
#######################################################
#                                                     #
#                        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   38 (  152),  selected   38 , name T0349AL381_4-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL381_4-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      13      M       1           -
LGA    S      14      R       2           -
LGA    A      15      E       3           -
LGA    V      16      L       4           -
LGA    G      17      L       5           -
LGA    A      18      R       6           -
LGA    L      19      T       7           -
LGA    -       -      N       8           -
LGA    L      20      D       9           #
LGA    D      24      A      10          4.380
LGA    I      25      V      11          2.629
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    -       -      S      14           -
LGA    G      26      A      15          1.104
LGA    H      27      V      16          3.183
LGA    L      28      G      17          3.340
LGA    -       -      A      18           -
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    V      29      D      21          0.781
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    -       -      I      25           -
LGA    -       -      G      26           -
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    P      45      R      47          3.211
LGA    R      46      V      48           -
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      L      49          4.072
LGA    -       -      V      50           -
LGA    V      50      H      51          2.828
LGA    H      51      E      52          3.871
LGA    E      52      D      53          2.927
LGA    D      53      D      54          2.773
LGA    D      54      -       -           -
LGA    L      55      L      55          0.956
LGA    A      56      A      56          2.441
LGA    G      57      G      57          2.754
LGA    A      58      A      58          1.713
LGA    R      59      R      59          0.654
LGA    R      60      R      60          1.612
LGA    L      61      L      61          3.006
LGA    L      62      L      62          2.809
LGA    T      63      T      63          1.291
LGA    D      64      D      64          3.304
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    A      65      L      67          1.095
LGA    G      66      A      68          1.375
LGA    L      67      H      69          2.504
LGA    -       -      E      70           -
LGA    A      68      L      71          2.071
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   38   57    5.0     26    2.62    46.15     33.132     0.955

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.494645 * X  +   0.849560 * Y  +  -0.183231 * Z  +  13.743636
  Y_new =   0.834244 * X  +   0.405032 * Y  +  -0.374147 * Z  + -62.886547
  Z_new =  -0.243646 * X  +  -0.337929 * Y  +  -0.909088 * Z  +  44.917934 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.785698    0.355895  [ DEG:  -159.6087     20.3913 ]
  Theta =   0.246123    2.895469  [ DEG:    14.1018    165.8982 ]
  Phi   =   2.105998   -1.035594  [ DEG:   120.6648    -59.3352 ]
 
# 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: T0349AL381_4-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL381_4-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38   57   5.0   26   2.62   46.15  33.132
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL381_4-D1
REMARK Aligment from pdb entry: 1g61A
ATOM      1  N   LEU    13     -12.632   4.968  10.832  1.00  0.00              
ATOM      2  CA  LEU    13     -11.251   4.511  10.658  1.00  0.00              
ATOM      3  C   LEU    13     -11.016   3.242  11.454  1.00  0.00              
ATOM      4  O   LEU    13     -10.419   2.279  10.955  1.00  0.00              
ATOM      5  N   SER    14     -11.495   3.213  12.726  1.00  0.00              
