
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0314AL243_1-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314AL243_1-D1.T0314_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      S       2           -
LGA    -       -      I       3           -
LGA    -       -      T       4           -
LGA    -       -      S       5           -
LGA    -       -      T       6           -
LGA    -       -      D       7           -
LGA    -       -      I       8           -
LGA    -       -      C       9           -
LGA    -       -      Q      10           -
LGA    -       -      A      11           -
LGA    -       -      A      12           -
LGA    -       -      D      13           -
LGA    -       -      A      14           -
LGA    -       -      L      15           -
LGA    -       -      K      16           -
LGA    -       -      G      17           -
LGA    -       -      F      18           -
LGA    -       -      V      19           -
LGA    -       -      G      20           -
LGA    -       -      F      21           -
LGA    -       -      N      22           -
LGA    -       -      R      23           -
LGA    -       -      K      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    -       -      R      27           -
LGA    -       -      Y      28           -
LGA    -       -      I      29           -
LGA    -       -      V      30           -
LGA    -       -      R      31           -
LGA    -       -      F      32           -
LGA    -       -      S      33           -
LGA    -       -      E      34           -
LGA    -       -      D      35           -
LGA    -       -      S      36           -
LGA    -       -      F      37           -
LGA    -       -      G      38           -
LGA    -       -      M      39           -
LGA    -       -      D      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      D      43           -
LGA    -       -      D      44           -
LGA    Q      10      S      45          4.719
LGA    -       -      I      46           -
LGA    -       -      T      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      S      50           -
LGA    -       -      E      51           -
LGA    A      11      F      52          3.602
LGA    A      12      V      53           -
LGA    D      13      W      54           -
LGA    A      14      S      55          4.667
LGA    L      15      -       -           -
LGA    K      16      -       -           -
LGA    G      17      S      56          4.171
LGA    R      23      V      57          2.315
LGA    K      24      R      58          3.096
LGA    -       -      D      59           -
LGA    -       -      D      60           -
LGA    T      25      V      61          1.996
LGA    G      26      M      62          4.446
LGA    R      27      R      63          0.510
LGA    Y      28      L      64          0.916
LGA    I      29      G      65          1.996
LGA    V      30      R      66          2.908
LGA    -       -      E      67           -
LGA    -       -      Q      68           -
LGA    R      31      L      69          2.113
LGA    -       -      Q      70           -
LGA    -       -      I      71           -
LGA    F      32      L      72          0.924
LGA    S      33      L      73           #
LGA    E      34      E      74          4.766
LGA    -       -      Q      75           -
LGA    D      35      N      76          2.145
LGA    S      36      I      77          3.461
LGA    -       -      N      78           -
LGA    -       -      E      79           -
LGA    -       -      R      80           -
LGA    -       -      L      81           -
LGA    -       -      N      82           -
LGA    F      37      I      83          4.366
LGA    G      38      G      84           #
LGA    M      39      -       -           -
LGA    D      40      -       -           -
LGA    V      41      -       -           -
LGA    A      42      -       -           -
LGA    D      43      -       -           -
LGA    D      44      -       -           -
LGA    S      45      E      85          5.119
LGA    I      46      P      86           #
LGA    T      47      L      87           -
LGA    P      48      -       -           -
