       7      Y       5           -
LGA    Y       8      M       6           -
LGA    -       -      D       7           -
LGA    -       -      Y       8           -
LGA    E     289      E     289          5.111
LGA    A     290      A     290          0.649
LGA    Y     291      Y     291          3.739
LGA    E     292      E     292          2.549
LGA    A     293      A     293          4.429
LGA    H     294      H     294          2.661
LGA    M     295      M     295          2.491
LGA    R     296      R     296          2.302
LGA    D     297      D     297          2.050
LGA    V     298      V     298          1.920
LGA    R     299      R     299          1.750
LGA    D     300      D     300          1.351
LGA    Y     301      Y     301          0.857
LGA    L     302      L     302          1.086
LGA    E     303      E     303          0.821
LGA    E     304      E     304          0.391
LGA    R     305      R     305          0.393
LGA    L     306      L     306          0.715
LGA    E     307      E     307          0.724
LGA    A     308      A     308          1.147
LGA    E     309      E     309          1.817
LGA    F     310      F     310          1.463
LGA    G     311      G     311           #
LGA    -       -      Q     312           -
LGA    -       -      K     313           -
LGA    -       -      R     314           -
LGA    Q     312      I     315          1.023
LGA    K     313      H     316          3.116
LGA    R     314      L     317          2.396
LGA    -       -      N     318           -
LGA    I     315      S     319          1.944
LGA    H     316      Q     320          1.361
LGA    L     317      F     321          5.178
LGA    -       -      P     322           -
LGA    N     318      G     323          3.577
LGA    S     319      T     324          1.553
LGA    Q     320      Q     325          3.791
LGA    F     321      R     326          1.131
LGA    -       -      L     327           -
LGA    -       -      P     328           -
LGA    -       -      N     329           -
LGA    -       -      T     330           -
LGA    -       -      C     331           -
LGA    -       -      N     332           -
LGA    -       -      F     333           -
LGA    -       -      S     334           -
LGA    -       -      I     335           -
LGA    -       -      R     336           -
LGA    -       -      G     337           -
LGA    -       -      P     338           -
LGA    -       -      R     339           -
LGA    -       -      L     340           -
LGA    -       -      Q     341           -
LGA    -       -      G     342           -
LGA    -       -      H     343           -
LGA    -       -      V     344           -
LGA    -       -      V     345           -
LGA    -       -      L     346           -
LGA    -       -      A     347           -
LGA    -       -      Q     348           -
LGA    -       -      C     349           -
LGA    -       -      R     350           -
LGA    -       -      V     351           -
LGA    -       -      L     352           -
LGA    -       -      M     353           -
LGA    -       -      A     354           -
LGA    -       -      S     355           -
LGA    -       -      V     356           -
LGA    -       -      G     357           -
LGA    -       -      A     358           -
LGA    -       -      A     359           -
LGA    -       -      C     360           -
LGA    -       -      H     361           -