ATOM      6  CA  SER    14     -11.267   2.013  13.526  1.00  0.00              
ATOM      7  C   SER    14     -11.966   0.788  12.939  1.00  0.00              
ATOM      8  O   SER    14     -11.377  -0.305  12.997  1.00  0.00              
ATOM      9  N   ALA    15     -13.164   0.948  12.388  1.00  0.00              
ATOM     10  CA  ALA    15     -13.897  -0.179  11.809  1.00  0.00              
ATOM     11  C   ALA    15     -13.121  -0.724  10.620  1.00  0.00              
ATOM     12  O   ALA    15     -12.979  -1.954  10.446  1.00  0.00              
ATOM     13  N   VAL    16     -12.575   0.140   9.761  1.00  0.00              
ATOM     14  CA  VAL    16     -11.775  -0.313   8.632  1.00  0.00              
ATOM     15  C   VAL    16     -10.496  -1.010   9.077  1.00  0.00              
ATOM     16  O   VAL    16     -10.137  -2.111   8.638  1.00  0.00              
ATOM     17  N   GLY    17      -9.802  -0.421  10.044  1.00  0.00              
ATOM     18  CA  GLY    17      -8.584  -0.987  10.581  1.00  0.00              
ATOM     19  C   GLY    17      -8.846  -2.373  11.139  1.00  0.00              
ATOM     20  O   GLY    17      -8.039  -3.299  10.964  1.00  0.00              
ATOM     21  N   ALA    18      -9.953  -2.572  11.825  1.00  0.00              
ATOM     22  CA  ALA    18     -10.238  -3.853  12.458  1.00  0.00              
ATOM     23  C   ALA    18     -10.521  -4.904  11.423  1.00  0.00              
ATOM     24  O   ALA    18     -10.110  -6.050  11.528  1.00  0.00              
ATOM     25  N   LEU    19     -11.317  -4.583  10.386  1.00  0.00              
ATOM     26  CA  LEU    19     -11.662  -5.651   9.448  1.00  0.00              
ATOM     27  C   LEU    19     -10.526  -5.974   8.505  1.00  0.00              
ATOM     28  O   LEU    19     -10.329  -7.141   8.142  1.00  0.00              
ATOM     29  N   LEU    20      -9.726  -4.984   8.119  1.00  0.00              
ATOM     30  CA  LEU    20      -8.589  -5.260   7.225  1.00  0.00              
ATOM     31  C   LEU    20      -7.342  -5.657   7.985  1.00  0.00              
ATOM     32  O   LEU    20      -6.381  -6.170   7.374  1.00  0.00              
ATOM     33  N   ASP    24      -7.327  -5.434   9.299  1.00  0.00              
ATOM     34  CA  ASP    24      -6.169  -5.705  10.196  1.00  0.00              
ATOM     35  C   ASP    24      -4.960  -4.928   9.688  1.00  0.00              
ATOM     36  O   ASP    24      -3.896  -5.485   9.496  1.00  0.00              
ATOM     37  N   ILE    25      -5.098  -3.624   9.476  1.00  0.00              
ATOM     38  CA  ILE    25      -4.044  -2.799   8.898  1.00  0.00              
ATOM     39  C   ILE    25      -3.779  -1.563   9.762  1.00  0.00              
ATOM     40  O   ILE    25      -4.624  -1.254  10.619  1.00  0.00              
ATOM     41  N   GLY    26      -2.692  -0.871   9.523  1.00  0.00              
ATOM     42  CA  GLY    26      -2.391   0.461   9.998  1.00  0.00              
ATOM     43  C   GLY    26      -2.972   1.462   8.988  1.00  0.00              
ATOM     44  O   GLY    26      -2.706   1.349   7.789  1.00  0.00              
ATOM     45  N   HIS    27      -3.759   2.394   9.475  1.00  0.00              
ATOM     46  CA  HIS    27      -4.506   3.297   8.618  1.00  0.00              
ATOM     47  C   HIS    27      -3.905   4.691   8.669  1.00  0.00              
ATOM     48  O   HIS    27      -3.619   5.199   9.752  1.00  0.00              
ATOM     49  N   LEU    28      -3.734   5.280   7.515  1.00  0.00              
ATOM     50  CA  LEU    28      -3.322   6.675   7.392  1.00  0.00              
ATOM     51  C   LEU    28      -4.409   7.478   6.686  1.00  0.00              
ATOM     52  O   LEU    28      -4.826   7.077   5.572  1.00  0.00              
ATOM     53  N   VAL    29      -4.843   8.579   7.291  1.00  0.00              
ATOM     54  CA  VAL    29      -5.721   9.520   6.603  1.00  0.00              
