
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS121_1-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      -       -           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      A       5          4.261
LGA    L      13      K       6          2.480
LGA    A      14      I       7          3.044
LGA    A      15      A       8          2.644
LGA    K      16      R       9          3.674
LGA    A      17      I      10          3.727
LGA    -       -      N      11           -
LGA    K      18      E      12          4.427
LGA    A      19      L      13          0.965
LGA    G      20      A      14          3.941
LGA    V      21      A      15          3.283
LGA    I      22      K      16           -
LGA    T      23      -       -           -
LGA    E      24      A      17          3.548
LGA    E      25      K      18          4.882
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    E      26      I      22          1.164
LGA    K      27      T      23          0.964
LGA    A      28      E      24          0.962
LGA    E      29      E      25          0.788
LGA    Q      30      E      26          0.990
LGA    Q      31      K      27          0.472
LGA    K      32      A      28          0.973
LGA    L      33      E      29          1.562
LGA    R      34      Q      30          1.405
LGA    Q      35      Q      31          0.345
LGA    E      36      K      32          2.388
LGA    Y      37      L      33          2.595
LGA    L      38      R      34          0.994
LGA    K      39      Q      35          2.206
LGA    G      40      E      36          3.945
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     27    2.69    11.11     54.709     0.967

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.158091 * X  +  -0.977615 * Y  +   0.138838 * Z  +  -2.071505
  Y_new =   0.547813 * X  +  -0.203819 * Y  +  -0.811393 * Z  +   0.783096
  Z_new =   0.821528 * X  +  -0.052217 * Y  +   0.567773 * Z  +  -7.262374 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.091710    3.049883  [ DEG:    -5.2546    174.7454 ]
  Theta =  -0.964085   -2.177507  [ DEG:   -55.2380   -124.7620 ]
  Phi   =   1.851748   -1.289844  [ DEG:   106.0974    -73.9026 ]
 
# 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_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS121_1-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   27   2.69   11.11  54.709
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS121_1-D1
PFRMAT    TS
TARGET    T0335
MODEL     1
PARENT    N/A
ATOM      5  N   ALA     5      -3.101  -2.249 -19.088  1.00  0.00          
ATOM      5  CA  ALA     5      -2.810  -3.611 -18.610  1.00  0.00          
ATOM      5  C   ALA     5      -1.867  -3.538 -17.409  1.00  0.00          
ATOM      5  O   ALA     5      -2.004  -4.276 -16.420  1.00  0.00          
ATOM      5  CB  ALA     5      -2.087  -4.379 -19.734  1.00  0.00          
ATOM      6  N   LYS     6      -0.917  -2.631 -17.529  1.00  0.00          
ATOM      6  CA  LYS     6       0.097  -2.394 -16.493  1.00  0.00          
ATOM      6  C   LYS     6      -0.611  -2.001 -15.193  1.00  0.00          
ATOM      6  O   LYS     6      -0.227  -2.409 -14.087  1.00  0.00          
ATOM      6  CB  LYS     6       0.987  -1.219 -16.939  1.00  0.00          
ATOM      7  N   ILE     7      -1.648  -1.203 -15.365  1.00  0.00          
ATOM      7  CA  ILE     7      -2.470  -0.705 -14.251  1.00  0.00          
ATOM      7  C   ILE     7      -2.968  -1.909 -13.452  1.00  0.00          
ATOM      7  O   ILE     7      -3.027  -1.896 -12.212  1.00  0.00          
ATOM      7  CB  ILE     7      -3.696   0.040 -14.825  1.00  0.00          
ATOM      8  N   ALA     8      -3.318  -2.940 -14.198  1.00  0.00          
ATOM      8  CA  ALA     8      -3.823  -4.199 -13.635  1.00  0.00          
ATOM      8  C   ALA     8      -2.739  -4.799 -12.738  1.00  0.00          
ATOM      8  O   ALA     8      -3.004  -5.320 -11.645  1.00  0.00          
ATOM      8  CB  ALA     8      -4.089  -5.165 -14.810  1.00  0.00          