LGA    -       -      S     362           -
LGA    -       -      D     363           -
LGA    -       -      H     364           -
LGA    -       -      G     365           -
LGA    -       -      D     366           -
LGA    -       -      Q     367           -
LGA    -       -      P     368           -
LGA    -       -      S     369           -
LGA    -       -      P     370           -
LGA    -       -      V     371           -
LGA    -       -      L     372           -
LGA    -       -      L     373           -
LGA    -       -      S     374           -
LGA    -       -      Y     375           -
LGA    -       -      G     376           -
LGA    -       -      V     377           -
LGA    -       -      P     378           -
LGA    -       -      F     379           -
LGA    -       -      D     380           -
LGA    -       -      V     381           -
LGA    -       -      A     382           -
LGA    -       -      R     383           -
LGA    -       -      N     384           -
LGA    -       -      A     385           -
LGA    -       -      L     386           -
LGA    -       -      R     387           -
LGA    -       -      L     388           -
LGA    -       -      S     389           -
LGA    -       -      V     390           -
LGA    -       -      G     391           -
LGA    -       -      R     392           -
LGA    -       -      S     393           -
LGA    -       -      T     394           -
LGA    -       -      T     395           -
LGA    -       -      R     396           -
LGA    -       -      A     397           -
LGA    -       -      E     398           -
LGA    -       -      V     399           -
LGA    -       -      D     400           -
LGA    -       -      L     401           -
LGA    -       -      V     402           -
LGA    -       -      V     403           -
LGA    -       -      Q     404           -
LGA    -       -      D     405           -
LGA    -       -      L     406           -
LGA    -       -      K     407           -
LGA    -       -      Q     408           -
LGA    -       -      A     409           -
LGA    -       -      V     410           -
LGA    -       -      A     411           -
LGA    -       -      Q     412           -
LGA    -       -      L     413           -
LGA    -       -      E     414           -
LGA    -       -      D     415           -
LGA    -       -      Q     416           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39  136    5.0     32    2.43    71.88     18.797     1.266

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.629450 * X  +   0.450781 * Y  +   0.632921 * Z  + -119.961273
  Y_new =   0.273917 * X  +  -0.890964 * Y  +   0.362150 * Z  +  62.277458
  Z_new =   0.727161 * X  +  -0.054587 * Y  +  -0.684294 * Z  +  24.935951 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.061989    0.079603  [ DEG:  -175.4391      4.5609 ]
  Theta =  -0.814176   -2.327416  [ DEG:   -46.6489   -133.3511 ]
  Phi   =   0.410453   -2.731140  [ DEG:    23.5172   -156.4828 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0339TS474_1-D1                               
REMARK     2: T0339_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0339TS474_1-D1.T0339_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39  136   5.0   32   2.43   71.88  18.797
REMARK  ---------------------------------------------------------- 
MOLECULE T0339TS474_1-D1
PFRMAT TS
TARGET T0339
MODEL 1
PARENT N/A
