
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0349AL243_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL243_5-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      11      M       1           -
LGA    L      12      R       2           -
LGA    L      13      E       3           -
LGA    S      14      L       4           -
LGA    A      15      L       5           -
LGA    V      16      -       -           -
LGA    G      17      -       -           -
LGA    A      18      -       -           -
LGA    L      19      -       -           -
LGA    L      20      -       -           -
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      R       6           #
LGA    G      26      T       7          3.369
LGA    -       -      N       8           -
LGA    H      27      D       9          2.987
LGA    L      28      A      10          1.769
LGA    V      29      V      11          5.327
LGA    P      45      L      12          3.266
LGA    R      46      L      13           -
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      S      14           #
LGA    V      50      A      15          4.530
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    H      51      A      18           #
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    -       -      D      21           -
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    -       -      I      25           -
LGA    E      52      G      26          2.882
LGA    D      53      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    -       -      V      50           -
LGA    -       -      H      51           -
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    D      54      D      54          1.351
LGA    L      55      L      55          0.779
LGA    A      56      A      56          0.632
LGA    G      57      G      57          0.805
LGA    A      58      A      58          0.483
LGA    R      59      R      59          1.185
LGA    R      60      R      60          1.188
LGA    L      61      L      61          0.561
LGA    L      62      L      62          0.687
LGA    T      63      T      63          1.362
LGA    D      64      D      64          1.539
LGA    A      65      A      65          1.598
LGA    G      66      G      66          3.930
LGA    L      67      L      67          2.015
LGA    A      68      A      68          3.544
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)   43   57    5.0     22    2.50    72.73     29.597     0.846

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.613093 * X  +   0.628932 * Y  +  -0.478081 * Z  +  -7.171939
  Y_new =  -0.667783 * X  +   0.089225 * Y  +  -0.738989 * Z  +  17.852909
  Z_new =  -0.422117 * X  +   0.772323 * Y  +   0.474693 * Z  +  17.139923 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.019689   -2.121904  [ DEG:    58.4239   -121.5761 ]
  Theta =   0.435779    2.705813  [ DEG:    24.9683    155.0317 ]
  Phi   =  -0.828069    2.313523  [ DEG:   -47.4449    132.5551 ]
 
# 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_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL243_5-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   57   5.0   22   2.50   72.73  29.597
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL243_5-D1
REMARK Aligment from pdb entry: 1pvmA
ATOM      1  N   VAL    11     -12.740 -11.540  10.960  1.00  0.00              
ATOM      2  CA  VAL    11     -12.003 -12.536  10.197  1.00  0.00              
ATOM      3  C   VAL    11     -10.907 -13.033  11.138  1.00  0.00              
ATOM      4  O   VAL    11     -10.291 -12.237  11.848  1.00  0.00              
ATOM      5  N   LEU    12     -10.665 -14.340  11.165  1.00  0.00              
ATOM      6  CA  LEU    12      -9.628 -14.874  12.042  1.00  0.00              
ATOM      7  C   LEU    12      -8.251 -14.561  11.464  1.00  0.00              
ATOM      8  O   LEU    12      -8.111 -14.289  10.271  1.00  0.00              
ATOM      9  N   LEU    13      -7.235 -14.598  12.317  1.00  0.00              
ATOM     10  CA  LEU    13      -5.872 -14.350  11.873  1.00  0.00              
ATOM     11  C   LEU    13      -5.524 -15.358  10.777  1.00  0.00              
ATOM     12  O   LEU    13      -4.872 -15.017   9.794  1.00  0.00              
