
#######################################################
#                                                     #
#                        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 T0335AL243_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL243_2-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           -
LGA    K       6      K       6           -
LGA    I       7      I       7           -
LGA    A       8      A       8           -
LGA    R       9      R       9           -
LGA    I      10      I      10           -
LGA    N      11      N      11           -
LGA    E      12      E      12           -
LGA    L      13      L      13           -
LGA    A      14      A      14           -
LGA    A      15      A      15           -
LGA    K      16      K      16           -
LGA    A      17      A      17           -
LGA    K      18      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    A      19      V      21           #
LGA    G      20      -       -           -
LGA    V      21      I      22          6.598
LGA    I      22      T      23          1.000
LGA    T      23      E      24          1.303
LGA    E      24      E      25          1.058
LGA    E      25      E      26          0.964
LGA    E      26      K      27          0.747
LGA    K      27      A      28          0.868
LGA    A      28      E      29          1.003
LGA    E      29      Q      30          0.959
LGA    Q      30      Q      31          1.037
LGA    Q      31      K      32          0.840
LGA    K      32      L      33          0.609
LGA    L      33      R      34          0.757
LGA    R      34      Q      35          0.660
LGA    Q      35      E      36          0.467
LGA    E      36      Y      37          0.532
LGA    Y      37      L      38          1.404
LGA    L      38      K      39          1.556
LGA    K      39      G      40          0.667
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     19    1.78    15.79     51.242     1.012

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.113477 * X  +   0.985998 * Y  +   0.122194 * Z  + -70.440033
  Y_new =  -0.849292 * X  +   0.160088 * Y  +  -0.503066 * Z  +  36.952633
  Z_new =  -0.515584 * X  +  -0.046692 * Y  +   0.855566 * Z  + -25.730377 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.054521    3.087072  [ DEG:    -3.1238    176.8762 ]
  Theta =   0.541689    2.599903  [ DEG:    31.0365    148.9635 ]
  Phi   =  -1.437970    1.703623  [ DEG:   -82.3896     97.6104 ]
 
# 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: T0335AL243_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL243_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   19   1.78   15.79  51.242
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL243_2-D1
REMARK Aligment from pdb entry: 2ayuA
ATOM     13  N   ALA     5      -9.956  17.102  35.724  1.00  0.00              
ATOM     14  CA  ALA     5     -10.984  17.050  34.708  1.00  0.00              
ATOM     15  C   ALA     5     -10.343  17.179  33.331  1.00  0.00              
ATOM     16  O   ALA     5     -10.260  16.207  32.583  1.00  0.00              
ATOM     17  N   LYS     6      -9.872  18.384  33.021  1.00  0.00              
ATOM     18  CA  LYS     6      -9.236  18.676  31.735  1.00  0.00              
ATOM     19  C   LYS     6      -8.039  17.785  31.419  1.00  0.00              
ATOM     20  O   LYS     6      -7.921  17.271  30.302  1.00  0.00              
ATOM     21  N   ILE     7      -7.149  17.636  32.400  1.00  0.00              
ATOM     22  CA  ILE     7      -5.954  16.809  32.262  1.00  0.00              