LGA    T      49      -       -           -
LGA    S      50      -       -           -
LGA    E      51      -       -           -
LGA    F      52      -       -           -
LGA    E      67      -       -           -
LGA    Q      68      L      88           #
LGA    L      69      V      89          3.160
LGA    -       -      Y      90           -
LGA    Q      70      L      91          4.422
LGA    I      71      R      92          4.477
LGA    L      72      R      93          4.101
LGA    L      73      -       -           -
LGA    E      74      Q      94          2.240
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      P      97           -
LGA    -       -      E      98           -
LGA    -       -      I      99           -
LGA    -       -      T     100           -
LGA    -       -      A     101           -
LGA    -       -      Q     102           -
LGA    -       -      R     103           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46  103    5.0     24    3.46     8.33     13.670     0.673

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.329472 * X  +  -0.245471 * Y  +   0.911697 * Z  +  36.488770
  Y_new =   0.943927 * X  +  -0.063952 * Y  +   0.323900 * Z  + -74.172455
  Z_new =  -0.021203 * X  +   0.967292 * Y  +   0.252777 * Z  + -12.986684 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.315188   -1.826405  [ DEG:    75.3547   -104.6453 ]
  Theta =   0.021205    3.120388  [ DEG:     1.2150    178.7850 ]
  Phi   =   1.906619   -1.234974  [ DEG:   109.2412    -70.7588 ]
 
# 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: T0314AL243_1-D1                               
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314AL243_1-D1.T0314_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46  103   5.0   24   3.46    8.33  13.670
REMARK  ---------------------------------------------------------- 
MOLECULE T0314AL243_1-D1
REMARK Aligment from pdb entry: 1bfi_
ATOM      1  N   GLN    10      20.011   6.553 -24.057  1.00  0.00              
ATOM      2  CA  GLN    10      18.810   6.747 -24.909  1.00  0.00              
ATOM      3  C   GLN    10      17.790   7.570 -24.123  1.00  0.00              
ATOM      4  O   GLN    10      17.076   8.389 -24.670  1.00  0.00              
ATOM      5  N   ALA    11      17.715   7.348 -22.840  1.00  0.00              
ATOM      6  CA  ALA    11      16.751   8.105 -22.000  1.00  0.00              
ATOM      7  C   ALA    11      17.046   9.604 -22.100  1.00  0.00              
ATOM      8  O   ALA    11      16.147  10.419 -22.118  1.00  0.00              
ATOM      9  N   ALA    12      18.296   9.976 -22.166  1.00  0.00              
ATOM     10  CA  ALA    12      18.624  11.425 -22.265  1.00  0.00              
ATOM     11  C   ALA    12      17.946  11.988 -23.513  1.00  0.00              
ATOM     12  O   ALA    12      17.331  13.033 -23.478  1.00  0.00              
ATOM     13  N   ASP    13      18.037  11.290 -24.611  1.00  0.00              
ATOM     14  CA  ASP    13      17.379  11.770 -25.851  1.00  0.00              
ATOM     15  C   ASP    13      15.872  11.832 -25.603  1.00  0.00              
ATOM     16  O   ASP    13      15.209  12.794 -25.945  1.00  0.00              
ATOM     17  N   ALA    14      15.331  10.817 -24.983  1.00  0.00              
ATOM     18  CA  ALA    14      13.875  10.808 -24.686  1.00  0.00              
ATOM     19  C   ALA    14      13.564  11.940 -23.712  1.00  0.00              
ATOM     20  O   ALA    14      12.569  12.623 -23.829  1.00  0.00              
ATOM     21  N   LEU    15      14.422  12.146 -22.749  1.00  0.00              
ATOM     22  CA  LEU    15      14.190  13.239 -21.766  1.00  0.00              
ATOM     23  C   LEU    15      14.520  14.566 -22.439  1.00  0.00              
ATOM     24  O   LEU    15      13.943  15.594 -22.144  1.00  0.00              
ATOM     25  N   LYS    16      15.433  14.535 -23.364  1.00  0.00              
ATOM     26  CA  LYS    16      15.805  15.767 -24.096  1.00  0.00              
ATOM     27  C   LYS    16      14.771  16.052 -25.180  1.00  0.00              
ATOM     28  O   LYS    16      14.344  15.164 -25.890  1.00  0.00              
