
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0335AL243_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL243_4-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      -       -           -
LGA    K       6      A       5          2.344
LGA    I       7      K       6          1.025
LGA    A       8      I       7          1.540
LGA    R       9      A       8          1.263
LGA    I      10      R       9          0.793
LGA    N      11      I      10          0.919
LGA    E      12      N      11          0.842
LGA    L      13      E      12          0.549
LGA    A      14      L      13          0.571
LGA    A      15      A      14          1.467
LGA    K      16      A      15          1.856
LGA    A      17      K      16          1.695
LGA    K      18      A      17          1.146
LGA    A      19      K      18          1.768
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    G      20      I      22          4.623
LGA    V      21      T      23           -
LGA    T      23      E      24           -
LGA    E      24      E      25           -
LGA    -       -      E      26           -
LGA    E      25      K      27          3.941
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    E      26      Q      30          0.637
LGA    K      27      Q      31          2.034
LGA    A      28      K      32          2.734
LGA    E      29      L      33          2.724
LGA    Q      30      R      34           -
LGA    Q      31      Q      35           -
LGA    K      32      E      36           -
LGA    L      33      Y      37           -
LGA    R      34      L      38           -
LGA    Q      35      K      39           -
LGA    E      36      G      40           -
LGA    Y      37      -       -           -
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   36    5.0     20    2.03     5.00     50.195     0.938

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.500117 * X  +  -0.640375 * Y  +   0.582927 * Z  + -13.137563
  Y_new =  -0.856249 * X  +  -0.466208 * Y  +   0.222458 * Z  +  -7.314725
  Z_new =   0.129308 * X  +  -0.610386 * Y  +  -0.781479 * Z  +  -1.710026 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.478504    0.663088  [ DEG:  -142.0078     37.9922 ]
  Theta =  -0.129671   -3.011921  [ DEG:    -7.4296   -172.5704 ]
  Phi   =  -1.042166    2.099427  [ DEG:   -59.7117    120.2883 ]
 
# 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_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL243_4-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   36   5.0   20   2.03    5.00  50.195
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL243_4-D1
REMARK Aligment from pdb entry: 2vsgA
ATOM      5  N   ALA     5       0.045  -6.449 -10.459  1.00  0.00              
ATOM      6  CA  ALA     5      -1.313  -6.535  -9.902  1.00  0.00              
ATOM      7  C   ALA     5      -1.467  -7.410  -8.635  1.00  0.00              
ATOM      8  O   ALA     5      -2.416  -7.218  -7.866  1.00  0.00              
ATOM      9  N   LYS     6      -0.566  -8.358  -8.334  1.00  0.00              
ATOM     10  CA  LYS     6      -0.668  -9.072  -7.076  1.00  0.00              
ATOM     11  C   LYS     6      -0.358  -8.069  -5.953  1.00  0.00              
ATOM     12  O   LYS     6      -1.198  -7.785  -5.089  1.00  0.00              
ATOM     13  N   ILE     7       0.806  -7.418  -5.994  1.00  0.00              
ATOM     14  CA  ILE     7       1.179  -6.414  -5.006  1.00  0.00              
