
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS121_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      -       -           -
LGA    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      -       -           -
LGA    R       9      A       5          2.281
LGA    I      10      K       6          0.622
LGA    N      11      I       7          1.898
LGA    E      12      A       8          1.923
LGA    L      13      R       9          0.810
LGA    A      14      I      10          0.582
LGA    A      15      N      11          0.668
LGA    K      16      E      12          0.631
LGA    A      17      L      13          1.000
LGA    K      18      A      14          1.348
LGA    A      19      A      15          1.261
LGA    G      20      K      16          0.997
LGA    V      21      -       -           -
LGA    I      22      -       -           -
LGA    T      23      A      17          5.524
LGA    E      24      K      18           -
LGA    -       -      A      19           -
LGA    E      25      G      20           #
LGA    E      26      V      21          2.634
LGA    K      27      -       -           -
LGA    A      28      I      22          4.441
LGA    E      29      T      23          3.447
LGA    Q      30      -       -           -
LGA    Q      31      -       -           -
LGA    K      32      E      24          3.512
LGA    L      33      E      25          2.434
LGA    R      34      E      26          1.608
LGA    Q      35      K      27          2.710
LGA    E      36      A      28          1.957
LGA    Y      37      E      29          1.459
LGA    L      38      Q      30          2.508
LGA    -       -      Q      31           -
LGA    K      39      K      32          1.938
LGA    G      40      L      33          4.596
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
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)   36   36    5.0     25    2.49     8.00     49.901     0.967

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.502220 * X  +  -0.038083 * Y  +  -0.863901 * Z  +   1.884325
  Y_new =  -0.700196 * X  +   0.604158 * Y  +   0.380419 * Z  +  -6.011302
  Z_new =   0.507446 * X  +   0.795954 * Y  +  -0.330086 * Z  +   3.867346 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.963915   -1.177678  [ DEG:   112.5240    -67.4760 ]
  Theta =  -0.532218   -2.609375  [ DEG:   -30.4938   -149.5062 ]
  Phi   =  -2.193011    0.948582  [ DEG:  -125.6502     54.3498 ]
 
# 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_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS121_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   25   2.49    8.00  49.901
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS121_2-D1
PFRMAT    TS
TARGET    T0335
MODEL     2
PARENT    N/A
ATOM      5  N   ALA     5      -6.753 -13.485   1.634  1.00  0.00          
ATOM      5  CA  ALA     5      -6.945 -12.563   0.505  1.00  0.00          
ATOM      5  C   ALA     5      -6.646 -13.299  -0.803  1.00  0.00          
ATOM      5  O   ALA     5      -7.321 -13.117  -1.827  1.00  0.00          
ATOM      5  CB  ALA     5      -5.924 -11.416   0.654  1.00  0.00          
ATOM      6  N   LYS     6      -5.622 -14.128  -0.730  1.00  0.00          
ATOM      6  CA  LYS     6      -5.164 -14.935  -1.869  1.00  0.00          
ATOM      6  C   LYS     6      -4.943 -14.039  -3.092  1.00  0.00          
ATOM      6  O   LYS     6      -5.193 -14.424  -4.242  1.00  0.00          
ATOM      6  CB  LYS     6      -6.269 -15.960  -2.184  1.00  0.00          
ATOM      7  N   ILE     7      -4.470 -12.841  -2.804  1.00  0.00          
ATOM      7  CA  ILE     7      -4.185 -11.822  -3.827  1.00  0.00          
ATOM      7  C   ILE     7      -2.851 -12.150  -4.505  1.00  0.00          
ATOM      7  O   ILE     7      -1.764 -11.909  -3.962  1.00  0.00          
ATOM      7  CB  ILE     7      -4.036 -10.469  -3.110  1.00  0.00          
ATOM      8  N   ALA     8      -2.971 -12.702  -5.697  1.00  0.00          
ATOM      8  CA  ALA     8      -1.817 -13.097  -6.522  1.00  0.00          
