
#######################################################
#                                                     #
#                        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 T0335TS252_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS252_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      A       5           #
LGA    R       9      K       6          3.013
LGA    I      10      I       7          4.878
LGA    N      11      A       8          4.305
LGA    E      12      -       -           -
LGA    L      13      R       9          4.343
LGA    A      14      I      10          1.394
LGA    A      15      N      11          1.277
LGA    K      16      E      12          2.411
LGA    A      17      L      13          3.596
LGA    K      18      -       -           -
LGA    A      19      -       -           -
LGA    G      20      A      14          2.012
LGA    V      21      A      15          3.029
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    I      22      K      18          2.966
LGA    T      23      A      19          3.912
LGA    E      24      G      20          3.776
LGA    E      25      V      21          3.435
LGA    E      26      I      22          4.690
LGA    K      27      T      23          3.081
LGA    A      28      E      24          3.771
LGA    E      29      E      25          3.731
LGA    Q      30      E      26          2.808
LGA    Q      31      K      27          1.867
LGA    K      32      A      28          1.831
LGA    L      33      E      29          3.592
LGA    R      34      Q      30          3.830
LGA    -       -      Q      31           -
LGA    -       -      K      32           -
LGA    Q      35      L      33          4.830
LGA    E      36      R      34          3.848
LGA    Y      37      Q      35           -
LGA    L      38      E      36           -
LGA    K      39      Y      37           -
LGA    G      40      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    3.44     8.00     42.948     0.706

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.769514 * X  +  -0.530668 * Y  +   0.355302 * Z  +  -3.631338
  Y_new =   0.630665 * X  +  -0.719042 * Y  +   0.291959 * Z  +  -7.510201
  Z_new =   0.100544 * X  +   0.448743 * Y  +   0.887987 * Z  +  -5.717066 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.467918   -2.673675  [ DEG:    26.8097   -153.1903 ]
  Theta =  -0.100714   -3.040879  [ DEG:    -5.7705   -174.2295 ]
  Phi   =   2.455036   -0.686556  [ DEG:   140.6632    -39.3368 ]
 
# 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: T0335TS252_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS252_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   25   3.44    8.00  42.948
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS252_1-D1
PFRMAT TS                                                                       
TARGET T0335                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM     21  N   ALA     5      -1.982   1.374  -8.925   1.0                    
ATOM     22  CA  ALA     5      -0.789   1.917  -8.286   1.0                    
ATOM     23  C   ALA     5       0.479   1.403  -8.960   1.0                    
ATOM     24  O   ALA     5       0.446   0.420  -9.700   1.0                    
ATOM     25  CB  ALA     5      -0.784   1.745  -7.542   0.0                    
ATOM     26  N   LYS     6       1.595   2.076  -8.699   1.0                    
ATOM     27  CA  LYS     6       2.876   1.690  -9.279   1.0                    
ATOM     28  C   LYS     6       3.332   0.332  -8.756   1.0                    
ATOM     29  O   LYS     6       4.453  -0.101  -9.023   1.0                    
ATOM     30  CB  LYS     6       4.874   3.706  -8.743   0.0                    
ATOM     31  N   ILE     7       2.456  -0.333  -8.010   1.0                    
ATOM     32  CA  ILE     7       2.768  -1.642  -7.448   1.0                    
ATOM     33  C   ILE     7       1.676  -2.656  -7.774   1.0                    
ATOM     34  O   ILE     7       0.490  -2.388  -7.585   1.0                    
ATOM     35  CB  ILE     7       3.002  -1.521  -5.677   0.0                    
ATOM     36  N   ALA     8       2.086  -3.821  -8.266   1.0                    
ATOM     37  CA  ALA     8       1.145  -4.877  -8.620   1.0                    
