
#######################################################
#                                                     #
#                        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 (  144),  selected   36 , name T0335TS035_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS035_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      A       5          2.719
LGA    K       6      K       6          1.418
LGA    I       7      I       7          0.845
LGA    A       8      A       8          1.467
LGA    R       9      R       9          1.336
LGA    I      10      I      10          0.736
LGA    N      11      N      11          0.998
LGA    E      12      E      12          0.731
LGA    L      13      L      13          1.782
LGA    A      14      A      14          1.827
LGA    A      15      A      15          0.997
LGA    K      16      K      16          1.058
LGA    A      17      A      17          3.053
LGA    K      18      K      18          2.870
LGA    A      19      A      19          1.115
LGA    G      20      G      20          2.221
LGA    V      21      V      21          1.980
LGA    I      22      I      22          1.274
LGA    T      23      T      23          1.943
LGA    E      24      E      24          2.071
LGA    E      25      E      25          1.570
LGA    E      26      E      26          0.691
LGA    K      27      K      27          0.945
LGA    A      28      A      28          0.816
LGA    E      29      E      29          0.714
LGA    Q      30      Q      30          0.803
LGA    Q      31      Q      31          0.488
LGA    K      32      K      32          0.782
LGA    L      33      L      33          0.570
LGA    R      34      R      34          0.703
LGA    Q      35      Q      35          0.425
LGA    E      36      E      36          0.627
LGA    Y      37      Y      37          1.180
LGA    L      38      L      38          1.586
LGA    K      39      K      39          1.590
LGA    G      40      G      40          1.523

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     36    1.48   100.00     93.847     2.280

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.665058 * X  +  -0.421008 * Y  +   0.616806 * Z  +   0.421066
  Y_new =   0.058910 * X  +  -0.852944 * Y  +  -0.518668 * Z  +   4.440650
  Z_new =   0.744464 * X  +  -0.308608 * Y  +   0.592059 * Z  + -13.279188 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.480499    2.661093  [ DEG:   -27.5306    152.4694 ]
  Theta =  -0.839732   -2.301861  [ DEG:   -48.1131   -131.8869 ]
  Phi   =   3.053245   -0.088348  [ DEG:   174.9380     -5.0620 ]
 
# 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: T0335TS035_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS035_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   36   1.48  100.00  93.847
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS035_4-D1
PFRMAT TS
TARGET T0335
MODEL  4  REFINED
PARENT N/A
ATOM     17  N   ALA     5       1.349 -10.404  -6.593  1.00  0.00
ATOM     18  CA  ALA     5       1.855 -10.533  -5.240  1.00  0.00
ATOM     19  C   ALA     5       1.966  -9.182  -4.553  1.00  0.00
