
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL242_1-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      A       5           -
LGA    K       6      K       6           -
LGA    -       -      I       7           -
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    I       7      L      13           #
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    A       8      K      16          4.227
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    R       9      A      19          2.118
LGA    I      10      G      20          1.984
LGA    N      11      V      21          1.219
LGA    E      12      I      22          3.290
LGA    L      13      T      23          3.752
LGA    A      14      E      24          0.994
LGA    A      15      E      25          4.975
LGA    -       -      E      26           -
LGA    K      16      K      27          3.020
LGA    A      17      A      28          4.401
LGA    -       -      E      29           -
LGA    K      18      Q      30          1.807
LGA    -       -      Q      31           -
LGA    -       -      K      32           -
LGA    A      19      L      33          1.501
LGA    G      20      R      34          0.917
LGA    -       -      Q      35           -
LGA    V      21      E      36          3.704
LGA    I      22      Y      37          4.729
LGA    T      23      L      38          4.136
LGA    E      24      -       -           -
LGA    E      25      -       -           -
LGA    E      26      -       -           -
LGA    K      27      -       -           -
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      K      39          3.858
LGA    Q      31      G      40          3.744
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    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     18    3.29    11.11     29.191     0.530

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.087359 * X  +   0.873252 * Y  +  -0.479374 * Z  +  11.128103
  Y_new =   0.440047 * X  +   0.397891 * Y  +   0.805010 * Z  +   2.588809
  Z_new =   0.893715 * X  +  -0.281272 * Y  +  -0.349513 * Z  +  -3.761244 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.463958    0.677634  [ DEG:  -141.1744     38.8256 ]
  Theta =  -1.105559   -2.036033  [ DEG:   -63.3439   -116.6561 ]
  Phi   =   1.374821   -1.766771  [ DEG:    78.7715   -101.2285 ]
 
# 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_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL242_1-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   3.29   11.11  29.191
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL242_1-D1
REMARK Aligment from pdb entry: 1d4b_A
ATOM     17  N   ALA     5     -20.059  -2.517   1.517  1.00  0.00              
ATOM     18  CA  ALA     5     -20.055  -1.077   1.914  1.00  0.00              
ATOM     19  C   ALA     5     -19.148  -0.865   3.131  1.00  0.00              
ATOM     20  O   ALA     5     -19.615  -0.692   4.243  1.00  0.00              
ATOM     21  N   LYS     6     -17.858  -0.876   2.930  1.00  0.00              
ATOM     22  CA  LYS     6     -16.919  -0.673   4.072  1.00  0.00              
ATOM     23  C   LYS     6     -16.924  -1.911   4.968  1.00  0.00              
ATOM     24  O   LYS     6     -17.945  -2.295   5.508  1.00  0.00              
ATOM     25  N   ILE     7     -15.792  -2.541   5.132  1.00  0.00              
ATOM     26  CA  ILE     7     -15.727  -3.756   5.995  1.00  0.00              
ATOM     27  C   ILE     7     -14.489  -3.711   6.895  1.00  0.00              
ATOM     28  O   ILE     7     -14.534  -4.103   8.045  1.00  0.00              
ATOM     29  N   ALA     8     -13.382  -3.236   6.384  1.00  0.00              
ATOM     30  CA  ALA     8     -12.144  -3.169   7.216  1.00  0.00              
ATOM     31  C   ALA     8     -11.517  -1.773   7.129  1.00  0.00              
ATOM     32  O   ALA     8     -10.314  -1.628   7.042  1.00  0.00              
ATOM     33  N   ARG     9     -12.326  -0.746   7.156  1.00  0.00              
ATOM     34  CA  ARG     9     -11.778   0.640   7.076  1.00  0.00              
ATOM     35  C   ARG     9     -10.945   0.951   8.324  1.00  0.00              
ATOM     36  O   ARG     9     -11.405   0.811   9.441  1.00  0.00              
ATOM     37  N   ILE    10      -9.722   1.376   8.141  1.00  0.00              
ATOM     38  CA  ILE    10      -8.858   1.698   9.314  1.00  0.00              
ATOM     39  C   ILE    10      -8.638   3.211   9.406  1.00  0.00              
ATOM     40  O   ILE    10      -8.617   3.906   8.409  1.00  0.00              
ATOM     41  N   ASN    11      -8.474   3.725  10.597  1.00  0.00              
ATOM     42  CA  ASN    11      -8.256   5.193  10.755  1.00  0.00              