ATOM     15  C   ILE     7       0.225  -5.246  -5.031  1.00  0.00              
ATOM     16  O   ILE     7      -0.095  -4.761  -3.955  1.00  0.00              
ATOM     17  N   ALA     8      -0.281  -4.765  -6.157  1.00  0.00              
ATOM     18  CA  ALA     8      -1.260  -3.685  -6.123  1.00  0.00              
ATOM     19  C   ALA     8      -2.432  -4.123  -5.294  1.00  0.00              
ATOM     20  O   ALA     8      -3.020  -3.279  -4.627  1.00  0.00              
ATOM     21  N   ARG     9      -2.760  -5.426  -5.352  1.00  0.00              
ATOM     22  CA  ARG     9      -3.888  -5.971  -4.619  1.00  0.00              
ATOM     23  C   ARG     9      -3.619  -5.875  -3.137  1.00  0.00              
ATOM     24  O   ARG     9      -4.401  -5.237  -2.435  1.00  0.00              
ATOM     25  N   ILE    10      -2.511  -6.459  -2.657  1.00  0.00              
ATOM     26  CA  ILE    10      -2.118  -6.364  -1.256  1.00  0.00              
ATOM     27  C   ILE    10      -2.237  -4.942  -0.746  1.00  0.00              
ATOM     28  O   ILE    10      -2.951  -4.710   0.230  1.00  0.00              
ATOM     29  N   ASN    11      -1.689  -3.988  -1.473  1.00  0.00              
ATOM     30  CA  ASN    11      -1.772  -2.624  -1.044  1.00  0.00              
ATOM     31  C   ASN    11      -3.178  -2.156  -0.938  1.00  0.00              
ATOM     32  O   ASN    11      -3.434  -1.359  -0.046  1.00  0.00              
ATOM     33  N   GLU    12      -4.081  -2.631  -1.788  1.00  0.00              
ATOM     34  CA  GLU    12      -5.473  -2.210  -1.717  1.00  0.00              
ATOM     35  C   GLU    12      -6.116  -2.784  -0.471  1.00  0.00              
ATOM     36  O   GLU    12      -6.707  -2.045   0.325  1.00  0.00              
ATOM     37  N   LEU    13      -5.989  -4.101  -0.308  1.00  0.00              
ATOM     38  CA  LEU    13      -6.652  -4.853   0.752  1.00  0.00              
ATOM     39  C   LEU    13      -6.392  -4.178   2.080  1.00  0.00              
ATOM     40  O   LEU    13      -7.338  -3.790   2.777  1.00  0.00              
ATOM     41  N   ALA    14      -5.096  -3.924   2.321  1.00  0.00              
ATOM     42  CA  ALA    14      -4.662  -3.298   3.545  1.00  0.00              
ATOM     43  C   ALA    14      -5.206  -1.907   3.689  1.00  0.00              
ATOM     44  O   ALA    14      -5.709  -1.615   4.771  1.00  0.00              
ATOM     45  N   ALA    15      -5.236  -1.044   2.689  1.00  0.00              
ATOM     46  CA  ALA    15      -5.837   0.261   2.918  1.00  0.00              
ATOM     47  C   ALA    15      -7.297   0.113   3.319  1.00  0.00              
ATOM     48  O   ALA    15      -7.733   0.752   4.281  1.00  0.00              
ATOM     49  N   LYS    16      -8.003  -0.837   2.677  1.00  0.00              
ATOM     50  CA  LYS    16      -9.417  -1.099   2.934  1.00  0.00              
ATOM     51  C   LYS    16      -9.643  -1.537   4.374  1.00  0.00              
ATOM     52  O   LYS    16     -10.542  -1.012   5.032  1.00  0.00              
ATOM     53  N   ALA    17      -8.831  -2.463   4.877  1.00  0.00              
ATOM     54  CA  ALA    17      -8.847  -2.832   6.271  1.00  0.00              
ATOM     55  C   ALA    17      -8.645  -1.577   7.116  1.00  0.00              
ATOM     56  O   ALA    17      -9.492  -1.169   7.919  1.00  0.00              
ATOM     57  N   LYS    18      -7.564  -0.850   6.853  1.00  0.00              
