
#######################################################
#                                                     #
#                        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 T0335AL333_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL333_2-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      -       -           -
LGA    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      A       5          1.939
LGA    R       9      K       6          1.438
LGA    I      10      I       7          1.653
LGA    N      11      A       8          1.441
LGA    E      12      R       9          0.519
LGA    L      13      I      10          0.401
LGA    A      14      N      11          1.770
LGA    A      15      E      12          1.825
LGA    K      16      L      13          2.360
LGA    -       -      A      14           -
LGA    A      17      A      15          1.130
LGA    K      18      K      16          2.407
LGA    A      19      A      17          1.864
LGA    G      20      K      18           -
LGA    V      21      A      19           -
LGA    I      22      G      20           -
LGA    T      23      V      21           -
LGA    E      24      I      22           -
LGA    E      25      T      23           -
LGA    E      26      -       -           -
LGA    K      27      -       -           -
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      -       -           -
LGA    Q      31      -       -           -
LGA    K      32      -       -           -
LGA    L      33      E      24          2.689
LGA    R      34      E      25          2.365
LGA    Q      35      -       -           -
LGA    E      36      E      26          4.023
LGA    Y      37      K      27          2.417
LGA    L      38      A      28          4.041
LGA    -       -      E      29           -
LGA    -       -      Q      30           -
LGA    -       -      Q      31           -
LGA    -       -      K      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    K      39      G      40          2.933
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     18    2.28    33.33     41.265     0.757

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.932043 * X  +  -0.349571 * Y  +   0.095369 * Z  + -15.628775
  Y_new =  -0.131098 * X  +  -0.079957 * Y  +   0.988140 * Z  + -83.626511
  Z_new =  -0.337800 * X  +  -0.933492 * Y  +  -0.120352 * Z  + 118.594078 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.699015    1.442577  [ DEG:   -97.3464     82.6536 ]
  Theta =   0.344578    2.797014  [ DEG:    19.7429    160.2571 ]
  Phi   =  -0.139739    3.001853  [ DEG:    -8.0065    171.9935 ]
 
# 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: T0335AL333_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL333_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   18   2.28   33.33  41.265
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL333_2-D1
REMARK Aligment from pdb entry: 1a8y
ATOM     17  N   ALA     5       6.761  -5.878  -5.976  1.00  0.00              
ATOM     18  CA  ALA     5       7.478  -6.491  -7.092  1.00  0.00              
ATOM     19  C   ALA     5       6.659  -7.690  -7.593  1.00  0.00              
ATOM     20  O   ALA     5       6.496  -8.733  -6.946  1.00  0.00              
ATOM     21  N   LYS     6       6.043  -7.479  -8.768  1.00  0.00              
ATOM     22  CA  LYS     6       5.154  -8.452  -9.418  1.00  0.00              
ATOM     23  C   LYS     6       3.729  -8.560  -8.837  1.00  0.00              
ATOM     24  O   LYS     6       3.550  -8.615  -7.620  1.00  0.00              
ATOM     25  N   ILE     7       2.724  -8.682  -9.732  1.00  0.00              