ATOM     23  C   ILE     7      -6.324  15.472  31.649  1.00  0.00              
ATOM     24  O   ILE     7      -5.699  15.014  30.688  1.00  0.00              
ATOM     25  N   ALA     8      -7.345  14.849  32.225  1.00  0.00              
ATOM     26  CA  ALA     8      -7.826  13.555  31.761  1.00  0.00              
ATOM     27  C   ALA     8      -8.113  13.528  30.259  1.00  0.00              
ATOM     28  O   ALA     8      -7.595  12.666  29.537  1.00  0.00              
ATOM     29  N   ARG     9      -8.947  14.467  29.811  1.00  0.00              
ATOM     30  CA  ARG     9      -9.318  14.606  28.402  1.00  0.00              
ATOM     31  C   ARG     9      -8.070  14.457  27.508  1.00  0.00              
ATOM     32  O   ARG     9      -8.056  13.684  26.540  1.00  0.00              
ATOM     33  N   ILE    10      -7.027  15.218  27.839  1.00  0.00              
ATOM     34  CA  ILE    10      -5.769  15.188  27.101  1.00  0.00              
ATOM     35  C   ILE    10      -5.147  13.799  27.169  1.00  0.00              
ATOM     36  O   ILE    10      -4.581  13.322  26.189  1.00  0.00              
ATOM     37  N   ASN    11      -5.243  13.156  28.328  1.00  0.00              
ATOM     38  CA  ASN    11      -4.706  11.813  28.465  1.00  0.00              
ATOM     39  C   ASN    11      -5.295  10.927  27.367  1.00  0.00              
ATOM     40  O   ASN    11      -4.587  10.117  26.762  1.00  0.00              
ATOM     41  N   GLU    12      -6.595  11.087  27.110  1.00  0.00              
ATOM     42  CA  GLU    12      -7.283  10.291  26.085  1.00  0.00              
ATOM     43  C   GLU    12      -6.933  10.791  24.690  1.00  0.00              
ATOM     44  O   GLU    12      -6.867  10.020  23.729  1.00  0.00              
ATOM     45  N   LEU    13      -6.716  12.094  24.584  1.00  0.00              
ATOM     46  CA  LEU    13      -6.338  12.680  23.315  1.00  0.00              
ATOM     47  C   LEU    13      -5.000  12.041  22.945  1.00  0.00              
ATOM     48  O   LEU    13      -4.741  11.698  21.792  1.00  0.00              
ATOM     49  N   ALA    14      -4.164  11.873  23.963  1.00  0.00              
ATOM     50  CA  ALA    14      -2.842  11.284  23.818  1.00  0.00              
ATOM     51  C   ALA    14      -2.971   9.824  23.350  1.00  0.00              
ATOM     52  O   ALA    14      -2.076   9.285  22.683  1.00  0.00              
ATOM     53  N   ALA    15      -4.095   9.198  23.707  1.00  0.00              
ATOM     54  CA  ALA    15      -4.382   7.807  23.328  1.00  0.00              
ATOM     55  C   ALA    15      -4.825   7.796  21.874  1.00  0.00              
ATOM     56  O   ALA    15      -4.392   6.966  21.075  1.00  0.00              
ATOM     57  N   LYS    16      -5.712   8.728  21.550  1.00  0.00              
ATOM     58  CA  LYS    16      -6.212   8.854  20.196  1.00  0.00              
ATOM     59  C   LYS    16      -5.041   9.068  19.253  1.00  0.00              
ATOM     60  O   LYS    16      -5.082   8.632  18.105  1.00  0.00              
ATOM     61  N   ALA    17      -3.997   9.733  19.749  1.00  0.00              
ATOM     62  CA  ALA    17      -2.805  10.004  18.949  1.00  0.00              
ATOM     63  C   ALA    17      -2.141   8.700  18.533  1.00  0.00              
ATOM     64  O   ALA    17      -1.812   8.526  17.357  1.00  0.00              
ATOM     65  N   LYS    18      -1.956   7.782  19.488  1.00  0.00              
ATOM     66  CA  LYS    18      -1.312   6.491  19.202  1.00  0.00              
ATOM     67  C   LYS    18      -2.114   5.634  18.232  1.00  0.00              
