
#######################################################
#                                                     #
#                        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   36 (  178),  selected   36 , name T0335TS556_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS556_2-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          3.834
LGA    K       6      K       6          2.484
LGA    I       7      I       7          1.503
LGA    A       8      A       8          1.674
LGA    R       9      R       9          1.778
LGA    I      10      I      10          1.034
LGA    N      11      N      11          0.607
LGA    E      12      E      12          0.785
LGA    L      13      L      13          1.100
LGA    A      14      A      14          0.430
LGA    A      15      A      15          0.865
LGA    K      16      K      16          1.056
LGA    A      17      A      17          0.937
LGA    K      18      K      18          0.830
LGA    A      19      A      19          2.456
LGA    G      20      G      20          2.392
LGA    V      21      V      21          0.526
LGA    I      22      I      22          1.735
LGA    T      23      T      23          2.967
LGA    E      24      E      24          4.082
LGA    E      25      E      25          4.816
LGA    E      26      E      26          3.308
LGA    K      27      K      27          0.811
LGA    A      28      A      28          1.224
LGA    E      29      E      29          3.038
LGA    Q      30      Q      30          4.743
LGA    Q      31      Q      31          4.128
LGA    K      32      K      32          3.838
LGA    L      33      -       -           -
LGA    R      34      -       -           -
LGA    Q      35      L      33          3.587
LGA    E      36      R      34           -
LGA    Y      37      Q      35           -
LGA    -       -      E      36           -
LGA    L      38      Y      37           #
LGA    K      39      L      38           -
LGA    G      40      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     29    2.55    96.55     66.552     1.093

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.436496 * X  +  -0.813187 * Y  +  -0.384966 * Z  +   0.384994
  Y_new =   0.463184 * X  +   0.569927 * Y  +  -0.678707 * Z  + -10.455236
  Z_new =   0.771318 * X  +   0.117943 * Y  +   0.625427 * Z  + -15.701181 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.186391   -2.955202  [ DEG:    10.6794   -169.3206 ]
  Theta =  -0.880909   -2.260684  [ DEG:   -50.4724   -129.5276 ]
  Phi   =   0.815054   -2.326539  [ DEG:    46.6991   -133.3009 ]
 
# 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: T0335TS556_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS556_2-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   29   2.55   96.55  66.552
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS556_2-D1
PFRMAT TS
TARGET T0335
MODEL 2
PARENT N/A
ATOM     21  N   ALA     5      -2.074  -9.255 -10.207  1.00 10.00
ATOM     22  CA  ALA     5      -2.228  -9.799  -8.864  1.00 10.00
ATOM     23  C   ALA     5      -1.562  -8.905  -7.827  1.00 10.00
ATOM     24  O   ALA     5      -2.044  -8.779  -6.701  1.00 10.00
ATOM     25  CB  ALA     5      -1.659 -11.209  -8.795  1.00 10.00
ATOM     26  N   LYS     6      -0.452  -8.284  -8.213  1.00 10.00
ATOM     27  CA  LYS     6       0.280  -7.396  -7.318  1.00 10.00
ATOM     28  C   LYS     6      -0.549  -6.170  -6.959  1.00 10.00
ATOM     29  O   LYS     6      -0.591  -5.755  -5.802  1.00 10.00
ATOM     30  CB  LYS     6       1.600  -6.980  -7.947  1.00 10.00
ATOM     31  N   ILE     7      -1.209  -5.595  -7.959  1.00 10.00
ATOM     32  CA  ILE     7      -2.054  -4.426  -7.747  1.00 10.00