ATOM     43  C   ASN    11      -6.965   5.458  11.532  1.00  0.00              
ATOM     44  O   ASN    11      -6.863   6.416  12.274  1.00  0.00              
ATOM     45  N   GLU    12      -5.978   4.618  11.368  1.00  0.00              
ATOM     46  CA  GLU    12      -4.693   4.824  12.098  1.00  0.00              
ATOM     47  C   GLU    12      -4.046   6.141  11.664  1.00  0.00              
ATOM     48  O   GLU    12      -4.183   6.566  10.534  1.00  0.00              
ATOM     49  N   LEU    13      -3.342   6.790  12.554  1.00  0.00              
ATOM     50  CA  LEU    13      -2.688   8.082  12.192  1.00  0.00              
ATOM     51  C   LEU    13      -1.584   7.848  11.151  1.00  0.00              
ATOM     52  O   LEU    13      -1.597   8.456  10.099  1.00  0.00              
ATOM     53  N   ALA    14      -0.660   6.974  11.473  1.00  0.00              
ATOM     54  CA  ALA    14       0.449   6.677  10.535  1.00  0.00              
ATOM     55  C   ALA    14      -0.053   5.807   9.376  1.00  0.00              
ATOM     56  O   ALA    14      -0.901   4.959   9.564  1.00  0.00              
ATOM     57  N   ALA    15       0.488   6.048   8.206  1.00  0.00              
ATOM     58  CA  ALA    15       0.079   5.268   7.012  1.00  0.00              
ATOM     59  C   ALA    15       0.678   3.855   7.068  1.00  0.00              
ATOM     60  O   ALA    15       1.802   3.680   7.492  1.00  0.00              
ATOM     61  N   LYS    16      -0.095   2.888   6.632  1.00  0.00              
ATOM     62  CA  LYS    16       0.379   1.483   6.639  1.00  0.00              
ATOM     63  C   LYS    16       1.399   1.259   5.518  1.00  0.00              
ATOM     64  O   LYS    16       1.340   1.886   4.479  1.00  0.00              
ATOM     65  N   ALA    17       2.332   0.368   5.720  1.00  0.00              
ATOM     66  CA  ALA    17       3.353   0.100   4.666  1.00  0.00              
ATOM     67  C   ALA    17       2.692  -0.545   3.444  1.00  0.00              
ATOM     68  O   ALA    17       2.072  -1.586   3.542  1.00  0.00              
ATOM     69  N   LYS    18       2.817   0.068   2.297  1.00  0.00              
ATOM     70  CA  LYS    18       2.192  -0.509   1.071  1.00  0.00              
ATOM     71  C   LYS    18       3.196  -0.500  -0.091  1.00  0.00              
ATOM     72  O   LYS    18       3.940   0.447  -0.254  1.00  0.00              
ATOM     73  N   ALA    19       3.189  -1.559  -0.866  1.00  0.00              
ATOM     74  CA  ALA    19       4.116  -1.656  -2.020  1.00  0.00              
ATOM     75  C   ALA    19       3.687  -0.700  -3.137  1.00  0.00              
ATOM     76  O   ALA    19       2.824  -1.010  -3.934  1.00  0.00              
ATOM     77  N   GLY    20       4.285   0.461  -3.198  1.00  0.00              
ATOM     78  CA  GLY    20       3.913   1.439  -4.261  1.00  0.00              
ATOM     79  C   GLY    20       4.875   1.323  -5.446  1.00  0.00              
ATOM     80  O   GLY    20       6.062   1.115  -5.278  1.00  0.00              
ATOM     81  N   VAL    21       4.372   1.456  -6.645  1.00  0.00              
ATOM     82  CA  VAL    21       5.253   1.354  -7.845  1.00  0.00              
ATOM     83  C   VAL    21       5.549   2.749  -8.403  1.00  0.00              
ATOM     84  O   VAL    21       4.659   3.455  -8.838  1.00  0.00              
ATOM     85  N   ILE    22       6.792   3.149  -8.395  1.00  0.00              
ATOM     86  CA  ILE    22       7.151   4.497  -8.926  1.00  0.00              
ATOM     87  C   ILE    22       7.833   4.362 -10.290  1.00  0.00              
ATOM     88  O   ILE    22       8.710   3.541 -10.477  1.00  0.00              
ATOM     89  N   THR    23       7.436   5.163 -11.244  1.00  0.00              
ATOM     90  CA  THR    23       8.060   5.083 -12.597  1.00  0.00              
ATOM     91  C   THR    23       8.494   6.477 -13.058  1.00  0.00              
ATOM     92  O   THR    23       7.828   7.459 -12.802  1.00  0.00              
ATOM     93  N   GLU    24       9.607   6.569 -13.736  1.00  0.00              
ATOM     94  CA  GLU    24      10.087   7.901 -14.212  1.00  0.00              
ATOM     95  C   GLU    24       9.333   8.313 -15.480  1.00  0.00              
ATOM     96  O   GLU    24       8.500   7.581 -15.977  1.00  0.00              
ATOM     97  N   GLU    25       9.604   9.493 -15.986  1.00  0.00              
ATOM     98  CA  GLU    25       8.896   9.990 -17.212  1.00  0.00              
ATOM     99  C   GLU    25       8.589   8.847 -18.198  1.00  0.00              
ATOM    100  O   GLU    25       7.517   8.275 -18.165  1.00  0.00              
ATOM    101  N   GLU    26       9.502   8.508 -19.079  1.00  0.00              