ATOM     68  O   LYS    18      -1.565   4.729  17.604  1.00  0.00              
ATOM     69  N   ALA    19      -3.413   5.923  18.119  1.00  0.00              
ATOM     70  CA  ALA    19      -4.300   5.211  17.199  1.00  0.00              
ATOM     71  C   ALA    19      -3.953   5.701  15.801  1.00  0.00              
ATOM     72  O   ALA    19      -3.708   4.899  14.894  1.00  0.00              
ATOM     73  N   GLY    20      -1.302   7.026  14.868  1.00  0.00              
ATOM     74  CA  GLY    20      -0.011   6.407  14.627  1.00  0.00              
ATOM     75  C   GLY    20      -0.078   5.025  13.970  1.00  0.00              
ATOM     76  O   GLY    20       0.677   4.722  13.041  1.00  0.00              
ATOM     77  N   VAL    21      -0.983   4.185  14.445  1.00  0.00              
ATOM     78  CA  VAL    21      -1.094   2.857  13.883  1.00  0.00              
ATOM     79  C   VAL    21      -1.546   2.923  12.414  1.00  0.00              
ATOM     80  O   VAL    21      -1.144   2.097  11.584  1.00  0.00              
ATOM     81  N   ILE    22      -2.372   3.915  12.095  1.00  0.00              
ATOM     82  CA  ILE    22      -2.870   4.102  10.726  1.00  0.00              
ATOM     83  C   ILE    22      -1.727   4.617   9.840  1.00  0.00              
ATOM     84  O   ILE    22      -1.456   4.104   8.741  1.00  0.00              
ATOM     85  N   THR    23      -1.083   5.665  10.348  1.00  0.00              
ATOM     86  CA  THR    23       0.020   6.326   9.677  1.00  0.00              
ATOM     87  C   THR    23       1.126   5.351   9.308  1.00  0.00              
ATOM     88  O   THR    23       1.929   5.623   8.405  1.00  0.00              
ATOM     89  N   GLU    24       1.177   4.218  10.008  1.00  0.00              
ATOM     90  CA  GLU    24       2.182   3.233   9.682  1.00  0.00              
ATOM     91  C   GLU    24       1.741   2.528   8.408  1.00  0.00              
ATOM     92  O   GLU    24       2.533   2.359   7.469  1.00  0.00              
ATOM     93  N   GLU    25       0.470   2.132   8.364  1.00  0.00              
ATOM     94  CA  GLU    25      -0.047   1.460   7.175  1.00  0.00              
ATOM     95  C   GLU    25       0.132   2.382   5.974  1.00  0.00              
ATOM     96  O   GLU    25       0.560   1.966   4.893  1.00  0.00              
ATOM     97  N   GLU    26      -0.196   3.649   6.177  1.00  0.00              
ATOM     98  CA  GLU    26      -0.049   4.625   5.117  1.00  0.00              
ATOM     99  C   GLU    26       1.341   4.516   4.506  1.00  0.00              
ATOM    100  O   GLU    26       1.495   4.309   3.307  1.00  0.00              
ATOM    101  N   LYS    27       2.350   4.677   5.354  1.00  0.00              
ATOM    102  CA  LYS    27       3.734   4.611   4.915  1.00  0.00              
ATOM    103  C   LYS    27       4.012   3.361   4.126  1.00  0.00              
ATOM    104  O   LYS    27       4.804   3.374   3.187  1.00  0.00              
ATOM    105  N   ALA    28       3.352   2.280   4.509  1.00  0.00              
ATOM    106  CA  ALA    28       3.541   1.016   3.822  1.00  0.00              
ATOM    107  C   ALA    28       3.023   1.027   2.385  1.00  0.00              
ATOM    108  O   ALA    28       3.748   0.672   1.448  1.00  0.00              
ATOM    109  N   GLU    29       1.772   1.436   2.210  1.00  0.00              
ATOM    110  CA  GLU    29       1.188   1.487   0.878  1.00  0.00              
ATOM    111  C   GLU    29       1.901   2.498  -0.014  1.00  0.00              
