
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0335AL243_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL243_1-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5           -
LGA    K       6      K       6           #
LGA    I       7      -       -           -
LGA    A       8      -       -           -
LGA    R       9      -       -           -
LGA    I      10      I       7          1.498
LGA    N      11      -       -           -
LGA    E      12      A       8          3.542
LGA    L      13      R       9          2.768
LGA    A      14      I      10          2.574
LGA    A      15      N      11          2.415
LGA    K      16      E      12          0.775
LGA    A      17      L      13          0.598
LGA    K      18      A      14          2.130
LGA    A      19      A      15          3.715
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    G      20      V      21          4.875
LGA    V      21      I      22          4.650
LGA    I      22      T      23          1.685
LGA    E      24      E      24          2.252
LGA    E      25      E      25          2.918
LGA    E      26      E      26          2.729
LGA    K      27      K      27          2.512
LGA    A      28      A      28          2.628
LGA    E      29      E      29          1.906
LGA    Q      30      Q      30          0.732
LGA    Q      31      Q      31          1.728
LGA    K      32      K      32          1.554
LGA    L      33      L      33          1.907
LGA    R      34      R      34          1.954
LGA    Q      35      Q      35          1.668
LGA    E      36      E      36          2.125
LGA    L      38      Y      37          3.035
LGA    K      39      L      38          3.206
LGA    -       -      K      39           -
LGA    G      40      G      40          1.449

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34   36    5.0     28    2.55    57.14     63.400     1.055

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.588071 * X  +   0.782431 * Y  +   0.204875 * Z  + -36.633575
  Y_new =   0.803919 * X  +   0.593265 * Y  +   0.041843 * Z  +   2.130997
  Z_new =  -0.088806 * X  +   0.189310 * Y  +  -0.977893 * Z  +  97.356644 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.950369   -0.191224  [ DEG:   169.0437    -10.9563 ]
  Theta =   0.088923    3.052669  [ DEG:     5.0949    174.9051 ]
  Phi   =   2.202356   -0.939237  [ DEG:   126.1857    -53.8143 ]
 
# 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: T0335AL243_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL243_1-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   36   5.0   28   2.55   57.14  63.400
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL243_1-D1
REMARK Aligment from pdb entry: 1dg3A
ATOM      5  N   ALA     5      -3.426  -7.486 -16.352  1.00  0.00              
ATOM      6  CA  ALA     5      -3.825  -8.433 -15.322  1.00  0.00              
ATOM      7  C   ALA     5      -3.035  -8.118 -14.053  1.00  0.00              
ATOM      8  O   ALA     5      -3.493  -8.375 -12.938  1.00  0.00              
ATOM      9  N   LYS     6      -1.845  -7.557 -14.232  1.00  0.00              
ATOM     10  CA  LYS     6      -1.005  -7.191 -13.104  1.00  0.00              
ATOM     11  C   LYS     6      -1.580  -5.960 -12.421  1.00  0.00              
ATOM     12  O   LYS     6      -1.742  -5.937 -11.203  1.00  0.00              
ATOM     13  N   ILE     7      -1.878  -4.930 -13.208  1.00  0.00              
ATOM     14  CA  ILE     7      -2.433  -3.702 -12.655  1.00  0.00              
ATOM     15  C   ILE     7      -3.718  -3.959 -11.877  1.00  0.00              
ATOM     16  O   ILE     7      -3.923  -3.382 -10.811  1.00  0.00              
ATOM     17  N   ALA     8      -4.581  -4.826 -12.400  1.00  0.00              
ATOM     18  CA  ALA     8      -5.836  -5.115 -11.717  1.00  0.00              
ATOM     19  C   ALA     8      -5.596  -5.871 -10.417  1.00  0.00              
ATOM     20  O   ALA     8      -6.274  -5.633  -9.420  1.00  0.00              
ATOM     21  N   ARG     9      -4.635  -6.787 -10.437  1.00  0.00              
ATOM     22  CA  ARG     9      -4.297  -7.562  -9.250  1.00  0.00              
ATOM     23  C   ARG     9      -3.755  -6.596  -8.201  1.00  0.00              
ATOM     24  O   ARG     9      -4.125  -6.649  -7.025  1.00  0.00              
ATOM     25  N   ILE    10      -2.870  -5.711  -8.649  1.00  0.00              
ATOM     26  CA  ILE    10      -2.258  -4.722  -7.779  1.00  0.00              
ATOM     27  C   ILE    10      -3.307  -3.841  -7.111  1.00  0.00              
