
#######################################################
#                                                     #
#                        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   48 (  200),  selected   48 , name T0316AL044_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL044_2-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284           -
LGA    S     285      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    T     286      V     293           #
LGA    S     287      H     294           #
LGA    L     288      F     295          3.328
LGA    -       -      T     296           -
LGA    E     289      R     297          2.404
LGA    A     290      E     298          2.873
LGA    S     291      M     299          3.115
LGA    Q     292      P     300          1.180
LGA    -       -      E     301           -
LGA    V     293      E     302          4.904
LGA    H     294      F     303          1.819
LGA    F     295      T     304          2.172
LGA    T     296      L     305           #
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    R     297      T     321          4.158
LGA    E     298      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    M     299      F     333           #
LGA    -       -      A     334           -
LGA    P     300      E     335          5.401
LGA    E     301      P     336          4.463
LGA    E     302      Q     337          3.712
LGA    F     303      R     338          3.381
LGA    L     305      A     339           #
LGA    C     307      -       -           -
LGA    T     308      I     340           #
LGA    A     309      -       -           -
LGA    E     327      -       -           -
LGA    T     329      -       -           -
LGA    E     330      -       -           -
LGA    V     331      -       -           -
LGA    I     332      -       -           -
LGA    F     333      -       -           -
LGA    A     334      -       -           -
LGA    E     335      -       -           -
LGA    P     336      -       -           -
LGA    Q     337      T     341          3.016
LGA    R     338      P     342          2.490
LGA    A     339      G     343          1.642
LGA    I     340      Q     344          1.974
LGA    T     341      A     345          2.917
LGA    P     342      V     346          2.807
LGA    G     343      -       -           -
LGA    Q     344      V     347          3.824
LGA    A     345      F     348          4.458
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    V     346      G     357          0.704
LGA    V     347      G     358           #
LGA    F     348      L     359           -
LGA    Y     349      I     360           -
LGA    D     350      D     361           -
LGA    G     351      N     362           -
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   90    5.0     22    3.26     0.00     15.203     0.656

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.721435 * X  +  -0.512901 * Y  +   0.465256 * Z  + -19.646820
  Y_new =  -0.648125 * X  +  -0.736714 * Y  +   0.192838 * Z  +  32.509132
  Z_new =   0.243854 * X  +  -0.440665 * Y  +  -0.863916 * Z  +  46.684608 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.669915    0.471678  [ DEG:  -152.9749     27.0252 ]
  Theta =  -0.246337   -2.895255  [ DEG:   -14.1141   -165.8859 ]
  Phi   =  -0.731921    2.409672  [ DEG:   -41.9360    138.0640 ]
 
# 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: T0316AL044_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_2-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   90   5.0   22   3.26    0.00  15.203
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_2-D3
REMARK Aligment from pdb entry: 1k92_A
ATOM    885  N   MET   284      26.029  -0.581   5.533  1.00  0.00              
ATOM    886  CA  MET   284      26.395  -0.593   6.951  1.00  0.00              
ATOM    887  C   MET   284      26.777   0.899   7.095  1.00  0.00              