ATOM     33  C   ILE     7      -3.218  -4.750  -6.819  1.00 10.00
ATOM     34  O   ILE     7      -3.559  -3.961  -5.937  1.00 10.00
ATOM     35  CB  ILE     7      -2.567  -3.894  -9.077  1.00 10.00
ATOM     36  N   ALA     8      -3.825  -5.914  -7.022  1.00 10.00
ATOM     37  CA  ALA     8      -4.936  -6.355  -6.188  1.00 10.00
ATOM     38  C   ALA     8      -4.510  -6.501  -4.734  1.00 10.00
ATOM     39  O   ALA     8      -5.236  -6.105  -3.821  1.00 10.00
ATOM     40  CB  ALA     8      -5.505  -7.665  -6.710  1.00 10.00
ATOM     41  N   ARG     9      -3.328  -7.072  -4.523  1.00 10.00
ATOM     42  CA  ARG     9      -2.811  -7.289  -3.178  1.00 10.00
ATOM     43  C   ARG     9      -2.567  -5.967  -2.461  1.00 10.00
ATOM     44  O   ARG     9      -2.893  -5.818  -1.284  1.00 10.00
ATOM     45  CB  ARG     9      -1.533  -8.111  -3.227  1.00 10.00
ATOM     46  N   ILE    10      -1.989  -5.008  -3.179  1.00 10.00
ATOM     47  CA  ILE    10      -1.729  -3.686  -2.623  1.00 10.00
ATOM     48  C   ILE    10      -3.028  -2.953  -2.317  1.00 10.00
ATOM     49  O   ILE    10      -3.167  -2.332  -1.262  1.00 10.00
ATOM     50  CB  ILE    10      -0.869  -2.870  -3.576  1.00 10.00
ATOM     51  N   ASN    11      -3.976  -3.026  -3.244  1.00 10.00
ATOM     52  CA  ASN    11      -5.278  -2.394  -3.061  1.00 10.00
ATOM     53  C   ASN    11      -5.995  -2.953  -1.839  1.00 10.00
ATOM     54  O   ASN    11      -6.607  -2.209  -1.073  1.00 10.00
ATOM     55  CB  ASN    11      -6.132  -2.570  -4.307  1.00 10.00
ATOM     56  N   GLU    12      -5.916  -4.267  -1.663  1.00 10.00
ATOM     57  CA  GLU    12      -6.568  -4.931  -0.541  1.00 10.00
ATOM     58  C   GLU    12      -6.034  -4.417   0.790  1.00 10.00
ATOM     59  O   GLU    12      -6.793  -4.205   1.735  1.00 10.00
ATOM     60  CB  GLU    12      -6.390  -6.438  -0.639  1.00 10.00
ATOM     61  N   LEU    13      -4.721  -4.219   0.857  1.00 10.00
ATOM     62  CA  LEU    13      -4.090  -3.671   2.051  1.00 10.00
ATOM     63  C   LEU    13      -4.554  -2.244   2.314  1.00 10.00
ATOM     64  O   LEU    13      -4.846  -1.876   3.452  1.00 10.00
ATOM     65  CB  LEU    13      -2.575  -3.722   1.921  1.00 10.00
ATOM     66  N   ALA    14      -4.620  -1.444   1.255  1.00 10.00
ATOM     67  CA  ALA    14      -5.042  -0.054   1.371  1.00 10.00
ATOM     68  C   ALA    14      -6.473   0.049   1.882  1.00 10.00
ATOM     69  O   ALA    14      -6.785   0.895   2.720  1.00 10.00
ATOM     70  CB  ALA    14      -4.904   0.656   0.033  1.00 10.00
ATOM     71  N   ALA    15      -7.341  -0.819   1.372  1.00 10.00
ATOM     72  CA  ALA    15      -8.740  -0.834   1.780  1.00 10.00
ATOM     73  C   ALA    15      -8.878  -1.167   3.260  1.00 10.00
ATOM     74  O   ALA    15      -9.716  -0.597   3.960  1.00 10.00
ATOM     75  CB  ALA    15      -9.530  -1.822   0.936  1.00 10.00
ATOM     76  N   LYS    16      -8.053  -2.095   3.732  1.00 10.00
ATOM     77  CA  LYS    16      -8.066  -2.490   5.135  1.00 10.00
ATOM     78  C   LYS    16      -7.540  -1.373   6.027  1.00 10.00
ATOM     79  O   LYS    16      -8.049  -1.152   7.126  1.00 10.00
ATOM     80  CB  LYS    16      -7.250  -3.758   5.337  1.00 10.00
ATOM     81  N   ALA    17      -6.521  -0.669   5.547  1.00 10.00
ATOM     82  CA  ALA    17      -5.920   0.423   6.303  1.00 10.00
ATOM     83  C   ALA    17      -6.933   1.529   6.570  1.00 10.00
ATOM     84  O   ALA    17      -7.022   2.045   7.684  1.00 10.00
ATOM     85  CB  ALA    17      -4.710   0.977   5.565  1.00 10.00
ATOM     86  N   LYS    18      -7.693   1.889   5.542  1.00 10.00
ATOM     87  CA  LYS    18      -8.698   2.940   5.663  1.00 10.00
