
#######################################################
#                                                     #
#                        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   40 (  160),  selected   40 , name T0349AL243_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL243_2-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    L       4      L       5          3.083
LGA    L       5      R       6          3.696
LGA    R       6      T       7          4.158
LGA    N       8      N       8          5.399
LGA    D       9      D       9          1.873
LGA    A      10      A      10          1.707
LGA    V      11      V      11          1.635
LGA    L      12      L      12          1.392
LGA    L      13      L      13          1.388
LGA    S      14      S      14          1.844
LGA    A      15      A      15          1.469
LGA    V      16      V      16          1.224
LGA    G      17      G      17          1.492
LGA    A      18      A      18          0.840
LGA    L      19      L      19          0.692
LGA    L      20      L      20          0.600
LGA    D      21      D      21          1.344
LGA    G      22      G      22          1.663
LGA    A      23      A      23          1.518
LGA    D      24      D      24          1.736
LGA    L      28      I      25          1.014
LGA    V      29      G      26          1.777
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    R      47      V      48          4.448
LGA    V      48      L      49          1.395
LGA    L      49      V      50          3.320
LGA    V      50      H      51          1.796
LGA    -       -      E      52           -
LGA    D      53      D      53          3.593
LGA    D      54      D      54          0.881
LGA    L      55      L      55          0.896
LGA    A      56      A      56          1.213
LGA    G      57      G      57          1.037
LGA    A      58      A      58          0.481
LGA    R      59      R      59          0.793
LGA    R      60      R      60          0.521
LGA    L      61      L      61          0.472
LGA    L      62      L      62          0.842
LGA    T      63      T      63          0.994
LGA    D      64      D      64          2.139
LGA    -       -      A      65           -
LGA    A      65      G      66          0.837
LGA    G      66      L      67          1.214
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40   57    5.0     40    2.06    75.00     62.854     1.849

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.886468 * X  +  -0.420787 * Y  +   0.192646 * Z  +   7.774568
  Y_new =  -0.432116 * X  +  -0.901617 * Y  +   0.019041 * Z  +  36.552559
  Z_new =   0.165681 * X  +  -0.100125 * Y  +  -0.981084 * Z  +  12.994175 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.039890    0.101703  [ DEG:  -174.1728      5.8272 ]
  Theta =  -0.166448   -2.975144  [ DEG:    -9.5368   -170.4632 ]
  Phi   =  -0.453564    2.688029  [ DEG:   -25.9873    154.0127 ]
 
# 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: T0349AL243_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL243_2-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40   57   5.0   40   2.06   75.00  62.854
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL243_2-D1
REMARK Aligment from pdb entry: 2f06A
ATOM      1  N   LEU     4       4.973  -0.983   1.653  1.00  0.00              
ATOM      2  CA  LEU     4       4.896  -2.452   1.745  1.00  0.00              
ATOM      3  C   LEU     4       3.770  -2.825   2.717  1.00  0.00              
ATOM      4  O   LEU     4       3.800  -2.442   3.868  1.00  0.00              
ATOM      5  N   LEU     5       2.723  -3.473   2.201  1.00  0.00              
ATOM      6  CA  LEU     5       1.531  -3.808   2.999  1.00  0.00              
ATOM      7  C   LEU     5       1.708  -5.297   3.227  1.00  0.00              
ATOM      8  O   LEU     5       1.571  -6.118   2.277  1.00  0.00              
ATOM      9  N   ARG     6       2.041  -5.661   4.446  1.00  0.00              
