
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0335AL381_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL381_1-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      10      A       5           -
LGA    N      11      K       6           -
LGA    E      12      I       7           -
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    L      13      A      15           #
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    A      14      K      18          4.916
LGA    K      16      A      19          3.889
LGA    A      17      -       -           -
LGA    K      18      G      20          0.455
LGA    A      19      -       -           -
LGA    G      20      V      21          1.492
LGA    V      21      -       -           -
LGA    I      22      I      22          2.593
LGA    T      23      T      23          0.978
LGA    E      24      E      24          0.813
LGA    E      25      E      25          1.105
LGA    E      26      E      26          0.666
LGA    K      27      K      27          0.788
LGA    A      28      A      28          0.652
LGA    E      29      E      29          1.036
LGA    Q      30      Q      30          0.723
LGA    Q      31      Q      31          0.806
LGA    K      32      K      32          0.589
LGA    L      33      L      33          1.382
LGA    R      34      R      34          1.426
LGA    Q      35      Q      35          0.925
LGA    E      36      E      36          1.082
LGA    Y      37      Y      37          1.609
LGA    L      38      L      38          1.167
LGA    K      39      K      39          0.420
LGA    G      40      G      40          3.663

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   30   36    5.0     23    1.85    82.61     59.562     1.178

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.933846 * X  +   0.049095 * Y  +   0.354289 * Z  +  -2.042714
  Y_new =  -0.245728 * X  +   0.631703 * Y  +  -0.735234 * Z  +  -7.587165
  Z_new =  -0.259902 * X  +  -0.773654 * Y  +  -0.577849 * Z  +  -4.829124 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.212316    0.929276  [ DEG:  -126.7564     53.2436 ]
  Theta =   0.262920    2.878672  [ DEG:    15.0642    164.9358 ]
  Phi   =  -2.884290    0.257302  [ DEG:  -165.2577     14.7423 ]
 
# 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: T0335AL381_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_1-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30   36   5.0   23   1.85   82.61  59.562
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_1-D1
REMARK Aligment from pdb entry: 1r2uA
ATOM      1  N   ILE    10     -23.568   2.074  -0.615  1.00  0.00              
ATOM      2  CA  ILE    10     -22.701   2.924   0.258  1.00  0.00              
ATOM      3  C   ILE    10     -21.890   2.035   1.202  1.00  0.00              
ATOM      4  O   ILE    10     -22.377   1.010   1.683  1.00  0.00              
ATOM      5  N   ASN    11     -20.646   2.445   1.458  1.00  0.00              
ATOM      6  CA  ASN    11     -19.764   1.685   2.345  1.00  0.00              
ATOM      7  C   ASN    11     -19.154   2.599   3.407  1.00  0.00              
ATOM      8  O   ASN    11     -18.519   3.606   3.088  1.00  0.00              
ATOM      9  N   GLU    12     -19.355   2.230   4.674  1.00  0.00              
ATOM     10  CA  GLU    12     -18.820   3.017   5.789  1.00  0.00              
ATOM     11  C   GLU    12     -17.700   2.261   6.518  1.00  0.00              
ATOM     12  O   GLU    12     -17.326   2.619   7.639  1.00  0.00              
ATOM     13  N   LEU    13     -17.151   1.226   5.869  1.00  0.00              
ATOM     14  CA  LEU    13     -16.063   0.448   6.470  1.00  0.00              
ATOM     15  C   LEU    13     -14.713   1.112   6.188  1.00  0.00              
ATOM     16  O   LEU    13     -13.761   0.942   6.946  1.00  0.00              
ATOM     17  N   ALA    14     -14.645   1.871   5.086  1.00  0.00              
ATOM     18  CA  ALA    14     -13.411   2.561   4.706  1.00  0.00              
ATOM     19  C   ALA    14     -13.083   3.660   5.712  1.00  0.00              
