
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0324AL242_3-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324AL242_3-D2.T0324_D2.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    S      17      S      17           -
LGA    -       -      Q      18           -
LGA    -       -      P      19           -
LGA    -       -      A      20           -
LGA    -       -      Y      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      V      24           -
LGA    -       -      M      25           -
LGA    Q      18      R      26           #
LGA    -       -      E      27           -
LGA    P      19      V      28          4.438
LGA    A      20      L      29           #
LGA    Y      21      A      30          4.652
LGA    T      22      T      31          1.972
LGA    T      23      Y      32          2.521
LGA    V      24      G      33          3.478
LGA    M      25      K      34          2.070
LGA    R      26      P      35          4.982
LGA    -       -      F      36           -
LGA    -       -      S      37           -
LGA    -       -      P      38           -
LGA    -       -      A      39           -
LGA    E      27      Q      40           #
LGA    V      28      A      41           -
LGA    -       -      Q      42           -
LGA    -       -      K      43           -
LGA    L      29      T      44          3.607
LGA    A      30      F      45           -
LGA    T      31      P      46           -
LGA    Y      32      M      47           #
LGA    G      33      A      48          0.830
LGA    K      34      A      49          1.138
LGA    V      73      E      50           #
LGA    -       -      Q      51           -
LGA    -       -      A      52           -
LGA    M      74      M      53          2.070
LGA    -       -      T      54           -
LGA    -       -      E      55           -
LGA    -       -      L      56           -
LGA    A      75      G      57          5.289
LGA    S      76      I      58          2.194
LGA    H      77      A      59          2.404
LGA    -       -      A      60           -
LGA    -       -      S      61           -
LGA    -       -      E      62           -
LGA    Y      78      F      63          3.951
LGA    D      79      D      64           #
LGA    -       -      H      65           -
LGA    -       -      F      66           -
LGA    Q      80      Q      67          2.804
LGA    -       -      A      68           -
LGA    -       -      Q      69           -
LGA    I      81      Y      70          3.850
LGA    -       -      E      71           -
LGA    -       -      D      72           -
LGA    -       -      V      73           -
LGA    -       -      M      74           -
LGA    -       -      A      75           -
LGA    -       -      S      76           -
LGA    -       -      H      77           -
LGA    -       -      Y      78           -
LGA    -       -      D      79           -
LGA    -       -      Q      80           -
LGA    -       -      I      81           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   65    5.0     17    3.33    17.65     16.522     0.495

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.979888 * X  +  -0.193004 * Y  +  -0.050685 * Z  +  27.107075
  Y_new =  -0.195659 * X  +  -0.979184 * Y  +  -0.053995 * Z  +  13.009408
  Z_new =  -0.039208 * X  +   0.062826 * Y  +  -0.997254 * Z  +  14.014947 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.078676   -0.062916  [ DEG:   176.3952     -3.6048 ]
  Theta =   0.039218    3.102374  [ DEG:     2.2470    177.7530 ]
  Phi   =  -0.197082    2.944510  [ DEG:   -11.2920    168.7080 ]
 
# 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: T0324AL242_3-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324AL242_3-D2.T0324_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   65   5.0   17   3.33   17.65  16.522
REMARK  ---------------------------------------------------------- 
MOLECULE T0324AL242_3-D2
REMARK Aligment from pdb entry: 1u7p_A
ATOM     65  N   SER    17      20.370   4.908   8.025  1.00  0.00              
ATOM     66  CA  SER    17      19.185   4.542   7.257  1.00  0.00              
ATOM     67  C   SER    17      19.291   5.088   5.847  1.00  0.00              
