
#######################################################
#                                                     #
#                        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 T0335TS307_3u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS307_3u-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      -       -           -
LGA    I       7      -       -           -
LGA    A       8      A       5          1.419
LGA    R       9      K       6          1.603
LGA    I      10      I       7          2.465
LGA    N      11      A       8          1.836
LGA    E      12      R       9          0.607
LGA    L      13      I      10          2.044
LGA    A      14      N      11          2.645
LGA    A      15      E      12          1.754
LGA    K      16      L      13          0.361
LGA    A      17      A      14          1.240
LGA    K      18      A      15          1.288
LGA    A      19      K      16          0.700
LGA    G      20      A      17          1.136
LGA    I      22      K      18          1.920
LGA    T      23      A      19          1.748
LGA    E      24      G      20          1.532
LGA    E      25      V      21          1.388
LGA    E      26      I      22          2.509
LGA    K      27      T      23          3.022
LGA    A      28      E      24          2.209
LGA    E      29      E      25          2.086
LGA    Q      30      E      26          1.844
LGA    Q      31      K      27          1.057
LGA    K      32      A      28          1.747
LGA    L      33      E      29          2.987
LGA    R      34      Q      30          2.818
LGA    -       -      Q      31           -
LGA    Q      35      K      32          1.679
LGA    E      36      L      33          0.929
LGA    L      38      R      34          2.082
LGA    K      39      Q      35          2.483
LGA    G      40      E      36          0.549
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)   34   36    5.0     31    1.87    12.90     77.424     1.574

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.149085 * X  +   0.804982 * Y  +   0.574262 * Z  +  -4.633420
  Y_new =  -0.269411 * X  +  -0.591849 * Y  +   0.759692 * Z  +   6.562946
  Z_new =   0.951416 * X  +  -0.041454 * Y  +   0.305107 * Z  +   5.666179 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.135039    3.006553  [ DEG:    -7.7372    172.2628 ]
  Theta =  -1.257801   -1.883792  [ DEG:   -72.0667   -107.9333 ]
  Phi   =  -2.076226    1.065366  [ DEG:  -118.9590     61.0410 ]
 
# 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: T0335TS307_3u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS307_3u-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   31   1.87   12.90  77.424
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS307_3u-D1
PFRMAT   TS
TARGET   T0335
MODEL    3  UNREFINED
PARENT   1e52_A
ATOM     1   N   ALA     5       3.195 -13.338  -9.276  1.00                    
ATOM     1   CA  ALA     5       3.680 -13.067  -7.890  1.00                    
ATOM     1   C   ALA     5       3.661 -11.561  -7.618  1.00                    
ATOM     1   O   ALA     5       2.978 -11.087  -6.731  1.00                    
ATOM     1   N   LYS     6       4.396 -10.808  -8.385  1.00                    
ATOM     1   CA  LYS     6       4.414  -9.331  -8.186  1.00                    
ATOM     1   C   LYS     6       2.980  -8.791  -8.289  1.00                    
ATOM     1   O   LYS     6       2.447  -8.229  -7.353  1.00                    
ATOM     1   N   ILE     7       2.356  -8.962  -9.423  1.00                    
ATOM     1   CA  ILE     7       0.959  -8.466  -9.599  1.00                    
ATOM     1   C   ILE     7       0.079  -8.925  -8.431  1.00                    
ATOM     1   O   ILE     7      -0.821  -8.227  -8.008  1.00                    
ATOM     1   N   ALA     8       0.335 -10.092  -7.905  1.00                    
ATOM     1   CA  ALA     8      -0.485 -10.589  -6.765  1.00                    
ATOM     1   C   ALA     8      -0.141  -9.811  -5.493  1.00                    
ATOM     1   O   ALA     8      -0.995  -9.526  -4.676  1.00                    
ATOM     1   N   ARG     9       1.105  -9.465  -5.318  1.00                    
ATOM     1   CA  ARG     9       1.504  -8.705  -4.100  1.00                    
ATOM     1   C   ARG     9       0.984  -7.268  -4.183  1.00                    
ATOM     1   O   ARG     9       0.439  -6.737  -3.235  1.00                    
ATOM     1   N   ILE    10       1.148  -6.633  -5.311  1.00                    
ATOM     1   CA  ILE    10       0.662  -5.230  -5.457  1.00                    