ATOM     29  N   GLY    17      14.363  17.283 -25.316  1.00  0.00              
ATOM     30  CA  GLY    17      13.362  17.623 -26.366  1.00  0.00              
ATOM     31  C   GLY    17      11.951  17.562 -25.779  1.00  0.00              
ATOM     32  O   GLY    17      10.988  17.943 -26.412  1.00  0.00              
ATOM     33  N   ARG    23      11.819  17.075 -24.579  1.00  0.00              
ATOM     34  CA  ARG    23      10.474  16.978 -23.958  1.00  0.00              
ATOM     35  C   ARG    23      10.224  18.197 -23.064  1.00  0.00              
ATOM     36  O   ARG    23      11.086  18.631 -22.329  1.00  0.00              
ATOM     37  N   LYS    24       9.041  18.742 -23.123  1.00  0.00              
ATOM     38  CA  LYS    24       8.722  19.930 -22.276  1.00  0.00              
ATOM     39  C   LYS    24       8.655  19.499 -20.809  1.00  0.00              
ATOM     40  O   LYS    24       8.547  18.330 -20.502  1.00  0.00              
ATOM     41  N   THR    25       8.730  20.434 -19.906  1.00  0.00              
ATOM     42  CA  THR    25       8.677  20.079 -18.459  1.00  0.00              
ATOM     43  C   THR    25       7.346  19.381 -18.161  1.00  0.00              
ATOM     44  O   THR    25       6.319  19.728 -18.710  1.00  0.00              
ATOM     45  N   GLY    26       7.351  18.400 -17.298  1.00  0.00              
ATOM     46  CA  GLY    26       6.080  17.683 -16.972  1.00  0.00              
ATOM     47  C   GLY    26       6.123  16.274 -17.561  1.00  0.00              
ATOM     48  O   GLY    26       5.546  15.345 -17.028  1.00  0.00              
ATOM     49  N   ARG    27       6.807  16.104 -18.653  1.00  0.00              
ATOM     50  CA  ARG    27       6.897  14.757 -19.274  1.00  0.00              
ATOM     51  C   ARG    27       7.877  13.899 -18.468  1.00  0.00              
ATOM     52  O   ARG    27       8.944  14.347 -18.098  1.00  0.00              
ATOM     53  N   TYR    28       7.534  12.665 -18.195  1.00  0.00              
ATOM     54  CA  TYR    28       8.470  11.801 -17.423  1.00  0.00              
ATOM     55  C   TYR    28       8.435  10.391 -18.003  1.00  0.00              
ATOM     56  O   TYR    28       7.531  10.034 -18.727  1.00  0.00              
ATOM     57  N   ILE    29       9.409   9.592 -17.698  1.00  0.00              
ATOM     58  CA  ILE    29       9.414   8.212 -18.243  1.00  0.00              
ATOM     59  C   ILE    29       9.752   7.232 -17.121  1.00  0.00              
ATOM     60  O   ILE    29      10.405   7.578 -16.157  1.00  0.00              
ATOM     61  N   VAL    30       9.323   6.012 -17.251  1.00  0.00              
ATOM     62  CA  VAL    30       9.627   5.001 -16.208  1.00  0.00              
ATOM     63  C   VAL    30      10.549   3.957 -16.822  1.00  0.00              
ATOM     64  O   VAL    30      10.369   3.557 -17.955  1.00  0.00              
ATOM     65  N   ARG    31      11.545   3.521 -16.107  1.00  0.00              
ATOM     66  CA  ARG    31      12.475   2.518 -16.690  1.00  0.00              
ATOM     67  C   ARG    31      13.042   1.649 -15.577  1.00  0.00              
ATOM     68  O   ARG    31      12.881   1.939 -14.407  1.00  0.00              
ATOM     69  N   PHE    32      13.720   0.590 -15.917  1.00  0.00              
ATOM     70  CA  PHE    32      14.301  -0.277 -14.865  1.00  0.00              
ATOM     71  C   PHE    32      15.784   0.033 -14.736  1.00  0.00              
ATOM     72  O   PHE    32      16.335   0.789 -15.508  1.00  0.00              
ATOM     73  N   SER    33      16.447  -0.575 -13.799  1.00  0.00              
ATOM     74  CA  SER    33      17.900  -0.334 -13.682  1.00  0.00              
ATOM     75  C   SER    33      18.532  -1.174 -14.784  1.00  0.00              
ATOM     76  O   SER    33      19.734  -1.320 -14.890  1.00  0.00              
ATOM     77  N   GLU    34      17.672  -1.700 -15.619  1.00  0.00              
ATOM     78  CA  GLU    34      18.083  -2.532 -16.782  1.00  0.00              
ATOM     79  C   GLU    34      18.273  -3.991 -16.354  1.00  0.00              
ATOM     80  O   GLU    34      17.440  -4.833 -16.613  1.00  0.00              