ATOM     10  CA  ARG     6       2.163  -7.058   4.807  1.00  0.00              
ATOM     11  C   ARG     6       0.784  -7.727   5.030  1.00  0.00              
ATOM     12  O   ARG     6      -0.231  -7.090   4.823  1.00  0.00              
ATOM     13  N   ASN     8       0.709  -9.005   5.384  1.00  0.00              
ATOM     14  CA  ASN     8      -0.624  -9.542   5.837  1.00  0.00              
ATOM     15  C   ASN     8      -1.642  -9.524   4.616  1.00  0.00              
ATOM     16  O   ASN     8      -1.322 -10.135   3.596  1.00  0.00              
ATOM     17  N   ASP     9      -2.807  -8.850   4.684  1.00  0.00              
ATOM     18  CA  ASP     9      -3.736  -8.588   3.494  1.00  0.00              
ATOM     19  C   ASP     9      -5.078  -7.898   3.882  1.00  0.00              
ATOM     20  O   ASP     9      -5.926  -7.693   3.002  1.00  0.00              
ATOM     21  N   ALA    10      -5.234  -7.495   5.161  1.00  0.00              
ATOM     22  CA  ALA    10      -6.493  -7.808   5.908  1.00  0.00              
ATOM     23  C   ALA    10      -7.231  -6.900   6.962  1.00  0.00              
ATOM     24  O   ALA    10      -8.156  -7.433   7.594  1.00  0.00              
ATOM     25  N   VAL    11      -6.809  -5.687   7.334  1.00  0.00              
ATOM     26  CA  VAL    11      -5.470  -5.421   7.752  1.00  0.00              
ATOM     27  C   VAL    11      -4.864  -4.044   7.648  1.00  0.00              
ATOM     28  O   VAL    11      -5.398  -3.020   8.108  1.00  0.00              
ATOM     29  N   LEU    12      -3.698  -4.101   7.049  1.00  0.00              
ATOM     30  CA  LEU    12      -2.692  -3.089   7.087  1.00  0.00              
ATOM     31  C   LEU    12      -3.002  -1.952   6.181  1.00  0.00              
ATOM     32  O   LEU    12      -2.556  -0.851   6.450  1.00  0.00              
ATOM     33  N   LEU    13      -3.758  -2.203   5.109  1.00  0.00              
ATOM     34  CA  LEU    13      -4.097  -1.095   4.206  1.00  0.00              
ATOM     35  C   LEU    13      -4.994  -0.043   4.942  1.00  0.00              
ATOM     36  O   LEU    13      -4.839   1.187   4.755  1.00  0.00              
ATOM     37  N   SER    14      -5.903  -0.539   5.769  1.00  0.00              
ATOM     38  CA  SER    14      -6.759   0.359   6.524  1.00  0.00              
ATOM     39  C   SER    14      -5.953   1.205   7.522  1.00  0.00              
ATOM     40  O   SER    14      -6.065   2.447   7.525  1.00  0.00              
ATOM     41  N   ALA    15      -5.109   0.549   8.301  1.00  0.00              
ATOM     42  CA  ALA    15      -4.161   1.266   9.151  1.00  0.00              
ATOM     43  C   ALA    15      -3.319   2.290   8.415  1.00  0.00              
ATOM     44  O   ALA    15      -3.107   3.334   8.970  1.00  0.00              
ATOM     45  N   VAL    16      -2.833   2.015   7.188  1.00  0.00              
ATOM     46  CA  VAL    16      -2.018   2.995   6.449  1.00  0.00              
ATOM     47  C   VAL    16      -2.861   4.201   6.113  1.00  0.00              
ATOM     48  O   VAL    16      -2.419   5.375   6.168  1.00  0.00              
ATOM     49  N   GLY    17      -4.074   3.950   5.691  1.00  0.00              
ATOM     50  CA  GLY    17      -4.920   5.106   5.328  1.00  0.00              
ATOM     51  C   GLY    17      -5.332   5.881   6.577  1.00  0.00              
ATOM     52  O   GLY    17      -5.550   7.104   6.498  1.00  0.00              
ATOM     53  N   ALA    18      -5.436   5.171   7.683  1.00  0.00              
ATOM     54  CA  ALA    18      -5.624   5.806   9.014  1.00  0.00              
ATOM     55  C   ALA    18      -4.449   6.682   9.518  1.00  0.00              
ATOM     56  O   ALA    18      -4.674   7.787   9.989  1.00  0.00              
ATOM     57  N   LEU    19      -3.225   6.179   9.510  1.00  0.00              
ATOM     58  CA  LEU    19      -2.003   7.030   9.625  1.00  0.00              
ATOM     59  C   LEU    19      -2.031   8.319   8.802  1.00  0.00              
ATOM     60  O   LEU    19      -1.805   9.401   9.340  1.00  0.00              
