
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0351AL381_2
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351AL381_2.T0351.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      L       3           -
LGA    T      48      Y       4          1.443
LGA    -       -      D       5           -
LGA    -       -      A       6           -
LGA    W      49      I       7          3.381
LGA    -       -      M       8           -
LGA    -       -      Y       9           -
LGA    -       -      K      10           -
LGA    -       -      Y      11           -
LGA    -       -      P      12           -
LGA    -       -      N      13           -
LGA    -       -      A      14           -
LGA    -       -      V      15           -
LGA    -       -      S      16           -
LGA    -       -      R      17           -
LGA    -       -      K      18           -
LGA    -       -      D      19           -
LGA    -       -      F      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      R      23           -
LGA    -       -      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    W      50      Y      30          3.885
LGA    E      51      I      31          4.758
LGA    E      52      E      32           -
LGA    L      53      -       -           -
LGA    Q      54      K      33          5.223
LGA    -       -      W      34           -
LGA    -       -      N      35           -
LGA    K      55      L      36          3.002
LGA    N      56      R      37          5.157
LGA    P      57      A      38          4.655
LGA    P      58      P      39          0.624
LGA    Y      59      L      40          4.190
LGA    E      60      P      41          1.444
LGA    P      61      T      42          1.609
LGA    P      62      Q      43          3.078
LGA    D      63      A      44          1.594
LGA    Q      64      E      45          1.842
LGA    V      65      L      46          2.037
LGA    E      66      E      47          1.187
LGA    L      67      T      48          1.022
LGA    L      68      W      49          1.287
LGA    A      69      W      50          0.791
LGA    Q      70      E      51          0.527
LGA    E      71      E      52          1.204
LGA    L      72      L      53          1.150
LGA    S      73      Q      54          0.510
LGA    Q      74      K      55          1.640
LGA    E      75      N      56          2.034
LGA    K      76      -       -           -
LGA    L      77      -       -           -
LGA    A      78      -       -           -
LGA    T      88      -       -           -
LGA    L      89      -       -           -
LGA    G      90      -       -           -
LGA    N      91      -       -           -
LGA    E      92      -       -           -
LGA    L      93      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37   56    5.0     26    2.72    15.38     34.662     0.921

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.764432 * X  +   0.402408 * Y  +  -0.503699 * Z  +  45.851036
  Y_new =  -0.516032 * X  +  -0.850247 * Y  +   0.103883 * Z  +  18.524385
  Z_new =  -0.386465 * X  +   0.339336 * Y  +   0.857611 * Z  +   1.155883 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.376773   -2.764820  [ DEG:    21.5875   -158.4125 ]
  Theta =   0.396796    2.744797  [ DEG:    22.7347    157.2653 ]
  Phi   =  -2.547806    0.593786  [ DEG:  -145.9785     34.0214 ]
 
# 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: T0351AL381_2                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351AL381_2.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   56   5.0   26   2.72   15.38  34.662
REMARK  ---------------------------------------------------------- 
MOLECULE T0351AL381_2
REMARK Aligment from pdb entry: 1q2hA
ATOM      1  N   THR    48      -2.612   2.716   5.783  1.00  0.00              
ATOM      2  CA  THR    48      -1.400   3.147   5.080  1.00  0.00              
