
#######################################################
#                                                     #
#                        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 T0335TS121_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS121_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      -       -           -
LGA    I       7      -       -           -
LGA    A       8      -       -           -
LGA    R       9      A       5          4.586
LGA    I      10      K       6          3.524
LGA    N      11      I       7          2.316
LGA    E      12      A       8          1.495
LGA    L      13      R       9          2.766
LGA    A      14      I      10          2.017
LGA    A      15      N      11          0.453
LGA    K      16      E      12          2.405
LGA    A      17      L      13          2.918
LGA    K      18      A      14          0.641
LGA    A      19      A      15          3.606
LGA    G      20      K      16          4.904
LGA    V      21      A      17          2.944
LGA    I      22      K      18          2.905
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    T      23      I      22          0.972
LGA    E      24      T      23          3.214
LGA    E      25      E      24          1.879
LGA    -       -      E      25           -
LGA    E      26      E      26          2.355
LGA    K      27      K      27          2.095
LGA    A      28      A      28          2.289
LGA    E      29      E      29          1.940
LGA    Q      30      Q      30          1.384
LGA    Q      31      Q      31          0.924
LGA    K      32      K      32          1.511
LGA    L      33      L      33          1.213
LGA    R      34      R      34          0.620
LGA    Q      35      Q      35          1.513
LGA    E      36      E      36          2.216
LGA    Y      37      Y      37          2.096
LGA    L      38      L      38          1.992
LGA    K      39      K      39          3.462
LGA    G      40      G      40          3.863

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     32    2.53    53.12     70.277     1.216

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.344190 * X  +   0.937898 * Y  +  -0.043363 * Z  +  -1.597162
  Y_new =  -0.809456 * X  +   0.273020 * Y  +  -0.519847 * Z  +   3.020135
  Z_new =  -0.475725 * X  +   0.214026 * Y  +   0.853158 * Z  +  -7.394751 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.245791   -2.895802  [ DEG:    14.0828   -165.9172 ]
  Theta =   0.495788    2.645805  [ DEG:    28.4066    151.5934 ]
  Phi   =  -1.168747    1.972846  [ DEG:   -66.9643    113.0357 ]
 
# 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: T0335TS121_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS121_4-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   32   2.53   53.12  70.277
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS121_4-D1
PFRMAT    TS
TARGET    T0335
MODEL     4
PARENT    N/A
ATOM      5  N   ALA     5      -0.362  -8.358 -16.813  1.00  0.00          
ATOM      5  CA  ALA     5      -1.202  -8.990 -15.783  1.00  0.00          
ATOM      5  C   ALA     5      -0.519  -8.903 -14.415  1.00  0.00          
ATOM      5  O   ALA     5      -1.155  -8.662 -13.379  1.00  0.00          
ATOM      5  CB  ALA     5      -1.345 -10.481 -16.138  1.00  0.00          