ATOM     13  N   SER    14      -5.978 -16.598  10.950  1.00  0.00              
ATOM     14  CA  SER    14      -5.723 -17.668   9.987  1.00  0.00              
ATOM     15  C   SER    14      -6.249 -17.294   8.604  1.00  0.00              
ATOM     16  O   SER    14      -5.514 -17.330   7.620  1.00  0.00              
ATOM     17  N   ALA    15      -7.523 -16.925   8.531  1.00  0.00              
ATOM     18  CA  ALA    15      -8.114 -16.561   7.252  1.00  0.00              
ATOM     19  C   ALA    15      -7.503 -15.300   6.658  1.00  0.00              
ATOM     20  O   ALA    15      -7.318 -15.207   5.445  1.00  0.00              
ATOM     21  N   VAL    16      -7.189 -14.329   7.506  1.00  0.00              
ATOM     22  CA  VAL    16      -6.594 -13.090   7.021  1.00  0.00              
ATOM     23  C   VAL    16      -5.210 -13.336   6.427  1.00  0.00              
ATOM     24  O   VAL    16      -4.870 -12.781   5.382  1.00  0.00              
ATOM     25  N   GLY    17      -4.411 -14.165   7.090  1.00  0.00              
ATOM     26  CA  GLY    17      -3.066 -14.456   6.605  1.00  0.00              
ATOM     27  C   GLY    17      -3.109 -15.277   5.324  1.00  0.00              
ATOM     28  O   GLY    17      -2.238 -15.131   4.461  1.00  0.00              
ATOM     29  N   ALA    18      -4.116 -16.135   5.186  1.00  0.00              
ATOM     30  CA  ALA    18      -4.230 -16.914   3.961  1.00  0.00              
ATOM     31  C   ALA    18      -4.450 -15.944   2.802  1.00  0.00              
ATOM     32  O   ALA    18      -3.900 -16.129   1.715  1.00  0.00              
ATOM     33  N   LEU    19      -5.246 -14.905   3.039  1.00  0.00              
ATOM     34  CA  LEU    19      -5.512 -13.893   2.020  1.00  0.00              
ATOM     35  C   LEU    19      -4.213 -13.155   1.677  1.00  0.00              
ATOM     36  O   LEU    19      -3.912 -12.923   0.507  1.00  0.00              
ATOM     37  N   LEU    20      -3.443 -12.792   2.701  1.00  0.00              
ATOM     38  CA  LEU    20      -2.174 -12.099   2.489  1.00  0.00              
ATOM     39  C   LEU    20      -1.210 -12.958   1.680  1.00  0.00              
ATOM     40  O   LEU    20      -0.595 -12.488   0.718  1.00  0.00              
ATOM     41  N   ASP    21      -1.071 -14.219   2.079  1.00  0.00              
ATOM     42  CA  ASP    21      -0.170 -15.129   1.385  1.00  0.00              
ATOM     43  C   ASP    21      -0.582 -15.417  -0.051  1.00  0.00              
ATOM     44  O   ASP    21       0.267 -15.486  -0.930  1.00  0.00              
ATOM     45  N   GLY    22      -1.878 -15.571  -0.302  1.00  0.00              
ATOM     46  CA  GLY    22      -2.334 -15.868  -1.655  1.00  0.00              
ATOM     47  C   GLY    22      -2.229 -14.674  -2.599  1.00  0.00              
ATOM     48  O   GLY    22      -2.017 -14.846  -3.797  1.00  0.00              
ATOM     49  N   ALA    23      -2.352 -13.465  -2.059  1.00  0.00              
ATOM     50  CA  ALA    23      -2.269 -12.254  -2.872  1.00  0.00              
ATOM     51  C   ALA    23      -0.896 -11.585  -2.852  1.00  0.00              
ATOM     52  O   ALA    23      -0.638 -10.674  -3.640  1.00  0.00              
ATOM     53  N   ASP    24      -0.022 -12.034  -1.958  1.00  0.00              
ATOM     54  CA  ASP    24       1.304 -11.437  -1.824  1.00  0.00              
ATOM     55  C   ASP    24       1.156  -9.959  -1.454  1.00  0.00              
ATOM     56  O   ASP    24       1.886  -9.104  -1.950  1.00  0.00              
ATOM     57  N   ILE    25       0.181  -9.675  -0.599  1.00  0.00              
ATOM     58  CA  ILE    25      -0.083  -8.321  -0.109  1.00  0.00              
ATOM     59  C   ILE    25      -0.113  -8.457   1.401  1.00  0.00              
ATOM     60  O   ILE    25      -1.026  -9.066   1.957  1.00  0.00              
ATOM     61  N   GLY    26       0.885  -7.890   2.066  1.00  0.00              
ATOM     62  CA  GLY    26       0.983  -8.023   3.505  1.00  0.00              
ATOM     63  C   GLY    26       0.466  -6.844   4.302  1.00  0.00              
ATOM     64  O   GLY    26       1.056  -6.411   5.290  1.00  0.00              
ATOM     65  N   HIS    27      -0.676  -6.343   3.858  1.00  0.00              
ATOM     66  CA  HIS    27      -1.325  -5.234   4.522  1.00  0.00              