ATOM    888  O   MET   284      27.637   1.420   6.346  1.00  0.00              
ATOM    889  N   SER   285      26.133   1.583   8.037  1.00  0.00              
ATOM    890  CA  SER   285      26.354   3.014   8.213  1.00  0.00              
ATOM    891  C   SER   285      26.738   3.402   9.633  1.00  0.00              
ATOM    892  O   SER   285      26.507   2.657  10.587  1.00  0.00              
ATOM    893  N   THR   286      27.347   4.578   9.753  1.00  0.00              
ATOM    894  CA  THR   286      27.690   5.116  11.070  1.00  0.00              
ATOM    895  C   THR   286      26.595   6.057  11.565  1.00  0.00              
ATOM    896  O   THR   286      26.324   7.100  10.945  1.00  0.00              
ATOM    897  N   SER   287      25.966   5.699  12.687  1.00  0.00              
ATOM    898  CA  SER   287      24.925   6.547  13.286  1.00  0.00              
ATOM    899  C   SER   287      25.543   7.788  13.916  1.00  0.00              
ATOM    900  O   SER   287      26.757   7.859  14.132  1.00  0.00              
ATOM    901  N   LEU   288      24.702   8.771  14.224  1.00  0.00              
ATOM    902  CA  LEU   288      25.182  10.014  14.826  1.00  0.00              
ATOM    903  C   LEU   288      25.990   9.748  16.100  1.00  0.00              
ATOM    904  O   LEU   288      27.016  10.397  16.346  1.00  0.00              
ATOM    905  N   GLU   289      25.552   8.763  16.877  1.00  0.00              
ATOM    906  CA  GLU   289      26.223   8.399  18.126  1.00  0.00              
ATOM    907  C   GLU   289      27.517   7.599  18.003  1.00  0.00              
ATOM    908  O   GLU   289      28.039   7.096  19.002  1.00  0.00              
ATOM    909  N   ALA   290      28.017   7.456  16.786  1.00  0.00              
ATOM    910  CA  ALA   290      29.268   6.751  16.543  1.00  0.00              
ATOM    911  C   ALA   290      29.228   5.263  16.849  1.00  0.00              
ATOM    912  O   ALA   290      30.082   4.737  17.563  1.00  0.00              
ATOM    913  N   SER   291      28.219   4.590  16.303  1.00  0.00              
ATOM    914  CA  SER   291      28.091   3.136  16.407  1.00  0.00              
ATOM    915  C   SER   291      27.427   2.787  15.084  1.00  0.00              
ATOM    916  O   SER   291      26.717   3.615  14.508  1.00  0.00              
ATOM    917  N   GLN   292      27.611   1.564  14.617  1.00  0.00              
ATOM    918  CA  GLN   292      27.088   1.188  13.302  1.00  0.00              
ATOM    919  C   GLN   292      25.746   0.470  13.280  1.00  0.00              
ATOM    920  O   GLN   292      25.413  -0.260  14.206  1.00  0.00              
ATOM    921  N   VAL   293      24.979   0.711  12.217  1.00  0.00              
ATOM    922  CA  VAL   293      23.698   0.027  11.991  1.00  0.00              
ATOM    923  C   VAL   293      23.696  -0.463  10.538  1.00  0.00              
ATOM    924  O   VAL   293      24.578  -0.132   9.744  1.00  0.00              
ATOM    925  N   HIS   294      22.711  -1.279  10.191  1.00  0.00              
ATOM    926  CA  HIS   294      22.609  -1.834   8.847  1.00  0.00              
ATOM    927  C   HIS   294      21.219  -1.590   8.297  1.00  0.00              
ATOM    928  O   HIS   294      20.243  -1.723   9.023  1.00  0.00              
ATOM    929  N   PHE   295      21.126  -1.231   7.025  1.00  0.00              
ATOM    930  CA  PHE   295      19.809  -1.057   6.445  1.00  0.00              
ATOM    931  C   PHE   295      19.737  -1.488   4.991  1.00  0.00              
ATOM    932  O   PHE   295      20.765  -1.601   4.308  1.00  0.00              
ATOM    933  N  ATHR   296      18.506  -1.749   4.557  1.00  0.00              
ATOM    934  N  BTHR   296      18.536  -1.786   4.500  1.00  0.00              
ATOM    935  CA ATHR   296      18.200  -2.100   3.175  1.00  0.00              
ATOM    936  CA BTHR   296      18.353  -2.130   3.080  1.00  0.00              