ATOM      9  N   ARG     9      -1.520  -4.708 -13.236  1.00  0.00          
ATOM      9  CA  ARG     9      -0.330  -5.220 -12.540  1.00  0.00          
ATOM      9  C   ARG     9      -0.200  -4.518 -11.185  1.00  0.00          
ATOM      9  O   ARG     9       0.157  -5.124 -10.165  1.00  0.00          
ATOM      9  CB  ARG     9       0.882  -4.856 -13.416  1.00  0.00          
ATOM     10  N   ILE    10      -0.498  -3.234 -11.212  1.00  0.00          
ATOM     10  CA  ILE    10      -0.440  -2.370 -10.023  1.00  0.00          
ATOM     10  C   ILE    10      -1.301  -2.966  -8.905  1.00  0.00          
ATOM     10  O   ILE    10      -0.945  -2.944  -7.719  1.00  0.00          
ATOM     10  CB  ILE    10      -1.102  -1.039 -10.429  1.00  0.00          
ATOM     11  N   ASN    11      -2.437  -3.492  -9.324  1.00  0.00          
ATOM     11  CA  ASN    11      -3.413  -4.118  -8.419  1.00  0.00          
ATOM     11  C   ASN    11      -2.786  -5.281  -7.646  1.00  0.00          
ATOM     11  O   ASN    11      -2.996  -5.455  -6.437  1.00  0.00          
ATOM     11  CB  ASN    11      -4.525  -4.723  -9.296  1.00  0.00          
ATOM     12  N   GLU    12      -2.016  -6.061  -8.379  1.00  0.00          
ATOM     12  CA  GLU    12      -1.315  -7.236  -7.838  1.00  0.00          
ATOM     12  C   GLU    12      -0.372  -6.834  -6.698  1.00  0.00          
ATOM     12  O   GLU    12      -0.300  -7.485  -5.647  1.00  0.00          
ATOM     12  CB  GLU    12      -0.457  -7.829  -8.969  1.00  0.00          
ATOM     13  N   LEU    13       0.338  -5.750  -6.944  1.00  0.00          
ATOM     13  CA  LEU    13       1.306  -5.189  -5.986  1.00  0.00          
ATOM     13  C   LEU    13       0.569  -4.845  -4.691  1.00  0.00          
ATOM     13  O   LEU    13       1.047  -5.104  -3.575  1.00  0.00          
ATOM     13  CB  LEU    13       1.822  -3.871  -6.598  1.00  0.00          
ATOM     14  N   ALA    14      -0.598  -4.258  -4.877  1.00  0.00          
ATOM     14  CA  ALA    14      -1.470  -3.842  -3.770  1.00  0.00          
ATOM     14  C   ALA    14      -1.843  -5.053  -2.910  1.00  0.00          
ATOM     14  O   ALA    14      -1.897  -4.989  -1.675  1.00  0.00          
ATOM     14  CB  ALA    14      -2.783  -3.359  -4.412  1.00  0.00          
ATOM     15  N   ALA    15      -2.095  -6.148  -3.603  1.00  0.00          
ATOM     15  CA  ALA    15      -2.472  -7.424  -2.977  1.00  0.00          
ATOM     15  C   ALA    15      -1.445  -7.820  -1.913  1.00  0.00          
ATOM     15  O   ALA    15      -1.780  -8.333  -0.835  1.00  0.00          
ATOM     15  CB  ALA    15      -2.405  -8.480  -4.098  1.00  0.00          
ATOM     16  N   LYS    16      -0.195  -7.565  -2.251  1.00  0.00          
ATOM     16  CA  LYS    16       0.950  -7.865  -1.378  1.00  0.00          
ATOM     16  C   LYS    16       0.764  -7.095  -0.070  1.00  0.00          
ATOM     16  O   LYS    16       1.001  -7.608   1.034  1.00  0.00          
ATOM     16  CB  LYS    16       2.205  -7.332  -2.102  1.00  0.00          
ATOM     17  N   ALA    17       0.336  -5.857  -0.231  1.00  0.00          
ATOM     17  CA  ALA    17       0.090  -4.942   0.892  1.00  0.00          
ATOM     17  C   ALA    17      -0.983  -5.545   1.800  1.00  0.00          
ATOM     17  O   ALA    17      -0.906  -5.486   3.036  1.00  0.00          
ATOM     17  CB  ALA    17      -0.481  -3.629   0.318  1.00  0.00          
ATOM     18  N   LYS    18      -1.975  -6.121   1.147  1.00  0.00          
ATOM     18  CA  LYS    18      -3.111  -6.763   1.824  1.00  0.00          
ATOM     18  C   LYS    18      -3.993  -5.633   2.359  1.00  0.00          
ATOM     18  O   LYS    18      -4.732  -5.786   3.344  1.00  0.00          
ATOM     18  CB  LYS    18      -2.588  -7.609   2.998  1.00  0.00          
ATOM     19  N   ALA    19      -3.890  -4.506   1.681  1.00  0.00          
ATOM     19  CA  ALA    19      -4.648  -3.295   2.024  1.00  0.00          