ATOM     81  N   ASP    35      16.967  -5.484 -10.398  1.00  0.00              
ATOM     82  CA  ASP    35      15.494  -5.431 -10.171  1.00  0.00              
ATOM     83  C   ASP    35      15.074  -4.062  -9.621  1.00  0.00              
ATOM     84  O   ASP    35      13.929  -3.856  -9.275  1.00  0.00              
ATOM     85  N   SER    36      15.980  -3.126  -9.529  1.00  0.00              
ATOM     86  CA  SER    36      15.603  -1.784  -8.996  1.00  0.00              
ATOM     87  C   SER    36      14.895  -0.990 -10.096  1.00  0.00              
ATOM     88  O   SER    36      15.231  -1.088 -11.259  1.00  0.00              
ATOM     89  N   PHE    37      13.911  -0.209  -9.740  1.00  0.00              
ATOM     90  CA  PHE    37      13.176   0.583 -10.769  1.00  0.00              
ATOM     91  C   PHE    37      13.439   2.075 -10.562  1.00  0.00              
ATOM     92  O   PHE    37      13.862   2.502  -9.505  1.00  0.00              
ATOM     93  N   GLY    38      13.197   2.878 -11.563  1.00  0.00              
ATOM     94  CA  GLY    38      13.437   4.335 -11.412  1.00  0.00              
ATOM     95  C   GLY    38      12.735   5.084 -12.544  1.00  0.00              
ATOM     96  O   GLY    38      12.674   4.617 -13.665  1.00  0.00              
ATOM     97  N   MET    39      12.215   6.248 -12.274  1.00  0.00              
ATOM     98  CA  MET    39      11.541   7.016 -13.354  1.00  0.00              
ATOM     99  C   MET    39      12.251   8.347 -13.494  1.00  0.00              
ATOM    100  O   MET    39      12.599   8.984 -12.523  1.00  0.00              
ATOM    101  N   ASP    40      12.489   8.766 -14.693  1.00  0.00              
ATOM    102  CA  ASP    40      13.203  10.050 -14.881  1.00  0.00              
ATOM    103  C   ASP    40      12.216  11.121 -15.325  1.00  0.00              
ATOM    104  O   ASP    40      11.284  10.861 -16.059  1.00  0.00              
ATOM    105  N   VAL    41      12.403  12.324 -14.865  1.00  0.00              
ATOM    106  CA  VAL    41      11.466  13.406 -15.238  1.00  0.00              
ATOM    107  C   VAL    41      12.245  14.569 -15.848  1.00  0.00              
ATOM    108  O   VAL    41      13.432  14.721 -15.637  1.00  0.00              
ATOM    109  N   ALA    42       9.645  -3.464  -2.904  1.00  0.00              
ATOM    110  CA  ALA    42      10.171  -4.484  -1.948  1.00  0.00              
ATOM    111  C   ALA    42       9.016  -4.983  -1.067  1.00  0.00              
ATOM    112  O   ALA    42       7.963  -4.382  -1.031  1.00  0.00              
ATOM    113  N   ASP    43       9.195  -6.072  -0.356  1.00  0.00              
ATOM    114  CA  ASP    43       8.085  -6.574   0.512  1.00  0.00              
ATOM    115  C   ASP    43       7.377  -5.366   1.120  1.00  0.00              
ATOM    116  O   ASP    43       6.174  -5.354   1.296  1.00  0.00              
ATOM    117  N   ASP    44       8.127  -4.345   1.430  1.00  0.00              
ATOM    118  CA  ASP    44       7.528  -3.117   2.017  1.00  0.00              
ATOM    119  C   ASP    44       8.170  -1.874   1.378  1.00  0.00              
ATOM    120  O   ASP    44       8.440  -0.898   2.050  1.00  0.00              
ATOM    121  N   SER    45       8.429  -1.902   0.091  1.00  0.00              
ATOM    122  CA  SER    45       9.063  -0.718  -0.572  1.00  0.00              
ATOM    123  C   SER    45       8.422  -0.475  -1.944  1.00  0.00              
ATOM    124  O   SER    45       7.844  -1.362  -2.536  1.00  0.00              
ATOM    125  N   ILE    46       5.986   6.086  -0.598  1.00  0.00              
ATOM    126  CA  ILE    46       5.119   5.339   0.356  1.00  0.00              
ATOM    127  C   ILE    46       5.556   5.640   1.789  1.00  0.00              
ATOM    128  O   ILE    46       6.475   5.041   2.312  1.00  0.00              
ATOM    129  N   THR    47       4.893   6.560   2.423  1.00  0.00              
ATOM    130  CA  THR    47       5.244   6.916   3.824  1.00  0.00              
ATOM    131  C   THR    47       4.028   6.647   4.709  1.00  0.00              
ATOM    132  O   THR    47       2.907   6.686   4.252  1.00  0.00              