ATOM    102  CA  GLU    26       9.210   7.404 -20.044  1.00  0.00              
ATOM    103  C   GLU    26       9.699   6.053 -19.506  1.00  0.00              
ATOM    104  O   GLU    26       8.912   5.195 -19.158  1.00  0.00              
ATOM    105  N   LYS    27      10.991   5.856 -19.438  1.00  0.00              
ATOM    106  CA  LYS    27      11.522   4.556 -18.924  1.00  0.00              
ATOM    107  C   LYS    27      12.925   4.726 -18.326  1.00  0.00              
ATOM    108  O   LYS    27      13.640   3.762 -18.133  1.00  0.00              
ATOM    109  N   ALA    28      13.337   5.935 -18.044  1.00  0.00              
ATOM    110  CA  ALA    28      14.706   6.141 -17.478  1.00  0.00              
ATOM    111  C   ALA    28      14.881   5.337 -16.184  1.00  0.00              
ATOM    112  O   ALA    28      15.824   4.582 -16.036  1.00  0.00              
ATOM    113  N   GLU    29      13.985   5.492 -15.247  1.00  0.00              
ATOM    114  CA  GLU    29      14.105   4.733 -13.966  1.00  0.00              
ATOM    115  C   GLU    29      12.763   4.091 -13.601  1.00  0.00              
ATOM    116  O   GLU    29      11.720   4.709 -13.701  1.00  0.00              
ATOM    117  N   GLN    30      12.783   2.856 -13.175  1.00  0.00              
ATOM    118  CA  GLN    30      11.513   2.170 -12.800  1.00  0.00              
ATOM    119  C   GLN    30      11.726   1.316 -11.547  1.00  0.00              
ATOM    120  O   GLN    30      12.273   0.232 -11.610  1.00  0.00              
ATOM    121  N   GLN    31      11.299   1.797 -10.409  1.00  0.00              
ATOM    122  CA  GLN    31      11.478   1.011  -9.153  1.00  0.00              
ATOM    123  C   GLN    31      10.185   1.028  -8.332  1.00  0.00              
ATOM    124  O   GLN    31       9.517   2.039  -8.229  1.00  0.00              
ATOM    125  N   LYS    32       9.827  -0.084  -7.747  1.00  0.00              
ATOM    126  CA  LYS    32       8.578  -0.133  -6.933  1.00  0.00              
ATOM    127  C   LYS    32       8.872  -0.796  -5.586  1.00  0.00              
ATOM    128  O   LYS    32       9.063  -1.994  -5.503  1.00  0.00              
ATOM    129  N   LEU    33       8.911  -0.027  -4.533  1.00  0.00              
ATOM    130  CA  LEU    33       9.193  -0.611  -3.189  1.00  0.00              
ATOM    131  C   LEU    33       8.129  -0.166  -2.181  1.00  0.00              
ATOM    132  O   LEU    33       7.399   0.777  -2.412  1.00  0.00              
ATOM    133  N   ARG    34       8.040  -0.838  -1.065  1.00  0.00              
ATOM    134  CA  ARG    34       7.025  -0.455  -0.039  1.00  0.00              
ATOM    135  C   ARG    34       7.526   0.741   0.776  1.00  0.00              
ATOM    136  O   ARG    34       8.621   0.728   1.303  1.00  0.00              
ATOM    137  N   GLN    35       6.732   1.773   0.881  1.00  0.00              
ATOM    138  CA  GLN    35       7.163   2.970   1.661  1.00  0.00              
ATOM    139  C   GLN    35       6.010   3.481   2.529  1.00  0.00              
ATOM    140  O   GLN    35       4.854   3.375   2.168  1.00  0.00              
ATOM    141  N   GLU    36       6.319   4.039   3.667  1.00  0.00              
ATOM    142  CA  GLU    36       5.247   4.563   4.564  1.00  0.00              
ATOM    143  C   GLU    36       5.588   5.990   5.003  1.00  0.00              
ATOM    144  O   GLU    36       6.378   6.200   5.901  1.00  0.00              
ATOM    145  N   TYR    37       4.998   6.971   4.372  1.00  0.00              
ATOM    146  CA  TYR    37       5.292   8.384   4.748  1.00  0.00              
ATOM    147  C   TYR    37       4.102   9.286   4.406  1.00  0.00              
ATOM    148  O   TYR    37       3.445   9.107   3.397  1.00  0.00              
ATOM    149  N   LEU    38       3.816  10.251   5.239  1.00  0.00              
ATOM    150  CA  LEU    38       2.664  11.161   4.966  1.00  0.00              
ATOM    151  C   LEU    38       3.116  12.385   4.157  1.00  0.00              
ATOM    152  O   LEU    38       2.882  12.470   2.966  1.00  0.00              
ATOM    153  N   LYS    39       3.747  13.337   4.793  1.00  0.00              
ATOM    154  CA  LYS    39       4.198  14.558   4.062  1.00  0.00              
ATOM    155  C   LYS    39       5.615  14.370   3.510  1.00  0.00              
ATOM    156  O   LYS    39       5.893  14.697   2.373  1.00  0.00              
ATOM    157  N   GLY    40       6.512  13.851   4.304  1.00  0.00              
ATOM    158  CA  GLY    40       7.910  13.649   3.822  1.00  0.00              
ATOM    159  C   GLY    40       7.934  12.713   2.608  1.00  0.00              
ATOM    160  O   GLY    40       8.903  12.658   1.876  1.00  0.00              
END
