
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0316AL044_3-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL044_3-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A     290      M     284           -
LGA    S     291      S     285           -
LGA    Q     292      T     286           -
LGA    V     293      S     287           -
LGA    H     294      L     288           -
LGA    F     295      E     289           -
LGA    T     296      A     290           -
LGA    R     297      S     291           -
LGA    E     298      Q     292           -
LGA    M     299      V     293           -
LGA    P     300      H     294           -
LGA    E     301      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    E     302      K     310          1.101
LGA    T     304      F     311          0.766
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    -       -      T     321           -
LGA    -       -      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    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    L     305      A     345          1.131
LGA    C     307      V     346          1.036
LGA    T     308      V     347          0.761
LGA    A     309      F     348          1.263
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    K     310      C     354          5.356
LGA    F     311      L     355          2.108
LGA    K     319      G     356          1.217
LGA    V     320      G     357          2.606
LGA    T     321      G     358          1.002
LGA    V     322      L     359          1.110
LGA    H     323      I     360          2.807
LGA    V     324      D     361          0.428
LGA    K     325      N     362          1.795
LGA    G     326      A     363          1.842
LGA    E     327      Y     364          1.639
LGA    K     328      R     365          3.170
LGA    T     329      D     366          5.495
LGA    E     330      -       -           -
LGA    V     331      -       -           -
LGA    I     332      -       -           -
LGA    E     335      -       -           -
LGA    P     336      -       -           -
LGA    R     338      -       -           -
LGA    A     339      -       -           -
LGA    I     340      -       -           -
LGA    T     341      -       -           -
LGA    P     342      G     367          3.811
LGA    G     343      Q     368          1.881
LGA    Q     344      V     369           -
LGA    V     346      C     370           -
LGA    V     347      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   90    5.0     21    2.45     0.00     18.833     0.825

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.359804 * X  +   0.747674 * Y  +  -0.558144 * Z  +  14.243083
  Y_new =   0.828890 * X  +  -0.018488 * Y  +  -0.559105 * Z  +  11.040723
  Z_new =  -0.428348 * X  +  -0.663809 * Y  +  -0.613087 * Z  +  58.631012 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.316493    0.825100  [ DEG:  -132.7253     47.2747 ]
  Theta =   0.442663    2.698929  [ DEG:    25.3627    154.6373 ]
  Phi   =   1.980332   -1.161261  [ DEG:   113.4647    -66.5353 ]
 
# 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_3-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_3-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   90   5.0   21   2.45    0.00  18.833
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_3-D3
REMARK Aligment from pdb entry: 1ni5_A
ATOM    805  N   ALA   290      40.636  18.815  -0.657  1.00  0.00              
ATOM    806  CA  ALA   290      41.208  20.033  -1.228  1.00  0.00              