ATOM     38  C   ALA     8       1.497  -6.186  -7.922   1.0                    
ATOM     39  O   ALA     8       0.620  -6.997  -7.624   1.0                    
ATOM     40  CB  ALA     8       1.127  -4.974  -9.377   0.0                    
ATOM     41  N   ARG     9       2.785  -6.386  -7.663   1.0                    
ATOM     42  CA  ARG     9       3.255  -7.596  -6.999   1.0                    
ATOM     43  C   ARG     9       2.677  -7.713  -5.593   1.0                    
ATOM     44  O   ARG     9       2.329  -8.806  -5.144   1.0                    
ATOM     45  CB  ARG     9       6.929  -7.654  -6.891   0.0                    
ATOM     46  N   ILE    10       2.575  -6.582  -4.903   1.0                    
ATOM     47  CA  ILE    10       2.040  -6.556  -3.548   1.0                    
ATOM     48  C   ILE    10       0.625  -7.125  -3.503   1.0                    
ATOM     49  O   ILE    10      -0.071  -7.163  -4.517   1.0                    
ATOM     50  CB  ILE    10       2.067  -4.889  -2.897   0.0                    
ATOM     51  N   ASN    11       0.208  -7.566  -2.321   1.0                    
ATOM     52  CA  ASN    11      -1.124  -8.133  -2.142   1.0                    
ATOM     53  C   ASN    11      -1.647  -7.879  -0.732   1.0                    
ATOM     54  O   ASN    11      -2.851  -7.735  -0.524   1.0                    
ATOM     55  CB  ASN    11      -1.106 -10.081  -2.537   0.0                    
ATOM     56  N   GLU    12      -0.733  -7.824   0.231   1.0                    
ATOM     57  CA  GLU    12      -1.101  -7.587   1.622   1.0                    
ATOM     58  C   GLU    12      -1.313  -6.101   1.891   1.0                    
ATOM     59  O   GLU    12      -1.874  -5.720   2.919   1.0                    
ATOM     60  CB  GLU    12       0.653  -8.518   3.163   0.0                    
ATOM     61  N   LEU    13      -0.862  -5.266   0.960   1.0                    
ATOM     62  CA  LEU    13      -1.003  -3.821   1.095   1.0                    
ATOM     63  C   LEU    13      -1.891  -3.248  -0.004   1.0                    
ATOM     64  O   LEU    13      -2.150  -2.045  -0.042   1.0                    
ATOM     65  CB  LEU    13       0.807  -2.935   1.073   0.0                    
ATOM     66  N   ALA    14      -2.356  -4.117  -0.896   1.0                    
ATOM     67  CA  ALA    14      -3.215  -3.700  -1.997   1.0                    
ATOM     68  C   ALA    14      -4.597  -3.295  -1.494   1.0                    
ATOM     69  O   ALA    14      -4.944  -3.539  -0.339   1.0                    
ATOM     70  CB  ALA    14      -3.272  -4.256  -2.516   0.0                    
ATOM     71  N   ALA    15      -5.383  -2.677  -2.371   1.0                    
ATOM     72  CA  ALA    15      -6.728  -2.239  -2.018   1.0                    
ATOM     73  C   ALA    15      -7.518  -3.361  -1.354   1.0                    
ATOM     74  O   ALA    15      -8.128  -3.166  -0.303   1.0                    
ATOM     75  CB  ALA    15      -7.095  -1.982  -2.635   0.0                    
ATOM     76  N   LYS    16      -7.503  -4.536  -1.976   1.0                    
ATOM     77  CA  LYS    16      -8.218  -5.692  -1.446   1.0                    
ATOM     78  C   LYS    16      -7.691  -6.084  -0.070   1.0                    
ATOM     79  O   LYS    16      -8.457  -6.479   0.809   1.0                    
ATOM     80  CB  LYS    16      -8.025  -7.919  -3.276   0.0                    
ATOM     81  N   ALA    17      -6.379  -5.972   0.110   1.0                    
ATOM     82  CA  ALA    17      -5.747  -6.314   1.378   1.0                    
ATOM     83  C   ALA    17      -6.173  -5.353   2.484   1.0                    
ATOM     84  O   ALA    17      -6.755  -4.302   2.215   1.0                    
ATOM     85  CB  ALA    17      -4.988  -6.318   1.306   0.0                    
ATOM     86  N   LYS    18      -5.879  -5.721   3.727   1.0                    
ATOM     87  CA  LYS    18      -6.230  -4.892   4.873   1.0                    
ATOM     88  C   LYS    18      -5.311  -3.680   4.981   1.0                    
ATOM     89  O   LYS    18      -5.749  -2.586   5.338   1.0                    
ATOM     90  CB  LYS    18      -6.140  -6.449   7.305   0.0                    
ATOM     91  N   ALA    19      -4.035  -3.882   4.669   1.0                    