ATOM     20  O   ALA    14     -11.918   3.947   5.976  1.00  0.00              
ATOM     21  N   LYS    16     -14.132   4.265   6.272  1.00  0.00              
ATOM     22  CA  LYS    16     -13.958   5.335   7.260  1.00  0.00              
ATOM     23  C   LYS    16     -13.627   4.739   8.622  1.00  0.00              
ATOM     24  O   LYS    16     -12.808   5.275   9.370  1.00  0.00              
ATOM     25  N   ALA    17     -14.270   3.614   8.928  1.00  0.00              
ATOM     26  CA  ALA    17     -14.039   2.926  10.199  1.00  0.00              
ATOM     27  C   ALA    17     -12.697   2.183  10.184  1.00  0.00              
ATOM     28  O   ALA    17     -12.091   1.962  11.232  1.00  0.00              
ATOM     29  N   LYS    18     -12.243   1.796   8.984  1.00  0.00              
ATOM     30  CA  LYS    18     -10.978   1.072   8.843  1.00  0.00              
ATOM     31  C   LYS    18      -9.797   2.036   8.733  1.00  0.00              
ATOM     32  O   LYS    18      -8.728   1.775   9.287  1.00  0.00              
ATOM     33  N   ALA    19      -9.994   3.153   8.018  1.00  0.00              
ATOM     34  CA  ALA    19      -8.923   4.143   7.855  1.00  0.00              
ATOM     35  C   ALA    19      -8.464   4.676   9.219  1.00  0.00              
ATOM     36  O   ALA    19      -7.289   4.997   9.406  1.00  0.00              
ATOM     37  N   GLY    20      -9.404   4.751  10.169  1.00  0.00              
ATOM     38  CA  GLY    20      -9.091   5.230  11.518  1.00  0.00              
ATOM     39  C   GLY    20      -8.305   4.175  12.307  1.00  0.00              
ATOM     40  O   GLY    20      -7.604   4.503  13.266  1.00  0.00              
ATOM     41  N   VAL    21      -8.426   2.904  11.895  1.00  0.00              
ATOM     42  CA  VAL    21      -7.716   1.815  12.574  1.00  0.00              
ATOM     43  C   VAL    21      -6.256   1.764  12.123  1.00  0.00              
ATOM     44  O   VAL    21      -5.353   1.536  12.931  1.00  0.00              
ATOM     45  N   ILE    22      -6.039   1.978  10.823  1.00  0.00              
ATOM     46  CA  ILE    22      -4.689   1.957  10.260  1.00  0.00              
ATOM     47  C   ILE    22      -3.860   3.127  10.789  1.00  0.00              
ATOM     48  O   ILE    22      -4.389   4.198  11.097  1.00  0.00              
ATOM     49  N   THR    23      -2.551   2.898  10.891  1.00  0.00              
ATOM     50  CA  THR    23      -1.628   3.925  11.386  1.00  0.00              
ATOM     51  C   THR    23      -0.861   4.564  10.229  1.00  0.00              
ATOM     52  O   THR    23      -0.896   4.080   9.095  1.00  0.00              
ATOM     53  N   GLU    24      -0.152   5.652  10.542  1.00  0.00              
ATOM     54  CA  GLU    24       0.646   6.355   9.536  1.00  0.00              
ATOM     55  C   GLU    24       1.800   5.468   9.070  1.00  0.00              
ATOM     56  O   GLU    24       2.221   5.532   7.915  1.00  0.00              
ATOM     57  N   GLU    25       2.296   4.634   9.990  1.00  0.00              
ATOM     58  CA  GLU    25       3.396   3.719   9.685  1.00  0.00              
ATOM     59  C   GLU    25       2.981   2.711   8.609  1.00  0.00              
ATOM     60  O   GLU    25       3.760   2.396   7.708  1.00  0.00              
ATOM     61  N   GLU    26       1.743   2.221   8.714  1.00  0.00              
ATOM     62  CA  GLU    26       1.216   1.254   7.745  1.00  0.00              
ATOM     63  C   GLU    26       1.166   1.874   6.351  1.00  0.00              
ATOM     64  O   GLU    26       1.600   1.263   5.374  1.00  0.00              
ATOM     65  N   LYS    27       0.646   3.104   6.274  1.00  0.00              
ATOM     66  CA  LYS    27       0.559   3.810   4.994  1.00  0.00              
ATOM     67  C   LYS    27       1.958   4.164   4.482  1.00  0.00              
ATOM     68  O   LYS    27       2.195   4.198   3.275  1.00  0.00              
ATOM     69  N   ALA    28       2.886   4.413   5.416  1.00  0.00              