ATOM     20  O   ALA     5       1.790  -9.068  -3.341  1.00  0.00
ATOM     21  N   LYS     6       2.261  -8.129  -5.312  1.00  0.00
ATOM     22  CA  LYS     6       2.298  -6.803  -4.728  1.00  0.00
ATOM     23  C   LYS     6       1.020  -6.032  -5.010  1.00  0.00
ATOM     24  O   LYS     6       0.613  -5.170  -4.231  1.00  0.00
ATOM     25  N   ILE     7       0.360  -6.322  -6.127  1.00  0.00
ATOM     26  CA  ILE     7      -0.880  -5.637  -6.436  1.00  0.00
ATOM     27  C   ILE     7      -1.981  -6.003  -5.454  1.00  0.00
ATOM     28  O   ILE     7      -2.728  -5.144  -4.988  1.00  0.00
ATOM     29  N   ALA     8      -2.104  -7.284  -5.119  1.00  0.00
ATOM     30  CA  ALA     8      -3.137  -7.695  -4.188  1.00  0.00
ATOM     31  C   ALA     8      -2.955  -7.042  -2.827  1.00  0.00
ATOM     32  O   ALA     8      -3.916  -6.602  -2.199  1.00  0.00
ATOM     33  N   ARG     9      -1.718  -6.969  -2.342  1.00  0.00
ATOM     34  CA  ARG     9      -1.482  -6.359  -1.048  1.00  0.00
ATOM     35  C   ARG     9      -1.804  -4.874  -1.062  1.00  0.00
ATOM     36  O   ARG     9      -2.501  -4.366  -0.186  1.00  0.00
ATOM     37  N   ILE    10      -1.302  -4.146  -2.057  1.00  0.00
ATOM     38  CA  ILE    10      -1.570  -2.722  -2.120  1.00  0.00
ATOM     39  C   ILE    10      -3.056  -2.438  -2.264  1.00  0.00
ATOM     40  O   ILE    10      -3.588  -1.511  -1.656  1.00  0.00
ATOM     41  N   ASN    11      -3.757  -3.230  -3.071  1.00  0.00
ATOM     42  CA  ASN    11      -5.193  -3.060  -3.186  1.00  0.00
ATOM     43  C   ASN    11      -5.890  -3.272  -1.852  1.00  0.00
ATOM     44  O   ASN    11      -6.843  -2.571  -1.515  1.00  0.00
ATOM     45  N   GLU    12      -5.432  -4.242  -1.066  1.00  0.00
ATOM     46  CA  GLU    12      -6.055  -4.490   0.219  1.00  0.00
ATOM     47  C   GLU    12      -5.684  -3.423   1.236  1.00  0.00
ATOM     48  O   GLU    12      -6.497  -3.030   2.070  1.00  0.00
ATOM     49  N   LEU    13      -4.449  -2.932   1.188  1.00  0.00
ATOM     50  CA  LEU    13      -4.057  -1.867   2.090  1.00  0.00
ATOM     51  C   LEU    13      -4.852  -0.596   1.834  1.00  0.00
ATOM     52  O   LEU    13      -5.188   0.140   2.759  1.00  0.00
ATOM     53  N   ALA    14      -5.169  -0.314   0.573  1.00  0.00
ATOM     54  CA  ALA    14      -6.005   0.833   0.276  1.00  0.00
ATOM     55  C   ALA    14      -7.414   0.652   0.816  1.00  0.00
ATOM     56  O   ALA    14      -8.009   1.580   1.361  1.00  0.00
ATOM     57  N   ALA    15      -7.977  -0.544   0.675  1.00  0.00
ATOM     58  CA  ALA    15      -9.319  -0.777   1.173  1.00  0.00
ATOM     59  C   ALA    15      -9.391  -0.617   2.683  1.00  0.00
ATOM     60  O   ALA    15     -10.366  -0.094   3.220  1.00  0.00
ATOM     61  N   LYS    16      -8.362  -1.064   3.397  1.00  0.00
ATOM     62  CA  LYS    16      -8.367  -0.924   4.840  1.00  0.00
ATOM     63  C   LYS    16      -8.377   0.536   5.263  1.00  0.00
ATOM     64  O   LYS    16      -9.050   0.917   6.219  1.00  0.00
ATOM     65  N   ALA    17      -7.632   1.384   4.558  1.00  0.00
ATOM     66  CA  ALA    17      -7.596   2.789   4.917  1.00  0.00
