
#######################################################
#                                                     #
#                        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 T0335AL242_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL242_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      -       -           -
LGA    R       9      -       -           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      -       -           -
LGA    A      14      A       5           #
LGA    A      15      K       6          5.853
LGA    K      16      I       7          4.471
LGA    A      17      -       -           -
LGA    K      18      -       -           -
LGA    A      19      -       -           -
LGA    G      20      -       -           -
LGA    V      21      -       -           -
LGA    I      22      -       -           -
LGA    T      23      -       -           -
LGA    E      24      -       -           -
LGA    E      25      A       8          3.277
LGA    E      26      R       9          0.661
LGA    K      27      I      10          3.300
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    A      28      L      13          1.401
LGA    E      29      A      14          4.473
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    Q      30      A      17          1.989
LGA    Q      31      K      18          2.706
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    K      32      I      22          2.164
LGA    L      33      T      23          1.346
LGA    R      34      E      24          1.700
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    Q      35      K      27          3.168
LGA    E      36      A      28          2.884
LGA    -       -      E      29           -
LGA    Y      37      Q      30          3.316
LGA    L      38      Q      31          3.764
LGA    -       -      K      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    K      39      Q      35          2.789
LGA    G      40      E      36          2.211
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     18    3.12     0.00     32.444     0.559

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.624862 * X  +   0.628209 * Y  +   0.463574 * Z  +  -3.485894
  Y_new =  -0.649673 * X  +  -0.089094 * Y  +  -0.754975 * Z  +   2.429893
  Z_new =  -0.432980 * X  +  -0.772927 * Y  +   0.463802 * Z  +  -1.737180 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.030334    2.111259  [ DEG:   -59.0338    120.9662 ]
  Theta =   0.447796    2.693796  [ DEG:    25.6568    154.3432 ]
  Phi   =  -2.336731    0.804862  [ DEG:  -133.8848     46.1152 ]
 
# 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: T0335AL242_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL242_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   3.12    0.00  32.444
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL242_2-D1
REMARK Aligment from pdb entry: 1q38_A
ATOM     17  N   ALA     5      -2.660  -2.635  15.015  1.00  0.00              
ATOM     18  CA  ALA     5      -3.893  -3.072  14.369  1.00  0.00              
ATOM     19  C   ALA     5      -5.115  -2.467  15.051  1.00  0.00              
ATOM     20  O   ALA     5      -5.183  -2.399  16.279  1.00  0.00              
ATOM     21  N   LYS     6      -6.079  -2.028  14.247  1.00  0.00              
ATOM     22  CA  LYS     6      -7.302  -1.431  14.770  1.00  0.00              
ATOM     23  C   LYS     6      -8.535  -2.146  14.219  1.00  0.00              
ATOM     24  O   LYS     6      -9.023  -1.815  13.138  1.00  0.00              
ATOM     25  N   ILE     7      -9.056  -3.145  14.955  1.00  0.00              