ATOM     26  CA  ILE     7       1.280  -8.723  -9.461  1.00  0.00              
ATOM     27  C   ILE     7       0.693  -9.477  -8.272  1.00  0.00              
ATOM     28  O   ILE     7      -0.509  -9.355  -8.053  1.00  0.00              
ATOM     29  N   ALA     8       1.423 -10.275  -7.490  1.00  0.00              
ATOM     30  CA  ALA     8       0.850 -10.903  -6.303  1.00  0.00              
ATOM     31  C   ALA     8       1.077 -10.080  -5.036  1.00  0.00              
ATOM     32  O   ALA     8       0.636 -10.461  -3.950  1.00  0.00              
ATOM     33  N   ARG     9       1.815  -8.967  -5.142  1.00  0.00              
ATOM     34  CA  ARG     9       2.005  -8.011  -4.054  1.00  0.00              
ATOM     35  C   ARG     9       1.153  -6.783  -4.357  1.00  0.00              
ATOM     36  O   ARG     9       0.735  -6.092  -3.433  1.00  0.00              
ATOM     37  N   ILE    10       0.875  -6.534  -5.649  1.00  0.00              
ATOM     38  CA  ILE    10       0.019  -5.473  -6.163  1.00  0.00              
ATOM     39  C   ILE    10      -1.402  -5.826  -5.814  1.00  0.00              
ATOM     40  O   ILE    10      -2.158  -4.983  -5.360  1.00  0.00              
ATOM     41  N   ASN    11      -1.825  -7.061  -6.028  1.00  0.00              
ATOM     42  CA  ASN    11      -3.153  -7.476  -5.601  1.00  0.00              
ATOM     43  C   ASN    11      -3.014  -8.065  -4.195  1.00  0.00              
ATOM     44  O   ASN    11      -3.066  -9.266  -3.927  1.00  0.00              
ATOM     45  N   GLU    12      -2.762  -7.115  -3.297  1.00  0.00              
ATOM     46  CA  GLU    12      -2.582  -7.270  -1.857  1.00  0.00              
ATOM     47  C   GLU    12      -2.758  -5.844  -1.347  1.00  0.00              
ATOM     48  O   GLU    12      -3.484  -5.561  -0.394  1.00  0.00              
ATOM     49  N   LEU    13      -2.055  -4.955  -2.061  1.00  0.00              
ATOM     50  CA  LEU    13      -2.118  -3.528  -1.907  1.00  0.00              
ATOM     51  C   LEU    13      -3.527  -3.094  -2.313  1.00  0.00              
ATOM     52  O   LEU    13      -4.231  -2.453  -1.535  1.00  0.00              
ATOM     53  N   ALA    14      -3.943  -3.467  -3.532  1.00  0.00              
ATOM     54  CA  ALA    14      -5.248  -3.148  -4.105  1.00  0.00              
ATOM     55  C   ALA    14      -6.436  -3.485  -3.219  1.00  0.00              
ATOM     56  O   ALA    14      -7.439  -2.775  -3.203  1.00  0.00              
ATOM     57  N   ALA    15      -6.308  -4.559  -2.444  1.00  0.00              
ATOM     58  CA  ALA    15      -7.324  -4.982  -1.499  1.00  0.00              
ATOM     59  C   ALA    15      -7.341  -4.240  -0.166  1.00  0.00              
ATOM     60  O   ALA    15      -8.353  -4.347   0.523  1.00  0.00              
ATOM     61  N   LYS    16      -6.307  -3.506   0.288  1.00  0.00              
ATOM     62  CA  LYS    16      -6.364  -2.794   1.561  1.00  0.00              
ATOM     63  C   LYS    16      -7.406  -1.700   1.424  1.00  0.00              
ATOM     64  O   LYS    16      -7.420  -0.942   0.447  1.00  0.00              
ATOM     65  N   ALA    17      -8.310  -1.643   2.401  1.00  0.00              
ATOM     66  CA  ALA    17      -9.364  -0.679   2.285  1.00  0.00              
ATOM     67  C   ALA    17      -9.704   0.012   3.568  1.00  0.00              
ATOM     68  O   ALA    17     -10.182   1.145   3.499  1.00  0.00              
ATOM     69  N   LYS    18      -9.446  -0.597   4.740  1.00  0.00              
ATOM     70  CA  LYS    18      -9.893   0.042   5.962  1.00  0.00              
