
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0335AL381_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL381_3-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    A       8      N      11          0.751
LGA    R       9      E      12          0.725
LGA    I      10      L      13          1.461
LGA    N      11      A      14          1.496
LGA    E      12      A      15          1.088
LGA    L      13      K      16          0.598
LGA    A      14      A      17          1.092
LGA    A      15      K      18          1.803
LGA    K      16      A      19          2.024
LGA    A      17      G      20          1.493
LGA    K      18      V      21          0.939
LGA    A      19      I      22          2.210
LGA    G      20      T      23          2.128
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    V      21      E      26          2.242
LGA    I      22      K      27          2.306
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    T      23      Q      30          1.637
LGA    -       -      Q      31           -
LGA    E      24      K      32          3.214
LGA    E      25      L      33          3.873
LGA    E      26      -       -           -
LGA    K      27      -       -           -
LGA    A      28      -       -           -
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      R      34           #
LGA    K      39      Q      35          5.232
LGA    G      40      E      36          2.049
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)   33   36    5.0     20    2.21     5.00     47.308     0.864

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.808820 * X  +   0.422538 * Y  +  -0.408989 * Z  + -14.851705
  Y_new =  -0.563518 * X  +   0.755724 * Y  +  -0.333659 * Z  +  29.424236
  Z_new =   0.168099 * X  +   0.500343 * Y  +   0.849353 * Z  + -21.517591 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.532357   -2.609236  [ DEG:    30.5018   -149.4982 ]
  Theta =  -0.168900   -2.972692  [ DEG:    -9.6773   -170.3227 ]
  Phi   =  -0.608519    2.533074  [ DEG:   -34.8656    145.1344 ]
 
# 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_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33   36   5.0   20   2.21    5.00  47.308
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_3-D1
REMARK Aligment from pdb entry: 1dpmA
ATOM      1  N   ALA     8      -4.419  -2.043  -2.822  1.00  0.00              
ATOM      2  CA  ALA     8      -5.843  -1.761  -2.792  1.00  0.00              
ATOM      3  C   ALA     8      -6.439  -2.403  -1.532  1.00  0.00              
ATOM      4  O   ALA     8      -7.375  -1.921  -0.971  1.00  0.00              
ATOM      5  N   ARG     9      -5.872  -3.520  -1.091  1.00  0.00              
ATOM      6  CA  ARG     9      -6.356  -4.168   0.087  1.00  0.00              
ATOM      7  C   ARG     9      -6.025  -3.339   1.305  1.00  0.00              
ATOM      8  O   ARG     9      -6.869  -3.134   2.200  1.00  0.00              
ATOM      9  N   ILE    10      -4.795  -2.847   1.317  1.00  0.00              
ATOM     10  CA  ILE    10      -4.305  -2.007   2.404  1.00  0.00              
ATOM     11  C   ILE    10      -5.165  -0.760   2.486  1.00  0.00              
ATOM     12  O   ILE    10      -5.581  -0.306   3.548  1.00  0.00              
ATOM     13  N   ASN    11      -5.425  -0.178   1.311  1.00  0.00              
ATOM     14  CA  ASN    11      -6.228   1.009   1.265  1.00  0.00              
ATOM     15  C   ASN    11      -7.613   0.809   1.844  1.00  0.00              
ATOM     16  O   ASN    11      -8.090   1.612   2.606  1.00  0.00              
ATOM     17  N   GLU    12      -8.262  -0.289   1.488  1.00  0.00              
ATOM     18  CA  GLU    12      -9.619  -0.622   1.968  1.00  0.00              
ATOM     19  C   GLU    12      -9.725  -0.857   3.488  1.00  0.00              
ATOM     20  O   GLU    12     -10.586  -0.334   4.179  1.00  0.00              
ATOM     21  N   LEU    13      -8.852  -1.655   4.051  1.00  0.00              
ATOM     22  CA  LEU    13      -8.941  -1.835   5.481  1.00  0.00              
ATOM     23  C   LEU    13      -8.475  -0.565   6.194  1.00  0.00              
ATOM     24  O   LEU    13      -8.908  -0.290   7.289  1.00  0.00              
ATOM     25  N   ALA    14      -7.568   0.219   5.579  1.00  0.00              