ATOM     88  C   LYS    18      -9.784   2.551   6.656  1.00 10.00
ATOM     89  O   LYS    18     -10.235   3.375   7.452  1.00 10.00
ATOM     90  CB  LYS    18      -9.306   3.250   4.303  1.00 10.00
ATOM     91  N   ALA    19     -10.202   1.291   6.606  1.00 10.00
ATOM     92  CA  ALA    19     -11.232   0.788   7.508  1.00 10.00
ATOM     93  C   ALA    19     -10.775   0.857   8.958  1.00 10.00
ATOM     94  O   ALA    19     -11.565   1.150   9.856  1.00 10.00
ATOM     95  CB  ALA    19     -11.613  -0.636   7.137  1.00 10.00
ATOM     96  N   GLY    20      -9.493   0.585   9.183  1.00 10.00
ATOM     97  CA  GLY    20      -8.924   0.633  10.524  1.00 10.00
ATOM     98  C   GLY    20      -8.441   2.036  10.868  1.00 10.00
ATOM     99  O   GLY    20      -7.745   2.237  11.864  1.00 10.00
ATOM    100  N   VAL    21      -8.815   3.005  10.039  1.00 10.00
ATOM    101  CA  VAL    21      -8.631   4.413  10.374  1.00 10.00
ATOM    102  C   VAL    21      -7.235   4.670  10.925  1.00 10.00
ATOM    103  O   VAL    21      -7.080   5.248  12.000  1.00 10.00
ATOM    104  CB  VAL    21      -9.688   4.864  11.369  1.00 10.00
ATOM    105  N   ILE    22      -6.222   4.237  10.183  1.00 10.00
ATOM    106  CA  ILE    22      -4.835   4.442  10.584  1.00 10.00
ATOM    107  C   ILE    22      -4.322   5.798  10.119  1.00 10.00
ATOM    108  O   ILE    22      -4.915   6.430   9.245  1.00 10.00
ATOM    109  CB  ILE    22      -3.955   3.326  10.042  1.00 10.00
ATOM    110  N   THR    23      -3.215   6.241  10.707  1.00 10.00
ATOM    111  CA  THR    23      -2.596   7.503  10.322  1.00 10.00
ATOM    112  C   THR    23      -1.809   7.357   9.026  1.00 10.00
ATOM    113  O   THR    23      -1.540   6.244   8.573  1.00 10.00
ATOM    114  CB  THR    23      -1.695   8.012  11.436  1.00 10.00
ATOM    115  N   GLU    24      -1.442   8.488   8.432  1.00 10.00
ATOM    116  CA  GLU    24      -0.692   8.488   7.181  1.00 10.00
ATOM    117  C   GLU    24       0.660   7.808   7.350  1.00 10.00
ATOM    118  O   GLU    24       1.099   7.054   6.482  1.00 10.00
ATOM    119  CB  GLU    24      -0.514   9.910   6.670  1.00 10.00
ATOM    120  N   GLU    25       1.318   8.081   8.472  1.00 10.00
ATOM    121  CA  GLU    25       2.620   7.492   8.759  1.00 10.00
ATOM    122  C   GLU    25       2.520   5.978   8.900  1.00 10.00
ATOM    123  O   GLU    25       3.420   5.245   8.490  1.00 10.00
ATOM    124  CB  GLU    25       3.214   8.105  10.017  1.00 10.00
ATOM    125  N   GLU    26       1.420   5.515   9.484  1.00 10.00
ATOM    126  CA  GLU    26       1.144   4.086   9.575  1.00 10.00
ATOM    127  C   GLU    26       0.895   3.484   8.199  1.00 10.00
ATOM    128  O   GLU    26       1.346   2.376   7.904  1.00 10.00
ATOM    129  CB  GLU    26      -0.044   3.833  10.491  1.00 10.00
ATOM    130  N   LYS    27       0.176   4.220   7.358  1.00 10.00
ATOM    131  CA  LYS    27      -0.053   3.804   5.980  1.00 10.00
ATOM    132  C   LYS    27       1.254   3.736   5.200  1.00 10.00
ATOM    133  O   LYS    27       1.485   2.798   4.438  1.00 10.00
ATOM    134  CB  LYS    27      -1.032   4.747   5.297  1.00 10.00
ATOM    135  N   ALA    28       2.106   4.736   5.397  1.00 10.00
ATOM    136  CA  ALA    28       3.421   4.758   4.765  1.00 10.00
ATOM    137  C   ALA    28       4.242   3.538   5.162  1.00 10.00
ATOM    138  O   ALA    28       4.890   2.914   4.321  1.00 10.00
ATOM    139  CB  ALA    28       4.160   6.038   5.125  1.00 10.00
ATOM    140  N   GLU    29       4.212   3.203   6.447  1.00 10.00
ATOM    141  CA  GLU    29       5.002   2.094   6.968  1.00 10.00
ATOM    142  C   GLU    29       4.445   0.754   6.505  1.00 10.00
ATOM    143  O   GLU    29       5.197  -0.187   6.250  1.00 10.00