ATOM     68  O   SER    17      20.189   5.879   5.554  1.00  0.00              
ATOM     69  N   GLN    18      18.380   4.651   4.979  1.00  0.00              
ATOM     70  CA  GLN    18      18.318   5.153   3.608  1.00  0.00              
ATOM     71  C   GLN    18      17.268   6.259   3.641  1.00  0.00              
ATOM     72  O   GLN    18      16.131   6.024   4.056  1.00  0.00              
ATOM     73  N   PRO    19      17.643   7.458   3.212  1.00  0.00              
ATOM     74  CA  PRO    19      16.712   8.577   3.223  1.00  0.00              
ATOM     75  C   PRO    19      15.530   8.391   2.260  1.00  0.00              
ATOM     76  O   PRO    19      14.486   9.019   2.430  1.00  0.00              
ATOM     77  N   ALA    20      15.680   7.518   1.265  1.00  0.00              
ATOM     78  CA  ALA    20      14.601   7.286   0.304  1.00  0.00              
ATOM     79  C   ALA    20      13.730   6.087   0.682  1.00  0.00              
ATOM     80  O   ALA    20      12.835   5.705  -0.073  1.00  0.00              
ATOM     81  N   TYR    21      13.972   5.513   1.856  1.00  0.00              
ATOM     82  CA  TYR    21      13.227   4.335   2.279  1.00  0.00              
ATOM     83  C   TYR    21      12.672   4.314   3.702  1.00  0.00              
ATOM     84  O   TYR    21      11.478   4.091   3.905  1.00  0.00              
ATOM     85  N   THR    22      13.539   4.535   4.683  1.00  0.00              
ATOM     86  CA  THR    22      13.145   4.463   6.084  1.00  0.00              
ATOM     87  C   THR    22      12.444   5.662   6.704  1.00  0.00              
ATOM     88  O   THR    22      11.916   5.567   7.809  1.00  0.00              
ATOM     89  N   THR    23      12.440   6.788   6.006  1.00  0.00              
ATOM     90  CA  THR    23      11.810   7.987   6.531  1.00  0.00              
ATOM     91  C   THR    23      10.806   8.573   5.557  1.00  0.00              
ATOM     92  O   THR    23      10.742   8.173   4.397  1.00  0.00              
ATOM     93  N   VAL    24      10.021   9.530   6.033  1.00  0.00              
ATOM     94  CA  VAL    24       9.008  10.167   5.203  1.00  0.00              
ATOM     95  C   VAL    24       9.158  11.688   5.297  1.00  0.00              
ATOM     96  O   VAL    24       8.652  12.318   6.227  1.00  0.00              
ATOM     97  N   MET    25       9.887  12.288   4.337  1.00  0.00              
ATOM     98  CA  MET    25      10.155  13.729   4.243  1.00  0.00              
ATOM     99  C   MET    25       8.876  14.511   3.933  1.00  0.00              
ATOM    100  O   MET    25       7.908  13.945   3.440  1.00  0.00              
ATOM    101  N   ARG    26       8.865  15.824   4.203  1.00  0.00              
ATOM    102  CA  ARG    26       9.957  16.624   4.771  1.00  0.00              
ATOM    103  C   ARG    26      10.166  16.376   6.262  1.00  0.00              
ATOM    104  O   ARG    26       9.378  15.679   6.912  1.00  0.00              
ATOM    105  N   GLU    27      11.228  16.967   6.798  1.00  0.00              
ATOM    106  CA  GLU    27      11.556  16.832   8.209  1.00  0.00              
ATOM    107  C   GLU    27      11.373  18.175   8.909  1.00  0.00              
ATOM    108  O   GLU    27      11.146  19.192   8.263  1.00  0.00              
ATOM    109  N   VAL    28      11.482  18.168  10.235  1.00  0.00              
ATOM    110  CA  VAL    28      11.339  19.390  11.022  1.00  0.00              
ATOM    111  C   VAL    28      11.852  19.163  12.440  1.00  0.00              
ATOM    112  O   VAL    28      11.816  18.041  12.945  1.00  0.00              
ATOM    113  N   LEU    29      12.328  20.228  13.077  1.00  0.00              
ATOM    114  CA  LEU    29      12.808  20.121  14.448  1.00  0.00              
ATOM    115  C   LEU    29      11.613  20.164  15.386  1.00  0.00              
ATOM    116  O   LEU    29      10.732  21.010  15.246  1.00  0.00              
ATOM    117  N   ALA    30      11.586  19.241  16.337  1.00  0.00              
ATOM    118  CA  ALA    30      10.500  19.167  17.300  1.00  0.00              
ATOM    119  C   ALA    30      10.776  20.137  18.446  1.00  0.00              
