
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0356AL044_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_2-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      -       -           -
LGA    A     315      N       7           #
LGA    I     316      D       8          2.562
LGA    Y     317      L       9          2.126
LGA    H     318      R      10          3.083
LGA    S     319      D      11           #
LGA    -       -      F      12           -
LGA    T     320      L      13          1.466
LGA    Y     321      T      14          3.566
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    T     322      E      17          3.353
LGA    G     323      Q      18          1.364
LGA    R     324      Q      19          1.724
LGA    P     325      G      20          1.913
LGA    P     326      E      21          2.997
LGA    D     327      L      22          1.224
LGA    E     328      K      23          3.736
LGA    P     329      -       -           -
LGA    A     330      -       -           -
LGA    V     331      R      24          1.383
LGA    L     332      I      25          1.336
LGA    G     333      T      26          3.452
LGA    -       -      L      27           -
LGA    A     335      P      28          5.016
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    L     336      F      52          0.658
LGA    N     337      E      53          2.420
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    E     338      P      61          2.080
LGA    P     342      V      62          1.101
LGA    I     343      L      63          3.337
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    L     344      I     316          2.624
LGA    Q     345      Y     317          2.960
LGA    K     346      H     318          2.251
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29  124    5.0     24    2.61     0.00     13.104     0.884

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.048821 * X  +   0.245197 * Y  +   0.968243 * Z  +  66.527306
  Y_new =   0.994024 * X  +   0.106694 * Y  +   0.023102 * Z  +  -3.805426
  Z_new =  -0.097641 * X  +   0.963584 * Y  +  -0.248941 * Z  +  85.023880 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.823617   -1.317976  [ DEG:   104.4856    -75.5144 ]
  Theta =   0.097797    3.043796  [ DEG:     5.6033    174.3967 ]
  Phi   =   1.619872   -1.521721  [ DEG:    92.8118    -87.1882 ]
 
# 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: T0356AL044_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_2-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29  124   5.0   24   2.61    0.00  13.104
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_2-D1
REMARK Aligment from pdb entry: 1xov_A
ATOM     97  N   ASP   314      84.851  74.078  81.854  1.00  0.00              
ATOM     98  CA  ASP   314      84.058  74.996  82.633  1.00  0.00              
ATOM     99  C   ASP   314      82.605  75.115  82.144  1.00  0.00              
ATOM    100  O   ASP   314      82.348  75.036  80.926  1.00  0.00              
ATOM    101  N   ALA   315      81.663  75.254  83.071  1.00  0.00              
ATOM    102  CA  ALA   315      80.305  75.534  82.744  1.00  0.00              
ATOM    103  C   ALA   315      79.803  76.621  83.676  1.00  0.00              
ATOM    104  O   ALA   315      80.275  76.743  84.809  1.00  0.00              
ATOM    105  N   ILE   316      78.825  77.378  83.187  1.00  0.00              
ATOM    106  CA  ILE   316      78.260  78.467  83.938  1.00  0.00              
ATOM    107  C   ILE   316      76.790  78.231  84.018  1.00  0.00              
ATOM    108  O   ILE   316      76.075  78.185  83.007  1.00  0.00              
ATOM    109  N   TYR   317      76.314  77.964  85.229  1.00  0.00              
ATOM    110  CA  TYR   317      74.901  77.766  85.443  1.00  0.00              
ATOM    111  C   TYR   317      74.103  79.034  85.613  1.00  0.00              
ATOM    112  O   TYR   317      74.440  79.872  86.424  1.00  0.00              