ATOM    133  N   PRO    48       4.233   6.385   5.968  1.00  0.00              
ATOM    134  CA  PRO    48       3.116   6.116   6.900  1.00  0.00              
ATOM    135  C   PRO    48       1.887   6.945   6.537  1.00  0.00              
ATOM    136  O   PRO    48       0.772   6.462   6.551  1.00  0.00              
ATOM    137  N   THR    49       2.084   8.185   6.189  1.00  0.00              
ATOM    138  CA  THR    49       0.933   9.035   5.797  1.00  0.00              
ATOM    139  C   THR    49       0.378   8.539   4.451  1.00  0.00              
ATOM    140  O   THR    49      -0.819   8.413   4.272  1.00  0.00              
ATOM    141  N   SER    50       1.248   8.248   3.509  1.00  0.00              
ATOM    142  CA  SER    50       0.785   7.751   2.170  1.00  0.00              
ATOM    143  C   SER    50       1.416   6.378   1.873  1.00  0.00              
ATOM    144  O   SER    50       2.553   6.123   2.207  1.00  0.00              
ATOM    145  N   GLU    51       0.689   5.487   1.249  1.00  0.00              
ATOM    146  CA  GLU    51       1.256   4.141   0.938  1.00  0.00              
ATOM    147  C   GLU    51       0.703   3.644  -0.401  1.00  0.00              
ATOM    148  O   GLU    51      -0.403   3.144  -0.484  1.00  0.00              
ATOM    149  N   PHE    52       1.464   3.783  -1.450  1.00  0.00              
ATOM    150  CA  PHE    52       0.986   3.327  -2.787  1.00  0.00              
ATOM    151  C   PHE    52       1.156   1.813  -2.922  1.00  0.00              
ATOM    152  O   PHE    52       2.207   1.266  -2.649  1.00  0.00              
ATOM    153  N   GLU    67       0.121   1.131  -3.336  1.00  0.00              
ATOM    154  CA  GLU    67       0.204  -0.352  -3.486  1.00  0.00              
ATOM    155  C   GLU    67       0.653  -0.738  -4.903  1.00  0.00              
ATOM    156  O   GLU    67       1.344  -1.718  -5.086  1.00  0.00              
ATOM    157  N   GLN    68       0.264   0.004  -5.913  1.00  0.00              
ATOM    158  CA  GLN    68       0.683  -0.369  -7.302  1.00  0.00              
ATOM    159  C   GLN    68       1.354   0.819  -7.999  1.00  0.00              
ATOM    160  O   GLN    68       1.129   1.964  -7.660  1.00  0.00              
ATOM    161  N   LEU    69       2.182   0.544  -8.979  1.00  0.00              
ATOM    162  CA  LEU    69       2.881   1.639  -9.716  1.00  0.00              
ATOM    163  C   LEU    69       1.874   2.446 -10.533  1.00  0.00              
ATOM    164  O   LEU    69       2.051   3.626 -10.768  1.00  0.00              
ATOM    165  N   GLN    70       0.820   1.817 -10.969  1.00  0.00              
ATOM    166  CA  GLN    70      -0.203   2.541 -11.771  1.00  0.00              
ATOM    167  C   GLN    70      -0.738   3.703 -10.928  1.00  0.00              
ATOM    168  O   GLN    70      -0.898   4.810 -11.404  1.00  0.00              
ATOM    169  N   ILE    71      -0.988   3.458  -9.670  1.00  0.00              
ATOM    170  CA  ILE    71      -1.485   4.538  -8.775  1.00  0.00              
ATOM    171  C   ILE    71      -0.362   5.560  -8.565  1.00  0.00              
ATOM    172  O   ILE    71      -0.599   6.747  -8.454  1.00  0.00              
ATOM    173  N   LEU    72       0.860   5.100  -8.505  1.00  0.00              
ATOM    174  CA  LEU    72       2.008   6.033  -8.313  1.00  0.00              
ATOM    175  C   LEU    72       2.037   7.036  -9.461  1.00  0.00              
ATOM    176  O   LEU    72       2.140   8.228  -9.258  1.00  0.00              
ATOM    177  N   LEU    73       1.959   6.554 -10.669  1.00  0.00              
ATOM    178  CA  LEU    73       1.998   7.469 -11.843  1.00  0.00              
ATOM    179  C   LEU    73       0.812   8.435 -11.785  1.00  0.00              
ATOM    180  O   LEU    73       0.952   9.612 -12.046  1.00  0.00              
ATOM    181  N   GLU    74      -0.354   7.952 -11.462  1.00  0.00              
ATOM    182  CA  GLU    74      -1.536   8.859 -11.411  1.00  0.00              
ATOM    183  C   GLU    74      -1.341   9.941 -10.339  1.00  0.00              
ATOM    184  O   GLU    74      -1.500  11.116 -10.604  1.00  0.00              
END