ATOM    937  C  ATHR   296      17.368  -0.921   2.711  1.00  0.00              
ATOM    938  C  BTHR   296      17.330  -1.099   2.603  1.00  0.00              
ATOM    939  O  ATHR   296      16.442  -0.466   3.425  1.00  0.00              
ATOM    940  O  BTHR   296      16.242  -0.947   3.176  1.00  0.00              
ATOM    941  N   ARG   297      17.706  -0.398   1.534  1.00  0.00              
ATOM    942  CA  ARG   297      16.993   0.756   1.027  1.00  0.00              
ATOM    943  C   ARG   297      16.398   0.706  -0.364  1.00  0.00              
ATOM    944  O   ARG   297      16.927   0.045  -1.239  1.00  0.00              
ATOM    945  N   GLU   298      15.290   1.437  -0.534  1.00  0.00              
ATOM    946  CA  GLU   298      14.603   1.561  -1.824  1.00  0.00              
ATOM    947  C   GLU   298      14.435   3.063  -2.108  1.00  0.00              
ATOM    948  O   GLU   298      14.094   3.828  -1.202  1.00  0.00              
ATOM    949  N   MET   299      14.645   3.477  -3.360  1.00  0.00              
ATOM    950  CA  MET   299      14.426   4.895  -3.758  1.00  0.00              
ATOM    951  C   MET   299      14.503   4.884  -5.284  1.00  0.00              
ATOM    952  O   MET   299      15.407   5.456  -5.891  1.00  0.00              
ATOM    953  N   PRO   300      13.510   4.274  -5.943  1.00  0.00              
ATOM    954  CA  PRO   300      13.550   4.200  -7.411  1.00  0.00              
ATOM    955  C   PRO   300      13.582   5.500  -8.212  1.00  0.00              
ATOM    956  O   PRO   300      14.342   5.616  -9.187  1.00  0.00              
ATOM    957  N   GLU   301      20.556  10.419 -14.268  1.00  0.00              
ATOM    958  CA  GLU   301      20.471  11.374 -15.369  1.00  0.00              
ATOM    959  C   GLU   301      21.161  12.702 -15.035  1.00  0.00              
ATOM    960  O   GLU   301      21.881  13.252 -15.861  1.00  0.00              
ATOM    961  N   GLU   302      20.968  13.196 -13.806  1.00  0.00              
ATOM    962  CA  GLU   302      21.571  14.449 -13.381  1.00  0.00              
ATOM    963  C   GLU   302      23.100  14.341 -13.447  1.00  0.00              
ATOM    964  O   GLU   302      23.752  15.225 -14.025  1.00  0.00              
ATOM    965  N   PHE   303      23.670  13.266 -12.895  1.00  0.00              
ATOM    966  CA  PHE   303      25.131  13.148 -12.950  1.00  0.00              
ATOM    967  C   PHE   303      25.668  12.961 -14.359  1.00  0.00              
ATOM    968  O   PHE   303      26.747  13.464 -14.669  1.00  0.00              
ATOM    969  N   LEU   305      24.951  12.250 -15.232  1.00  0.00              
ATOM    970  CA  LEU   305      25.460  12.115 -16.582  1.00  0.00              
ATOM    971  C   LEU   305      25.519  13.512 -17.232  1.00  0.00              
ATOM    972  O   LEU   305      26.506  13.843 -17.886  1.00  0.00              
ATOM    973  N   CYS   307      24.472  14.330 -17.051  1.00  0.00              
ATOM    974  CA  CYS   307      24.518  15.693 -17.620  1.00  0.00              
ATOM    975  C   CYS   307      25.664  16.505 -16.982  1.00  0.00              
ATOM    976  O   CYS   307      26.382  17.220 -17.690  1.00  0.00              
ATOM    977  N   THR   308      25.834  16.398 -15.662  1.00  0.00              
ATOM    978  CA  THR   308      26.920  17.113 -14.977  1.00  0.00              
ATOM    979  C   THR   308      28.279  16.816 -15.661  1.00  0.00              
ATOM    980  O   THR   308      29.088  17.734 -15.936  1.00  0.00              
ATOM    981  N   ALA   309      28.540  15.541 -15.947  1.00  0.00              
ATOM    982  CA  ALA   309      29.797  15.168 -16.580  1.00  0.00              
ATOM    983  C   ALA   309      29.956  15.717 -17.996  1.00  0.00              
ATOM    984  O   ALA   309      31.071  15.823 -18.492  1.00  0.00              
ATOM    985  N   GLU   327      28.851  16.070 -18.652  1.00  0.00              
ATOM    986  CA  GLU   327      28.983  16.612 -19.996  1.00  0.00              