ATOM      8  C   ALA     8      -0.887 -11.910  -6.792  1.00  0.00          
ATOM      8  O   ALA     8       0.347 -12.021  -6.756  1.00  0.00          
ATOM      8  CB  ALA     8      -2.364 -13.583  -7.872  1.00  0.00          
ATOM      9  N   ARG     9      -1.517 -10.782  -7.062  1.00  0.00          
ATOM      9  CA  ARG     9      -0.817  -9.520  -7.352  1.00  0.00          
ATOM      9  C   ARG     9      -0.551  -8.769  -6.045  1.00  0.00          
ATOM      9  O   ARG     9      -1.472  -8.372  -5.319  1.00  0.00          
ATOM      9  CB  ARG     9      -1.745  -8.645  -8.209  1.00  0.00          
ATOM     10  N   ILE    10       0.728  -8.589  -5.776  1.00  0.00          
ATOM     10  CA  ILE    10       1.206  -7.892  -4.572  1.00  0.00          
ATOM     10  C   ILE    10       0.637  -6.471  -4.549  1.00  0.00          
ATOM     10  O   ILE    10       0.223  -5.948  -3.505  1.00  0.00          
ATOM     10  CB  ILE    10       2.744  -7.796  -4.628  1.00  0.00          
ATOM     11  N   ASN    11       0.631  -5.875  -5.726  1.00  0.00          
ATOM     11  CA  ASN    11       0.128  -4.508  -5.930  1.00  0.00          
ATOM     11  C   ASN    11      -1.342  -4.428  -5.513  1.00  0.00          
ATOM     11  O   ASN    11      -1.789  -3.474  -4.861  1.00  0.00          
ATOM     11  CB  ASN    11       0.215  -4.204  -7.438  1.00  0.00          
ATOM     12  N   GLU    12      -2.070  -5.455  -5.909  1.00  0.00          
ATOM     12  CA  GLU    12      -3.505  -5.580  -5.618  1.00  0.00          
ATOM     12  C   GLU    12      -3.669  -5.573  -4.096  1.00  0.00          
ATOM     12  O   GLU    12      -4.606  -4.983  -3.539  1.00  0.00          
ATOM     12  CB  GLU    12      -4.001  -6.936  -6.159  1.00  0.00          
ATOM     13  N   LEU    13      -2.732  -6.241  -3.451  1.00  0.00          
ATOM     13  CA  LEU    13      -2.698  -6.362  -1.985  1.00  0.00          
ATOM     13  C   LEU    13      -2.715  -4.972  -1.341  1.00  0.00          
ATOM     13  O   LEU    13      -3.365  -4.732  -0.315  1.00  0.00          
ATOM     13  CB  LEU    13      -1.330  -6.994  -1.663  1.00  0.00          
ATOM     14  N   ALA    14      -1.983  -4.076  -1.976  1.00  0.00          
ATOM     14  CA  ALA    14      -1.858  -2.679  -1.529  1.00  0.00          
ATOM     14  C   ALA    14      -3.235  -2.018  -1.443  1.00  0.00          
ATOM     14  O   ALA    14      -3.556  -1.285  -0.494  1.00  0.00          
ATOM     14  CB  ALA    14      -1.092  -1.949  -2.650  1.00  0.00          
ATOM     15  N   ALA    15      -4.029  -2.298  -2.460  1.00  0.00          
ATOM     15  CA  ALA    15      -5.396  -1.768  -2.578  1.00  0.00          
ATOM     15  C   ALA    15      -6.221  -2.242  -1.380  1.00  0.00          
ATOM     15  O   ALA    15      -7.001  -1.488  -0.780  1.00  0.00          
ATOM     15  CB  ALA    15      -6.041  -2.360  -3.847  1.00  0.00          
ATOM     16  N   LYS    16      -6.023  -3.507  -1.059  1.00  0.00          
ATOM     16  CA  LYS    16      -6.713  -4.167   0.059  1.00  0.00          
ATOM     16  C   LYS    16      -6.383  -3.436   1.361  1.00  0.00          
ATOM     16  O   LYS    16      -7.247  -3.196   2.217  1.00  0.00          
ATOM     16  CB  LYS    16      -6.188  -5.614   0.163  1.00  0.00          
ATOM     17  N   ALA    17      -5.114  -3.092   1.479  1.00  0.00          
ATOM     17  CA  ALA    17      -4.581  -2.382   2.650  1.00  0.00          
ATOM     17  C   ALA    17      -5.315  -1.048   2.804  1.00  0.00          
ATOM     17  O   ALA    17      -5.687  -0.627   3.908  1.00  0.00          
ATOM     17  CB  ALA    17      -3.092  -2.071   2.391  1.00  0.00          
ATOM     18  N   LYS    18      -5.509  -0.406   1.667  1.00  0.00          
ATOM     18  CA  LYS    18      -6.194   0.893   1.586  1.00  0.00          
ATOM     18  C   LYS    18      -7.604   0.740   2.160  1.00  0.00          
ATOM     18  O   LYS    18      -8.121   1.613   2.872  1.00  0.00          
ATOM     18  CB  LYS    18      -6.323   1.269   0.096  1.00  0.00          
ATOM     19  N   ALA    19      -8.199  -0.391   1.829  1.00  0.00          