ATOM     26  CA  ALA    14      -7.138   1.410   6.272  1.00  0.00              
ATOM     27  C   ALA    14      -8.281   2.378   6.523  1.00  0.00              
ATOM     28  O   ALA    14      -8.385   2.994   7.587  1.00  0.00              
ATOM     29  N   ALA    15      -9.109   2.511   5.501  1.00  0.00              
ATOM     30  CA  ALA    15     -10.279   3.391   5.452  1.00  0.00              
ATOM     31  C   ALA    15     -11.358   2.949   6.469  1.00  0.00              
ATOM     32  O   ALA    15     -11.906   3.739   7.241  1.00  0.00              
ATOM     33  N   LYS    16     -11.592   1.665   6.452  1.00  0.00              
ATOM     34  CA  LYS    16     -12.561   0.970   7.252  1.00  0.00              
ATOM     35  C   LYS    16     -12.214   0.922   8.726  1.00  0.00              
ATOM     36  O   LYS    16     -13.081   1.098   9.542  1.00  0.00              
ATOM     37  N   ALA    17     -10.962   0.702   9.077  1.00  0.00              
ATOM     38  CA  ALA    17     -10.529   0.644  10.508  1.00  0.00              
ATOM     39  C   ALA    17     -10.111   1.964  11.066  1.00  0.00              
ATOM     40  O   ALA    17      -9.871   2.072  12.262  1.00  0.00              
ATOM     41  N   LYS    18      -9.965   2.952  10.172  1.00  0.00              
ATOM     42  CA  LYS    18      -9.526   4.273  10.522  1.00  0.00              
ATOM     43  C   LYS    18      -8.135   4.269  11.146  1.00  0.00              
ATOM     44  O   LYS    18      -7.857   4.870  12.174  1.00  0.00              
ATOM     45  N   ALA    19      -7.234   3.541  10.518  1.00  0.00              
ATOM     46  CA  ALA    19      -5.867   3.502  10.985  1.00  0.00              
ATOM     47  C   ALA    19      -4.940   3.863   9.809  1.00  0.00              
ATOM     48  O   ALA    19      -5.163   3.396   8.669  1.00  0.00              
ATOM     49  N   GLY    20      -3.907   4.675  10.066  1.00  0.00              
ATOM     50  CA  GLY    20      -3.021   5.013   9.005  1.00  0.00              
ATOM     51  C   GLY    20      -2.145   3.787   8.658  1.00  0.00              
ATOM     52  O   GLY    20      -1.684   3.004   9.508  1.00  0.00              
ATOM     53  N   VAL    21      -1.905   3.604   7.391  1.00  0.00              
ATOM     54  CA  VAL    21      -1.057   2.513   6.951  1.00  0.00              
ATOM     55  C   VAL    21       0.004   3.047   6.007  1.00  0.00              
ATOM     56  O   VAL    21      -0.309   3.707   5.022  1.00  0.00              
ATOM     57  N   ILE    22       1.249   2.774   6.344  1.00  0.00              
ATOM     58  CA  ILE    22       2.403   3.103   5.533  1.00  0.00              
ATOM     59  C   ILE    22       2.813   1.861   4.734  1.00  0.00              
ATOM     60  O   ILE    22       2.996   0.793   5.307  1.00  0.00              
ATOM     61  N   THR    23       2.858   2.014   3.391  1.00  0.00              
ATOM     62  CA  THR    23       3.214   0.958   2.407  1.00  0.00              
ATOM     63  C   THR    23       4.734   0.928   2.161  1.00  0.00              
ATOM     64  O   THR    23       5.466   1.903   2.443  1.00  0.00              
ATOM     65  N   GLU    24       5.208  -0.223   1.675  1.00  0.00              
ATOM     66  CA  GLU    24       6.623  -0.376   1.459  1.00  0.00              
ATOM     67  C   GLU    24       6.989  -0.786   0.050  1.00  0.00              
ATOM     68  O   GLU    24       6.200  -1.325  -0.729  1.00  0.00              
ATOM     69  N   GLU    25       8.237  -0.534  -0.244  1.00  0.00              
ATOM     70  CA  GLU    25       8.797  -0.949  -1.473  1.00  0.00              
ATOM     71  C   GLU    25       9.986  -1.784  -1.014  1.00  0.00              
ATOM     72  O   GLU    25      10.174  -1.954   0.215  1.00  0.00              
ATOM     73  N   GLU    26      10.752  -2.327  -1.974  1.00  0.00              
ATOM     74  CA  GLU    26      11.909  -3.130  -1.662  1.00  0.00              
ATOM     75  C   GLU    26      11.662  -4.550  -2.070  1.00  0.00              
ATOM     76  O   GLU    26      10.770  -4.833  -2.874  1.00  0.00              
ATOM     77  N   LYS    27      12.462  -5.453  -1.521  1.00  0.00              
ATOM     78  CA  LYS    27      12.272  -6.852  -1.859  1.00  0.00              