ATOM      1  N   LYS     3     -80.566  -3.615   0.997  1.00 46.37
ATOM      2  CA  LYS     3     -79.584  -3.866   2.050  1.00 42.89
ATOM      3  C   LYS     3     -78.217  -3.405   1.546  1.00 40.67
ATOM      4  O   LYS     3     -77.712  -3.907   0.537  1.00 42.94
ATOM      5  N   VAL     4     -77.622  -2.444   2.238  1.00 35.15
ATOM      6  CA  VAL     4     -76.334  -1.922   1.823  1.00 30.37
ATOM      7  C   VAL     4     -75.276  -2.149   2.893  1.00 29.19
ATOM      8  O   VAL     4     -75.258  -1.472   3.920  1.00 27.90
ATOM      9  N   TYR     5     -74.392  -3.107   2.650  1.00 27.67
ATOM     10  CA  TYR     5     -73.350  -3.412   3.613  1.00 26.94
ATOM     11  C   TYR     5     -72.059  -2.647   3.320  1.00 27.77
ATOM     12  O   TYR     5     -71.320  -3.003   2.397  1.00 28.43
ATOM     13  N   MET     6     -71.799  -1.605   4.115  1.00 26.85
ATOM     14  CA  MET     6     -70.602  -0.771   3.966  1.00 25.68
ATOM     15  C   MET     6     -69.675  -0.863   5.187  1.00 26.88
ATOM     16  O   MET     6     -69.073   0.134   5.589  1.00 26.98
ATOM     17  N   ASP     7     -69.540  -2.061   5.754  1.00 26.53
ATOM     18  CA  ASP     7     -68.716  -2.255   6.946  1.00 25.72
ATOM     19  C   ASP     7     -67.766  -3.441   6.786  1.00 26.01
ATOM     20  O   ASP     7     -67.612  -4.249   7.706  1.00 24.77
ATOM     21  N   TYR     8     -67.111  -3.531   5.634  1.00 25.94
ATOM     22  CA  TYR     8     -66.203  -4.638   5.366  1.00 25.87
ATOM     23  C   TYR     8     -64.843  -4.625   6.062  1.00 27.51
ATOM     24  O   TYR     8     -64.072  -5.569   5.916  1.00 28.42
ATOM   1145  N   GLU   289       4.147 -24.795  15.131  1.00 30.21
ATOM   1146  CA  GLU   289       5.230 -24.157  14.383  1.00 31.01
ATOM   1147  C   GLU   289       5.383 -24.776  12.985  1.00 29.75
ATOM   1148  O   GLU   289       4.505 -25.502  12.536  1.00 30.35
ATOM   1149  N   ALA   290       6.491 -24.472  12.306  1.00 27.72
ATOM   1150  CA  ALA   290       6.713 -24.983  10.960  1.00 26.08
ATOM   1151  C   ALA   290       5.618 -24.465  10.036  1.00 25.57
ATOM   1152  O   ALA   290       5.154 -25.177   9.147  1.00 23.37
ATOM   1153  N   TYR   291       5.182 -23.225  10.262  1.00 26.95
ATOM   1154  CA  TYR   291       4.120 -22.633   9.456  1.00 26.16
ATOM   1155  C   TYR   291       2.803 -23.366   9.646  1.00 24.97
ATOM   1156  O   TYR   291       2.128 -23.684   8.672  1.00 24.00
ATOM   1157  N   GLU   292       2.425 -23.620  10.900  1.00 22.71
ATOM   1158  CA  GLU   292       1.185 -24.322  11.175  1.00 23.26
ATOM   1159  C   GLU   292       1.272 -25.710  10.526  1.00 22.69
ATOM   1160  O   GLU   292       0.299 -26.180   9.944  1.00 21.92
ATOM   1161  N   ALA   293       2.439 -26.356  10.638  1.00 21.29
ATOM   1162  CA  ALA   293       2.603 -27.690  10.032  1.00 21.50
ATOM   1163  C   ALA   293       2.543 -27.628   8.514  1.00 21.55
ATOM   1164  O   ALA   293       1.899 -28.474   7.880  1.00 22.28
ATOM   1165  N   HIS   294       3.169 -26.613   7.919  1.00 22.44
ATOM   1166  CA  HIS   294       3.099 -26.452   6.481  1.00 23.37
ATOM   1167  C   HIS   294       1.646 -26.205   6.036  1.00 23.71
ATOM   1168  O   HIS   294       1.187 -26.783   5.037  1.00 22.99
ATOM   1169  N   MET   295       0.899 -25.366   6.761  1.00  9.99
ATOM   1170  CA  MET   295      -0.497 -25.735   6.576  1.00  9.99
ATOM   1171  C   MET   295      -0.832 -25.850   5.099  1.00  9.99
ATOM   1172  O   MET   295      -1.598 -26.722   4.699  1.00  9.99