ATOM      3  C   THR    48      -1.438   2.723   3.614  1.00  0.00              
ATOM      4  O   THR    48      -0.977   3.448   2.728  1.00  0.00              
ATOM      5  N   TRP    49      -1.992   1.537   3.378  1.00  0.00              
ATOM      6  CA  TRP    49      -2.146   0.977   2.039  1.00  0.00              
ATOM      7  C   TRP    49      -3.035   1.908   1.198  1.00  0.00              
ATOM      8  O   TRP    49      -2.677   2.293   0.085  1.00  0.00              
ATOM      9  N   TRP    50      -4.195   2.267   1.739  1.00  0.00              
ATOM     10  CA  TRP    50      -5.110   3.154   1.024  1.00  0.00              
ATOM     11  C   TRP    50      -4.463   4.505   0.761  1.00  0.00              
ATOM     12  O   TRP    50      -4.626   5.086  -0.314  1.00  0.00              
ATOM     13  N   GLU    51      -3.712   4.997   1.737  1.00  0.00              
ATOM     14  CA  GLU    51      -3.052   6.289   1.606  1.00  0.00              
ATOM     15  C   GLU    51      -1.942   6.197   0.555  1.00  0.00              
ATOM     16  O   GLU    51      -1.695   7.151  -0.189  1.00  0.00              
ATOM     17  N   GLU    52      -1.283   5.043   0.483  1.00  0.00              
ATOM     18  CA  GLU    52      -0.216   4.848  -0.496  1.00  0.00              
ATOM     19  C   GLU    52      -0.793   4.808  -1.913  1.00  0.00              
ATOM     20  O   GLU    52      -0.196   5.345  -2.845  1.00  0.00              
ATOM     21  N   LEU    53      -1.946   4.163  -2.071  1.00  0.00              
ATOM     22  CA  LEU    53      -2.574   4.053  -3.379  1.00  0.00              
ATOM     23  C   LEU    53      -3.212   5.366  -3.822  1.00  0.00              
ATOM     24  O   LEU    53      -3.477   5.561  -5.006  1.00  0.00              
ATOM     25  N   GLN    54      -3.464   6.254  -2.866  1.00  0.00              
ATOM     26  CA  GLN    54      -4.031   7.556  -3.179  1.00  0.00              
ATOM     27  C   GLN    54      -2.917   8.440  -3.723  1.00  0.00              
ATOM     28  O   GLN    54      -3.125   9.209  -4.664  1.00  0.00              
ATOM     29  N   LYS    55      -1.735   8.329  -3.121  1.00  0.00              
ATOM     30  CA  LYS    55      -0.586   9.119  -3.546  1.00  0.00              
ATOM     31  C   LYS    55       0.083   8.535  -4.786  1.00  0.00              
ATOM     32  O   LYS    55       0.841   9.223  -5.472  1.00  0.00              
ATOM     33  N   ASN    56      -0.206   7.273  -5.076  1.00  0.00              
ATOM     34  CA  ASN    56       0.380   6.589  -6.220  1.00  0.00              
ATOM     35  C   ASN    56      -0.696   5.737  -6.895  1.00  0.00              
ATOM     36  O   ASN    56      -0.608   4.518  -6.915  1.00  0.00              
ATOM     37  N   PRO    57      -1.730   6.382  -7.470  1.00  0.00              
ATOM     38  CA  PRO    57      -2.829   5.674  -8.140  1.00  0.00              
ATOM     39  C   PRO    57      -2.436   4.650  -9.203  1.00  0.00              
ATOM     40  O   PRO    57      -3.188   3.716  -9.483  1.00  0.00              
ATOM     41  N   PRO    58      -1.262   4.810  -9.803  1.00  0.00              
ATOM     42  CA  PRO    58      -0.843   3.847 -10.811  1.00  0.00              
ATOM     43  C   PRO    58      -0.742   2.455 -10.168  1.00  0.00              
ATOM     44  O   PRO    58      -0.872   1.438 -10.844  1.00  0.00              
ATOM     45  N   TYR    59      -0.512   2.418  -8.859  1.00  0.00              
ATOM     46  CA  TYR    59      -0.395   1.153  -8.130  1.00  0.00              
ATOM     47  C   TYR    59      -1.743   0.524  -7.771  1.00  0.00              
ATOM     48  O   TYR    59      -1.812  -0.669  -7.464  1.00  0.00              
ATOM     49  N   GLU    60      -2.811   1.320  -7.795  1.00  0.00              
ATOM     50  CA  GLU    60      -4.137   0.804  -7.451  1.00  0.00              
ATOM     51  C   GLU    60      -4.757   0.027  -8.600  1.00  0.00              