ATOM     26  CA  ILE     7     -10.231  -3.911  14.530  1.00  0.00              
ATOM     27  C   ILE     7     -11.530  -3.118  14.646  1.00  0.00              
ATOM     28  O   ILE     7     -12.008  -2.847  15.747  1.00  0.00              
ATOM     29  N   ALA     8     -12.095  -2.759  13.497  1.00  0.00              
ATOM     30  CA  ALA     8     -13.347  -2.006  13.446  1.00  0.00              
ATOM     31  C   ALA     8     -13.274  -0.728  14.284  1.00  0.00              
ATOM     32  O   ALA     8     -14.017  -0.571  15.255  1.00  0.00              
ATOM     33  N   ARG     9     -12.383   0.212  13.916  1.00  0.00              
ATOM     34  CA  ARG     9     -12.228   1.477  14.633  1.00  0.00              
ATOM     35  C   ARG     9     -13.210   2.539  14.142  1.00  0.00              
ATOM     36  O   ARG     9     -14.233   2.216  13.538  1.00  0.00              
ATOM     37  N   ILE    10     -11.143  -2.258   7.439  1.00  0.00              
ATOM     38  CA  ILE    10      -9.868  -2.468   6.764  1.00  0.00              
ATOM     39  C   ILE    10      -9.961  -2.071   5.293  1.00  0.00              
ATOM     40  O   ILE    10     -10.983  -2.280   4.648  1.00  0.00              
ATOM     41  N   ASN    11      -8.878  -1.507   4.769  1.00  0.00              
ATOM     42  CA  ASN    11      -8.824  -1.092   3.371  1.00  0.00              
ATOM     43  C   ASN    11      -8.004  -2.096   2.566  1.00  0.00              
ATOM     44  O   ASN    11      -7.049  -2.673   3.080  1.00  0.00              
ATOM     45  N   GLU    12      -8.371  -2.298   1.307  1.00  0.00              
ATOM     46  CA  GLU    12      -7.652  -3.234   0.451  1.00  0.00              
ATOM     47  C   GLU    12      -6.971  -2.499  -0.695  1.00  0.00              
ATOM     48  O   GLU    12      -7.612  -1.772  -1.449  1.00  0.00              
ATOM     49  N   LEU    13      -5.670  -2.697  -0.821  1.00  0.00              
ATOM     50  CA  LEU    13      -4.911  -2.056  -1.881  1.00  0.00              
ATOM     51  C   LEU    13      -4.404  -3.092  -2.870  1.00  0.00              
ATOM     52  O   LEU    13      -3.576  -3.938  -2.531  1.00  0.00              
ATOM     53  N   ALA    14      -4.903  -3.021  -4.096  1.00  0.00              
ATOM     54  CA  ALA    14      -4.495  -3.952  -5.135  1.00  0.00              
ATOM     55  C   ALA    14      -3.763  -3.219  -6.245  1.00  0.00              
ATOM     56  O   ALA    14      -4.247  -2.213  -6.761  1.00  0.00              
ATOM     57  N   ALA    15      -2.593  -3.726  -6.613  1.00  0.00              
ATOM     58  CA  ALA    15      -1.812  -3.102  -7.666  1.00  0.00              
ATOM     59  C   ALA    15      -1.120  -4.134  -8.543  1.00  0.00              
ATOM     60  O   ALA    15      -0.759  -5.221  -8.086  1.00  0.00              
ATOM     61  N   LYS    16      -0.947  -3.775  -9.811  1.00  0.00              
ATOM     62  CA  LYS    16      -0.304  -4.649 -10.784  1.00  0.00              
ATOM     63  C   LYS    16       0.292  -3.824 -11.924  1.00  0.00              
ATOM     64  O   LYS    16      -0.288  -2.821 -12.340  1.00  0.00              
ATOM     65  N   ALA    17       1.463  -4.231 -12.442  1.00  0.00              
ATOM     66  CA  ALA    17       2.132  -3.516 -13.534  1.00  0.00              
ATOM     67  C   ALA    17       1.252  -3.396 -14.770  1.00  0.00              
ATOM     68  O   ALA    17       0.987  -4.383 -15.456  1.00  0.00              
ATOM     69  N   LYS    18       0.804  -2.177 -15.048  1.00  0.00              
ATOM     70  CA  LYS    18      -0.045  -1.915 -16.200  1.00  0.00              