ATOM     28  O   ILE    10      -3.294  -3.666  -5.891  1.00  0.00              
ATOM     29  N   ASN    11      -4.210  -3.283  -7.914  1.00  0.00              
ATOM     30  CA  ASN    11      -5.265  -2.423  -7.388  1.00  0.00              
ATOM     31  C   ASN    11      -6.098  -3.168  -6.351  1.00  0.00              
ATOM     32  O   ASN    11      -6.448  -2.612  -5.313  1.00  0.00              
ATOM     33  N   GLU    12      -6.407  -4.428  -6.635  1.00  0.00              
ATOM     34  CA  GLU    12      -7.193  -5.250  -5.721  1.00  0.00              
ATOM     35  C   GLU    12      -6.480  -5.445  -4.384  1.00  0.00              
ATOM     36  O   GLU    12      -7.122  -5.492  -3.332  1.00  0.00              
ATOM     37  N   LEU    13      -5.157  -5.564  -4.425  1.00  0.00              
ATOM     38  CA  LEU    13      -4.384  -5.761  -3.199  1.00  0.00              
ATOM     39  C   LEU    13      -4.277  -4.464  -2.407  1.00  0.00              
ATOM     40  O   LEU    13      -4.276  -4.488  -1.173  1.00  0.00              
ATOM     41  N   ALA    14      -4.180  -3.335  -3.108  1.00  0.00              
ATOM     42  CA  ALA    14      -4.107  -2.042  -2.437  1.00  0.00              
ATOM     43  C   ALA    14      -5.412  -1.890  -1.672  1.00  0.00              
ATOM     44  O   ALA    14      -5.427  -1.460  -0.515  1.00  0.00              
ATOM     45  N   ALA    15      -6.513  -2.244  -2.331  1.00  0.00              
ATOM     46  CA  ALA    15      -7.825  -2.161  -1.702  1.00  0.00              
ATOM     47  C   ALA    15      -7.842  -3.011  -0.431  1.00  0.00              
ATOM     48  O   ALA    15      -8.320  -2.569   0.615  1.00  0.00              
ATOM     49  N   LYS    16      -7.320  -4.230  -0.522  1.00  0.00              
ATOM     50  CA  LYS    16      -7.282  -5.110   0.639  1.00  0.00              
ATOM     51  C   LYS    16      -6.472  -4.482   1.774  1.00  0.00              
ATOM     52  O   LYS    16      -6.856  -4.561   2.940  1.00  0.00              
ATOM     53  N   ALA    17      -5.354  -3.856   1.424  1.00  0.00              
ATOM     54  CA  ALA    17      -4.491  -3.201   2.403  1.00  0.00              
ATOM     55  C   ALA    17      -5.266  -2.109   3.140  1.00  0.00              
ATOM     56  O   ALA    17      -5.266  -2.052   4.374  1.00  0.00              
ATOM     57  N   LYS    18      -5.927  -1.244   2.376  1.00  0.00              
ATOM     58  CA  LYS    18      -6.703  -0.150   2.954  1.00  0.00              
ATOM     59  C   LYS    18      -7.856  -0.647   3.814  1.00  0.00              
ATOM     60  O   LYS    18      -8.320   0.061   4.713  1.00  0.00              
ATOM     61  N   ALA    19      -8.312  -1.866   3.546  1.00  0.00              
ATOM     62  CA  ALA    19      -9.417  -2.439   4.300  1.00  0.00              
ATOM     63  C   ALA    19      -8.992  -3.027   5.645  1.00  0.00              
ATOM     64  O   ALA    19      -9.837  -3.293   6.500  1.00  0.00              
ATOM     65  N   GLY    20      -7.279  -0.471  11.833  1.00  0.00              
ATOM     66  CA  GLY    20      -6.345   0.220  12.720  1.00  0.00              
ATOM     67  C   GLY    20      -4.883   0.034  12.322  1.00  0.00              
ATOM     68  O   GLY    20      -4.081  -0.504  13.089  1.00  0.00              
ATOM     69  N   VAL    21      -4.535   0.470  11.116  1.00  0.00              
ATOM     70  CA  VAL    21      -3.156   0.347  10.657  1.00  0.00              
ATOM     71  C   VAL    21      -2.305   1.458  11.268  1.00  0.00              
ATOM     72  O   VAL    21      -1.095   1.312  11.422  1.00  0.00              
ATOM     73  N   ILE    22      -2.941   2.572  11.619  1.00  0.00              
ATOM     74  CA  ILE    22      -2.198   3.666  12.221  1.00  0.00              
ATOM     75  C   ILE    22      -1.762   4.760  11.265  1.00  0.00              
ATOM     76  O   ILE    22      -1.974   4.668  10.055  1.00  0.00              
ATOM     77  N   GLU    24      -1.125   5.789  11.820  1.00  0.00              
ATOM     78  CA  GLU    24      -0.670   6.949  11.056  1.00  0.00              
ATOM     79  C   GLU    24       0.345   6.720   9.930  1.00  0.00              
ATOM     80  O   GLU    24       0.498   7.578   9.063  1.00  0.00              
ATOM     81  N   GLU    25       1.033   5.581   9.926  1.00  0.00              
ATOM     82  CA  GLU    25       2.040   5.318   8.897  1.00  0.00              
ATOM     83  C   GLU    25       1.520   4.544   7.683  1.00  0.00              