ATOM     67  C   ALA    17      -8.934   3.465   4.661  1.00  0.00
ATOM     68  O   ALA    17      -9.205   4.549   5.176  1.00  0.00
ATOM     69  N   LYS    18      -9.794   2.842   3.862  1.00  0.00
ATOM     70  CA  LYS    18     -11.079   3.445   3.571  1.00  0.00
ATOM     71  C   LYS    18     -12.097   3.146   4.660  1.00  0.00
ATOM     72  O   LYS    18     -13.144   3.788   4.746  1.00  0.00
ATOM     73  N   ALA    19     -11.814   2.164   5.511  1.00  0.00
ATOM     74  CA  ALA    19     -12.755   1.820   6.560  1.00  0.00
ATOM     75  C   ALA    19     -12.332   2.392   7.902  1.00  0.00
ATOM     76  O   ALA    19     -13.077   2.337   8.879  1.00  0.00
ATOM     77  N   GLY    20     -11.129   2.953   7.979  1.00  0.00
ATOM     78  CA  GLY    20     -10.669   3.515   9.235  1.00  0.00
ATOM     79  C   GLY    20      -9.251   4.050   9.121  1.00  0.00
ATOM     80  O   GLY    20      -8.506   3.691   8.211  1.00  0.00
ATOM     81  N   VAL    21      -8.848   4.920  10.044  1.00  0.00
ATOM     82  CA  VAL    21      -7.509   5.472   9.984  1.00  0.00
ATOM     83  C   VAL    21      -6.451   4.397  10.169  1.00  0.00
ATOM     84  O   VAL    21      -6.570   3.529  11.032  1.00  0.00
ATOM     85  N   ILE    22      -5.394   4.430   9.362  1.00  0.00
ATOM     86  CA  ILE    22      -4.356   3.424   9.485  1.00  0.00
ATOM     87  C   ILE    22      -3.306   3.826  10.507  1.00  0.00
ATOM     88  O   ILE    22      -3.065   5.010  10.739  1.00  0.00
ATOM     89  N   THR    23      -2.659   2.850  11.139  1.00  0.00
ATOM     90  CA  THR    23      -1.561   3.167  12.031  1.00  0.00
ATOM     91  C   THR    23      -0.371   3.735  11.275  1.00  0.00
ATOM     92  O   THR    23      -0.316   3.683  10.047  1.00  0.00
ATOM     93  N   GLU    24       0.604   4.287  11.991  1.00  0.00
ATOM     94  CA  GLU    24       1.785   4.804  11.328  1.00  0.00
ATOM     95  C   GLU    24       2.529   3.711  10.577  1.00  0.00
ATOM     96  O   GLU    24       2.982   3.909   9.451  1.00  0.00
ATOM     97  N   GLU    25       2.668   2.534  11.182  1.00  0.00
ATOM     98  CA  GLU    25       3.361   1.452  10.513  1.00  0.00
ATOM     99  C   GLU    25       2.615   0.993   9.270  1.00  0.00
ATOM    100  O   GLU    25       3.222   0.613   8.269  1.00  0.00
ATOM    101  N   GLU    26       1.286   1.019   9.307  1.00  0.00
ATOM    102  CA  GLU    26       0.521   0.647   8.133  1.00  0.00
ATOM    103  C   GLU    26       0.620   1.700   7.043  1.00  0.00
ATOM    104  O   GLU    26       0.669   1.383   5.856  1.00  0.00
ATOM    105  N   LYS    27       0.648   2.975   7.422  1.00  0.00
ATOM    106  CA  LYS    27       0.762   4.025   6.428  1.00  0.00
ATOM    107  C   LYS    27       2.090   3.956   5.691  1.00  0.00
ATOM    108  O   LYS    27       2.157   4.176   4.482  1.00  0.00
ATOM    109  N   ALA    28       3.171   3.648   6.400  1.00  0.00
ATOM    110  CA  ALA    28       4.463   3.556   5.749  1.00  0.00
ATOM    111  C   ALA    28       4.491   2.442   4.716  1.00  0.00
ATOM    112  O   ALA    28       5.023   2.605   3.619  1.00  0.00
ATOM    113  N   GLU    29       3.918   1.287   5.042  1.00  0.00