ATOM     71  C   LYS    18       0.779  -1.887 -17.482  1.00  0.00              
ATOM     72  O   LYS    18       0.258  -2.111 -18.575  1.00  0.00              
ATOM     73  N   ALA    19       2.070  -1.608 -17.337  1.00  0.00              
ATOM     74  CA  ALA    19       2.974  -1.545 -18.479  1.00  0.00              
ATOM     75  C   ALA    19       3.695  -2.876 -18.681  1.00  0.00              
ATOM     76  O   ALA    19       4.198  -3.161 -19.767  1.00  0.00              
ATOM     77  N   GLY    20       3.739  -3.685 -17.627  1.00  0.00              
ATOM     78  CA  GLY    20       4.397  -4.985 -17.689  1.00  0.00              
ATOM     79  C   GLY    20       3.377  -6.118 -17.614  1.00  0.00              
ATOM     80  O   GLY    20       3.747  -7.292 -17.619  1.00  0.00              
ATOM     81  N   VAL    21       2.096  -5.746 -17.551  1.00  0.00              
ATOM     82  CA  VAL    21       0.990  -6.707 -17.479  1.00  0.00              
ATOM     83  C   VAL    21       1.369  -7.966 -16.692  1.00  0.00              
ATOM     84  O   VAL    21       1.780  -8.976 -17.263  1.00  0.00              
ATOM     85  N   ILE    22       1.225  -7.893 -15.371  1.00  0.00              
ATOM     86  CA  ILE    22       1.552  -9.027 -14.525  1.00  0.00              
ATOM     87  C   ILE    22       0.426  -9.387 -13.575  1.00  0.00              
ATOM     88  O   ILE    22      -0.749  -9.230 -13.907  1.00  0.00              
ATOM     89  N   THR    23       0.785  -9.875 -12.391  1.00  0.00              
ATOM     90  CA  THR    23      -0.204 -10.263 -11.391  1.00  0.00              
ATOM     91  C   THR    23      -0.433  -9.137 -10.386  1.00  0.00              
ATOM     92  O   THR    23       0.417  -8.264 -10.213  1.00  0.00              
ATOM     93  N   GLU    24      -1.588  -9.166  -9.726  1.00  0.00              
ATOM     94  CA  GLU    24      -1.931  -8.149  -8.737  1.00  0.00              
ATOM     95  C   GLU    24      -1.414  -8.533  -7.353  1.00  0.00              
ATOM     96  O   GLU    24      -0.910  -9.637  -7.150  1.00  0.00              
ATOM     97  N   GLU    25      -1.563  -7.615  -6.404  1.00  0.00              
ATOM     98  CA  GLU    25      -1.133  -7.844  -5.028  1.00  0.00              
ATOM     99  C   GLU    25      -2.094  -7.142  -4.077  1.00  0.00              
ATOM    100  O   GLU    25      -2.755  -6.185  -4.467  1.00  0.00              
ATOM    101  N   GLU    26      -2.188  -7.623  -2.842  1.00  0.00              
ATOM    102  CA  GLU    26      -3.103  -7.023  -1.877  1.00  0.00              
ATOM    103  C   GLU    26      -2.394  -6.579  -0.602  1.00  0.00              
ATOM    104  O   GLU    26      -1.514  -7.268  -0.085  1.00  0.00              
ATOM    105  N   LYS    27      -2.812  -5.421  -0.097  1.00  0.00              
ATOM    106  CA  LYS    27      -2.260  -4.854   1.127  1.00  0.00              
ATOM    107  C   LYS    27      -3.380  -4.223   1.948  1.00  0.00              
ATOM    108  O   LYS    27      -3.979  -3.230   1.532  1.00  0.00              
ATOM    109  N   ALA    28      -3.682  -4.817   3.098  1.00  0.00              
ATOM    110  CA  ALA    28      -4.758  -4.321   3.948  1.00  0.00              
ATOM    111  C   ALA    28      -4.274  -3.307   4.979  1.00  0.00              
ATOM    112  O   ALA    28      -3.339  -3.565   5.738  1.00  0.00              
ATOM    113  N   GLU    29      -4.943  -2.156   5.009  1.00  0.00              
ATOM    114  CA  GLU    29      -4.624  -1.089   5.952  1.00  0.00              
ATOM    115  C   GLU    29      -5.916  -0.497   6.517  1.00  0.00              