ATOM     1   C   ILE    10      -0.823  -5.148  -5.099  1.00                    
ATOM     1   O   ILE    10      -1.226  -4.374  -4.253  1.00                    
ATOM     1   N   ASN    11      -1.640  -5.939  -5.737  1.00                    
ATOM     1   CA  ASN    11      -3.099  -5.905  -5.432  1.00                    
ATOM     1   C   ASN    11      -3.344  -6.265  -3.964  1.00                    
ATOM     1   O   ASN    11      -4.363  -5.926  -3.394  1.00                    
ATOM     1   N   GLU    12      -2.420  -6.949  -3.350  1.00                    
ATOM     1   CA  GLU    12      -2.600  -7.332  -1.920  1.00                    
ATOM     1   C   GLU    12      -2.252  -6.154  -1.004  1.00                    
ATOM     1   O   GLU    12      -2.948  -5.873  -0.049  1.00                    
ATOM     1   N   LEU    13      -1.180  -5.467  -1.287  1.00                    
ATOM     1   CA  LEU    13      -0.786  -4.311  -0.429  1.00                    
ATOM     1   C   LEU    13      -1.752  -3.140  -0.632  1.00                    
ATOM     1   O   LEU    13      -2.168  -2.497   0.312  1.00                    
ATOM     1   N   ALA    14      -2.111  -2.857  -1.854  1.00                    
ATOM     1   CA  ALA    14      -3.049  -1.725  -2.112  1.00                    
ATOM     1   C   ALA    14      -4.392  -1.980  -1.420  1.00                    
ATOM     1   O   ALA    14      -4.968  -1.097  -0.817  1.00                    
ATOM     1   N   ALA    15      -4.894  -3.181  -1.504  1.00                    
ATOM     1   CA  ALA    15      -6.199  -3.491  -0.854  1.00                    
ATOM     1   C   ALA    15      -6.057  -3.385   0.666  1.00                    
ATOM     1   O   ALA    15      -7.024  -3.201   1.377  1.00                    
ATOM     1   N   LYS    16      -4.859  -3.499   1.171  1.00                    
ATOM     1   CA  LYS    16      -4.660  -3.405   2.647  1.00                    
ATOM     1   C   LYS    16      -4.806  -1.953   3.111  1.00                    
ATOM     1   O   LYS    16      -5.377  -1.677   4.149  1.00                    
ATOM     1   N   ALA    17      -4.295  -1.022   2.353  1.00                    
ATOM     1   CA  ALA    17      -4.404   0.411   2.752  1.00                    
ATOM     1   C   ALA    17      -5.864   0.774   3.039  1.00                    
ATOM     1   O   ALA    17      -6.187   1.324   4.073  1.00                    
ATOM     1   N   LYS    18      -6.749   0.477   2.123  1.00                    
ATOM     1   CA  LYS    18      -8.190   0.809   2.332  1.00                    
ATOM     1   C   LYS    18      -8.661   0.328   3.708  1.00                    
ATOM     1   O   LYS    18      -9.336   1.038   4.426  1.00                    
ATOM     1   N   ALA    19      -8.315  -0.874   4.079  1.00                    
ATOM     1   CA  ALA    19      -8.746  -1.400   5.406  1.00                    
ATOM     1   C   ALA    19      -8.377  -0.411   6.519  1.00                    
ATOM     1   O   ALA    19      -9.221   0.275   7.058  1.00                    
ATOM     1   N   GLY    20      -7.123  -0.342   6.870  1.00                    
ATOM     1   CA  GLY    20      -6.699   0.593   7.952  1.00                    
ATOM     1   C   GLY    20      -7.147   2.024   7.639  1.00                    
ATOM     1   O   GLY    20      -7.817   2.656   8.432  1.00                    
ATOM     1   N   ILE    22      -6.784   2.539   6.491  1.00                    
ATOM     1   CA  ILE    22      -7.191   3.933   6.124  1.00                    
ATOM     1   C   ILE    22      -8.684   4.138   6.406  1.00                    
ATOM     1   O   ILE    22      -9.122   5.222   6.736  1.00                    
ATOM     1   N   THR    23      -9.462   3.095   6.297  1.00                    
ATOM     1   CA  THR    23     -10.920   3.219   6.578  1.00                    
ATOM     1   C   THR    23     -11.146   3.181   8.092  1.00                    
ATOM     1   O   THR    23     -12.018   3.843   8.619  1.00                    
ATOM     1   N   GLU    24     -10.352   2.418   8.794  1.00                    
ATOM     1   CA  GLU    24     -10.502   2.342  10.275  1.00                    
ATOM     1   C   GLU    24      -9.533   3.321  10.941  1.00                    
ATOM     1   O   GLU    24      -9.141   3.151  12.079  1.00                    
ATOM     1   N   GLU    25      -9.144   4.346  10.232  1.00                    
ATOM     1   CA  GLU    25      -8.200   5.350  10.803  1.00                    
ATOM     1   C   GLU    25      -6.925   4.670  11.309  1.00                    