ATOM     92  CA  ALA    19      -3.052  -2.807   4.730   1.0                    
ATOM     93  C   ALA    19      -3.285  -1.783   3.624   1.0                    
ATOM     94  O   ALA    19      -3.132  -0.580   3.835   1.0                    
ATOM     95  CB  ALA    19      -2.345  -3.090   4.688   0.0                    
ATOM     96  N   GLY    20      -3.655  -2.269   2.443   1.0                    
ATOM     97  CA  GLY    20      -3.909  -1.399   1.303   1.0                    
ATOM     98  C   GLY    20      -5.122  -0.507   1.547   1.0                    
ATOM     99  O   GLY    20      -5.907  -0.245   0.637   1.0                    
ATOM    100  N   VAL    21      -5.267  -0.043   2.784   1.0                    
ATOM    101  CA  VAL    21      -6.384   0.820   3.152   1.0                    
ATOM    102  C   VAL    21      -5.938   2.273   3.282   1.0                    
ATOM    103  O   VAL    21      -4.775   2.552   3.574   1.0                    
ATOM    104  CB  VAL    21      -7.000   0.356   4.405   0.0                    
ATOM    105  N   ILE    22      -6.871   3.195   3.065   1.0                    
ATOM    106  CA  ILE    22      -6.577   4.619   3.157   1.0                    
ATOM    107  C   ILE    22      -7.511   5.313   4.143   1.0                    
ATOM    108  O   ILE    22      -7.200   6.387   4.656   1.0                    
ATOM    109  CB  ILE    22      -6.686   5.386   1.543   0.0                    
ATOM    110  N   THR    23      -8.656   4.691   4.402   1.0                    
ATOM    111  CA  THR    23      -9.638   5.247   5.326   1.0                    
ATOM    112  C   THR    23      -9.160   5.138   6.770   1.0                    
ATOM    113  O   THR    23      -9.341   6.061   7.565   1.0                    
ATOM    114  CB  THR    23     -10.922   4.583   5.163   0.0                    
ATOM    115  N   GLU    24      -8.549   4.006   7.102   1.0                    
ATOM    116  CA  GLU    24      -8.045   3.774   8.451   1.0                    
ATOM    117  C   GLU    24      -6.962   4.783   8.815   1.0                    
ATOM    118  O   GLU    24      -6.068   5.064   8.017   1.0                    
ATOM    119  CB  GLU    24      -7.171   1.427   8.668   0.0                    
ATOM    120  N   GLU    25      -7.047   5.325  10.026   1.0                    
ATOM    121  CA  GLU    25      -6.075   6.304  10.497   1.0                    
ATOM    122  C   GLU    25      -5.249   5.748  11.653   1.0                    
ATOM    123  O   GLU    25      -4.066   6.060  11.788   1.0                    
ATOM    124  CB  GLU    25      -7.232   8.427  11.183   0.0                    
ATOM    125  N   GLU    26      -5.881   4.923  12.482   1.0                    
ATOM    126  CA  GLU    26      -5.206   4.323  13.626   1.0                    
ATOM    127  C   GLU    26      -4.050   3.433  13.181   1.0                    
ATOM    128  O   GLU    26      -3.016   3.364  13.843   1.0                    
ATOM    129  CB  GLU    26      -6.839   3.014  15.019   0.0                    
ATOM    130  N   LYS    27      -4.234   2.753  12.053   1.0                    
ATOM    131  CA  LYS    27      -3.208   1.867  11.517   1.0                    
ATOM    132  C   LYS    27      -1.982   2.653  11.063   1.0                    
ATOM    133  O   LYS    27      -2.105   3.683  10.401   1.0                    
ATOM    134  CB  LYS    27      -4.270   0.299   9.336   0.0                    
ATOM    135  N   ALA    28      -0.802   2.159  11.424   1.0                    
ATOM    136  CA  ALA    28       0.448   2.814  11.054   1.0                    
ATOM    137  C   ALA    28       1.064   2.167   9.817   1.0                    
ATOM    138  O   ALA    28       1.741   2.830   9.032   1.0                    
ATOM    139  CB  ALA    28       0.939   2.798  11.638   0.0                    
ATOM    140  N   GLU    29       0.825   0.870   9.652   1.0                    
ATOM    141  CA  GLU    29       1.356   0.133   8.512   1.0                    
ATOM    142  C   GLU    29       0.502   0.350   7.268   1.0                    
ATOM    143  O   GLU    29       1.009   0.347   6.147   1.0                    
ATOM    144  CB  GLU    29       1.521  -2.316   9.053   0.0                    
ATOM    145  N   GLN    30      -0.798   0.537   7.475   1.0                    