ATOM     19  C   ALA    19      -5.436  -2.903   0.773  1.00  0.00          
ATOM     19  O   ALA    19      -4.920  -2.900  -0.355  1.00  0.00          
ATOM     19  CB  ALA    19      -3.655  -2.181   2.406  1.00  0.00          
ATOM     20  N   GLY    20      -6.692  -2.576   1.012  1.00  0.00          
ATOM     20  CA  GLY    20      -7.627  -2.167  -0.046  1.00  0.00          
ATOM     20  C   GLY    20      -7.265  -0.867  -0.768  1.00  0.00          
ATOM     20  O   GLY    20      -7.177  -0.804  -2.002  1.00  0.00          
ATOM     21  N   VAL    21      -7.061   0.158   0.038  1.00  0.00          
ATOM     21  CA  VAL    21      -6.702   1.500  -0.445  1.00  0.00          
ATOM     21  C   VAL    21      -5.219   1.775  -0.179  1.00  0.00          
ATOM     21  O   VAL    21      -4.644   1.348   0.831  1.00  0.00          
ATOM     21  CB  VAL    21      -7.535   2.521   0.351  1.00  0.00          
ATOM     22  N   ILE    22      -4.628   2.496  -1.113  1.00  0.00          
ATOM     22  CA  ILE    22      -3.206   2.875  -1.056  1.00  0.00          
ATOM     22  C   ILE    22      -2.962   3.653   0.238  1.00  0.00          
ATOM     22  O   ILE    22      -1.850   3.685   0.786  1.00  0.00          
ATOM     22  CB  ILE    22      -2.905   3.797  -2.252  1.00  0.00          
ATOM     23  N   THR    23      -4.031   4.275   0.701  1.00  0.00          
ATOM     23  CA  THR    23      -4.019   5.081   1.931  1.00  0.00          
ATOM     23  C   THR    23      -5.201   4.791   2.866  1.00  0.00          
ATOM     23  O   THR    23      -6.226   5.483   2.860  1.00  0.00          
ATOM     23  CB  THR    23      -4.154   6.550   1.487  1.00  0.00          
ATOM     24  N   GLU    24      -5.025   3.754   3.662  1.00  0.00          
ATOM     24  CA  GLU    24      -6.034   3.301   4.638  1.00  0.00          
ATOM     24  C   GLU    24      -6.275   4.444   5.623  1.00  0.00          
ATOM     24  O   GLU    24      -7.409   4.724   6.041  1.00  0.00          
ATOM     24  CB  GLU    24      -5.446   2.119   5.433  1.00  0.00          
ATOM     25  N   GLU    25      -5.178   5.088   5.974  1.00  0.00          
ATOM     25  CA  GLU    25      -5.182   6.221   6.911  1.00  0.00          
ATOM     25  C   GLU    25      -5.627   5.741   8.296  1.00  0.00          
ATOM     25  O   GLU    25      -5.870   6.532   9.217  1.00  0.00          
ATOM     25  CB  GLU    25      -6.211   7.255   6.420  1.00  0.00          
ATOM     26  N   GLU    26      -5.724   4.430   8.409  1.00  0.00          
ATOM     26  CA  GLU    26      -6.136   3.757   9.653  1.00  0.00          
ATOM     26  C   GLU    26      -5.165   4.087  10.787  1.00  0.00          
ATOM     26  O   GLU    26      -5.558   4.360  11.931  1.00  0.00          
ATOM     26  CB  GLU    26      -6.066   2.240   9.402  1.00  0.00          
ATOM     27  N   LYS    27      -3.893   4.052  10.433  1.00  0.00          
ATOM     27  CA  LYS    27      -2.795   4.336  11.365  1.00  0.00          
ATOM     27  C   LYS    27      -1.588   4.774  10.529  1.00  0.00          
ATOM     27  O   LYS    27      -1.445   4.424   9.350  1.00  0.00          
ATOM     27  CB  LYS    27      -2.424   3.058  12.139  1.00  0.00          
ATOM     28  N   ALA    28      -0.733   5.542  11.178  1.00  0.00          
ATOM     28  CA  ALA    28       0.494   6.075  10.565  1.00  0.00          
ATOM     28  C   ALA    28       1.353   4.950   9.982  1.00  0.00          
ATOM     28  O   ALA    28       1.910   5.053   8.880  1.00  0.00          
ATOM     28  CB  ALA    28       1.295   6.759  11.688  1.00  0.00          
ATOM     29  N   GLU    29       1.438   3.883  10.755  1.00  0.00          
ATOM     29  CA  GLU    29       2.212   2.688  10.389  1.00  0.00          
ATOM     29  C   GLU    29       1.656   2.086   9.096  1.00  0.00          
ATOM     29  O   GLU    29       2.397   1.697   8.181  1.00  0.00          
ATOM     29  CB  GLU    29       2.047   1.631  11.500  1.00  0.00          
ATOM     30  N   GLN    30       0.339   2.024   9.055  1.00  0.00          