ATOM     70  CA  ALA    28       4.267   4.745   5.054  1.00  0.00              
ATOM     71  C   ALA    28       4.915   3.561   4.333  1.00  0.00              
ATOM     72  O   ALA    28       5.553   3.730   3.292  1.00  0.00              
ATOM     73  N   GLU    29       4.723   2.360   4.892  1.00  0.00              
ATOM     74  CA  GLU    29       5.271   1.142   4.288  1.00  0.00              
ATOM     75  C   GLU    29       4.562   0.858   2.965  1.00  0.00              
ATOM     76  O   GLU    29       5.192   0.476   1.981  1.00  0.00              
ATOM     77  N   GLN    30       3.240   1.058   2.966  1.00  0.00              
ATOM     78  CA  GLN    30       2.426   0.834   1.768  1.00  0.00              
ATOM     79  C   GLN    30       2.873   1.756   0.631  1.00  0.00              
ATOM     80  O   GLN    30       2.959   1.334  -0.524  1.00  0.00              
ATOM     81  N   GLN    31       3.161   3.018   0.974  1.00  0.00              
ATOM     82  CA  GLN    31       3.605   3.999  -0.021  1.00  0.00              
ATOM     83  C   GLN    31       4.952   3.584  -0.615  1.00  0.00              
ATOM     84  O   GLN    31       5.138   3.620  -1.830  1.00  0.00              
ATOM     85  N   LYS    32       5.881   3.181   0.258  1.00  0.00              
ATOM     86  CA  LYS    32       7.206   2.747  -0.195  1.00  0.00              
ATOM     87  C   LYS    32       7.089   1.459  -1.009  1.00  0.00              
ATOM     88  O   LYS    32       7.709   1.321  -2.064  1.00  0.00              
ATOM     89  N   LEU    33       6.270   0.526  -0.509  1.00  0.00              
ATOM     90  CA  LEU    33       6.048  -0.754  -1.192  1.00  0.00              
ATOM     91  C   LEU    33       5.402  -0.535  -2.564  1.00  0.00              
ATOM     92  O   LEU    33       5.539  -1.366  -3.462  1.00  0.00              
ATOM     93  N   ARG    34       4.700   0.593  -2.715  1.00  0.00              
ATOM     94  CA  ARG    34       4.046   0.916  -3.979  1.00  0.00              
ATOM     95  C   ARG    34       5.028   1.626  -4.913  1.00  0.00              
ATOM     96  O   ARG    34       5.230   1.205  -6.050  1.00  0.00              
ATOM     97  N   GLN    35       5.625   2.712  -4.410  1.00  0.00              
ATOM     98  CA  GLN    35       6.580   3.511  -5.190  1.00  0.00              
ATOM     99  C   GLN    35       7.707   2.662  -5.788  1.00  0.00              
ATOM    100  O   GLN    35       8.125   2.899  -6.922  1.00  0.00              
ATOM    101  N   GLU    36       8.205   1.681  -5.023  1.00  0.00              
ATOM    102  CA  GLU    36       9.295   0.821  -5.515  1.00  0.00              
ATOM    103  C   GLU    36       8.910   0.157  -6.839  1.00  0.00              
ATOM    104  O   GLU    36       9.741   0.016  -7.738  1.00  0.00              
ATOM    105  N   TYR    37       7.637  -0.236  -6.953  1.00  0.00              
ATOM    106  CA  TYR    37       7.144  -0.870  -8.175  1.00  0.00              
ATOM    107  C   TYR    37       6.775   0.190  -9.218  1.00  0.00              
ATOM    108  O   TYR    37       6.872  -0.051 -10.422  1.00  0.00              
ATOM    109  N   LEU    38       6.351   1.369  -8.739  1.00  0.00              
ATOM    110  CA  LEU    38       5.970   2.469  -9.633  1.00  0.00              
ATOM    111  C   LEU    38       7.169   3.387  -9.905  1.00  0.00              
ATOM    112  O   LEU    38       7.029   4.610 -10.002  1.00  0.00              
ATOM    113  N   LYS    39       8.353   2.783 -10.043  1.00  0.00              
ATOM    114  CA  LYS    39       9.568   3.553 -10.321  1.00  0.00              
ATOM    115  C   LYS    39       9.564   4.044 -11.773  1.00  0.00              
ATOM    116  O   LYS    39      10.122   5.098 -12.083  1.00  0.00              
ATOM    117  N   GLY    40       8.919   3.269 -12.653  1.00  0.00              
ATOM    118  CA  GLY    40       8.834   3.630 -14.068  1.00  0.00              
ATOM    119  C   GLY    40       7.556   3.058 -14.695  1.00  0.00              
ATOM    120  O   GLY    40       7.573   2.546 -15.819  1.00  0.00              
END