ATOM     61  N   LEU    20      -2.311   8.216   7.517  1.00  0.00              
ATOM     62  CA  LEU    20      -2.370   9.386   6.667  1.00  0.00              
ATOM     63  C   LEU    20      -3.523  10.330   6.985  1.00  0.00              
ATOM     64  O   LEU    20      -3.299  11.539   6.985  1.00  0.00              
ATOM     65  N   ASP    21      -4.729   9.797   7.263  1.00  0.00              
ATOM     66  CA  ASP    21      -5.874  10.602   7.692  1.00  0.00              
ATOM     67  C   ASP    21      -5.577  11.417   8.945  1.00  0.00              
ATOM     68  O   ASP    21      -6.040  12.571   9.086  1.00  0.00              
ATOM     69  N   GLY    22      -4.885  10.792   9.897  1.00  0.00              
ATOM     70  CA  GLY    22      -4.626  11.435  11.191  1.00  0.00              
ATOM     71  C   GLY    22      -3.719  12.683  11.011  1.00  0.00              
ATOM     72  O   GLY    22      -3.781  13.641  11.818  1.00  0.00              
ATOM     73  N   ALA    23      -2.890  12.669   9.955  1.00  0.00              
ATOM     74  CA  ALA    23      -2.014  13.780   9.690  1.00  0.00              
ATOM     75  C   ALA    23      -2.655  14.867   8.795  1.00  0.00              
ATOM     76  O   ALA    23      -1.982  15.893   8.471  1.00  0.00              
ATOM     77  N   ASP    24      -3.928  14.659   8.417  1.00  0.00              
ATOM     78  CA  ASP    24      -4.668  15.476   7.435  1.00  0.00              
ATOM     79  C   ASP    24      -3.885  15.492   6.123  1.00  0.00              
ATOM     80  O   ASP    24      -3.712  16.543   5.499  1.00  0.00              
ATOM     81  N   LEU    28      -3.394  14.304   5.732  1.00  0.00              
ATOM     82  CA  LEU    28      -2.709  14.116   4.481  1.00  0.00              
ATOM     83  C   LEU    28      -3.722  13.550   3.536  1.00  0.00              
ATOM     84  O   LEU    28      -4.338  12.509   3.797  1.00  0.00              
ATOM     85  N   VAL    29      -3.940  14.287   2.447  1.00  0.00              
ATOM     86  CA  VAL    29      -4.827  13.847   1.359  1.00  0.00              
ATOM     87  C   VAL    29      -4.105  12.933   0.359  1.00  0.00              
ATOM     88  O   VAL    29      -2.960  13.198  -0.099  1.00  0.00              
ATOM    139  N   ARG    47       1.293   2.102  -4.044  1.00  0.00              
ATOM    140  CA  ARG    47       1.898   3.244  -4.681  1.00  0.00              
ATOM    141  C   ARG    47       0.969   4.439  -4.557  1.00  0.00              
ATOM    142  O   ARG    47      -0.227   4.330  -4.842  1.00  0.00              
ATOM    143  N   VAL    48       1.512   5.576  -4.160  1.00  0.00              
ATOM    144  CA  VAL    48       0.685   6.608  -3.608  1.00  0.00              
ATOM    145  C   VAL    48       1.229   7.979  -3.952  1.00  0.00              
ATOM    146  O   VAL    48       2.400   8.259  -3.731  1.00  0.00              
ATOM    147  N   LEU    49       0.354   8.814  -4.494  1.00  0.00              
ATOM    148  CA  LEU    49       0.576  10.272  -4.565  1.00  0.00              
ATOM    149  C   LEU    49      -0.200  10.961  -3.435  1.00  0.00              
ATOM    150  O   LEU    49      -1.422  10.850  -3.376  1.00  0.00              
ATOM    151  N   VAL    50       0.508  11.629  -2.513  1.00  0.00              
ATOM    152  CA  VAL    50      -0.148  12.289  -1.386  1.00  0.00              
ATOM    153  C   VAL    50       0.097  13.834  -1.389  1.00  0.00              
ATOM    154  O   VAL    50       0.940  14.319  -2.166  1.00  0.00              
ATOM    155  N   ASP    53      -0.601  14.562  -0.505  1.00  0.00              
ATOM    156  CA  ASP    53      -0.508  16.052  -0.455  1.00  0.00              
ATOM    157  C   ASP    53       0.801  16.613   0.142  1.00  0.00              
ATOM    158  O   ASP    53       1.209  17.744  -0.179  1.00  0.00              
ATOM    159  N   ASP    54       1.445  15.818   0.999  1.00  0.00              
ATOM    160  CA  ASP    54       2.711  16.171   1.628  1.00  0.00              