ATOM    807  C   ALA   290      40.546  21.237  -0.587  1.00  0.00              
ATOM    808  O   ALA   290      39.326  21.282  -0.431  1.00  0.00              
ATOM    809  N   SER   291      38.576  24.237   0.333  1.00  0.00              
ATOM    810  CA  SER   291      37.377  24.774  -0.315  1.00  0.00              
ATOM    811  C   SER   291      37.372  26.288  -0.426  1.00  0.00              
ATOM    812  O   SER   291      38.039  26.984   0.345  1.00  0.00              
ATOM    813  N   GLN   292      36.607  26.787  -1.392  1.00  0.00              
ATOM    814  CA  GLN   292      36.474  28.223  -1.595  1.00  0.00              
ATOM    815  C   GLN   292      35.476  28.692  -0.547  1.00  0.00              
ATOM    816  O   GLN   292      34.518  27.983  -0.239  1.00  0.00              
ATOM    817  N   VAL   293      35.695  29.884  -0.009  1.00  0.00              
ATOM    818  CA  VAL   293      34.806  30.430   1.008  1.00  0.00              
ATOM    819  C   VAL   293      33.342  30.373   0.580  1.00  0.00              
ATOM    820  O   VAL   293      32.450  30.221   1.417  1.00  0.00              
ATOM    821  N   HIS   294      33.091  30.476  -0.721  1.00  0.00              
ATOM    822  CA  HIS   294      31.722  30.422  -1.204  1.00  0.00              
ATOM    823  C   HIS   294      31.265  28.972  -1.230  1.00  0.00              
ATOM    824  O   HIS   294      30.083  28.674  -1.041  1.00  0.00              
ATOM    825  N   PHE   295      27.672  24.662   0.646  1.00  0.00              
ATOM    826  CA  PHE   295      27.563  23.426   1.393  1.00  0.00              
ATOM    827  C   PHE   295      26.474  23.502   2.451  1.00  0.00              
ATOM    828  O   PHE   295      25.624  22.618   2.540  1.00  0.00              
ATOM    829  N   THR   296      26.487  24.562   3.248  1.00  0.00              
ATOM    830  CA  THR   296      25.488  24.712   4.297  1.00  0.00              
ATOM    831  C   THR   296      24.091  25.084   3.800  1.00  0.00              
ATOM    832  O   THR   296      23.099  24.485   4.210  1.00  0.00              
ATOM    833  N   ARG   297      24.014  26.076   2.924  1.00  0.00              
ATOM    834  CA  ARG   297      22.739  26.525   2.397  1.00  0.00              
ATOM    835  C   ARG   297      22.055  25.541   1.456  1.00  0.00              
ATOM    836  O   ARG   297      20.832  25.409   1.479  1.00  0.00              
ATOM    837  N   GLU   298      22.840  24.845   0.637  1.00  0.00              
ATOM    838  CA  GLU   298      22.285  23.920  -0.352  1.00  0.00              
ATOM    839  C   GLU   298      22.318  22.445   0.024  1.00  0.00              
ATOM    840  O   GLU   298      21.661  21.627  -0.617  1.00  0.00              
ATOM    841  N   MET   299      23.082  22.089   1.044  1.00  0.00              
ATOM    842  CA  MET   299      23.164  20.683   1.420  1.00  0.00              
ATOM    843  C   MET   299      22.597  20.431   2.812  1.00  0.00              
ATOM    844  O   MET   299      21.582  19.750   2.963  1.00  0.00              
ATOM    845  N   PRO   300      19.195  21.423   3.116  1.00  0.00              
ATOM    846  CA  PRO   300      18.373  20.825   2.068  1.00  0.00              
ATOM    847  C   PRO   300      17.639  19.641   2.685  1.00  0.00              
ATOM    848  O   PRO   300      18.091  19.073   3.690  1.00  0.00              
ATOM    849  N   GLU   301      16.509  19.282   2.080  1.00  0.00              
ATOM    850  CA  GLU   301      15.671  18.172   2.530  1.00  0.00              
ATOM    851  C   GLU   301      16.318  16.826   2.173  1.00  0.00              