ATOM      6  N   LYS     6       0.784  -9.106 -14.451  1.00  0.00          
ATOM      6  CA  LYS     6       1.635  -9.069 -13.252  1.00  0.00          
ATOM      6  C   LYS     6       1.509  -7.730 -12.519  1.00  0.00          
ATOM      6  O   LYS     6       1.434  -7.662 -11.283  1.00  0.00          
ATOM      6  CB  LYS     6       3.096  -9.166 -13.726  1.00  0.00          
ATOM      7  N   ILE     7       1.488  -6.680 -13.319  1.00  0.00          
ATOM      7  CA  ILE     7       1.372  -5.300 -12.825  1.00  0.00          
ATOM      7  C   ILE     7       0.058  -5.210 -12.047  1.00  0.00          
ATOM      7  O   ILE     7      -0.034  -4.577 -10.983  1.00  0.00          
ATOM      7  CB  ILE     7       1.330  -4.340 -14.034  1.00  0.00          
ATOM      8  N   ALA     8      -0.943  -5.860 -12.609  1.00  0.00          
ATOM      8  CA  ALA     8      -2.293  -5.905 -12.030  1.00  0.00          
ATOM      8  C   ALA     8      -2.220  -6.530 -10.635  1.00  0.00          
ATOM      8  O   ALA     8      -2.866  -6.080  -9.679  1.00  0.00          
ATOM      8  CB  ALA     8      -3.157  -6.828 -12.915  1.00  0.00          
ATOM      9  N   ARG     9      -1.417  -7.575 -10.555  1.00  0.00          
ATOM      9  CA  ARG     9      -1.199  -8.327  -9.309  1.00  0.00          
ATOM      9  C   ARG     9      -0.635  -7.360  -8.267  1.00  0.00          
ATOM      9  O   ARG     9      -1.014  -7.372  -7.086  1.00  0.00          
ATOM      9  CB  ARG     9      -0.106  -9.391  -9.555  1.00  0.00          
ATOM     10  N   ILE    10       0.275  -6.529  -8.743  1.00  0.00          
ATOM     10  CA  ILE    10       0.945  -5.517  -7.914  1.00  0.00          
ATOM     10  C   ILE    10      -0.131  -4.582  -7.356  1.00  0.00          
ATOM     10  O   ILE    10      -0.095  -4.163  -6.190  1.00  0.00          
ATOM     10  CB  ILE    10       1.857  -4.715  -8.865  1.00  0.00          
ATOM     11  N   ASN    11      -1.079  -4.276  -8.222  1.00  0.00          
ATOM     11  CA  ASN    11      -2.208  -3.394  -7.895  1.00  0.00          
ATOM     11  C   ASN    11      -2.999  -3.953  -6.711  1.00  0.00          
ATOM     11  O   ASN    11      -3.418  -3.225  -5.800  1.00  0.00          
ATOM     11  CB  ASN    11      -3.150  -3.386  -9.117  1.00  0.00          
ATOM     12  N   GLU    12      -3.186  -5.259  -6.759  1.00  0.00          
ATOM     12  CA  GLU    12      -3.919  -6.001  -5.724  1.00  0.00          
ATOM     12  C   GLU    12      -3.215  -5.788  -4.382  1.00  0.00          
ATOM     12  O   GLU    12      -3.846  -5.604  -3.331  1.00  0.00          
ATOM     12  CB  GLU    12      -3.877  -7.511  -6.035  1.00  0.00          
ATOM     13  N   LEU    13      -1.897  -5.819  -4.455  1.00  0.00          
ATOM     13  CA  LEU    13      -1.024  -5.637  -3.286  1.00  0.00          
ATOM     13  C   LEU    13      -1.337  -4.261  -2.699  1.00  0.00          
ATOM     13  O   LEU    13      -1.416  -4.070  -1.474  1.00  0.00          
ATOM     13  CB  LEU    13       0.443  -5.616  -3.768  1.00  0.00          
ATOM     14  N   ALA    14      -1.510  -3.319  -3.607  1.00  0.00          
ATOM     14  CA  ALA    14      -1.819  -1.924  -3.262  1.00  0.00          
ATOM     14  C   ALA    14      -3.142  -1.886  -2.493  1.00  0.00          