ATOM     30  CA  GLN    30      -0.403   1.481   7.907  1.00  0.00          
ATOM     30  C   GLN    30      -0.026   2.336   6.695  1.00  0.00          
ATOM     30  O   GLN    30       0.141   1.841   5.570  1.00  0.00          
ATOM     30  CB  GLN    30      -1.914   1.649   8.169  1.00  0.00          
ATOM     31  N   GLN    31       0.099   3.622   6.964  1.00  0.00          
ATOM     31  CA  GLN    31       0.454   4.621   5.946  1.00  0.00          
ATOM     31  C   GLN    31       1.777   4.253   5.266  1.00  0.00          
ATOM     31  O   GLN    31       1.948   4.389   4.047  1.00  0.00          
ATOM     31  CB  GLN    31       0.638   5.945   6.711  1.00  0.00          
ATOM     32  N   LYS    32       2.696   3.788   6.092  1.00  0.00          
ATOM     32  CA  LYS    32       4.038   3.374   5.650  1.00  0.00          
ATOM     32  C   LYS    32       3.973   2.260   4.602  1.00  0.00          
ATOM     32  O   LYS    32       4.654   2.291   3.567  1.00  0.00          
ATOM     32  CB  LYS    32       4.756   2.795   6.885  1.00  0.00          
ATOM     33  N   LEU    33       3.136   1.285   4.906  1.00  0.00          
ATOM     33  CA  LEU    33       2.920   0.116   4.041  1.00  0.00          
ATOM     33  C   LEU    33       2.392   0.590   2.684  1.00  0.00          
ATOM     33  O   LEU    33       2.778   0.090   1.618  1.00  0.00          
ATOM     33  CB  LEU    33       1.850  -0.781   4.688  1.00  0.00          
ATOM     34  N   ARG    34       1.507   1.566   2.763  1.00  0.00          
ATOM     34  CA  ARG    34       0.872   2.170   1.582  1.00  0.00          
ATOM     34  C   ARG    34       1.902   2.709   0.586  1.00  0.00          
ATOM     34  O   ARG    34       1.780   2.549  -0.636  1.00  0.00          
ATOM     34  CB  ARG    34       0.096   3.391   2.107  1.00  0.00          
ATOM     35  N   GLN    35       2.913   3.347   1.146  1.00  0.00          
ATOM     35  CA  GLN    35       4.014   3.944   0.374  1.00  0.00          
ATOM     35  C   GLN    35       4.690   2.852  -0.456  1.00  0.00          
ATOM     35  O   GLN    35       5.041   3.042  -1.630  1.00  0.00          
ATOM     35  CB  GLN    35       5.050   4.510   1.366  1.00  0.00          
ATOM     36  N   GLU    36       4.856   1.713   0.189  1.00  0.00          
ATOM     36  CA  GLU    36       5.484   0.533  -0.420  1.00  0.00          
ATOM     36  C   GLU    36       4.704   0.071  -1.655  1.00  0.00          
ATOM     36  O   GLU    36       5.272  -0.252  -2.706  1.00  0.00          
ATOM     36  CB  GLU    36       5.473  -0.606   0.618  1.00  0.00          
ATOM     37  N   TYR    37       3.395   0.050  -1.492  1.00  0.00          
ATOM     37  CA  TYR    37       2.457  -0.361  -2.550  1.00  0.00          
ATOM     37  C   TYR    37       2.572   0.517  -3.797  1.00  0.00          
ATOM     37  O   TYR    37       2.626   0.035  -4.938  1.00  0.00          
ATOM     37  CB  TYR    37       1.036  -0.159  -1.989  1.00  0.00          
ATOM     38  N   LEU    38       2.605   1.812  -3.540  1.00  0.00          
ATOM     38  CA  LEU    38       2.712   2.833  -4.592  1.00  0.00          
ATOM     38  C   LEU    38       3.999   2.637  -5.397  1.00  0.00          
ATOM     38  O   LEU    38       4.029   2.768  -6.628  1.00  0.00          
ATOM     38  CB  LEU    38       2.746   4.206  -3.895  1.00  0.00          
ATOM     39  N   LYS    39       5.050   2.320  -4.664  1.00  0.00          
ATOM     39  CA  LYS    39       6.385   2.086  -5.234  1.00  0.00          
ATOM     39  C   LYS    39       6.340   0.971  -6.280  1.00  0.00          
ATOM     39  O   LYS    39       6.982   1.038  -7.340  1.00  0.00          
ATOM     39  CB  LYS    39       7.321   1.635  -4.096  1.00  0.00          
ATOM     40  N   GLY    40       5.568  -0.045  -5.947  1.00  0.00          
ATOM     40  CA  GLY    40       5.380  -1.223  -6.806  1.00  0.00          
ATOM     40  C   GLY    40       4.607  -0.773  -8.051  1.00  0.00          
ATOM     40  O   GLY    40       4.883  -1.193  -9.182  1.00  0.00          
TER
END