ATOM    161  C   ASP    54       3.576  14.897   1.770  1.00  0.00              
ATOM    162  O   ASP    54       3.509  14.209   2.800  1.00  0.00              
ATOM    163  N   LEU    55       4.354  14.546   0.718  1.00  0.00              
ATOM    164  CA  LEU    55       5.083  13.257   0.794  1.00  0.00              
ATOM    165  C   LEU    55       6.112  13.111   1.939  1.00  0.00              
ATOM    166  O   LEU    55       6.222  12.029   2.505  1.00  0.00              
ATOM    167  N   ALA    56       6.783  14.190   2.324  1.00  0.00              
ATOM    168  CA  ALA    56       7.795  14.141   3.390  1.00  0.00              
ATOM    169  C   ALA    56       7.163  13.912   4.777  1.00  0.00              
ATOM    170  O   ALA    56       7.669  13.104   5.565  1.00  0.00              
ATOM    171  N   GLY    57       6.069  14.619   5.044  1.00  0.00              
ATOM    172  CA  GLY    57       5.321  14.442   6.300  1.00  0.00              
ATOM    173  C   GLY    57       4.735  13.019   6.339  1.00  0.00              
ATOM    174  O   GLY    57       4.794  12.354   7.378  1.00  0.00              
ATOM    175  N   ALA    58       4.168  12.572   5.211  1.00  0.00              
ATOM    176  CA  ALA    58       3.622  11.225   5.082  1.00  0.00              
ATOM    177  C   ALA    58       4.650  10.145   5.298  1.00  0.00              
ATOM    178  O   ALA    58       4.406   9.209   6.104  1.00  0.00              
ATOM    179  N   ARG    59       5.781  10.269   4.616  1.00  0.00              
ATOM    180  CA  ARG    59       6.898   9.352   4.845  1.00  0.00              
ATOM    181  C   ARG    59       7.334   9.232   6.319  1.00  0.00              
ATOM    182  O   ARG    59       7.552   8.136   6.836  1.00  0.00              
ATOM    183  N   ARG    60       7.494  10.348   7.004  1.00  0.00              
ATOM    184  CA  ARG    60       7.983  10.249   8.387  1.00  0.00              
ATOM    185  C   ARG    60       6.923   9.643   9.343  1.00  0.00              
ATOM    186  O   ARG    60       7.280   8.884  10.256  1.00  0.00              
ATOM    187  N   LEU    61       5.644   9.978   9.126  1.00  0.00              
ATOM    188  CA  LEU    61       4.526   9.383   9.861  1.00  0.00              
ATOM    189  C   LEU    61       4.462   7.832   9.697  1.00  0.00              
ATOM    190  O   LEU    61       4.357   7.047  10.684  1.00  0.00              
ATOM    191  N   LEU    62       4.570   7.394   8.456  1.00  0.00              
ATOM    192  CA  LEU    62       4.634   5.987   8.154  1.00  0.00              
ATOM    193  C   LEU    62       5.823   5.267   8.790  1.00  0.00              
ATOM    194  O   LEU    62       5.604   4.229   9.400  1.00  0.00              
ATOM    195  N   THR    63       7.055   5.786   8.657  1.00  0.00              
ATOM    196  CA  THR    63       8.243   5.217   9.364  1.00  0.00              
ATOM    197  C   THR    63       8.059   5.151  10.885  1.00  0.00              
ATOM    198  O   THR    63       8.489   4.190  11.539  1.00  0.00              
ATOM    199  N   ASP    64       7.468   6.211  11.443  1.00  0.00              
ATOM    200  CA  ASP    64       7.147   6.315  12.864  1.00  0.00              
ATOM    201  C   ASP    64       6.180   5.212  13.302  1.00  0.00              
ATOM    202  O   ASP    64       6.247   4.758  14.451  1.00  0.00              
ATOM    203  N   ALA    65       5.231   4.868  12.428  1.00  0.00              
ATOM    204  CA  ALA    65       4.285   3.784  12.662  1.00  0.00              
ATOM    205  C   ALA    65       4.768   2.416  12.168  1.00  0.00              
ATOM    206  O   ALA    65       3.970   1.473  12.087  1.00  0.00              
ATOM    207  N   GLY    66       6.062   2.338  11.816  1.00  0.00              
ATOM    208  CA  GLY    66       6.791   1.088  11.546  1.00  0.00              
ATOM    209  C   GLY    66       6.413   0.474  10.210  1.00  0.00              
ATOM    210  O   GLY    66       6.592  -0.747  10.025  1.00  0.00              
END