ATOM    852  O   GLU   301      16.641  16.580   1.006  1.00  0.00              
ATOM    853  N   GLU   302      20.340  15.718  -1.287  1.00  0.00              
ATOM    854  CA  GLU   302      21.208  16.889  -1.460  1.00  0.00              
ATOM    855  C   GLU   302      22.620  16.489  -1.908  1.00  0.00              
ATOM    856  O   GLU   302      23.175  15.502  -1.420  1.00  0.00              
ATOM    857  N   THR   304      23.201  17.264  -2.823  1.00  0.00              
ATOM    858  CA  THR   304      24.532  16.950  -3.321  1.00  0.00              
ATOM    859  C   THR   304      25.283  18.117  -3.963  1.00  0.00              
ATOM    860  O   THR   304      24.789  18.747  -4.900  1.00  0.00              
ATOM    861  N   LEU   305      29.999  16.248  -1.415  1.00  0.00              
ATOM    862  CA  LEU   305      29.535  16.320  -0.042  1.00  0.00              
ATOM    863  C   LEU   305      28.035  16.204  -0.131  1.00  0.00              
ATOM    864  O   LEU   305      27.421  16.809  -1.012  1.00  0.00              
ATOM    865  N   CYS   307      27.435  15.440   0.771  1.00  0.00              
ATOM    866  CA  CYS   307      25.991  15.295   0.741  1.00  0.00              
ATOM    867  C   CYS   307      25.394  15.110   2.118  1.00  0.00              
ATOM    868  O   CYS   307      26.117  15.007   3.109  1.00  0.00              
ATOM    869  N   THR   308      24.068  15.077   2.180  1.00  0.00              
ATOM    870  CA  THR   308      23.391  14.907   3.455  1.00  0.00              
ATOM    871  C   THR   308      22.659  13.580   3.606  1.00  0.00              
ATOM    872  O   THR   308      21.919  13.145   2.715  1.00  0.00              
ATOM    873  N   ALA   309      22.879  12.947   4.752  1.00  0.00              
ATOM    874  CA  ALA   309      22.225  11.688   5.082  1.00  0.00              
ATOM    875  C   ALA   309      22.272  11.516   6.594  1.00  0.00              
ATOM    876  O   ALA   309      23.332  11.660   7.227  1.00  0.00              
ATOM    877  N   LYS   310      21.104  11.227   7.160  1.00  0.00              
ATOM    878  CA  LYS   310      20.945  11.035   8.594  1.00  0.00              
ATOM    879  C   LYS   310      21.393  12.258   9.378  1.00  0.00              
ATOM    880  O   LYS   310      22.088  12.146  10.384  1.00  0.00              
ATOM    881  N   PHE   311      20.984  13.430   8.897  1.00  0.00              
ATOM    882  CA  PHE   311      21.308  14.694   9.548  1.00  0.00              
ATOM    883  C   PHE   311      22.811  14.822   9.734  1.00  0.00              
ATOM    884  O   PHE   311      23.300  15.213  10.792  1.00  0.00              
ATOM    885  N   LYS   319      23.537  14.490   8.682  1.00  0.00              
ATOM    886  CA  LYS   319      24.986  14.542   8.704  1.00  0.00              
ATOM    887  C   LYS   319      25.501  14.888   7.332  1.00  0.00              
ATOM    888  O   LYS   319      24.862  14.577   6.324  1.00  0.00              
ATOM    889  N   VAL   320      26.666  15.520   7.294  1.00  0.00              
ATOM    890  CA  VAL   320      27.286  15.863   6.028  1.00  0.00              
ATOM    891  C   VAL   320      28.376  14.829   5.798  1.00  0.00              
ATOM    892  O   VAL   320      29.136  14.503   6.711  1.00  0.00              
ATOM    893  N   THR   321      28.434  14.308   4.578  1.00  0.00              
ATOM    894  CA  THR   321      29.411  13.285   4.222  1.00  0.00              
ATOM    895  C   THR   321      30.349  13.728   3.111  1.00  0.00              