ATOM     19  CA  ALA    19      -9.555  -0.741   2.272  1.00  0.00          
ATOM     19  C   ALA    19      -9.530  -1.105   3.758  1.00  0.00          
ATOM     19  O   ALA    19     -10.500  -0.900   4.502  1.00  0.00          
ATOM     19  CB  ALA    19      -9.987  -1.986   1.476  1.00  0.00          
ATOM     20  N   GLY    20      -8.395  -1.648   4.160  1.00  0.00          
ATOM     20  CA  GLY    20      -8.156  -2.072   5.548  1.00  0.00          
ATOM     20  C   GLY    20      -8.828  -3.425   5.793  1.00  0.00          
ATOM     20  O   GLY    20      -9.731  -3.569   6.630  1.00  0.00          
ATOM     21  N   VAL    21      -8.361  -4.403   5.038  1.00  0.00          
ATOM     21  CA  VAL    21      -8.865  -5.782   5.110  1.00  0.00          
ATOM     21  C   VAL    21      -8.559  -6.318   6.511  1.00  0.00          
ATOM     21  O   VAL    21      -9.318  -7.107   7.093  1.00  0.00          
ATOM     21  CB  VAL    21      -8.090  -6.640   4.095  1.00  0.00          
ATOM     22  N   ILE    22      -7.432  -5.863   7.026  1.00  0.00          
ATOM     22  CA  ILE    22      -6.947  -6.249   8.361  1.00  0.00          
ATOM     22  C   ILE    22      -6.534  -4.978   9.107  1.00  0.00          
ATOM     22  O   ILE    22      -5.418  -4.462   8.957  1.00  0.00          
ATOM     22  CB  ILE    22      -5.701  -7.133   8.171  1.00  0.00          
ATOM     23  N   THR    23      -7.464  -4.497   9.911  1.00  0.00          
ATOM     23  CA  THR    23      -7.276  -3.284  10.723  1.00  0.00          
ATOM     23  C   THR    23      -8.050  -3.451  12.035  1.00  0.00          
ATOM     23  O   THR    23      -9.255  -3.186  12.123  1.00  0.00          
ATOM     23  CB  THR    23      -7.884  -2.097   9.952  1.00  0.00          
ATOM     24  N   GLU    24      -7.320  -3.895  13.040  1.00  0.00          
ATOM     24  CA  GLU    24      -7.863  -4.126  14.389  1.00  0.00          
ATOM     24  C   GLU    24      -8.460  -2.837  14.959  1.00  0.00          
ATOM     24  O   GLU    24      -9.530  -2.828  15.583  1.00  0.00          
ATOM     24  CB  GLU    24      -6.691  -4.557  15.287  1.00  0.00          
ATOM     25  N   GLU    25      -7.736  -1.759  14.722  1.00  0.00          
ATOM     25  CA  GLU    25      -8.124  -0.416  15.179  1.00  0.00          
ATOM     25  C   GLU    25      -7.947   0.548  14.002  1.00  0.00          
ATOM     25  O   GLU    25      -7.008   0.441  13.202  1.00  0.00          
ATOM     25  CB  GLU    25      -7.169  -0.000  16.312  1.00  0.00          
ATOM     26  N   GLU    26      -8.875   1.483  13.928  1.00  0.00          
ATOM     26  CA  GLU    26      -8.896   2.512  12.875  1.00  0.00          
ATOM     26  C   GLU    26      -8.465   3.875  13.423  1.00  0.00          
ATOM     26  O   GLU    26      -9.190   4.537  14.179  1.00  0.00          
ATOM     26  CB  GLU    26     -10.345   2.658  12.376  1.00  0.00          
ATOM     27  N   LYS    27      -7.272   4.266  13.016  1.00  0.00          
ATOM     27  CA  LYS    27      -6.665   5.543  13.422  1.00  0.00          
ATOM     27  C   LYS    27      -6.063   6.094  12.125  1.00  0.00          
ATOM     27  O   LYS    27      -5.468   5.368  11.319  1.00  0.00          
ATOM     27  CB  LYS    27      -5.544   5.275  14.443  1.00  0.00          
ATOM     28  N   ALA    28      -6.240   7.391  11.957  1.00  0.00          
ATOM     28  CA  ALA    28      -5.744   8.125  10.782  1.00  0.00          
ATOM     28  C   ALA    28      -4.233   7.954  10.609  1.00  0.00          
ATOM     28  O   ALA    28      -3.722   7.715   9.505  1.00  0.00          
ATOM     28  CB  ALA    28      -6.032   9.619  11.012  1.00  0.00          
ATOM     29  N   GLU    29      -3.544   8.082  11.726  1.00  0.00          
ATOM     29  CA  GLU    29      -2.080   7.956  11.787  1.00  0.00          
ATOM     29  C   GLU    29      -1.657   6.553  11.344  1.00  0.00          
ATOM     29  O   GLU    29      -0.705   6.367  10.573  1.00  0.00          
ATOM     29  CB  GLU    29      -1.619   8.134  13.246  1.00  0.00          
ATOM     30  N   GLN    30      -2.394   5.584  11.855  1.00  0.00          