ATOM     71  C   LYS    18      -9.003   1.124   6.543  1.00  0.00              
ATOM     72  O   LYS    18      -9.384   1.820   7.493  1.00  0.00              
ATOM     73  N   ALA    19      -7.851   1.283   5.879  1.00  0.00              
ATOM     74  CA  ALA    19      -6.880   2.324   6.194  1.00  0.00              
ATOM     75  C   ALA    19      -6.462   3.158   4.967  1.00  0.00              
ATOM     76  O   ALA    19      -6.698   2.819   3.794  1.00  0.00              
ATOM     77  N   GLY    20      13.030   5.147  -9.042  1.00  0.00              
ATOM     78  CA  GLY    20      13.970   4.485  -9.919  1.00  0.00              
ATOM     79  C   GLY    20      14.464   3.185  -9.313  1.00  0.00              
ATOM     80  O   GLY    20      14.398   2.151  -9.966  1.00  0.00              
ATOM     81  N   VAL    21      15.003   3.230  -8.089  1.00  0.00              
ATOM     82  CA  VAL    21      15.459   2.073  -7.319  1.00  0.00              
ATOM     83  C   VAL    21      15.725   2.490  -5.884  1.00  0.00              
ATOM     84  O   VAL    21      15.463   3.643  -5.546  1.00  0.00              
ATOM     85  N   ILE    22      16.229   1.587  -5.014  1.00  0.00              
ATOM     86  CA  ILE    22      16.372   1.866  -3.593  1.00  0.00              
ATOM     87  C   ILE    22      17.236   3.062  -3.204  1.00  0.00              
ATOM     88  O   ILE    22      17.187   3.542  -2.065  1.00  0.00              
ATOM     89  N   THR    23      18.001   3.540  -4.204  1.00  0.00              
ATOM     90  CA  THR    23      19.009   4.583  -4.082  1.00  0.00              
ATOM     91  C   THR    23      18.552   5.988  -4.373  1.00  0.00              
ATOM     92  O   THR    23      19.179   6.916  -3.878  1.00  0.00              
ATOM     93  N   GLU    24      17.455   6.103  -5.138  1.00  0.00              
ATOM     94  CA  GLU    24      16.751   7.323  -5.510  1.00  0.00              
ATOM     95  C   GLU    24      16.549   8.231  -4.328  1.00  0.00              
ATOM     96  O   GLU    24      15.933   7.848  -3.351  1.00  0.00              
ATOM     97  N   GLU    25      17.081   9.447  -4.409  1.00  0.00              
ATOM     98  CA  GLU    25      16.971  10.507  -3.420  1.00  0.00              
ATOM     99  C   GLU    25      15.556  10.752  -2.904  1.00  0.00              
ATOM    100  O   GLU    25      15.325  11.161  -1.767  1.00  0.00              
ATOM    101  N   GLU    26      14.581  10.440  -3.755  1.00  0.00              
ATOM    102  CA  GLU    26      13.173  10.648  -3.475  1.00  0.00              
ATOM    103  C   GLU    26      12.505   9.509  -2.744  1.00  0.00              
ATOM    104  O   GLU    26      11.511   9.704  -2.048  1.00  0.00              
ATOM    105  N   LYS    27      13.084   8.321  -2.913  1.00  0.00              
ATOM    106  CA  LYS    27      12.692   7.131  -2.204  1.00  0.00              
ATOM    107  C   LYS    27      13.201   7.254  -0.766  1.00  0.00              
ATOM    108  O   LYS    27      12.478   6.892   0.150  1.00  0.00              
ATOM    109  N   ALA    28      14.417   7.738  -0.479  1.00  0.00              
ATOM    110  CA  ALA    28      14.888   7.971   0.886  1.00  0.00              
ATOM    111  C   ALA    28      13.992   9.015   1.536  1.00  0.00              
ATOM    112  O   ALA    28      13.707   8.953   2.731  1.00  0.00              
ATOM    113  N   GLU    29      13.455   9.967   0.756  1.00  0.00              
ATOM    114  CA  GLU    29      12.483  10.877   1.310  1.00  0.00              
ATOM    115  C   GLU    29      11.230  10.089   1.686  1.00  0.00              