ATOM    896  O   THR   321      29.925  14.326   2.121  1.00  0.00              
ATOM    897  N   VAL   322      31.629  13.435   3.278  1.00  0.00              
ATOM    898  CA  VAL   322      32.608  13.750   2.251  1.00  0.00              
ATOM    899  C   VAL   322      32.918  12.407   1.636  1.00  0.00              
ATOM    900  O   VAL   322      33.514  11.550   2.284  1.00  0.00              
ATOM    901  N   HIS   323      32.498  12.205   0.395  1.00  0.00              
ATOM    902  CA  HIS   323      32.739  10.924  -0.243  1.00  0.00              
ATOM    903  C   HIS   323      33.177  11.027  -1.690  1.00  0.00              
ATOM    904  O   HIS   323      32.855  12.000  -2.385  1.00  0.00              
ATOM    905  N   VAL   324      33.917  10.005  -2.126  1.00  0.00              
ATOM    906  CA  VAL   324      34.433   9.913  -3.489  1.00  0.00              
ATOM    907  C   VAL   324      33.304   9.667  -4.467  1.00  0.00              
ATOM    908  O   VAL   324      32.737   8.575  -4.512  1.00  0.00              
ATOM    909  N   LYS   325      32.974  10.690  -5.246  1.00  0.00              
ATOM    910  CA  LYS   325      31.912  10.576  -6.226  1.00  0.00              
ATOM    911  C   LYS   325      32.038   9.264  -7.006  1.00  0.00              
ATOM    912  O   LYS   325      33.139   8.725  -7.185  1.00  0.00              
ATOM    913  N   GLY   326      30.896   8.752  -7.458  1.00  0.00              
ATOM    914  CA  GLY   326      30.829   7.500  -8.202  1.00  0.00              
ATOM    915  C   GLY   326      29.536   7.512  -8.994  1.00  0.00              
ATOM    916  O   GLY   326      28.472   7.807  -8.449  1.00  0.00              
ATOM    917  N   GLU   327      29.626   7.188 -10.277  1.00  0.00              
ATOM    918  CA  GLU   327      28.454   7.191 -11.130  1.00  0.00              
ATOM    919  C   GLU   327      27.509   6.039 -10.873  1.00  0.00              
ATOM    920  O   GLU   327      27.933   4.901 -10.658  1.00  0.00              
ATOM    921  N   LYS   328      26.219   6.358 -10.899  1.00  0.00              
ATOM    922  CA  LYS   328      25.180   5.366 -10.686  1.00  0.00              
ATOM    923  C   LYS   328      25.300   4.172 -11.610  1.00  0.00              
ATOM    924  O   LYS   328      26.103   4.175 -12.550  1.00  0.00              
ATOM    925  N   THR   329      20.749   1.328 -14.035  1.00  0.00              
ATOM    926  CA  THR   329      20.353   0.858 -15.353  1.00  0.00              
ATOM    927  C   THR   329      21.279  -0.228 -15.897  1.00  0.00              
ATOM    928  O   THR   329      20.982  -0.856 -16.911  1.00  0.00              
ATOM    929  N   GLU   330      22.396  -0.462 -15.217  1.00  0.00              
ATOM    930  CA  GLU   330      23.337  -1.469 -15.682  1.00  0.00              
ATOM    931  C   GLU   330      22.998  -2.886 -15.221  1.00  0.00              
ATOM    932  O   GLU   330      22.401  -3.095 -14.158  1.00  0.00              
ATOM    933  N   VAL   331      23.381  -3.845 -16.060  1.00  0.00              
ATOM    934  CA  VAL   331      23.186  -5.269 -15.828  1.00  0.00              
ATOM    935  C   VAL   331      24.391  -5.977 -16.432  1.00  0.00              
ATOM    936  O   VAL   331      24.490  -6.129 -17.647  1.00  0.00              
ATOM    937  N   ILE   332      25.318  -6.385 -15.575  1.00  0.00              
ATOM    938  CA  ILE   332      26.521  -7.062 -16.022  1.00  0.00              
ATOM    939  C   ILE   332      26.385  -8.567 -15.808  1.00  0.00              
ATOM    940  O   ILE   332      26.433  -9.054 -14.671  1.00  0.00              