ATOM     58  CA  LYS    18      -7.176   0.182   7.776  1.00  0.00              
ATOM     59  C   LYS    18      -7.648   1.545   7.341  1.00  0.00              
ATOM     60  O   LYS    18      -6.955   2.540   7.502  1.00  0.00              
ATOM     61  N   ALA    19      -8.852   1.578   6.784  1.00  0.00              
ATOM     62  CA  ALA    19      -9.532   2.777   6.308  1.00  0.00              
ATOM     63  C   ALA    19      -8.715   3.931   5.737  1.00  0.00              
ATOM     64  O   ALA    19      -9.158   5.087   5.845  1.00  0.00              
ATOM     65  N   GLY    20      -7.557   3.620   5.127  1.00  0.00              
ATOM     66  CA  GLY    20      -6.651   4.614   4.555  1.00  0.00              
ATOM     67  C   GLY    20      -6.545   4.440   3.041  1.00  0.00              
ATOM     68  O   GLY    20      -7.384   3.768   2.434  1.00  0.00              
ATOM     69  N   VAL    21      -5.538   5.054   2.414  1.00  0.00              
ATOM     70  CA  VAL    21      -5.371   4.991   0.977  1.00  0.00              
ATOM     71  C   VAL    21      -4.226   4.088   0.520  1.00  0.00              
ATOM     72  O   VAL    21      -3.254   3.861   1.253  1.00  0.00              
ATOM     73  N   THR    23      -4.300   3.570  -0.704  1.00  0.00              
ATOM     74  CA  THR    23      -3.318   2.635  -1.230  1.00  0.00              
ATOM     75  C   THR    23      -1.977   3.335  -1.404  1.00  0.00              
ATOM     76  O   THR    23      -0.916   2.744  -1.198  1.00  0.00              
ATOM     77  N   GLU    24      -2.014   4.635  -1.718  1.00  0.00              
ATOM     78  CA  GLU    24      -0.828   5.464  -1.887  1.00  0.00              
ATOM     79  C   GLU    24       0.046   5.593  -0.626  1.00  0.00              
ATOM     80  O   GLU    24       1.208   5.989  -0.708  1.00  0.00              
ATOM     81  N   GLU    25      -0.484   5.261   0.556  1.00  0.00              
ATOM     82  CA  GLU    25       0.278   5.334   1.785  1.00  0.00              
ATOM     83  C   GLU    25       1.165   4.104   1.941  1.00  0.00              
ATOM     84  O   GLU    25       2.040   4.056   2.811  1.00  0.00              
ATOM     85  N   GLU    26       0.988   3.065   1.122  1.00  0.00              
ATOM     86  CA  GLU    26       1.725   1.824   1.294  1.00  0.00              
ATOM     87  C   GLU    26       2.886   1.770   0.323  1.00  0.00              
ATOM     88  O   GLU    26       2.920   0.968  -0.611  1.00  0.00              
ATOM     89  N   LYS    27       3.925   2.572   0.550  1.00  0.00              
ATOM     90  CA  LYS    27       5.004   2.674  -0.429  1.00  0.00              
ATOM     91  C   LYS    27       6.157   1.692  -0.258  1.00  0.00              
ATOM     92  O   LYS    27       7.092   1.680  -1.051  1.00  0.00              
ATOM     93  N   ALA    28       6.039   0.745   0.660  1.00  0.00              
ATOM     94  CA  ALA    28       7.128  -0.147   1.029  1.00  0.00              
ATOM     95  C   ALA    28       7.159  -1.423   0.190  1.00  0.00              
ATOM     96  O   ALA    28       7.307  -2.544   0.680  1.00  0.00              
ATOM     97  N   GLU    29       7.093  -1.247  -1.125  1.00  0.00              
ATOM     98  CA  GLU    29       6.967  -2.325  -2.101  1.00  0.00              
ATOM     99  C   GLU    29       7.708  -3.621  -1.852  1.00  0.00              
ATOM    100  O   GLU    29       7.071  -4.614  -1.507  1.00  0.00              
ATOM    101  N   GLN    30       9.031  -3.678  -1.954  1.00  0.00              