ATOM   1173  N   ARG   296      -0.246 -24.982   4.284  1.00  9.99
ATOM   1174  CA  ARG   296      -0.500 -25.007   2.845  1.00  9.99
ATOM   1175  C   ARG   296      -0.029 -26.332   2.254  1.00  9.99
ATOM   1176  O   ARG   296      -0.683 -26.904   1.382  1.00  9.99
ATOM   1177  N   ASP   297       1.106 -26.817   2.743  1.00  9.99
ATOM   1178  CA  ASP   297       1.670 -28.074   2.274  1.00  9.99
ATOM   1179  C   ASP   297       0.712 -29.208   2.657  1.00  9.99
ATOM   1180  O   ASP   297       0.222 -29.945   1.795  1.00  9.99
ATOM   1181  N   VAL   298       0.440 -29.343   3.953  1.00  9.99
ATOM   1182  CA  VAL   298      -0.466 -30.374   4.419  1.00  9.99
ATOM   1183  C   VAL   298      -1.761 -30.348   3.619  1.00  9.99
ATOM   1184  O   VAL   298      -2.291 -31.398   3.262  1.00  9.99
ATOM   1185  N   ARG   299      -2.274 -29.155   3.326  1.00  9.99
ATOM   1186  CA  ARG   299      -3.516 -29.056   2.571  1.00  9.99
ATOM   1187  C   ARG   299      -3.387 -29.578   1.143  1.00  9.99
ATOM   1188  O   ARG   299      -4.302 -30.233   0.637  1.00  9.99
ATOM   1189  N   ASP   300      -2.264 -29.298   0.487  1.00  9.99
ATOM   1190  CA  ASP   300      -2.121 -29.762  -0.889  1.00  9.99
ATOM   1191  C   ASP   300      -2.118 -31.287  -0.909  1.00  9.99
ATOM   1192  O   ASP   300      -2.762 -31.905  -1.758  1.00  9.99
ATOM   1193  N   TYR   301      -1.414 -31.894   0.040  1.00  9.99
ATOM   1194  CA  TYR   301      -1.373 -33.348   0.108  1.00  9.99
ATOM   1195  C   TYR   301      -2.784 -33.908   0.298  1.00  9.99
ATOM   1196  O   TYR   301      -3.118 -34.976  -0.221  1.00  9.99
ATOM   1197  N   LEU   302      -3.611 -33.186   1.043  1.00  9.99
ATOM   1198  CA  LEU   302      -4.979 -33.609   1.271  1.00  9.99
ATOM   1199  C   LEU   302      -5.791 -33.505  -0.008  1.00  9.99
ATOM   1200  O   LEU   302      -6.455 -34.456  -0.405  1.00  9.99
ATOM   1201  N   GLU   303      -5.742 -32.337  -0.642  1.00  9.99
ATOM   1202  CA  GLU   303      -6.489 -32.111  -1.872  1.00  9.99
ATOM   1203  C   GLU   303      -6.129 -33.192  -2.873  1.00  9.99
ATOM   1204  O   GLU   303      -6.989 -33.768  -3.535  1.00  9.99
ATOM   1205  N   GLU   304      -4.835 -33.455  -2.967  1.00  9.99
ATOM   1206  CA  GLU   304      -4.320 -34.454  -3.878  1.00  9.99
ATOM   1207  C   GLU   304      -5.000 -35.794  -3.594  1.00  9.99
ATOM   1208  O   GLU   304      -5.722 -36.315  -4.441  1.00  9.99
ATOM   1209  N   ARG   305      -4.785 -36.328  -2.392  1.00  9.99
ATOM   1210  CA  ARG   305      -5.377 -37.600  -2.013  1.00  9.99
ATOM   1211  C   ARG   305      -6.896 -37.688  -2.057  1.00  9.99
ATOM   1212  O   ARG   305      -7.449 -38.731  -2.421  1.00  9.99
ATOM   1213  N   LEU   306      -7.583 -36.610  -1.693  1.00  9.99
ATOM   1214  CA  LEU   306      -9.037 -36.640  -1.695  1.00  9.99
ATOM   1215  C   LEU   306      -9.613 -36.690  -3.095  1.00  9.99
ATOM   1216  O   LEU   306     -10.629 -37.345  -3.327  1.00  9.99
ATOM   1217  N   GLU   307      -8.978 -35.998  -4.033  1.00  9.99
ATOM   1218  CA  GLU   307      -9.473 -36.016  -5.405  1.00  9.99
ATOM   1219  C   GLU   307      -9.245 -37.419  -5.961  1.00  9.99
ATOM   1220  O   GLU   307     -10.034 -37.916  -6.767  1.00  9.99
ATOM   1221  N   ALA   308      -8.172 -38.060  -5.504  1.00  9.99
ATOM   1222  CA  ALA   308      -7.847 -39.411  -5.935  1.00  9.99
ATOM   1223  C   ALA   308      -8.856 -40.406  -5.377  1.00  9.99
ATOM   1224  O   ALA   308      -8.739 -41.608  -5.603  1.00  9.99