ATOM    114  CA  GLU    29       3.912   0.187   4.097  1.00  0.00
ATOM    115  C   GLU    29       3.165   0.549   2.822  1.00  0.00
ATOM    116  O   GLU    29       3.570   0.180   1.722  1.00  0.00
ATOM    117  N   GLN    30       2.061   1.279   2.946  1.00  0.00
ATOM    118  CA  GLN    30       1.316   1.671   1.764  1.00  0.00
ATOM    119  C   GLN    30       2.131   2.589   0.868  1.00  0.00
ATOM    120  O   GLN    30       2.091   2.480  -0.357  1.00  0.00
ATOM    121  N   GLN    31       2.886   3.512   1.457  1.00  0.00
ATOM    122  CA  GLN    31       3.684   4.417   0.655  1.00  0.00
ATOM    123  C   GLN    31       4.837   3.695  -0.023  1.00  0.00
ATOM    124  O   GLN    31       5.140   3.936  -1.190  1.00  0.00
ATOM    125  N   LYS    32       5.504   2.794   0.694  1.00  0.00
ATOM    126  CA  LYS    32       6.602   2.060   0.096  1.00  0.00
ATOM    127  C   LYS    32       6.139   1.231  -1.092  1.00  0.00
ATOM    128  O   LYS    32       6.812   1.163  -2.119  1.00  0.00
ATOM    129  N   LEU    33       4.983   0.585  -0.976  1.00  0.00
ATOM    130  CA  LEU    33       4.481  -0.208  -2.082  1.00  0.00
ATOM    131  C   LEU    33       4.156   0.658  -3.288  1.00  0.00
ATOM    132  O   LEU    33       4.453   0.298  -4.426  1.00  0.00
ATOM    133  N   ARG    34       3.540   1.815  -3.065  1.00  0.00
ATOM    134  CA  ARG    34       3.211   2.686  -4.177  1.00  0.00
ATOM    135  C   ARG    34       4.459   3.197  -4.876  1.00  0.00
ATOM    136  O   ARG    34       4.535   3.221  -6.104  1.00  0.00
ATOM    137  N   GLN    35       5.463   3.617  -4.112  1.00  0.00
ATOM    138  CA  GLN    35       6.676   4.126  -4.722  1.00  0.00
ATOM    139  C   GLN    35       7.346   3.078  -5.595  1.00  0.00
ATOM    140  O   GLN    35       7.934   3.392  -6.629  1.00  0.00
ATOM    141  N   GLU    36       7.274   1.811  -5.197  1.00  0.00
ATOM    142  CA  GLU    36       7.912   0.768  -5.977  1.00  0.00
ATOM    143  C   GLU    36       7.018   0.288  -7.108  1.00  0.00
ATOM    144  O   GLU    36       7.438   0.213  -8.262  1.00  0.00
ATOM    145  N   TYR    37       5.767  -0.045  -6.804  1.00  0.00
ATOM    146  CA  TYR    37       4.863  -0.495  -7.843  1.00  0.00
ATOM    147  C   TYR    37       4.616   0.591  -8.878  1.00  0.00
ATOM    148  O   TYR    37       4.665   0.345 -10.082  1.00  0.00
ATOM    149  N   LEU    38       4.344   1.815  -8.432  1.00  0.00
ATOM    150  CA  LEU    38       4.113   2.894  -9.371  1.00  0.00
ATOM    151  C   LEU    38       5.364   3.217 -10.172  1.00  0.00
ATOM    152  O   LEU    38       5.295   3.536 -11.358  1.00  0.00
ATOM    153  N   LYS    39       6.533   3.142  -9.542  1.00  0.00
ATOM    154  CA  LYS    39       7.762   3.420 -10.259  1.00  0.00
ATOM    155  C   LYS    39       7.969   2.451 -11.412  1.00  0.00
ATOM    156  O   LYS    39       8.375   2.842 -12.505  1.00  0.00
ATOM    157  N   GLY    40       7.692   1.169 -11.194  1.00  0.00
ATOM    158  CA  GLY    40       7.830   0.204 -12.268  1.00  0.00
ATOM    159  C   GLY    40       6.777   0.411 -13.344  1.00  0.00
ATOM    160  O   GLY    40       7.067   0.347 -14.537  1.00  0.00
TER
END