ATOM    102  CA  GLN    30       9.696  -4.961  -1.815  1.00  0.00              
ATOM    103  C   GLN    30       9.609  -5.622  -0.446  1.00  0.00              
ATOM    104  O   GLN    30       9.646  -6.853  -0.423  1.00  0.00              
ATOM    105  N   GLN    31       9.458  -4.912   0.684  1.00  0.00              
ATOM    106  CA  GLN    31       9.313  -5.625   1.947  1.00  0.00              
ATOM    107  C   GLN    31       7.867  -6.045   2.152  1.00  0.00              
ATOM    108  O   GLN    31       7.633  -7.082   2.781  1.00  0.00              
ATOM    109  N   LYS    32       6.861  -5.339   1.602  1.00  0.00              
ATOM    110  CA  LYS    32       5.471  -5.831   1.617  1.00  0.00              
ATOM    111  C   LYS    32       5.465  -7.182   0.920  1.00  0.00              
ATOM    112  O   LYS    32       5.041  -8.209   1.466  1.00  0.00              
ATOM    113  N   LEU    33       6.069  -7.155  -0.262  1.00  0.00              
ATOM    114  CA  LEU    33       6.308  -8.297  -1.113  1.00  0.00              
ATOM    115  C   LEU    33       6.949  -9.434  -0.324  1.00  0.00              
ATOM    116  O   LEU    33       6.559 -10.598  -0.449  1.00  0.00              
ATOM    117  N   ARG    34       7.934  -9.107   0.515  1.00  0.00              
ATOM    118  CA  ARG    34       8.638 -10.084   1.330  1.00  0.00              
ATOM    119  C   ARG    34       7.711 -10.788   2.320  1.00  0.00              
ATOM    120  O   ARG    34       7.752 -12.015   2.420  1.00  0.00              
ATOM    121  N   GLN    35       6.882 -10.028   3.042  1.00  0.00              
ATOM    122  CA  GLN    35       6.011 -10.579   4.068  1.00  0.00              
ATOM    123  C   GLN    35       5.077 -11.619   3.503  1.00  0.00              
ATOM    124  O   GLN    35       4.999 -12.765   3.964  1.00  0.00              
ATOM    125  N   GLU    36       4.356 -11.164   2.481  1.00  0.00              
ATOM    126  CA  GLU    36       3.324 -11.967   1.888  1.00  0.00              
ATOM    127  C   GLU    36       3.865 -12.999   0.919  1.00  0.00              
ATOM    128  O   GLU    36       3.658 -14.191   1.146  1.00  0.00              
ATOM    129  N   TYR    37       4.599 -12.595  -0.120  1.00  0.00              
ATOM    130  CA  TYR    37       5.021 -13.553  -1.122  1.00  0.00              
ATOM    131  C   TYR    37       6.274 -14.278  -0.684  1.00  0.00              
ATOM    132  O   TYR    37       6.313 -15.508  -0.766  1.00  0.00              
ATOM    133  N   LEU    38      12.270 -14.305  -3.191  1.00  0.00              
ATOM    134  CA  LEU    38      12.336 -15.334  -4.226  1.00  0.00              
ATOM    135  C   LEU    38      11.073 -16.199  -4.055  1.00  0.00              
ATOM    136  O   LEU    38      11.021 -17.389  -4.398  1.00  0.00              
ATOM    137  N   LYS    39       9.994 -15.537  -3.585  1.00  0.00              
ATOM    138  CA  LYS    39       8.697 -16.110  -3.250  1.00  0.00              
ATOM    139  C   LYS    39       8.917 -17.097  -2.131  1.00  0.00              
ATOM    140  O   LYS    39       8.643 -16.746  -0.995  1.00  0.00              
ATOM    141  N   GLY    40       9.459 -18.283  -2.398  1.00  0.00              
ATOM    142  CA  GLY    40       9.772 -19.301  -1.408  1.00  0.00              
ATOM    143  C   GLY    40       8.609 -19.702  -0.479  1.00  0.00              
ATOM    144  O   GLY    40       8.154 -20.854  -0.549  1.00  0.00              
END