ATOM    112  O   GLU    29       1.864   2.402  -1.249  1.00  0.00              
ATOM    113  N   GLN    30       2.561   3.454   0.636  1.00  0.00              
ATOM    114  CA  GLN    30       3.325   4.496  -0.040  1.00  0.00              
ATOM    115  C   GLN    30       4.633   3.910  -0.547  1.00  0.00              
ATOM    116  O   GLN    30       4.991   4.059  -1.710  1.00  0.00              
ATOM    117  N   GLN    31       5.348   3.249   0.349  1.00  0.00              
ATOM    118  CA  GLN    31       6.619   2.651   0.000  1.00  0.00              
ATOM    119  C   GLN    31       6.396   1.730  -1.179  1.00  0.00              
ATOM    120  O   GLN    31       7.238   1.632  -2.080  1.00  0.00              
ATOM    121  N   LYS    32       5.252   1.048  -1.153  1.00  0.00              
ATOM    122  CA  LYS    32       4.870   0.125  -2.216  1.00  0.00              
ATOM    123  C   LYS    32       4.632   0.911  -3.486  1.00  0.00              
ATOM    124  O   LYS    32       5.285   0.666  -4.503  1.00  0.00              
ATOM    125  N   LEU    33       3.691   1.858  -3.406  1.00  0.00              
ATOM    126  CA  LEU    33       3.340   2.717  -4.532  1.00  0.00              
ATOM    127  C   LEU    33       4.599   3.255  -5.198  1.00  0.00              
ATOM    128  O   LEU    33       4.652   3.404  -6.421  1.00  0.00              
ATOM    129  N   ARG    34       5.607   3.549  -4.383  1.00  0.00              
ATOM    130  CA  ARG    34       6.879   4.068  -4.869  1.00  0.00              
ATOM    131  C   ARG    34       7.615   3.017  -5.674  1.00  0.00              
ATOM    132  O   ARG    34       8.079   3.275  -6.786  1.00  0.00              
ATOM    133  N   GLN    35       7.719   1.824  -5.107  1.00  0.00              
ATOM    134  CA  GLN    35       8.403   0.744  -5.791  1.00  0.00              
ATOM    135  C   GLN    35       7.685   0.467  -7.116  1.00  0.00              
ATOM    136  O   GLN    35       8.296   0.068  -8.106  1.00  0.00              
ATOM    137  N   GLU    36       6.378   0.700  -7.123  1.00  0.00              
ATOM    138  CA  GLU    36       5.576   0.479  -8.310  1.00  0.00              
ATOM    139  C   GLU    36       6.079   1.310  -9.463  1.00  0.00              
ATOM    140  O   GLU    36       6.206   0.818 -10.592  1.00  0.00              
ATOM    141  N   TYR    37       6.350   2.580  -9.185  1.00  0.00              
ATOM    142  CA  TYR    37       6.828   3.469 -10.221  1.00  0.00              
ATOM    143  C   TYR    37       8.307   3.361 -10.480  1.00  0.00              
ATOM    144  O   TYR    37       8.776   3.714 -11.565  1.00  0.00              
ATOM    145  N   LEU    38       9.046   2.855  -9.497  1.00  0.00              
ATOM    146  CA  LEU    38      10.470   2.690  -9.698  1.00  0.00              
ATOM    147  C   LEU    38      10.547   1.807 -10.921  1.00  0.00              
ATOM    148  O   LEU    38      11.400   1.983 -11.792  1.00  0.00              
ATOM    149  N   LYS    39       9.617   0.860 -10.972  1.00  0.00              
ATOM    150  CA  LYS    39       9.528  -0.088 -12.064  1.00  0.00              
ATOM    151  C   LYS    39       9.311   0.625 -13.382  1.00  0.00              
ATOM    152  O   LYS    39       9.971   0.325 -14.378  1.00  0.00              
ATOM    153  N   GLY    40       8.389   1.577 -13.386  1.00  0.00              
ATOM    154  CA  GLY    40       8.093   2.324 -14.595  1.00  0.00              
ATOM    155  C   GLY    40       9.258   3.221 -15.036  1.00  0.00              
ATOM    156  O   GLY    40       9.338   3.609 -16.211  1.00  0.00              
END