ATOM    113  N   HIS   318      73.012  79.145  84.877  1.00  0.00              
ATOM    114  CA  HIS   318      71.990  80.168  85.163  1.00  0.00              
ATOM    115  C   HIS   318      70.756  79.441  85.676  1.00  0.00              
ATOM    116  O   HIS   318      69.860  78.961  84.941  1.00  0.00              
ATOM    117  N   SER   319      70.711  79.350  86.988  1.00  0.00              
ATOM    118  CA  SER   319      69.778  78.450  87.642  1.00  0.00              
ATOM    119  C   SER   319      68.304  78.714  87.306  1.00  0.00              
ATOM    120  O   SER   319      67.541  77.770  87.089  1.00  0.00              
ATOM    121  N   THR   320      67.898  79.982  87.360  1.00  0.00              
ATOM    122  CA  THR   320      66.542  80.422  87.047  1.00  0.00              
ATOM    123  C   THR   320      66.601  81.953  87.033  1.00  0.00              
ATOM    124  O   THR   320      67.696  82.505  87.256  1.00  0.00              
ATOM    125  N   TYR   321      65.501  82.603  86.681  1.00  0.00              
ATOM    126  CA  TYR   321      65.483  84.048  86.552  1.00  0.00              
ATOM    127  C   TYR   321      65.132  84.693  87.903  1.00  0.00              
ATOM    128  O   TYR   321      64.289  84.196  88.667  1.00  0.00              
ATOM    129  N   THR   322      65.735  85.855  88.156  1.00  0.00              
ATOM    130  CA  THR   322      65.434  86.627  89.375  1.00  0.00              
ATOM    131  C   THR   322      64.191  87.517  89.250  1.00  0.00              
ATOM    132  O   THR   322      63.692  88.068  90.245  1.00  0.00              
ATOM    133  N   GLY   323      63.683  87.639  88.021  1.00  0.00              
ATOM    134  CA  GLY   323      62.646  88.604  87.675  1.00  0.00              
ATOM    135  C   GLY   323      61.410  87.964  87.055  1.00  0.00              
ATOM    136  O   GLY   323      60.700  88.579  86.253  1.00  0.00              
ATOM    137  N   ARG   324      61.106  86.755  87.523  1.00  0.00              
ATOM    138  CA  ARG   324      59.996  86.005  87.030  1.00  0.00              
ATOM    139  C   ARG   324      59.359  85.331  88.257  1.00  0.00              
ATOM    140  O   ARG   324      60.024  84.685  89.075  1.00  0.00              
ATOM    141  N   PRO   325      58.061  85.527  88.456  1.00  0.00              
ATOM    142  CA  PRO   325      57.427  84.941  89.629  1.00  0.00              
ATOM    143  C   PRO   325      57.395  83.410  89.646  1.00  0.00              
ATOM    144  O   PRO   325      57.454  82.782  90.722  1.00  0.00              
ATOM    145  N   PRO   326      57.210  82.810  88.448  1.00  0.00              
ATOM    146  CA  PRO   326      57.205  81.346  88.363  1.00  0.00              
ATOM    147  C   PRO   326      58.509  80.832  88.979  1.00  0.00              
ATOM    148  O   PRO   326      58.530  79.941  89.807  1.00  0.00              
ATOM    149  N   ASP   327      59.602  81.423  88.551  1.00  0.00              
ATOM    150  CA  ASP   327      60.945  81.000  88.990  1.00  0.00              
ATOM    151  C   ASP   327      61.173  81.255  90.469  1.00  0.00              
ATOM    152  O   ASP   327      61.764  80.455  91.176  1.00  0.00              
ATOM    153  N   GLU   328      60.682  82.400  90.973  1.00  0.00              
ATOM    154  CA  GLU   328      60.754  82.650  92.413  1.00  0.00              
ATOM    155  C   GLU   328      59.973  81.632  93.233  1.00  0.00              
ATOM    156  O   GLU   328      60.476  81.148  94.257  1.00  0.00              
ATOM    157  N   PRO   329      58.722  81.342  92.841  1.00  0.00              
ATOM    158  CA  PRO   329      57.925  80.328  93.523  1.00  0.00              
ATOM    159  C   PRO   329      58.651  79.005  93.579  1.00  0.00              
ATOM    160  O   PRO   329      58.639  78.334  94.630  1.00  0.00              
ATOM    161  N   ALA   330      62.006  78.194  93.193  1.00  0.00              
ATOM    162  CA  ALA   330      63.236  78.041  93.958  1.00  0.00              