ATOM    987  C   GLU   327      28.996  18.136 -20.058  1.00  0.00              
ATOM    988  O   GLU   327      29.281  18.702 -21.120  1.00  0.00              
ATOM    989  N   THR   329      28.749  18.780 -18.913  1.00  0.00              
ATOM    990  CA  THR   329      28.612  20.237 -18.825  1.00  0.00              
ATOM    991  C   THR   329      29.654  20.987 -18.003  1.00  0.00              
ATOM    992  O   THR   329      30.084  22.077 -18.400  1.00  0.00              
ATOM    993  N   GLU   330      30.077  20.418 -16.879  1.00  0.00              
ATOM    994  CA  GLU   330      31.004  21.127 -16.010  1.00  0.00              
ATOM    995  C   GLU   330      32.469  20.726 -16.051  1.00  0.00              
ATOM    996  O   GLU   330      32.825  19.572 -16.379  1.00  0.00              
ATOM    997  N   VAL   331      33.328  21.689 -15.697  1.00  0.00              
ATOM    998  CA  VAL   331      34.763  21.418 -15.700  1.00  0.00              
ATOM    999  C   VAL   331      35.199  20.571 -14.511  1.00  0.00              
ATOM   1000  O   VAL   331      34.421  20.351 -13.582  1.00  0.00              
ATOM   1001  N   ILE   332      36.436  20.068 -14.553  1.00  0.00              
ATOM   1002  CA  ILE   332      36.885  19.159 -13.511  1.00  0.00              
ATOM   1003  C   ILE   332      36.885  19.724 -12.097  1.00  0.00              
ATOM   1004  O   ILE   332      36.437  19.054 -11.164  1.00  0.00              
ATOM   1005  N   PHE   333      37.379  20.947 -11.926  1.00  0.00              
ATOM   1006  CA  PHE   333      37.388  21.550 -10.584  1.00  0.00              
ATOM   1007  C   PHE   333      35.966  21.641 -10.031  1.00  0.00              
ATOM   1008  O   PHE   333      35.735  21.431  -8.823  1.00  0.00              
ATOM   1009  N   ALA   334      35.016  21.976 -10.903  1.00  0.00              
ATOM   1010  CA  ALA   334      33.633  22.137 -10.483  1.00  0.00              
ATOM   1011  C   ALA   334      32.994  20.787 -10.140  1.00  0.00              
ATOM   1012  O   ALA   334      32.275  20.666  -9.149  1.00  0.00              
ATOM   1013  N   GLU   335      34.611  18.195  -9.094  1.00  0.00              
ATOM   1014  CA  GLU   335      35.182  17.722  -7.860  1.00  0.00              
ATOM   1015  C   GLU   335      34.604  18.461  -6.655  1.00  0.00              
ATOM   1016  O   GLU   335      34.398  17.850  -5.601  1.00  0.00              
ATOM   1017  N   PRO   336      34.284  19.751  -6.819  1.00  0.00              
ATOM   1018  CA  PRO   336      33.653  20.465  -5.713  1.00  0.00              
ATOM   1019  C   PRO   336      32.228  19.886  -5.502  1.00  0.00              
ATOM   1020  O   PRO   336      31.765  19.741  -4.363  1.00  0.00              
ATOM   1021  N   GLN   337      31.522  19.529  -6.578  1.00  0.00              
ATOM   1022  CA  GLN   337      30.209  18.913  -6.427  1.00  0.00              
ATOM   1023  C   GLN   337      30.339  17.611  -5.621  1.00  0.00              
ATOM   1024  O   GLN   337      29.569  17.378  -4.685  1.00  0.00              
ATOM   1025  N   ARG   338      31.308  16.755  -5.959  1.00  0.00              
ATOM   1026  CA  ARG   338      31.436  15.509  -5.195  1.00  0.00              
ATOM   1027  C   ARG   338      31.814  15.734  -3.739  1.00  0.00              
ATOM   1028  O   ARG   338      31.202  15.150  -2.834  1.00  0.00              
ATOM   1029  N   ALA   339      32.807  16.582  -3.494  1.00  0.00              
ATOM   1030  CA  ALA   339      33.265  16.835  -2.130  1.00  0.00              
ATOM   1031  C   ALA   339      32.230  17.542  -1.276  1.00  0.00              
ATOM   1032  O   ALA   339      31.908  17.087  -0.165  1.00  0.00              
ATOM   1033  N   ILE   340      31.698  18.638  -1.793  1.00  0.00              
ATOM   1034  CA  ILE   340      30.703  19.401  -1.045  1.00  0.00              
ATOM   1035  C   ILE   340      29.406  18.632  -0.893  1.00  0.00              