ATOM    941  N   GLU   335      26.202  -9.324 -16.913  1.00  0.00              
ATOM    942  CA  GLU   335      26.047 -10.786 -16.933  1.00  0.00              
ATOM    943  C   GLU   335      27.275 -11.493 -16.402  1.00  0.00              
ATOM    944  O   GLU   335      28.395 -11.001 -16.547  1.00  0.00              
ATOM    945  N   PRO   336      34.439 -17.864 -11.961  1.00  0.00              
ATOM    946  CA  PRO   336      35.548 -16.908 -11.933  1.00  0.00              
ATOM    947  C   PRO   336      35.033 -15.529 -11.507  1.00  0.00              
ATOM    948  O   PRO   336      33.878 -15.193 -11.758  1.00  0.00              
ATOM    949  N   ARG   338      35.878 -14.713 -10.854  1.00  0.00              
ATOM    950  CA  ARG   338      35.450 -13.378 -10.420  1.00  0.00              
ATOM    951  C   ARG   338      34.906 -12.525 -11.570  1.00  0.00              
ATOM    952  O   ARG   338      35.285 -12.714 -12.731  1.00  0.00              
ATOM    953  N   ALA   339      34.013 -11.593 -11.243  1.00  0.00              
ATOM    954  CA  ALA   339      33.434 -10.702 -12.247  1.00  0.00              
ATOM    955  C   ALA   339      33.848  -9.259 -11.982  1.00  0.00              
ATOM    956  O   ALA   339      33.538  -8.708 -10.926  1.00  0.00              
ATOM    957  N   ILE   340      34.540  -8.647 -12.938  1.00  0.00              
ATOM    958  CA  ILE   340      34.979  -7.260 -12.792  1.00  0.00              
ATOM    959  C   ILE   340      33.761  -6.344 -12.934  1.00  0.00              
ATOM    960  O   ILE   340      33.017  -6.439 -13.905  1.00  0.00              
ATOM    961  N   THR   341      33.556  -5.465 -11.962  1.00  0.00              
ATOM    962  CA  THR   341      32.411  -4.555 -11.995  1.00  0.00              
ATOM    963  C   THR   341      32.716  -3.231 -12.702  1.00  0.00              
ATOM    964  O   THR   341      33.869  -2.801 -12.788  1.00  0.00              
ATOM    965  N   PRO   342      31.676  -2.563 -13.216  1.00  0.00              
ATOM    966  CA  PRO   342      31.855  -1.288 -13.912  1.00  0.00              
ATOM    967  C   PRO   342      32.298  -0.160 -12.972  1.00  0.00              
ATOM    968  O   PRO   342      32.407  -0.359 -11.756  1.00  0.00              
ATOM    969  N   GLY   343      32.556   1.013 -13.553  1.00  0.00              
ATOM    970  CA  GLY   343      32.966   2.201 -12.815  1.00  0.00              
ATOM    971  C   GLY   343      33.820   1.877 -11.591  1.00  0.00              
ATOM    972  O   GLY   343      33.490   2.266 -10.464  1.00  0.00              
ATOM    973  N   GLN   344      35.724  -6.084  -7.880  1.00  0.00              
ATOM    974  CA  GLN   344      35.335  -7.369  -8.448  1.00  0.00              
ATOM    975  C   GLN   344      34.318  -8.002  -7.503  1.00  0.00              
ATOM    976  O   GLN   344      34.055  -7.473  -6.428  1.00  0.00              
ATOM    977  N   VAL   346      33.747  -9.128  -7.905  1.00  0.00              
ATOM    978  CA  VAL   346      32.754  -9.824  -7.092  1.00  0.00              
ATOM    979  C   VAL   346      32.923 -11.331  -7.351  1.00  0.00              
ATOM    980  O   VAL   346      33.321 -11.722  -8.451  1.00  0.00              
ATOM    981  N   VAL   347      31.713 -15.756  -6.026  1.00  0.00              
ATOM    982  CA  VAL   347      30.960 -16.708  -5.204  1.00  0.00              
ATOM    983  C   VAL   347      31.886 -17.759  -4.608  1.00  0.00              
ATOM    984  O   VAL   347      32.350 -18.648  -5.315  1.00  0.00              
END