ATOM    116  O   GLU    29      -6.643   0.201   5.813  1.00  0.00              
ATOM    117  N   GLN    30      -6.232  -0.781   7.795  1.00  0.00              
ATOM    118  CA  GLN    30      -7.457  -0.286   8.435  1.00  0.00              
ATOM    119  C   GLN    30      -7.487   1.233   8.572  1.00  0.00              
ATOM    120  O   GLN    30      -7.016   1.787   9.565  1.00  0.00              
ATOM    121  N   GLN    31      -8.057   1.900   7.572  1.00  0.00              
ATOM    122  CA  GLN    31      -8.151   3.347   7.605  1.00  0.00              
ATOM    123  C   GLN    31      -6.808   4.024   7.418  1.00  0.00              
ATOM    124  O   GLN    31      -5.912   3.473   6.779  1.00  0.00              
ATOM    125  N   LYS    32      -6.672   5.223   7.975  1.00  0.00              
ATOM    126  CA  LYS    32      -5.429   5.981   7.865  1.00  0.00              
ATOM    127  C   LYS    32      -4.681   5.999   9.196  1.00  0.00              
ATOM    128  O   LYS    32      -4.607   7.030   9.864  1.00  0.00              
ATOM    129  N   LEU    33      -4.123   4.852   9.572  1.00  0.00              
ATOM    130  CA  LEU    33      -3.376   4.741  10.820  1.00  0.00              
ATOM    131  C   LEU    33      -2.070   5.522  10.736  1.00  0.00              
ATOM    132  O   LEU    33      -1.587   6.054  11.736  1.00  0.00              
ATOM    133  N   ARG    34      -1.508   5.588   9.533  1.00  0.00              
ATOM    134  CA  ARG    34      -0.258   6.307   9.307  1.00  0.00              
ATOM    135  C   ARG    34       0.038   6.420   7.815  1.00  0.00              
ATOM    136  O   ARG    34      -0.730   5.939   6.982  1.00  0.00              
ATOM    137  N   GLN    35       1.155   7.061   7.484  1.00  0.00              
ATOM    138  CA  GLN    35       1.550   7.238   6.091  1.00  0.00              
ATOM    139  C   GLN    35       2.136   5.948   5.521  1.00  0.00              
ATOM    140  O   GLN    35       3.257   5.564   5.853  1.00  0.00              
ATOM    141  N   GLU    36       1.367   5.284   4.661  1.00  0.00              
ATOM    142  CA  GLU    36       1.807   4.037   4.045  1.00  0.00              
ATOM    143  C   GLU    36       1.774   4.138   2.523  1.00  0.00              
ATOM    144  O   GLU    36       0.705   4.249   1.923  1.00  0.00              
ATOM    145  N   TYR    37       2.951   4.097   1.905  1.00  0.00              
ATOM    146  CA  TYR    37       3.055   4.185   0.453  1.00  0.00              
ATOM    147  C   TYR    37       3.900   3.046  -0.112  1.00  0.00              
ATOM    148  O   TYR    37       5.027   2.816   0.329  1.00  0.00              
ATOM    149  N   LEU    38       3.349   2.338  -1.095  1.00  0.00              
ATOM    150  CA  LEU    38       4.052   1.227  -1.727  1.00  0.00              
ATOM    151  C   LEU    38       4.989   1.736  -2.819  1.00  0.00              
ATOM    152  O   LEU    38       4.560   2.422  -3.747  1.00  0.00              
ATOM    153  N   LYS    39       6.268   1.396  -2.700  1.00  0.00              
ATOM    154  CA  LYS    39       7.264   1.822  -3.676  1.00  0.00              
ATOM    155  C   LYS    39       7.988   0.621  -4.278  1.00  0.00              
ATOM    156  O   LYS    39       7.462  -0.492  -4.288  1.00  0.00              
ATOM    157  N   GLY    40       9.195   0.856  -4.784  1.00  0.00              
ATOM    158  CA  GLY    40       9.968  -0.215  -5.386  1.00  0.00              
ATOM    159  C   GLY    40       9.783  -0.272  -6.888  1.00  0.00              
ATOM    160  O   GLY    40      10.131  -1.265  -7.529  1.00  0.00              
END