ATOM    120  O   ALA    30      11.854  20.729  18.524  1.00  0.00              
ATOM    121  N   THR    31       9.800  20.300  19.333  1.00  0.00              
ATOM    122  CA  THR    31       9.946  21.204  20.467  1.00  0.00              
ATOM    123  C   THR    31      11.046  20.741  21.418  1.00  0.00              
ATOM    124  O   THR    31      11.647  21.553  22.121  1.00  0.00              
ATOM    125  N   TYR    32      11.307  19.437  21.436  1.00  0.00              
ATOM    126  CA  TYR    32      12.334  18.877  22.310  1.00  0.00              
ATOM    127  C   TYR    32      13.717  18.881  21.662  1.00  0.00              
ATOM    128  O   TYR    32      14.640  18.225  22.144  1.00  0.00              
ATOM    129  N   GLY    33      13.853  19.618  20.563  1.00  0.00              
ATOM    130  CA  GLY    33      15.135  19.711  19.878  1.00  0.00              
ATOM    131  C   GLY    33      15.462  18.616  18.874  1.00  0.00              
ATOM    132  O   GLY    33      16.428  18.733  18.123  1.00  0.00              
ATOM    133  N   LYS    34      14.667  17.552  18.852  1.00  0.00              
ATOM    134  CA  LYS    34      14.918  16.454  17.932  1.00  0.00              
ATOM    135  C   LYS    34      14.490  16.770  16.498  1.00  0.00              
ATOM    136  O   LYS    34      13.741  17.714  16.249  1.00  0.00              
ATOM    137  N   VAL    73      14.992  15.983  15.554  1.00  0.00              
ATOM    138  CA  VAL    73      14.614  16.136  14.157  1.00  0.00              
ATOM    139  C   VAL    73      13.580  15.041  13.932  1.00  0.00              
ATOM    140  O   VAL    73      13.769  13.900  14.357  1.00  0.00              
ATOM    141  N   MET    74      12.482  15.388  13.279  1.00  0.00              
ATOM    142  CA  MET    74      11.428  14.412  13.048  1.00  0.00              
ATOM    143  C   MET    74      10.943  14.419  11.608  1.00  0.00              
ATOM    144  O   MET    74      11.103  15.409  10.898  1.00  0.00              
ATOM    145  N   ALA    75      10.349  13.308  11.188  1.00  0.00              
ATOM    146  CA  ALA    75       9.807  13.198   9.843  1.00  0.00              
ATOM    147  C   ALA    75       8.286  13.148   9.984  1.00  0.00              
ATOM    148  O   ALA    75       7.765  13.145  11.103  1.00  0.00              
ATOM    149  N   SER    76       7.579  13.111   8.861  1.00  0.00              
ATOM    150  CA  SER    76       6.117  13.092   8.861  1.00  0.00              
ATOM    151  C   SER    76       5.458  12.016   9.727  1.00  0.00              
ATOM    152  O   SER    76       4.310  12.173  10.144  1.00  0.00              
ATOM    153  N   HIS    77       6.169  10.926   9.993  1.00  0.00              
ATOM    154  CA  HIS    77       5.605   9.847  10.798  1.00  0.00              
ATOM    155  C   HIS    77       6.065   9.870  12.250  1.00  0.00              
ATOM    156  O   HIS    77       5.980   8.862  12.955  1.00  0.00              
ATOM    157  N   TYR    78       6.545  11.029  12.688  1.00  0.00              
ATOM    158  CA  TYR    78       6.989  11.183  14.061  1.00  0.00              
ATOM    159  C   TYR    78       8.238  10.416  14.454  1.00  0.00              
ATOM    160  O   TYR    78       8.499  10.220  15.643  1.00  0.00              
ATOM    161  N   ASP    79       9.018   9.978  13.470  1.00  0.00              
ATOM    162  CA  ASP    79      10.243   9.241  13.761  1.00  0.00              
ATOM    163  C   ASP    79      11.353  10.164  14.243  1.00  0.00              
ATOM    164  O   ASP    79      11.520  11.274  13.745  1.00  0.00              
ATOM    165  N   GLN    80      12.115   9.689  15.215  1.00  0.00              
ATOM    166  CA  GLN    80      13.231  10.458  15.732  1.00  0.00              
ATOM    167  C   GLN    80      14.370  10.204  14.747  1.00  0.00              
ATOM    168  O   GLN    80      14.815   9.071  14.604  1.00  0.00              
ATOM    169  N   ILE    81      14.825  11.248  14.062  1.00  0.00              
ATOM    170  CA  ILE    81      15.905  11.100  13.087  1.00  0.00              
ATOM    171  C   ILE    81      17.231  11.484  13.735  1.00  0.00              
ATOM    172  O   ILE    81      17.376  12.595  14.230  1.00  0.00              
END