ATOM     79  C   LYS    27      12.635  -7.660  -0.657  1.00  0.00              
ATOM     80  O   LYS    27      13.511  -7.255   0.123  1.00  0.00              
ATOM     81  N   ALA    28      17.590  -8.638 -12.578  1.00  0.00              
ATOM     82  CA  ALA    28      17.871  -7.230 -12.750  1.00  0.00              
ATOM     83  C   ALA    28      19.175  -6.775 -12.157  1.00  0.00              
ATOM     84  O   ALA    28      19.739  -7.388 -11.245  1.00  0.00              
ATOM     85  N   GLU    29      19.630  -5.632 -12.665  1.00  0.00              
ATOM     86  CA  GLU    29      20.875  -5.020 -12.189  1.00  0.00              
ATOM     87  C   GLU    29      20.578  -4.062 -11.062  1.00  0.00              
ATOM     88  O   GLU    29      19.407  -3.713 -10.814  1.00  0.00              
ATOM     89  N   GLN    30      21.631  -3.644 -10.367  1.00  0.00              
ATOM     90  CA  GLN    30      21.452  -2.717  -9.268  1.00  0.00              
ATOM     91  C   GLN    30      20.749  -1.464  -9.815  1.00  0.00              
ATOM     92  O   GLN    30      19.837  -0.938  -9.231  1.00  0.00              
ATOM     93  N   GLN    31      21.145  -1.019 -10.994  1.00  0.00              
ATOM     94  CA  GLN    31      20.544   0.133 -11.582  1.00  0.00              
ATOM     95  C   GLN    31      19.056  -0.072 -11.905  1.00  0.00              
ATOM     96  O   GLN    31      18.265   0.817 -11.691  1.00  0.00              
ATOM     97  N   LYS    32      18.667  -1.246 -12.410  1.00  0.00              
ATOM     98  CA  LYS    32      17.276  -1.448 -12.703  1.00  0.00              
ATOM     99  C   LYS    32      16.473  -1.553 -11.423  1.00  0.00              
ATOM    100  O   LYS    32      15.378  -1.029 -11.339  1.00  0.00              
ATOM    101  N   LEU    33      17.037  -2.235 -10.436  1.00  0.00              
ATOM    102  CA  LEU    33      16.361  -2.369  -9.168  1.00  0.00              
ATOM    103  C   LEU    33      16.115  -0.977  -8.560  1.00  0.00              
ATOM    104  O   LEU    33      15.002  -0.673  -8.139  1.00  0.00              
ATOM    105  N   ARG    34      17.145  -0.108  -8.558  1.00  0.00              
ATOM    106  CA  ARG    34      17.020   1.257  -8.024  1.00  0.00              
ATOM    107  C   ARG    34      15.841   1.972  -8.667  1.00  0.00              
ATOM    108  O   ARG    34      15.051   2.660  -8.012  1.00  0.00              
ATOM    109  N   GLN    35      15.718   1.792  -9.978  1.00  0.00              
ATOM    110  CA  GLN    35      14.623   2.424 -10.695  1.00  0.00              
ATOM    111  C   GLN    35      13.254   1.911 -10.208  1.00  0.00              
ATOM    112  O   GLN    35      12.304   2.648 -10.052  1.00  0.00              
ATOM    113  N   GLU    36      13.149   0.625  -9.992  1.00  0.00              
ATOM    114  CA  GLU    36      11.881   0.093  -9.560  1.00  0.00              
ATOM    115  C   GLU    36      11.487   0.709  -8.218  1.00  0.00              
ATOM    116  O   GLU    36      10.384   1.209  -8.025  1.00  0.00              
ATOM    117  N   TYR    37      12.442   0.698  -7.295  1.00  0.00              
ATOM    118  CA  TYR    37      12.248   1.250  -5.975  1.00  0.00              
ATOM    119  C   TYR    37      11.807   2.667  -6.017  1.00  0.00              
ATOM    120  O   TYR    37      10.876   3.059  -5.291  1.00  0.00              
ATOM    121  N   LEU    38      12.474   3.454  -6.857  1.00  0.00              
ATOM    122  CA  LEU    38      12.121   4.867  -6.962  1.00  0.00              
ATOM    123  C   LEU    38      10.727   5.037  -7.521  1.00  0.00              
ATOM    124  O   LEU    38       9.980   5.952  -7.165  1.00  0.00              
ATOM    125  N   LYS    39      10.412   4.158  -8.445  1.00  0.00              
ATOM    126  CA  LYS    39       9.107   4.190  -9.081  1.00  0.00              
ATOM    127  C   LYS    39       7.976   4.126  -8.052  1.00  0.00              
ATOM    128  O   LYS    39       7.010   4.908  -8.095  1.00  0.00              
ATOM    129  N   GLY    40       8.092   3.109  -7.155  1.00  0.00              
ATOM    130  CA  GLY    40       7.122   2.834  -6.103  1.00  0.00              
ATOM    131  C   GLY    40       7.010   3.952  -5.107  1.00  0.00              
ATOM    132  O   GLY    40       5.937   4.258  -4.614  1.00  0.00              
END