ATOM     67  C   HIS    27      -2.777  -5.245   4.084  1.00  0.00              
ATOM     68  O   HIS    27      -3.057  -5.183   2.888  1.00  0.00              
ATOM     69  N   LEU    28      -3.691  -5.346   5.043  1.00  0.00              
ATOM     70  CA  LEU    28      -5.117  -5.360   4.746  1.00  0.00              
ATOM     71  C   LEU    28      -5.865  -4.302   5.537  1.00  0.00              
ATOM     72  O   LEU    28      -5.613  -4.111   6.729  1.00  0.00              
ATOM     73  N   VAL    29      -9.071  -3.141   7.425  1.00  0.00              
ATOM     74  CA  VAL    29     -10.121  -3.868   8.128  1.00  0.00              
ATOM     75  C   VAL    29     -11.345  -2.987   8.354  1.00  0.00              
ATOM     76  O   VAL    29     -11.218  -1.836   8.774  1.00  0.00              
ATOM    121  N   PRO    45      -1.138  -5.796   9.631  1.00  0.00              
ATOM    122  CA  PRO    45       0.192  -5.860   9.038  1.00  0.00              
ATOM    123  C   PRO    45       0.932  -7.064   9.598  1.00  0.00              
ATOM    124  O   PRO    45       0.499  -7.661  10.584  1.00  0.00              
ATOM    125  N   ARG    46       2.056  -7.407   8.975  1.00  0.00              
ATOM    126  CA  ARG    46       2.867  -8.524   9.434  1.00  0.00              
ATOM    127  C   ARG    46       3.336  -8.302  10.861  1.00  0.00              
ATOM    128  O   ARG    46       3.245  -9.194  11.692  1.00  0.00              
ATOM    129  N   ARG    47       3.847  -7.104  11.136  1.00  0.00              
ATOM    130  CA  ARG    47       4.350  -6.784  12.465  1.00  0.00              
ATOM    131  C   ARG    47       3.262  -6.876  13.523  1.00  0.00              
ATOM    132  O   ARG    47       3.513  -7.335  14.635  1.00  0.00              
ATOM    133  N   VAL    48      -5.922  -7.758  16.857  1.00  0.00              
ATOM    134  CA  VAL    48      -4.529  -7.798  16.430  1.00  0.00              
ATOM    135  C   VAL    48      -4.105  -6.585  15.594  1.00  0.00              
ATOM    136  O   VAL    48      -3.020  -6.030  15.790  1.00  0.00              
ATOM    137  N   LEU    49      -4.969  -6.187  14.669  1.00  0.00              
ATOM    138  CA  LEU    49      -4.724  -5.066  13.760  1.00  0.00              
ATOM    139  C   LEU    49      -4.328  -3.759  14.434  1.00  0.00              
ATOM    140  O   LEU    49      -4.658  -3.519  15.603  1.00  0.00              
ATOM    141  N   VAL    50      -3.628  -2.914  13.677  1.00  0.00              
ATOM    142  CA  VAL    50      -3.246  -1.597  14.169  1.00  0.00              
ATOM    143  C   VAL    50      -4.550  -0.814  14.265  1.00  0.00              
ATOM    144  O   VAL    50      -5.313  -0.741  13.294  1.00  0.00              
ATOM    145  N   HIS    51      -4.795  -0.243  15.438  1.00  0.00              
ATOM    146  CA  HIS    51      -6.002   0.526  15.708  1.00  0.00              
ATOM    147  C   HIS    51      -5.666   1.582  16.761  1.00  0.00              
ATOM    148  O   HIS    51      -4.989   1.280  17.739  1.00  0.00              
ATOM    149  N   GLU    52      -3.891  14.278   0.201  1.00  0.00              
ATOM    150  CA  GLU    52      -3.157  15.448  -0.274  1.00  0.00              
ATOM    151  C   GLU    52      -1.784  15.617   0.389  1.00  0.00              
ATOM    152  O   GLU    52      -1.064  16.581   0.112  1.00  0.00              
ATOM    153  N   ASP    53      -1.426  14.683   1.266  1.00  0.00              
ATOM    154  CA  ASP    53      -0.132  14.723   1.942  1.00  0.00              
ATOM    155  C   ASP    53       0.995  14.552   0.932  1.00  0.00              
ATOM    156  O   ASP    53       0.873  13.777  -0.019  1.00  0.00              
ATOM    157  N   ASP    54       2.096  15.267   1.141  1.00  0.00              
ATOM    158  CA  ASP    54       3.249  15.132   0.266  1.00  0.00              
ATOM    159  C   ASP    54       3.954  13.862   0.745  1.00  0.00              
ATOM    160  O   ASP    54       3.885  13.525   1.929  1.00  0.00              
ATOM    161  N   LEU    55       4.626  13.160  -0.161  1.00  0.00              
ATOM    162  CA  LEU    55       5.318  11.933   0.220  1.00  0.00              
ATOM    163  C   LEU    55       6.254  12.133   1.402  1.00  0.00              