ATOM     30  CA  GLN    30      -2.161   4.162  11.562  1.00  0.00          
ATOM     30  C   GLN    30      -2.262   3.909  10.057  1.00  0.00          
ATOM     30  O   GLN    30      -1.478   3.155   9.463  1.00  0.00          
ATOM     30  CB  GLN    30      -3.276   3.349  12.247  1.00  0.00          
ATOM     31  N   GLN    31      -3.247   4.561   9.467  1.00  0.00          
ATOM     31  CA  GLN    31      -3.524   4.462   8.026  1.00  0.00          
ATOM     31  C   GLN    31      -2.300   4.870   7.201  1.00  0.00          
ATOM     31  O   GLN    31      -1.946   4.238   6.197  1.00  0.00          
ATOM     31  CB  GLN    31      -4.666   5.454   7.737  1.00  0.00          
ATOM     32  N   LYS    32      -1.673   5.940   7.656  1.00  0.00          
ATOM     32  CA  LYS    32      -0.474   6.503   7.014  1.00  0.00          
ATOM     32  C   LYS    32       0.667   5.484   6.995  1.00  0.00          
ATOM     32  O   LYS    32       1.343   5.273   5.977  1.00  0.00          
ATOM     32  CB  LYS    32      -0.004   7.692   7.875  1.00  0.00          
ATOM     33  N   LEU    33       0.853   4.867   8.147  1.00  0.00          
ATOM     33  CA  LEU    33       1.895   3.851   8.350  1.00  0.00          
ATOM     33  C   LEU    33       1.696   2.666   7.402  1.00  0.00          
ATOM     33  O   LEU    33       2.647   2.112   6.834  1.00  0.00          
ATOM     33  CB  LEU    33       1.788   3.340   9.799  1.00  0.00          
ATOM     34  N   ARG    34       0.435   2.300   7.255  1.00  0.00          
ATOM     34  CA  ARG    34       0.018   1.186   6.391  1.00  0.00          
ATOM     34  C   ARG    34       0.497   1.418   4.956  1.00  0.00          
ATOM     34  O   ARG    34       0.983   0.507   4.271  1.00  0.00          
ATOM     34  CB  ARG    34      -1.522   1.148   6.380  1.00  0.00          
ATOM     35  N   GLN    35       0.344   2.658   4.530  1.00  0.00          
ATOM     35  CA  GLN    35       0.737   3.100   3.184  1.00  0.00          
ATOM     35  C   GLN    35       2.237   2.858   2.997  1.00  0.00          
ATOM     35  O   GLN    35       2.700   2.396   1.945  1.00  0.00          
ATOM     35  CB  GLN    35       0.479   4.612   3.055  1.00  0.00          
ATOM     36  N   GLU    36       2.970   3.184   4.044  1.00  0.00          
ATOM     36  CA  GLU    36       4.432   3.033   4.079  1.00  0.00          
ATOM     36  C   GLU    36       4.868   1.584   3.853  1.00  0.00          
ATOM     36  O   GLU    36       5.788   1.289   3.077  1.00  0.00          
ATOM     36  CB  GLU    36       4.894   3.431   5.495  1.00  0.00          
ATOM     37  N   TYR    37       4.180   0.701   4.553  1.00  0.00          
ATOM     37  CA  TYR    37       4.433  -0.745   4.487  1.00  0.00          
ATOM     37  C   TYR    37       4.246  -1.243   3.052  1.00  0.00          
ATOM     37  O   TYR    37       5.017  -2.064   2.535  1.00  0.00          
ATOM     37  CB  TYR    37       3.410  -1.472   5.380  1.00  0.00          
ATOM     38  N   LEU    38       3.205  -0.720   2.432  1.00  0.00          
ATOM     38  CA  LEU    38       2.841  -1.059   1.048  1.00  0.00          
ATOM     38  C   LEU    38       4.009  -0.744   0.110  1.00  0.00          
ATOM     38  O   LEU    38       4.339  -1.507  -0.808  1.00  0.00          
ATOM     38  CB  LEU    38       1.674  -0.133   0.650  1.00  0.00          
ATOM     39  N   LYS    39       4.615   0.400   0.373  1.00  0.00          
ATOM     39  CA  LYS    39       5.761   0.896  -0.404  1.00  0.00          
ATOM     39  C   LYS    39       6.865  -0.153  -0.288  1.00  0.00          
ATOM     39  O   LYS    39       7.595  -0.450  -1.248  1.00  0.00          
ATOM     39  CB  LYS    39       6.270   2.209   0.231  1.00  0.00          
ATOM     40  N   GLY    40       6.960  -0.698   0.910  1.00  0.00          
ATOM     40  CA  GLY    40       7.953  -1.729   1.241  1.00  0.00          
ATOM     40  C   GLY    40       7.622  -2.987   0.434  1.00  0.00          
ATOM     40  O   GLY    40       8.506  -3.703  -0.057  1.00  0.00          
TER
END