ATOM     84  O   GLU    25       2.282   4.229   6.775  1.00  0.00              
ATOM     85  N   GLU    26       0.226   4.252   7.668  1.00  0.00              
ATOM     86  CA  GLU    26      -0.378   3.489   6.581  1.00  0.00              
ATOM     87  C   GLU    26       0.005   3.970   5.180  1.00  0.00              
ATOM     88  O   GLU    26       0.479   3.183   4.357  1.00  0.00              
ATOM     89  N   LYS    27      -0.196   5.257   4.913  1.00  0.00              
ATOM     90  CA  LYS    27       0.116   5.825   3.608  1.00  0.00              
ATOM     91  C   LYS    27       1.584   5.822   3.243  1.00  0.00              
ATOM     92  O   LYS    27       1.956   5.412   2.146  1.00  0.00              
ATOM     93  N   ALA    28       2.416   6.297   4.160  1.00  0.00              
ATOM     94  CA  ALA    28       3.852   6.357   3.937  1.00  0.00              
ATOM     95  C   ALA    28       4.424   4.970   3.637  1.00  0.00              
ATOM     96  O   ALA    28       5.225   4.805   2.718  1.00  0.00              
ATOM     97  N   GLU    29       4.002   3.977   4.416  1.00  0.00              
ATOM     98  CA  GLU    29       4.466   2.602   4.243  1.00  0.00              
ATOM     99  C   GLU    29       4.110   2.041   2.856  1.00  0.00              
ATOM    100  O   GLU    29       4.971   1.509   2.160  1.00  0.00              
ATOM    101  N   GLN    30       2.851   2.177   2.453  1.00  0.00              
ATOM    102  CA  GLN    30       2.419   1.671   1.149  1.00  0.00              
ATOM    103  C   GLN    30       3.079   2.387  -0.031  1.00  0.00              
ATOM    104  O   GLN    30       3.560   1.744  -0.963  1.00  0.00              
ATOM    105  N   GLN    31       3.102   3.717   0.005  1.00  0.00              
ATOM    106  CA  GLN    31       3.694   4.474  -1.090  1.00  0.00              
ATOM    107  C   GLN    31       5.179   4.195  -1.239  1.00  0.00              
ATOM    108  O   GLN    31       5.696   4.140  -2.353  1.00  0.00              
ATOM    109  N   LYS    32       5.874   4.021  -0.122  1.00  0.00              
ATOM    110  CA  LYS    32       7.298   3.728  -0.191  1.00  0.00              
ATOM    111  C   LYS    32       7.467   2.356  -0.840  1.00  0.00              
ATOM    112  O   LYS    32       8.425   2.117  -1.579  1.00  0.00              
ATOM    113  N   LEU    33       6.532   1.456  -0.555  1.00  0.00              
ATOM    114  CA  LEU    33       6.579   0.118  -1.127  1.00  0.00              
ATOM    115  C   LEU    33       6.329   0.200  -2.626  1.00  0.00              
ATOM    116  O   LEU    33       7.105  -0.317  -3.429  1.00  0.00              
ATOM    117  N   ARG    34       5.234   0.853  -2.993  1.00  0.00              
ATOM    118  CA  ARG    34       4.869   1.000  -4.396  1.00  0.00              
ATOM    119  C   ARG    34       5.966   1.714  -5.181  1.00  0.00              
ATOM    120  O   ARG    34       6.254   1.358  -6.323  1.00  0.00              
ATOM    121  N   GLN    35       6.583   2.712  -4.559  1.00  0.00              
ATOM    122  CA  GLN    35       7.657   3.460  -5.201  1.00  0.00              
ATOM    123  C   GLN    35       8.793   2.521  -5.592  1.00  0.00              
ATOM    124  O   GLN    35       9.361   2.638  -6.676  1.00  0.00              
ATOM    125  N   GLU    36       9.112   1.584  -4.705  1.00  0.00              
ATOM    126  CA  GLU    36      10.188   0.627  -4.943  1.00  0.00              
ATOM    127  C   GLU    36       9.865  -0.435  -5.997  1.00  0.00              
ATOM    128  O   GLU    36      10.761  -1.136  -6.462  1.00  0.00              
ATOM    129  N   LEU    38       8.595  -0.567  -6.365  1.00  0.00              
ATOM    130  CA  LEU    38       8.207  -1.564  -7.362  1.00  0.00              
ATOM    131  C   LEU    38       7.947  -0.915  -8.719  1.00  0.00              
ATOM    132  O   LEU    38       7.752  -1.599  -9.723  1.00  0.00              
ATOM    133  N   LYS    39       7.951   0.412  -8.726  1.00  0.00              
ATOM    134  CA  LYS    39       7.711   1.211  -9.921  1.00  0.00              
ATOM    135  C   LYS    39       8.508   0.723 -11.131  1.00  0.00              
ATOM    136  O   LYS    39       7.962   0.557 -12.223  1.00  0.00              
ATOM    137  N   GLY    40       9.798   0.490 -10.930  1.00  0.00              
ATOM    138  CA  GLY    40      10.659   0.019 -12.004  1.00  0.00              
ATOM    139  C   GLY    40      10.194  -1.348 -12.500  1.00  0.00              
ATOM    140  O   GLY    40      10.061  -1.573 -13.702  1.00  0.00              
END