ATOM     52  O   GLU    60      -5.371   0.609  -9.504  1.00  0.00              
ATOM     53  N   PRO    61      -4.608  -1.293  -8.538  1.00  0.00              
ATOM     54  CA  PRO    61      -5.107  -2.203  -9.558  1.00  0.00              
ATOM     55  C   PRO    61      -5.851  -3.346  -8.883  1.00  0.00              
ATOM     56  O   PRO    61      -5.817  -3.477  -7.663  1.00  0.00              
ATOM     57  N   PRO    62      -6.531  -4.197  -9.669  1.00  0.00              
ATOM     58  CA  PRO    62      -7.255  -5.309  -9.050  1.00  0.00              
ATOM     59  C   PRO    62      -6.337  -6.275  -8.300  1.00  0.00              
ATOM     60  O   PRO    62      -6.814  -7.097  -7.525  1.00  0.00              
ATOM     61  N   ASP    63      -5.027  -6.171  -8.533  1.00  0.00              
ATOM     62  CA  ASP    63      -4.062  -7.054  -7.871  1.00  0.00              
ATOM     63  C   ASP    63      -3.471  -6.480  -6.578  1.00  0.00              
ATOM     64  O   ASP    63      -2.986  -7.231  -5.724  1.00  0.00              
ATOM     65  N   GLN    64      -3.494  -5.157  -6.459  1.00  0.00              
ATOM     66  CA  GLN    64      -2.926  -4.457  -5.308  1.00  0.00              
ATOM     67  C   GLN    64      -3.262  -4.993  -3.908  1.00  0.00              
ATOM     68  O   GLN    64      -2.360  -5.239  -3.101  1.00  0.00              
ATOM     69  N   VAL    65      -4.546  -5.157  -3.607  1.00  0.00              
ATOM     70  CA  VAL    65      -4.930  -5.628  -2.285  1.00  0.00              
ATOM     71  C   VAL    65      -4.225  -6.899  -1.853  1.00  0.00              
ATOM     72  O   VAL    65      -3.649  -6.976  -0.750  1.00  0.00              
ATOM     73  N   GLU    66      -4.285  -7.898  -2.725  1.00  0.00              
ATOM     74  CA  GLU    66      -3.669  -9.190  -2.472  1.00  0.00              
ATOM     75  C   GLU    66      -2.145  -9.099  -2.403  1.00  0.00              
ATOM     76  O   GLU    66      -1.526  -9.668  -1.502  1.00  0.00              
ATOM     77  N   LEU    67      -1.550  -8.388  -3.356  1.00  0.00              
ATOM     78  CA  LEU    67      -0.095  -8.230  -3.426  1.00  0.00              
ATOM     79  C   LEU    67       0.491  -7.563  -2.184  1.00  0.00              
ATOM     80  O   LEU    67       1.434  -8.077  -1.575  1.00  0.00              
ATOM     81  N   LEU    68      -0.068  -6.410  -1.828  1.00  0.00              
ATOM     82  CA  LEU    68       0.392  -5.646  -0.676  1.00  0.00              
ATOM     83  C   LEU    68       0.188  -6.367   0.653  1.00  0.00              
ATOM     84  O   LEU    68       1.127  -6.501   1.436  1.00  0.00              
ATOM     85  N   ALA    69      -1.037  -6.819   0.914  1.00  0.00              
ATOM     86  CA  ALA    69      -1.337  -7.478   2.177  1.00  0.00              
ATOM     87  C   ALA    69      -0.511  -8.732   2.379  1.00  0.00              
ATOM     88  O   ALA    69      -0.021  -8.991   3.482  1.00  0.00              
ATOM     89  N   GLN    70      -0.350  -9.514   1.320  1.00  0.00              
ATOM     90  CA  GLN    70       0.421 -10.737   1.454  1.00  0.00              
ATOM     91  C   GLN    70       1.904 -10.470   1.660  1.00  0.00              
ATOM     92  O   GLN    70       2.560 -11.187   2.419  1.00  0.00              
ATOM     93  N   GLU    71       2.432  -9.438   1.009  1.00  0.00              
ATOM     94  CA  GLU    71       3.852  -9.119   1.162  1.00  0.00              
ATOM     95  C   GLU    71       4.091  -8.558   2.572  1.00  0.00              
ATOM     96  O   GLU    71       5.096  -8.873   3.216  1.00  0.00              
ATOM     97  N   LEU    72       3.170  -7.730   3.052  1.00  0.00              
ATOM     98  CA  LEU    72       3.309  -7.191   4.403  1.00  0.00              
ATOM     99  C   LEU    72       3.241  -8.345   5.409  1.00  0.00              