ATOM   1225  N   GLU   309      -9.842 -39.905  -4.638  1.00  9.99
ATOM   1226  CA  GLU   309     -10.872 -40.763  -4.065  1.00  9.99
ATOM   1227  C   GLU   309     -12.240 -40.345  -4.573  1.00  9.99
ATOM   1228  O   GLU   309     -13.256 -40.899  -4.155  1.00  9.99
ATOM   1229  N   PHE   310     -12.261 -39.358  -5.465  1.00  9.99
ATOM   1230  CA  PHE   310     -13.512 -38.897  -6.039  1.00  9.99
ATOM   1231  C   PHE   310     -14.115 -37.659  -5.406  1.00  9.99
ATOM   1232  O   PHE   310     -15.222 -37.242  -5.765  1.00  9.99
ATOM   1233  N   GLY   311     -13.390 -37.051  -4.476  1.00  9.99
ATOM   1234  CA  GLY   311     -13.894 -35.872  -3.788  1.00  9.99
ATOM   1235  C   GLY   311     -14.055 -34.651  -4.681  1.00  9.99
ATOM   1236  O   GLY   311     -13.215 -34.398  -5.541  1.00  9.99
ATOM   1237  N   GLN   312     -15.144 -33.909  -4.487  1.00  9.99
ATOM   1238  CA  GLN   312     -15.351 -32.665  -5.223  1.00  9.99
ATOM   1239  C   GLN   312     -14.738 -31.624  -4.296  1.00  9.99
ATOM   1240  O   GLN   312     -14.987 -31.639  -3.091  1.00  9.99
ATOM   1241  N   LYS   313     -13.925 -30.734  -4.844  1.00  9.99
ATOM   1242  CA  LYS   313     -13.310 -29.698  -4.038  1.00  9.99
ATOM   1243  C   LYS   313     -14.150 -28.441  -4.197  1.00  9.99
ATOM   1244  O   LYS   313     -14.266 -27.898  -5.291  1.00  9.99
ATOM   1245  N   ARG   314     -14.738 -27.986  -3.100  1.00  9.99
ATOM   1246  CA  ARG   314     -15.582 -26.800  -3.114  1.00  9.99
ATOM   1247  C   ARG   314     -14.784 -25.519  -2.887  1.00  9.99
ATOM   1248  O   ARG   314     -15.080 -24.476  -3.473  1.00  9.99
ATOM   1249  N   ILE   315     -13.770 -25.604  -2.034  1.00  9.99
ATOM   1250  CA  ILE   315     -12.928 -24.459  -1.724  1.00  9.99
ATOM   1251  C   ILE   315     -12.134 -24.034  -2.943  1.00  9.99
ATOM   1252  O   ILE   315     -11.542 -24.872  -3.611  1.00  9.99
ATOM   1253  N   HIS   316     -12.135 -22.726  -3.267  1.00  9.99
ATOM   1254  CA  HIS   316     -11.385 -22.221  -4.420  1.00  9.99
ATOM   1255  C   HIS   316      -9.917 -22.103  -4.019  1.00  9.99
ATOM   1256  O   HIS   316      -9.502 -21.133  -3.384  1.00  9.99
ATOM   1257  N   LEU   317      -9.137 -23.104  -4.396  1.00  9.99
ATOM   1258  CA  LEU   317      -7.727 -23.147  -4.052  1.00  9.99
ATOM   1259  C   LEU   317      -6.917 -21.870  -4.289  1.00  9.99
ATOM   1260  O   LEU   317      -6.079 -21.509  -3.465  1.00  9.99
ATOM   1261  N   ASN   318      -7.178 -21.166  -5.383  1.00  9.99
ATOM   1262  CA  ASN   318      -6.404 -19.965  -5.687  1.00  9.99
ATOM   1263  C   ASN   318      -6.624 -18.752  -4.796  1.00  9.99
ATOM   1264  O   ASN   318      -5.807 -17.835  -4.801  1.00  9.99
ATOM   1265  N   SER   319      -7.712 -18.732  -4.032  1.00  9.99
ATOM   1266  CA  SER   319      -7.992 -17.574  -3.195  1.00  9.99
ATOM   1267  C   SER   319      -8.669 -17.928  -1.859  1.00  9.99
ATOM   1268  O   SER   319      -9.743 -17.403  -1.515  1.00  9.99
ATOM   1269  N   GLN   320      -8.020 -18.799  -1.091  1.00  9.99
ATOM   1270  CA  GLN   320      -8.574 -19.235   0.185  1.00  9.99
ATOM   1271  C   GLN   320      -7.539 -19.336   1.296  1.00  9.99
ATOM   1272  O   GLN   320      -6.337 -19.198   1.057  1.00  9.99
ATOM   1273  N   PHE   321      -8.023 -19.580   2.512  1.00  9.99
ATOM   1274  CA  PHE   321      -7.151 -19.738   3.672  1.00  9.99
ATOM   1275  C   PHE   321      -6.317 -21.010   3.483  1.00  9.99
ATOM   1276  O   PHE   321      -6.834 -22.057   3.090  1.00  9.99
TER
END