ATOM     55  C   VAL    29      -4.857  10.585   5.955  1.00  0.00              
ATOM     56  O   VAL    29      -4.056  11.236   6.618  1.00  0.00              
ATOM    117  N   PRO    45       1.360  -1.983  -2.769  1.00  0.00              
ATOM    118  CA  PRO    45       1.368  -3.412  -2.405  1.00  0.00              
ATOM    119  C   PRO    45       2.384  -3.541  -1.265  1.00  0.00              
ATOM    120  O   PRO    45       2.733  -2.531  -0.622  1.00  0.00              
ATOM    121  N   ARG    46       2.843  -4.764  -0.975  1.00  0.00              
ATOM    122  CA  ARG    46       3.800  -4.921   0.155  1.00  0.00              
ATOM    123  C   ARG    46       5.120  -4.212  -0.125  1.00  0.00              
ATOM    124  O   ARG    46       5.832  -3.836   0.825  1.00  0.00              
ATOM    125  N   ARG    47       5.465  -4.057  -1.401  1.00  0.00              
ATOM    126  CA  ARG    47       6.793  -3.585  -1.817  1.00  0.00              
ATOM    127  C   ARG    47       6.843  -2.110  -2.188  1.00  0.00              
ATOM    128  O   ARG    47       7.921  -1.513  -2.022  1.00  0.00              
ATOM    129  N   VAL    48       5.740  -1.554  -2.700  1.00  0.00              
ATOM    130  CA  VAL    48       5.847  -0.229  -3.273  1.00  0.00              
ATOM    131  C   VAL    48       4.577   0.564  -3.092  1.00  0.00              
ATOM    132  O   VAL    48       3.481   0.012  -2.834  1.00  0.00              
ATOM    133  N   LEU    49       4.703   1.870  -3.243  1.00  0.00              
ATOM    134  CA  LEU    49       3.579   2.812  -3.212  1.00  0.00              
ATOM    135  C   LEU    49       3.765   3.752  -4.381  1.00  0.00              
ATOM    136  O   LEU    49       4.814   4.423  -4.441  1.00  0.00              
ATOM    137  N   VAL    50       1.128  14.815  -6.417  1.00  0.00              
ATOM    138  CA  VAL    50       1.253  14.712  -4.964  1.00  0.00              
ATOM    139  C   VAL    50       2.015  15.925  -4.455  1.00  0.00              
ATOM    140  O   VAL    50       2.985  16.384  -5.060  1.00  0.00              
ATOM    141  N   HIS    51       1.579  16.466  -3.326  1.00  0.00              
ATOM    142  CA  HIS    51       2.163  17.685  -2.781  1.00  0.00              
ATOM    143  C   HIS    51       3.266  17.367  -1.803  1.00  0.00              
ATOM    144  O   HIS    51       3.245  16.290  -1.192  1.00  0.00              
ATOM    145  N   GLU    52       4.252  18.237  -1.628  1.00  0.00              
ATOM    146  CA  GLU    52       5.353  17.940  -0.722  1.00  0.00              
ATOM    147  C   GLU    52       4.891  17.600   0.670  1.00  0.00              
ATOM    148  O   GLU    52       5.434  16.673   1.289  1.00  0.00              
ATOM    149  N   ASP    53       3.913  18.289   1.222  1.00  0.00              
ATOM    150  CA  ASP    53       3.454  18.005   2.594  1.00  0.00              
ATOM    151  C   ASP    53       2.796  16.640   2.625  1.00  0.00              
ATOM    152  O   ASP    53       2.927  15.953   3.641  1.00  0.00              
ATOM    153  N   ASP    54       2.107  16.267   1.547  1.00  0.00              
ATOM    154  CA  ASP    54       1.473  14.933   1.512  1.00  0.00              
ATOM    155  C   ASP    54       2.514  13.834   1.472  1.00  0.00              
ATOM    156  O   ASP    54       2.407  12.834   2.161  1.00  0.00              
ATOM    157  N   LEU    55       3.543  14.011   0.642  1.00  0.00              
ATOM    158  CA  LEU    55       4.629  13.060   0.558  1.00  0.00              
ATOM    159  C   LEU    55       5.308  12.923   1.917  1.00  0.00              
ATOM    160  O   LEU    55       5.565  11.829   2.387  1.00  0.00              
ATOM    161  N   ALA    56       5.588  14.054   2.566  1.00  0.00              
ATOM    162  CA  ALA    56       6.170  14.040   3.875  1.00  0.00              
ATOM    163  C   ALA    56       5.305  13.257   4.885  1.00  0.00              