ATOM   1036  O   ILE   340      28.756  18.705   0.145  1.00  0.00              
ATOM   1037  N   THR   341      29.030  17.870  -1.927  1.00  0.00              
ATOM   1038  CA  THR   341      27.818  17.069  -1.827  1.00  0.00              
ATOM   1039  C   THR   341      27.924  15.989  -0.751  1.00  0.00              
ATOM   1040  O   THR   341      26.985  15.801   0.039  1.00  0.00              
ATOM   1041  N  APRO   342      29.049  15.273  -0.690  1.00  0.00              
ATOM   1042  N  BPRO   342      29.064  15.303  -0.698  1.00  0.00              
ATOM   1043  CA APRO   342      29.176  14.257   0.352  1.00  0.00              
ATOM   1044  CA BPRO   342      29.260  14.260   0.298  1.00  0.00              
ATOM   1045  C  APRO   342      29.090  14.924   1.724  1.00  0.00              
ATOM   1046  C  BPRO   342      29.240  14.841   1.728  1.00  0.00              
ATOM   1047  O  APRO   342      28.374  14.451   2.612  1.00  0.00              
ATOM   1048  O  BPRO   342      28.741  14.207   2.665  1.00  0.00              
ATOM   1049  N   GLY   343      29.819  16.032   1.900  1.00  0.00              
ATOM   1050  CA  GLY   343      29.836  16.714   3.203  1.00  0.00              
ATOM   1051  C   GLY   343      28.416  17.128   3.568  1.00  0.00              
ATOM   1052  O   GLY   343      27.996  16.963   4.718  1.00  0.00              
ATOM   1053  N   GLN   344      27.675  17.649   2.589  1.00  0.00              
ATOM   1054  CA  GLN   344      26.291  18.040   2.802  1.00  0.00              
ATOM   1055  C   GLN   344      25.432  16.824   3.172  1.00  0.00              
ATOM   1056  O   GLN   344      24.540  16.935   4.009  1.00  0.00              
ATOM   1057  N   ALA   345      25.693  15.675   2.534  1.00  0.00              
ATOM   1058  CA  ALA   345      24.945  14.463   2.859  1.00  0.00              
ATOM   1059  C   ALA   345      25.145  14.071   4.319  1.00  0.00              
ATOM   1060  O   ALA   345      24.197  13.638   5.003  1.00  0.00              
ATOM   1061  N   VAL   346      26.375  14.213   4.822  1.00  0.00              
ATOM   1062  CA  VAL   346      26.628  13.857   6.209  1.00  0.00              
ATOM   1063  C   VAL   346      25.869  14.822   7.131  1.00  0.00              
ATOM   1064  O   VAL   346      25.257  14.403   8.116  1.00  0.00              
ATOM   1065  N   VAL   347      25.883  16.119   6.807  1.00  0.00              
ATOM   1066  CA  VAL   347      25.173  17.105   7.618  1.00  0.00              
ATOM   1067  C   VAL   347      23.661  16.799   7.602  1.00  0.00              
ATOM   1068  O   VAL   347      22.999  16.880   8.637  1.00  0.00              
ATOM   1069  N   PHE   348      23.130  16.433   6.434  1.00  0.00              
ATOM   1070  CA  PHE   348      21.718  16.079   6.298  1.00  0.00              
ATOM   1071  C   PHE   348      21.393  14.892   7.220  1.00  0.00              
ATOM   1072  O   PHE   348      20.424  14.902   7.971  1.00  0.00              
ATOM   1073  N   TYR   349      22.234  13.875   7.163  1.00  0.00              
ATOM   1074  CA  TYR   349      22.064  12.696   8.023  1.00  0.00              
ATOM   1075  C   TYR   349      22.089  13.048   9.528  1.00  0.00              
ATOM   1076  O   TYR   349      21.384  12.433  10.345  1.00  0.00              
ATOM   1077  N   ASP   350      22.903  14.033   9.897  1.00  0.00              
ATOM   1078  CA  ASP   350      23.034  14.473  11.285  1.00  0.00              
ATOM   1079  C   ASP   350      21.883  15.332  11.791  1.00  0.00              
ATOM   1080  O   ASP   350      21.850  15.667  12.972  1.00  0.00              
ATOM   1081  N   GLY   351      20.973  15.719  10.890  1.00  0.00              
ATOM   1082  CA  GLY   351      19.861  16.585  11.265  1.00  0.00              
ATOM   1083  C   GLY   351      20.256  18.054  11.176  1.00  0.00              
ATOM   1084  O   GLY   351      19.593  18.919  11.766  1.00  0.00              
END