ATOM    164  O   LEU    55       6.458  11.211   2.192  1.00  0.00              
ATOM    165  N   ALA    56       6.823  13.327   1.536  1.00  0.00              
ATOM    166  CA  ALA    56       7.721  13.594   2.660  1.00  0.00              
ATOM    167  C   ALA    56       6.937  13.629   3.968  1.00  0.00              
ATOM    168  O   ALA    56       7.458  13.275   5.029  1.00  0.00              
ATOM    169  N   GLY    57       5.683  14.059   3.892  1.00  0.00              
ATOM    170  CA  GLY    57       4.839  14.126   5.076  1.00  0.00              
ATOM    171  C   GLY    57       4.456  12.712   5.493  1.00  0.00              
ATOM    172  O   GLY    57       4.387  12.398   6.681  1.00  0.00              
ATOM    173  N   ALA    58       4.203  11.862   4.506  1.00  0.00              
ATOM    174  CA  ALA    58       3.848  10.476   4.781  1.00  0.00              
ATOM    175  C   ALA    58       5.040   9.774   5.423  1.00  0.00              
ATOM    176  O   ALA    58       4.878   9.022   6.383  1.00  0.00              
ATOM    177  N   ARG    59       6.237  10.025   4.898  1.00  0.00              
ATOM    178  CA  ARG    59       7.444   9.417   5.447  1.00  0.00              
ATOM    179  C   ARG    59       7.589   9.782   6.924  1.00  0.00              
ATOM    180  O   ARG    59       7.898   8.930   7.757  1.00  0.00              
ATOM    181  N   ARG    60       7.363  11.053   7.245  1.00  0.00              
ATOM    182  CA  ARG    60       7.470  11.523   8.621  1.00  0.00              
ATOM    183  C   ARG    60       6.435  10.831   9.506  1.00  0.00              
ATOM    184  O   ARG    60       6.713  10.478  10.656  1.00  0.00              
ATOM    185  N   LEU    61       5.238  10.641   8.959  1.00  0.00              
ATOM    186  CA  LEU    61       4.165   9.984   9.689  1.00  0.00              
ATOM    187  C   LEU    61       4.508   8.519   9.955  1.00  0.00              
ATOM    188  O   LEU    61       4.357   8.029  11.077  1.00  0.00              
ATOM    189  N   LEU    62       4.955   7.814   8.921  1.00  0.00              
ATOM    190  CA  LEU    62       5.301   6.409   9.086  1.00  0.00              
ATOM    191  C   LEU    62       6.414   6.259  10.111  1.00  0.00              
ATOM    192  O   LEU    62       6.304   5.464  11.042  1.00  0.00              
ATOM    193  N   THR    63       7.481   7.031   9.934  1.00  0.00              
ATOM    194  CA  THR    63       8.628   6.975  10.834  1.00  0.00              
ATOM    195  C   THR    63       8.265   7.299  12.284  1.00  0.00              
ATOM    196  O   THR    63       8.729   6.641  13.212  1.00  0.00              
ATOM    197  N   ASP    64       7.442   8.321  12.475  1.00  0.00              
ATOM    198  CA  ASP    64       7.026   8.722  13.812  1.00  0.00              
ATOM    199  C   ASP    64       6.270   7.586  14.509  1.00  0.00              
ATOM    200  O   ASP    64       6.332   7.431  15.732  1.00  0.00              
ATOM    201  N   ALA    65       5.571   6.784  13.711  1.00  0.00              
ATOM    202  CA  ALA    65       4.759   5.687  14.228  1.00  0.00              
ATOM    203  C   ALA    65       5.344   4.289  14.104  1.00  0.00              
ATOM    204  O   ALA    65       4.679   3.316  14.467  1.00  0.00              
ATOM    205  N   GLY    66       6.572   4.190  13.601  1.00  0.00              
ATOM    206  CA  GLY    66       7.217   2.897  13.432  1.00  0.00              
ATOM    207  C   GLY    66       6.515   2.002  12.424  1.00  0.00              
ATOM    208  O   GLY    66       6.558   0.775  12.532  1.00  0.00              
ATOM    209  N   LEU    67       5.883   2.618  11.433  1.00  0.00              
ATOM    210  CA  LEU    67       5.141   1.897  10.401  1.00  0.00              
ATOM    211  C   LEU    67       5.885   1.799   9.070  1.00  0.00              
ATOM    212  O   LEU    67       6.789   2.590   8.798  1.00  0.00              
ATOM    213  N   ALA    68       5.503   0.825   8.244  1.00  0.00              
ATOM    214  CA  ALA    68       6.089   0.698   6.913  1.00  0.00              
ATOM    215  C   ALA    68       4.985   0.818   5.852  1.00  0.00              
ATOM    216  O   ALA    68       5.231   0.702   4.652  1.00  0.00              
END