ATOM     1   O   GLU    25      -6.290   5.133  12.236  1.00                    
ATOM     1   N   GLU    26      -6.534   3.586  10.698  1.00                    
ATOM     1   CA  GLU    26      -5.289   2.890  11.136  1.00                    
ATOM     1   C   GLU    26      -4.199   3.055  10.070  1.00                    
ATOM     1   O   GLU    26      -3.255   2.295  10.009  1.00                    
ATOM     1   N   LYS    27      -4.336   4.046   9.226  1.00                    
ATOM     1   CA  LYS    27      -3.335   4.281   8.149  1.00                    
ATOM     1   C   LYS    27      -1.941   4.573   8.713  1.00                    
ATOM     1   O   LYS    27      -0.983   4.630   7.973  1.00                    
ATOM     1   N   ALA    28      -1.798   4.761  10.003  1.00                    
ATOM     1   CA  ALA    28      -0.440   5.044  10.562  1.00                    
ATOM     1   C   ALA    28       0.558   4.018  10.017  1.00                    
ATOM     1   O   ALA    28       1.420   4.332   9.219  1.00                    
ATOM     1   N   GLU    29       0.420   2.792  10.421  1.00                    
ATOM     1   CA  GLU    29       1.327   1.730   9.906  1.00                    
ATOM     1   C   GLU    29       0.838   1.256   8.530  1.00                    
ATOM     1   O   GLU    29       1.569   0.648   7.774  1.00                    
ATOM     1   N   GLN    30      -0.407   1.515   8.214  1.00                    
ATOM     1   CA  GLN    30      -0.967   1.069   6.904  1.00                    
ATOM     1   C   GLN    30      -0.500   1.968   5.755  1.00                    
ATOM     1   O   GLN    30      -0.016   1.495   4.747  1.00                    
ATOM     1   N   GLN    31      -0.654   3.258   5.885  1.00                    
ATOM     1   CA  GLN    31      -0.231   4.171   4.783  1.00                    
ATOM     1   C   GLN    31       1.208   3.872   4.362  1.00                    
ATOM     1   O   GLN    31       1.608   4.159   3.253  1.00                    
ATOM     1   N   LYS    32       1.989   3.285   5.228  1.00                    
ATOM     1   CA  LYS    32       3.395   2.964   4.849  1.00                    
ATOM     1   C   LYS    32       3.402   2.131   3.567  1.00                    
ATOM     1   O   LYS    32       4.298   2.232   2.752  1.00                    
ATOM     1   N   LEU    33       2.398   1.316   3.376  1.00                    
ATOM     1   CA  LEU    33       2.337   0.486   2.139  1.00                    
ATOM     1   C   LEU    33       2.456   1.393   0.914  1.00                    
ATOM     1   O   LEU    33       2.944   0.995  -0.126  1.00                    
ATOM     1   N   ARG    34       2.025   2.620   1.040  1.00                    
ATOM     1   CA  ARG    34       2.120   3.577  -0.104  1.00                    
ATOM     1   C   ARG    34       3.537   3.539  -0.694  1.00                    
ATOM     1   O   ARG    34       3.727   3.688  -1.885  1.00                    
ATOM     1   N   GLN    35       4.525   3.332   0.130  1.00                    
ATOM     1   CA  GLN    35       5.922   3.275  -0.385  1.00                    
ATOM     1   C   GLN    35       6.133   1.978  -1.169  1.00                    
ATOM     1   O   GLN    35       6.812   1.952  -2.176  1.00                    
ATOM     1   N   GLU    36       5.549   0.901  -0.716  1.00                    
ATOM     1   CA  GLU    36       5.708  -0.393  -1.437  1.00                    
ATOM     1   C   GLU    36       4.760  -0.443  -2.638  1.00                    
ATOM     1   O   GLU    36       5.078  -0.997  -3.672  1.00                    
ATOM     1   N   LEU    38       3.595   0.134  -2.509  1.00                    
ATOM     1   CA  LEU    38       2.625   0.122  -3.641  1.00                    
ATOM     1   C   LEU    38       3.162   0.956  -4.807  1.00                    
ATOM     1   O   LEU    38       2.978   0.621  -5.960  1.00                    
ATOM     1   N   LYS    39       3.824   2.042  -4.515  1.00                    
ATOM     1   CA  LYS    39       4.372   2.898  -5.606  1.00                    
ATOM     1   C   LYS    39       5.639   2.267  -6.189  1.00                    
ATOM     1   O   LYS    39       5.820   2.211  -7.389  1.00                    
ATOM     1   N   GLY    40       6.517   1.793  -5.349  1.00                    
ATOM     1   CA  GLY    40       7.772   1.166  -5.856  1.00                    
ATOM     1   C   GLY    40       7.446  -0.096  -6.659  1.00                    
ATOM     1   O   GLY    40       7.988  -0.324  -7.722  1.00                    
TER
END