ATOM    144  CB  GLU    29       5.057   2.150   8.487  1.00 10.00
ATOM    145  N   GLN    30       3.124   0.675   6.395  1.00 10.00
ATOM    146  CA  GLN    30       2.471  -0.500   5.830  1.00 10.00
ATOM    147  C   GLN    30       2.740  -0.614   4.334  1.00 10.00
ATOM    148  O   GLN    30       2.785  -1.714   3.784  1.00 10.00
ATOM    149  CB  GLN    30       0.975  -0.457   6.100  1.00 10.00
ATOM    150  N   GLN    31       2.918   0.530   3.683  1.00 10.00
ATOM    151  CA  GLN    31       3.192   0.560   2.251  1.00 10.00
ATOM    152  C   GLN    31       4.566  -0.017   1.940  1.00 10.00
ATOM    153  O   GLN    31       4.741  -0.730   0.952  1.00 10.00
ATOM    154  CB  GLN    31       3.077   1.981   1.719  1.00 10.00
ATOM    155  N   LYS    32       5.540   0.297   2.789  1.00 10.00
ATOM    156  CA  LYS    32       6.902  -0.191   2.607  1.00 10.00
ATOM    157  C   LYS    32       6.959  -1.710   2.703  1.00 10.00
ATOM    158  O   LYS    32       7.576  -2.371   1.867  1.00 10.00
ATOM    159  CB  LYS    32       7.832   0.443   3.629  1.00 10.00
ATOM    160  N   LEU    33       6.313  -2.258   3.726  1.00 10.00
ATOM    161  CA  LEU    33       6.273  -3.702   3.922  1.00 10.00
ATOM    162  C   LEU    33       5.493  -4.388   2.809  1.00 10.00
ATOM    163  O   LEU    33       5.844  -5.487   2.378  1.00 10.00
ATOM    164  CB  LEU    33       5.669  -4.037   5.278  1.00 10.00
ATOM    165  N   ARG    34       4.435  -3.733   2.343  1.00 10.00
ATOM    166  CA  ARG    34       3.607  -4.276   1.273  1.00 10.00
ATOM    167  C   ARG    34       4.434  -4.550   0.023  1.00 10.00
ATOM    168  O   ARG    34       4.248  -5.569  -0.643  1.00 10.00
ATOM    169  CB  ARG    34       2.461  -3.328   0.955  1.00 10.00
ATOM    170  N   GLN    35       5.345  -3.635  -0.291  1.00 10.00
ATOM    171  CA  GLN    35       6.196  -3.774  -1.465  1.00 10.00
ATOM    172  C   GLN    35       7.092  -5.001  -1.354  1.00 10.00
ATOM    173  O   GLN    35       7.233  -5.766  -2.309  1.00 10.00
ATOM    174  CB  GLN    35       7.035  -2.520  -1.663  1.00 10.00
ATOM    175  N   GLU    36       7.695  -5.183  -0.185  1.00 10.00
ATOM    176  CA  GLU    36       8.566  -6.328   0.058  1.00 10.00
ATOM    177  C   GLU    36       7.815  -7.640  -0.121  1.00 10.00
ATOM    178  O   GLU    36       8.285  -8.546  -0.809  1.00 10.00
ATOM    179  CB  GLU    36       9.172  -6.246   1.451  1.00 10.00
ATOM    180  N   TYR    37       6.645  -7.736   0.502  1.00 10.00
ATOM    181  CA  TYR    37       5.837  -8.947   0.431  1.00 10.00
ATOM    182  C   TYR    37       5.294  -9.164  -0.977  1.00 10.00
ATOM    183  O   TYR    37       5.262 -10.291  -1.472  1.00 10.00
ATOM    184  CB  TYR    37       4.697  -8.884   1.435  1.00 10.00
ATOM    185  N   LEU    38       4.870  -8.080  -1.616  1.00 10.00
ATOM    186  CA  LEU    38       4.310  -8.153  -2.960  1.00 10.00
ATOM    187  C   LEU    38       5.253  -8.877  -3.911  1.00 10.00
ATOM    188  O   LEU    38       4.817  -9.629  -4.782  1.00 10.00
ATOM    189  CB  LEU    38       3.997  -6.759  -3.480  1.00 10.00
ATOM    190  N   LYS    39       6.551  -8.647  -3.738  1.00 10.00
ATOM    191  CA  LYS    39       7.561  -9.293  -4.568  1.00 10.00
ATOM    192  C   LYS    39       7.485 -10.809  -4.449  1.00 10.00
ATOM    193  O   LYS    39       7.517 -11.522  -5.453  1.00 10.00
ATOM    194  CB  LYS    39       8.950  -8.798  -4.194  1.00 10.00
ATOM    195  N   GLY    40       7.383 -11.296  -3.218  1.00 10.00
ATOM    196  CA  GLY    40       7.300 -12.730  -2.966  1.00 10.00
ATOM    197  C   GLY    40       5.970 -13.297  -3.445  1.00 10.00
ATOM    198  O   GLY    40       5.913 -14.408  -3.974  1.00 10.00
TER
END