ATOM    164  O   ALA    56       5.840  12.437   5.676  1.00  0.00              
ATOM    165  N   GLY    57       4.015  13.496   4.902  1.00  0.00              
ATOM    166  CA  GLY    57       3.053  12.858   5.779  1.00  0.00              
ATOM    167  C   GLY    57       3.079  11.342   5.548  1.00  0.00              
ATOM    168  O   GLY    57       3.092  10.539   6.501  1.00  0.00              
ATOM    169  N   ALA    58       3.042  10.954   4.283  1.00  0.00              
ATOM    170  CA  ALA    58       3.053   9.514   3.968  1.00  0.00              
ATOM    171  C   ALA    58       4.364   8.866   4.366  1.00  0.00              
ATOM    172  O   ALA    58       4.349   7.800   5.013  1.00  0.00              
ATOM    173  N   ARG    59       5.498   9.448   4.045  1.00  0.00              
ATOM    174  CA  ARG    59       6.778   8.834   4.416  1.00  0.00              
ATOM    175  C   ARG    59       6.918   8.804   5.932  1.00  0.00              
ATOM    176  O   ARG    59       7.485   7.824   6.458  1.00  0.00              
ATOM    177  N   ARG    60       6.432   9.811   6.643  1.00  0.00              
ATOM    178  CA  ARG    60       6.531   9.790   8.107  1.00  0.00              
ATOM    179  C   ARG    60       5.705   8.635   8.669  1.00  0.00              
ATOM    180  O   ARG    60       6.175   7.923   9.586  1.00  0.00              
ATOM    181  N   LEU    61       4.505   8.418   8.160  1.00  0.00              
ATOM    182  CA  LEU    61       3.663   7.295   8.593  1.00  0.00              
ATOM    183  C   LEU    61       4.360   5.975   8.340  1.00  0.00              
ATOM    184  O   LEU    61       4.381   5.067   9.186  1.00  0.00              
ATOM    185  N   LEU    62       4.980   5.827   7.162  1.00  0.00              
ATOM    186  CA  LEU    62       5.705   4.562   6.877  1.00  0.00              
ATOM    187  C   LEU    62       6.849   4.410   7.869  1.00  0.00              
ATOM    188  O   LEU    62       7.056   3.302   8.422  1.00  0.00              
ATOM    189  N   THR    63       7.619   5.454   8.127  1.00  0.00              
ATOM    190  CA  THR    63       8.777   5.360   9.028  1.00  0.00              
ATOM    191  C   THR    63       8.304   4.973  10.417  1.00  0.00              
ATOM    192  O   THR    63       8.892   4.126  11.120  1.00  0.00              
ATOM    193  N   ASP    64       7.250   5.624  10.911  1.00  0.00              
ATOM    194  CA  ASP    64       6.697   5.359  12.247  1.00  0.00              
ATOM    195  C   ASP    64       6.286   3.913  12.436  1.00  0.00              
ATOM    196  O   ASP    64       6.295   3.386  13.560  1.00  0.00              
ATOM    197  N   ALA    65       5.897   3.248  11.344  1.00  0.00              
ATOM    198  CA  ALA    65       5.480   1.871  11.368  1.00  0.00              
ATOM    199  C   ALA    65       6.553   0.912  10.890  1.00  0.00              
ATOM    200  O   ALA    65       6.293  -0.287  10.687  1.00  0.00              
ATOM    201  N   GLY    66       7.770   1.425  10.731  1.00  0.00              
ATOM    202  CA  GLY    66       8.890   0.596  10.236  1.00  0.00              
ATOM    203  C   GLY    66       8.599  -0.101   8.919  1.00  0.00              
ATOM    204  O   GLY    66       9.029  -1.253   8.709  1.00  0.00              
ATOM    205  N   LEU    67       7.932   0.589   8.006  1.00  0.00              
ATOM    206  CA  LEU    67       7.587   0.062   6.708  1.00  0.00              
ATOM    207  C   LEU    67       8.504   0.637   5.633  1.00  0.00              
ATOM    208  O   LEU    67       8.565   1.851   5.436  1.00  0.00              
ATOM    209  N   ALA    68       9.201  -0.232   4.953  1.00  0.00              
ATOM    210  CA  ALA    68      10.155   0.147   3.921  1.00  0.00              
ATOM    211  C   ALA    68       9.548  -0.187   2.565  1.00  0.00              
ATOM    212  O   ALA    68       9.641  -1.345   2.116  1.00  0.00              
END