ATOM     14  O   ALA    14      -3.306  -1.155  -1.506  1.00  0.00          
ATOM     14  CB  ALA    14      -1.953  -1.144  -4.586  1.00  0.00          
ATOM     15  N   ALA    15      -4.069  -2.692  -2.976  1.00  0.00          
ATOM     15  CA  ALA    15      -5.412  -2.811  -2.391  1.00  0.00          
ATOM     15  C   ALA    15      -5.379  -3.261  -0.927  1.00  0.00          
ATOM     15  O   ALA    15      -6.079  -2.721  -0.059  1.00  0.00          
ATOM     15  CB  ALA    15      -6.172  -3.916  -3.149  1.00  0.00          
ATOM     16  N   LYS    16      -4.548  -4.259  -0.689  1.00  0.00          
ATOM     16  CA  LYS    16      -4.362  -4.845   0.648  1.00  0.00          
ATOM     16  C   LYS    16      -3.890  -3.723   1.575  1.00  0.00          
ATOM     16  O   LYS    16      -4.294  -3.622   2.743  1.00  0.00          
ATOM     16  CB  LYS    16      -3.253  -5.915   0.575  1.00  0.00          
ATOM     17  N   ALA    17      -3.028  -2.893   1.019  1.00  0.00          
ATOM     17  CA  ALA    17      -2.448  -1.745   1.730  1.00  0.00          
ATOM     17  C   ALA    17      -3.548  -0.793   2.207  1.00  0.00          
ATOM     17  O   ALA    17      -3.527  -0.279   3.334  1.00  0.00          
ATOM     17  CB  ALA    17      -1.637  -0.989   0.660  1.00  0.00          
ATOM     18  N   LYS    18      -4.500  -0.581   1.319  1.00  0.00          
ATOM     18  CA  LYS    18      -5.652   0.298   1.570  1.00  0.00          
ATOM     18  C   LYS    18      -6.428  -0.201   2.791  1.00  0.00          
ATOM     18  O   LYS    18      -6.895   0.578   3.635  1.00  0.00          
ATOM     18  CB  LYS    18      -6.579   0.219   0.343  1.00  0.00          
ATOM     19  N   ALA    19      -6.546  -1.514   2.853  1.00  0.00          
ATOM     19  CA  ALA    19      -7.252  -2.204   3.942  1.00  0.00          
ATOM     19  C   ALA    19      -6.395  -2.219   5.210  1.00  0.00          
ATOM     19  O   ALA    19      -6.882  -2.435   6.328  1.00  0.00          
ATOM     19  CB  ALA    19      -7.499  -3.654   3.489  1.00  0.00          
ATOM     20  N   GLY    20      -5.115  -1.983   4.997  1.00  0.00          
ATOM     20  CA  GLY    20      -4.114  -1.951   6.075  1.00  0.00          
ATOM     20  C   GLY    20      -4.654  -1.141   7.257  1.00  0.00          
ATOM     20  O   GLY    20      -4.245   0.000   7.511  1.00  0.00          
ATOM     21  N   VAL    21      -5.577  -1.767   7.962  1.00  0.00          
ATOM     21  CA  VAL    21      -6.229  -1.171   9.139  1.00  0.00          
ATOM     21  C   VAL    21      -6.714   0.244   8.812  1.00  0.00          
ATOM     21  O   VAL    21      -7.085   1.030   9.693  1.00  0.00          
ATOM     21  CB  VAL    21      -5.175  -1.044  10.255  1.00  0.00          
ATOM     22  N   ILE    22      -6.697   0.538   7.526  1.00  0.00          
ATOM     22  CA  ILE    22      -7.121   1.843   6.991  1.00  0.00          
ATOM     22  C   ILE    22      -6.678   2.960   7.943  1.00  0.00          
ATOM     22  O   ILE    22      -7.233   4.066   7.959  1.00  0.00          
ATOM     22  CB  ILE    22      -8.659   1.853   6.926  1.00  0.00          
ATOM     23  N   THR    23      -5.668   2.632   8.726  1.00  0.00          
ATOM     23  CA  THR    23      -5.085   3.554   9.715  1.00  0.00          