ATOM    163  C   ALA   330      62.988  78.127  95.456  1.00  0.00              
ATOM    164  O   ALA   330      63.823  77.702  96.232  1.00  0.00              
ATOM    165  N   VAL   331      61.848  78.703  95.832  1.00  0.00              
ATOM    166  CA  VAL   331      61.448  78.826  97.250  1.00  0.00              
ATOM    167  C   VAL   331      60.525  77.713  97.768  1.00  0.00              
ATOM    168  O   VAL   331      60.050  77.758  98.895  1.00  0.00              
ATOM    169  N   LEU   332      60.258  76.706  96.951  1.00  0.00              
ATOM    170  CA  LEU   332      59.548  75.531  97.409  1.00  0.00              
ATOM    171  C   LEU   332      60.366  74.761  98.443  1.00  0.00              
ATOM    172  O   LEU   332      61.595  74.795  98.462  1.00  0.00              
ATOM    173  N   GLY   333      59.654  74.038  99.311  1.00  0.00              
ATOM    174  CA  GLY   333      60.341  73.387 100.411  1.00  0.00              
ATOM    175  C   GLY   333      61.329  72.363  99.891  1.00  0.00              
ATOM    176  O   GLY   333      61.006  71.576  99.024  1.00  0.00              
ATOM    177  N   ALA   335      62.557  72.416 100.390  1.00  0.00              
ATOM    178  CA  ALA   335      63.605  71.492  99.979  1.00  0.00              
ATOM    179  C   ALA   335      64.184  71.643  98.584  1.00  0.00              
ATOM    180  O   ALA   335      64.945  70.783  98.138  1.00  0.00              
ATOM    181  N   LEU   336      63.872  72.745  97.911  1.00  0.00              
ATOM    182  CA  LEU   336      64.351  72.932  96.546  1.00  0.00              
ATOM    183  C   LEU   336      65.855  73.106  96.495  1.00  0.00              
ATOM    184  O   LEU   336      66.481  72.635  95.548  1.00  0.00              
ATOM    185  N   ASN   337      66.491  73.788  97.452  1.00  0.00              
ATOM    186  CA  ASN   337      67.942  73.887  97.309  1.00  0.00              
ATOM    187  C   ASN   337      68.601  72.513  97.380  1.00  0.00              
ATOM    188  O   ASN   337      69.573  72.278  96.653  1.00  0.00              
ATOM    189  N   GLU   338      68.095  71.659  98.278  1.00  0.00              
ATOM    190  CA  GLU   338      68.582  70.258  98.332  1.00  0.00              
ATOM    191  C   GLU   338      68.401  69.567  96.997  1.00  0.00              
ATOM    192  O   GLU   338      69.298  68.880  96.499  1.00  0.00              
ATOM    193  N   PRO   342      67.221  69.712  96.424  1.00  0.00              
ATOM    194  CA  PRO   342      66.931  69.068  95.134  1.00  0.00              
ATOM    195  C   PRO   342      67.834  69.582  94.029  1.00  0.00              
ATOM    196  O   PRO   342      68.201  68.835  93.128  1.00  0.00              
ATOM    197  N   ILE   343      68.192  70.857  94.087  1.00  0.00              
ATOM    198  CA  ILE   343      69.095  71.417  93.084  1.00  0.00              
ATOM    199  C   ILE   343      70.501  70.952  93.314  1.00  0.00              
ATOM    200  O   ILE   343      71.225  70.718  92.363  1.00  0.00              
ATOM    201  N   LEU   344      70.915  70.807  94.567  1.00  0.00              
ATOM    202  CA  LEU   344      72.265  70.264  94.838  1.00  0.00              
ATOM    203  C   LEU   344      72.393  68.847  94.262  1.00  0.00              
ATOM    204  O   LEU   344      73.435  68.485  93.709  1.00  0.00              
ATOM    205  N   GLN   345      71.333  68.063  94.394  1.00  0.00              
ATOM    206  CA  GLN   345      71.273  66.707  93.809  1.00  0.00              
ATOM    207  C   GLN   345      71.350  66.738  92.279  1.00  0.00              
ATOM    208  O   GLN   345      72.126  66.034  91.659  1.00  0.00              
ATOM    209  N   LYS   346      70.540  67.585  91.673  1.00  0.00              
ATOM    210  CA  LYS   346      70.527  67.752  90.219  1.00  0.00              
ATOM    211  C   LYS   346      71.890  68.105  89.669  1.00  0.00              
ATOM    212  O   LYS   346      72.327  67.540  88.646  1.00  0.00              
END