ATOM    116  O   GLU    29      10.786  10.169   2.825  1.00  0.00              
ATOM    117  N   GLN    30       7.679   7.359   5.836  1.00  0.00              
ATOM    118  CA  GLN    30       7.042   6.148   6.314  1.00  0.00              
ATOM    119  C   GLN    30       7.387   5.812   7.755  1.00  0.00              
ATOM    120  O   GLN    30       6.586   5.243   8.488  1.00  0.00              
ATOM    121  N   GLN    31       8.598   6.161   8.157  1.00  0.00              
ATOM    122  CA  GLN    31       9.066   5.909   9.499  1.00  0.00              
ATOM    123  C   GLN    31       8.306   6.712  10.540  1.00  0.00              
ATOM    124  O   GLN    31       8.036   6.256  11.655  1.00  0.00              
ATOM    125  N   LYS    32       7.938   7.931  10.185  1.00  0.00              
ATOM    126  CA  LYS    32       7.224   8.803  11.095  1.00  0.00              
ATOM    127  C   LYS    32       5.804   8.278  11.351  1.00  0.00              
ATOM    128  O   LYS    32       5.276   8.543  12.427  1.00  0.00              
ATOM    129  N   LEU    33       5.203   7.520  10.413  1.00  0.00              
ATOM    130  CA  LEU    33       3.862   6.918  10.476  1.00  0.00              
ATOM    131  C   LEU    33       3.804   5.409  10.739  1.00  0.00              
ATOM    132  O   LEU    33       2.723   4.817  10.856  1.00  0.00              
ATOM    133  N   ARG    34       4.984   4.785  10.819  1.00  0.00              
ATOM    134  CA  ARG    34       5.162   3.375  11.085  1.00  0.00              
ATOM    135  C   ARG    34       4.827   3.066  12.518  1.00  0.00              
ATOM    136  O   ARG    34       5.365   3.733  13.384  1.00  0.00              
ATOM    137  N   GLN    35       4.001   2.082  12.863  1.00  0.00              
ATOM    138  CA  GLN    35       3.381   1.123  11.951  1.00  0.00              
ATOM    139  C   GLN    35       1.960   1.388  11.462  1.00  0.00              
ATOM    140  O   GLN    35       1.413   0.594  10.702  1.00  0.00              
ATOM    141  N   GLU    36       1.354   2.512  11.854  1.00  0.00              
ATOM    142  CA  GLU    36      -0.043   2.806  11.575  1.00  0.00              
ATOM    143  C   GLU    36      -0.484   3.126  10.156  1.00  0.00              
ATOM    144  O   GLU    36      -1.642   2.839   9.858  1.00  0.00              
ATOM    145  N   TYR    37       0.316   3.792   9.297  1.00  0.00              
ATOM    146  CA  TYR    37      -0.086   4.033   7.931  1.00  0.00              
ATOM    147  C   TYR    37       0.924   3.374   7.035  1.00  0.00              
ATOM    148  O   TYR    37       2.132   3.623   7.143  1.00  0.00              
ATOM    149  N   LEU    38       0.404   2.478   6.177  1.00  0.00              
ATOM    150  CA  LEU    38       1.114   1.814   5.096  1.00  0.00              
ATOM    151  C   LEU    38       1.525   2.624   3.895  1.00  0.00              
ATOM    152  O   LEU    38       0.702   3.187   3.178  1.00  0.00              
ATOM    153  N   LYS    39       8.160  -0.538 -13.535  1.00  0.00              
ATOM    154  CA  LYS    39       7.358   0.350 -14.349  1.00  0.00              
ATOM    155  C   LYS    39       6.073  -0.329 -14.792  1.00  0.00              
ATOM    156  O   LYS    39       5.114   0.350 -15.131  1.00  0.00              
ATOM    157  N   GLY    40       6.028  -1.662 -14.739  1.00  0.00              
ATOM    158  CA  GLY    40       4.830  -2.448 -15.017  1.00  0.00              
ATOM    159  C   GLY    40       3.742  -2.262 -13.948  1.00  0.00              
ATOM    160  O   GLY    40       2.546  -2.230 -14.253  1.00  0.00              
END