ATOM     23  C   THR    23      -4.207   4.541   8.940  1.00  0.00          
ATOM     23  O   THR    23      -3.626   4.221   7.894  1.00  0.00          
ATOM     23  CB  THR    23      -4.196   2.768  10.693  1.00  0.00          
ATOM     24  N   GLU    24      -4.131   5.739   9.488  1.00  0.00          
ATOM     24  CA  GLU    24      -3.341   6.838   8.909  1.00  0.00          
ATOM     24  C   GLU    24      -1.895   6.364   8.757  1.00  0.00          
ATOM     24  O   GLU    24      -1.213   6.645   7.762  1.00  0.00          
ATOM     24  CB  GLU    24      -3.364   8.026   9.894  1.00  0.00          
ATOM     25  N   GLU    25      -1.457   5.641   9.772  1.00  0.00          
ATOM     25  CA  GLU    25      -0.098   5.085   9.831  1.00  0.00          
ATOM     25  C   GLU    25      -0.022   4.164   8.614  1.00  0.00          
ATOM     25  O   GLU    25       1.013   4.053   7.936  1.00  0.00          
ATOM     25  CB  GLU    25       0.029   4.202  11.095  1.00  0.00          
ATOM     26  N   GLU    26      -1.144   3.516   8.364  1.00  0.00          
ATOM     26  CA  GLU    26      -1.292   2.580   7.242  1.00  0.00          
ATOM     26  C   GLU    26      -0.933   3.287   5.933  1.00  0.00          
ATOM     26  O   GLU    26      -0.304   2.718   5.031  1.00  0.00          
ATOM     26  CB  GLU    26      -2.784   2.186   7.186  1.00  0.00          
ATOM     27  N   LYS    27      -1.351   4.536   5.864  1.00  0.00          
ATOM     27  CA  LYS    27      -1.115   5.398   4.696  1.00  0.00          
ATOM     27  C   LYS    27       0.382   5.518   4.401  1.00  0.00          
ATOM     27  O   LYS    27       0.834   5.416   3.251  1.00  0.00          
ATOM     27  CB  LYS    27      -1.647   6.810   5.023  1.00  0.00          
ATOM     28  N   ALA    28       1.126   5.735   5.469  1.00  0.00          
ATOM     28  CA  ALA    28       2.589   5.882   5.411  1.00  0.00          
ATOM     28  C   ALA    28       3.224   4.603   4.865  1.00  0.00          
ATOM     28  O   ALA    28       4.055   4.623   3.945  1.00  0.00          
ATOM     28  CB  ALA    28       3.111   6.110   6.847  1.00  0.00          
ATOM     29  N   GLU    29       2.809   3.501   5.460  1.00  0.00          
ATOM     29  CA  GLU    29       3.290   2.162   5.091  1.00  0.00          
ATOM     29  C   GLU    29       2.904   1.930   3.630  1.00  0.00          
ATOM     29  O   GLU    29       3.670   1.374   2.828  1.00  0.00          
ATOM     29  CB  GLU    29       2.563   1.112   5.960  1.00  0.00          
ATOM     30  N   GLN    30       1.702   2.373   3.317  1.00  0.00          
ATOM     30  CA  GLN    30       1.131   2.254   1.968  1.00  0.00          
ATOM     30  C   GLN    30       2.038   2.927   0.935  1.00  0.00          
ATOM     30  O   GLN    30       2.240   2.432  -0.183  1.00  0.00          
ATOM     30  CB  GLN    30      -0.209   3.016   1.969  1.00  0.00          
ATOM     31  N   GLN    31       2.572   4.062   1.344  1.00  0.00          
ATOM     31  CA  GLN    31       3.474   4.872   0.510  1.00  0.00          
ATOM     31  C   GLN    31       4.669   4.022   0.070  1.00  0.00          
ATOM     31  O   GLN    31       5.127   4.078  -1.080  1.00  0.00          
ATOM     31  CB  GLN    31       4.007   6.020   1.393  1.00  0.00          
ATOM     32  N   LYS    32       5.150   3.240   1.019  1.00  0.00          