ATOM    146  CA  GLN    30      -1.725   0.755   6.371   1.0                    
ATOM    147  C   GLN    30      -1.602   2.171   5.819   1.0                    
ATOM    148  O   GLN    30      -1.689   2.385   4.609   1.0                    
ATOM    149  CB  GLN    30      -4.071   0.300   7.102   0.0                    
ATOM    150  N   GLN    31      -1.401   3.134   6.712   1.0                    
ATOM    151  CA  GLN    31      -1.266   4.530   6.316   1.0                    
ATOM    152  C   GLN    31       0.050   4.771   5.584   1.0                    
ATOM    153  O   GLN    31       0.104   5.533   4.618   1.0                    
ATOM    154  CB  GLN    31      -1.442   6.023   8.312   0.0                    
ATOM    155  N   LYS    32       1.109   4.117   6.050   1.0                    
ATOM    156  CA  LYS    32       2.426   4.260   5.440   1.0                    
ATOM    157  C   LYS    32       2.405   3.834   3.976   1.0                    
ATOM    158  O   LYS    32       2.914   4.543   3.107   1.0                    
ATOM    159  CB  LYS    32       4.387   2.729   6.910   0.0                    
ATOM    160  N   LEU    33       1.814   2.675   3.710   1.0                    
ATOM    161  CA  LEU    33       1.725   2.154   2.351   1.0                    
ATOM    162  C   LEU    33       0.807   3.014   1.489   1.0                    
ATOM    163  O   LEU    33      -0.246   3.461   1.942   1.0                    
ATOM    164  CB  LEU    33       1.088   0.243   2.371   0.0                    
ATOM    165  N   ARG    34       1.214   3.241   0.244   1.0                    
ATOM    166  CA  ARG    34       0.429   4.048  -0.682   1.0                    
ATOM    167  C   ARG    34       0.504   3.489  -2.099   1.0                    
ATOM    168  O   ARG    34      -0.521   3.233  -2.732   1.0                    
ATOM    169  CB  ARG    34       1.562   7.544  -0.615   0.0                    
ATOM    170  N   GLN    35       1.724   3.302  -2.592   1.0                    
ATOM    171  CA  GLN    35       1.935   2.773  -3.935   1.0                    
ATOM    172  C   GLN    35       1.311   1.390  -4.088   1.0                    
ATOM    173  O   GLN    35       0.760   1.060  -5.139   1.0                    
ATOM    174  CB  GLN    35       4.375   2.695  -4.467   0.0                    
ATOM    175  N   GLU    36       1.399   0.586  -3.034   1.0                    
ATOM    176  CA  GLU    36       0.842  -0.761  -3.048   1.0                    
ATOM    177  C   GLU    36      -0.681  -0.729  -3.098   1.0                    
ATOM    178  O   GLU    36      -1.313  -1.628  -3.652   1.0                    
ATOM    179  CB  GLU    36       1.632  -2.058  -1.045   0.0                    
ATOM    180  N   TYR    37      -1.265   0.313  -2.513   1.0                    
ATOM    181  CA  TYR    37      -2.715   0.463  -2.489   1.0                    
ATOM    182  C   TYR    37      -3.268   0.700  -3.891   1.0                    
ATOM    183  O   TYR    37      -2.609   1.306  -4.734   1.0                    
ATOM    184  CB  TYR    37      -3.595   2.966  -0.442   0.0                    
ATOM    185  N   LEU    38      -4.483   0.217  -4.131   1.0                    
ATOM    186  CA  LEU    38      -5.127   0.375  -5.429   1.0                    
ATOM    187  C   LEU    38      -6.421   1.173  -5.309   1.0                    
ATOM    188  O   LEU    38      -6.794   1.908  -6.224   1.0                    
ATOM    189  CB  LEU    38      -5.481  -1.424  -6.260   0.0                    
ATOM    190  N   LYS    39      -7.101   1.022  -4.178   1.0                    
ATOM    191  CA  LYS    39      -8.354   1.727  -3.937   1.0                    
ATOM    192  C   LYS    39      -8.119   3.223  -3.754   1.0                    
ATOM    193  O   LYS    39      -7.230   3.635  -3.009   1.0                    
ATOM    194  CB  LYS    39      -9.703   0.626  -1.632   0.0                    
ATOM    195  N   GLY    40      -8.922   4.031  -4.440   1.0                    
ATOM    196  CA  GLY    40      -8.803   5.482  -4.355   1.0                    
ATOM    197  C   GLY    40      -7.814   6.015  -5.387   1.0                    
ATOM    198  O   GLY    40      -7.567   7.219  -5.458   1.0                    
TER                                                                             
END