ATOM    100  O   LEU    72       4.088  -8.461   6.294  1.00  0.00              
ATOM    101  N   SER    73       2.239  -9.207   5.261  1.00  0.00              
ATOM    102  CA  SER    73       2.065 -10.322   6.184  1.00  0.00              
ATOM    103  C   SER    73       3.279 -11.255   6.227  1.00  0.00              
ATOM    104  O   SER    73       3.687 -11.689   7.308  1.00  0.00              
ATOM    105  N   GLN    74       3.862 -11.567   5.071  1.00  0.00              
ATOM    106  CA  GLN    74       5.030 -12.456   5.052  1.00  0.00              
ATOM    107  C   GLN    74       6.229 -11.820   5.752  1.00  0.00              
ATOM    108  O   GLN    74       6.916 -12.472   6.535  1.00  0.00              
ATOM    109  N   GLU    75       6.470 -10.543   5.480  1.00  0.00              
ATOM    110  CA  GLU    75       7.599  -9.847   6.079  1.00  0.00              
ATOM    111  C   GLU    75       7.387  -9.636   7.575  1.00  0.00              
ATOM    112  O   GLU    75       8.334  -9.714   8.357  1.00  0.00              
ATOM    113  N   LYS    76       6.147  -9.354   7.968  1.00  0.00              
ATOM    114  CA  LYS    76       5.821  -9.154   9.380  1.00  0.00              
ATOM    115  C   LYS    76       6.194 -10.415  10.153  1.00  0.00              
ATOM    116  O   LYS    76       6.895 -10.360  11.163  1.00  0.00              
ATOM    117  N   LEU    77       5.707 -11.559   9.679  1.00  0.00              
ATOM    118  CA  LEU    77       5.988 -12.817  10.354  1.00  0.00              
ATOM    119  C   LEU    77       7.488 -13.109  10.442  1.00  0.00              
ATOM    120  O   LEU    77       7.964 -13.554  11.489  1.00  0.00              
ATOM    121  N   ALA    78       8.232 -12.864   9.364  1.00  0.00              
ATOM    122  CA  ALA    78       9.680 -13.099   9.380  1.00  0.00              
ATOM    123  C   ALA    78      10.336 -12.232  10.445  1.00  0.00              
ATOM    124  O   ALA    78      11.077 -12.726  11.295  1.00  0.00              
ATOM    125  N   THR    88      10.072 -10.932  10.385  1.00  0.00              
ATOM    126  CA  THR    88      10.631  -9.989  11.357  1.00  0.00              
ATOM    127  C   THR    88      10.225 -10.345  12.790  1.00  0.00              
ATOM    128  O   THR    88      11.031 -10.230  13.724  1.00  0.00              
ATOM    129  N   LEU    89       8.977 -10.771  12.961  1.00  0.00              
ATOM    130  CA  LEU    89       8.460 -11.154  14.272  1.00  0.00              
ATOM    131  C   LEU    89       9.336 -12.247  14.893  1.00  0.00              
ATOM    132  O   LEU    89       9.804 -12.124  16.027  1.00  0.00              
ATOM    133  N   GLY    90       9.565 -13.315  14.142  1.00  0.00              
ATOM    134  CA  GLY    90      10.393 -14.392  14.655  1.00  0.00              
ATOM    135  C   GLY    90      11.770 -13.906  15.059  1.00  0.00              
ATOM    136  O   GLY    90      12.263 -14.220  16.145  1.00  0.00              
ATOM    137  N   ASN    91      12.394 -13.122  14.188  1.00  0.00              
ATOM    138  CA  ASN    91      13.731 -12.595  14.447  1.00  0.00              
ATOM    139  C   ASN    91      13.844 -11.702  15.685  1.00  0.00              
ATOM    140  O   ASN    91      14.802 -11.815  16.450  1.00  0.00              
ATOM    141  N   GLU    92      12.883 -10.806  15.883  1.00  0.00              
ATOM    142  CA  GLU    92      12.932  -9.912  17.037  1.00  0.00              
ATOM    143  C   GLU    92      12.674 -10.685  18.326  1.00  0.00              
ATOM    144  O   GLU    92      13.302 -10.418  19.354  1.00  0.00              
ATOM    145  N   LEU    93      11.758 -11.647  18.276  1.00  0.00              
ATOM    146  CA  LEU    93      11.474 -12.445  19.464  1.00  0.00              
ATOM    147  C   LEU    93      12.754 -13.154  19.916  1.00  0.00              
ATOM    148  O   LEU    93      13.111 -13.103  21.093  1.00  0.00              
END