ATOM     32  CA  LYS    32       6.295   2.340   0.811  1.00  0.00          
ATOM     32  C   LYS    32       5.986   1.298  -0.265  1.00  0.00          
ATOM     32  O   LYS    32       6.776   1.055  -1.190  1.00  0.00          
ATOM     32  CB  LYS    32       6.548   1.588   2.137  1.00  0.00          
ATOM     33  N   LEU    33       4.819   0.699  -0.113  1.00  0.00          
ATOM     33  CA  LEU    33       4.325  -0.334  -1.033  1.00  0.00          
ATOM     33  C   LEU    33       4.162   0.224  -2.449  1.00  0.00          
ATOM     33  O   LEU    33       4.531  -0.407  -3.450  1.00  0.00          
ATOM     33  CB  LEU    33       2.927  -0.793  -0.574  1.00  0.00          
ATOM     34  N   ARG    34       3.601   1.418  -2.495  1.00  0.00          
ATOM     34  CA  ARG    34       3.351   2.138  -3.752  1.00  0.00          
ATOM     34  C   ARG    34       4.652   2.341  -4.531  1.00  0.00          
ATOM     34  O   ARG    34       4.718   2.168  -5.757  1.00  0.00          
ATOM     34  CB  ARG    34       2.795   3.541  -3.436  1.00  0.00          
ATOM     35  N   GLN    35       5.676   2.710  -3.783  1.00  0.00          
ATOM     35  CA  GLN    35       7.019   2.960  -4.328  1.00  0.00          
ATOM     35  C   GLN    35       7.574   1.700  -4.996  1.00  0.00          
ATOM     35  O   GLN    35       8.100   1.730  -6.119  1.00  0.00          
ATOM     35  CB  GLN    35       7.939   3.295  -3.134  1.00  0.00          
ATOM     36  N   GLU    36       7.440   0.605  -4.273  1.00  0.00          
ATOM     36  CA  GLU    36       7.905  -0.715  -4.724  1.00  0.00          
ATOM     36  C   GLU    36       7.172  -1.159  -5.990  1.00  0.00          
ATOM     36  O   GLU    36       7.775  -1.605  -6.977  1.00  0.00          
ATOM     36  CB  GLU    36       7.558  -1.728  -3.612  1.00  0.00          
ATOM     37  N   TYR    37       5.861  -1.023  -5.926  1.00  0.00          
ATOM     37  CA  TYR    37       4.963  -1.389  -7.031  1.00  0.00          
ATOM     37  C   TYR    37       5.272  -0.577  -8.293  1.00  0.00          
ATOM     37  O   TYR    37       5.295  -1.096  -9.417  1.00  0.00          
ATOM     37  CB  TYR    37       3.532  -1.040  -6.579  1.00  0.00          
ATOM     38  N   LEU    38       5.505   0.703  -8.066  1.00  0.00          
ATOM     38  CA  LEU    38       5.823   1.662  -9.135  1.00  0.00          
ATOM     38  C   LEU    38       7.050   1.215  -9.933  1.00  0.00          
ATOM     38  O   LEU    38       7.104   1.318 -11.167  1.00  0.00          
ATOM     38  CB  LEU    38       6.180   3.006  -8.472  1.00  0.00          
ATOM     39  N   LYS    39       8.023   0.719  -9.190  1.00  0.00          
ATOM     39  CA  LYS    39       9.291   0.229  -9.753  1.00  0.00          
ATOM     39  C   LYS    39       9.050  -0.873 -10.785  1.00  0.00          
ATOM     39  O   LYS    39       9.692  -0.935 -11.843  1.00  0.00          
ATOM     39  CB  LYS    39      10.107  -0.377  -8.598  1.00  0.00          
ATOM     40  N   GLY    40       8.109  -1.734 -10.442  1.00  0.00          
ATOM     40  CA  GLY    40       7.716  -2.870 -11.286  1.00  0.00          
ATOM     40  C   GLY    40       6.758  -2.392 -12.380  1.00  0.00          
ATOM     40  O   GLY    40       6.987  -2.582 -13.583  1.00  0.00          
TER
END
