
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0335AL381_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL381_5-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           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    E      26      V      21          2.959
LGA    K      27      I      22          3.507
LGA    A      28      T      23          1.803
LGA    E      29      E      24          2.417
LGA    Q      30      E      25          2.222
LGA    Q      31      E      26          2.003
LGA    -       -      K      27           -
LGA    K      32      A      28          1.386
LGA    -       -      E      29           -
LGA    -       -      Q      30           -
LGA    L      33      Q      31          1.418
LGA    R      34      K      32          3.511
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    Q      35      Q      35          2.206
LGA    E      36      E      36          1.781
LGA    -       -      Y      37           -
LGA    Y      37      L      38          3.045
LGA    L      38      K      39          3.241
LGA    K      39      G      40          5.174
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   36    5.0     14    2.80    21.43     29.509     0.482

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.724827 * X  +   0.354397 * Y  +  -0.590786 * Z  +  24.280092
  Y_new =   0.688820 * X  +  -0.388177 * Y  +   0.612246 * Z  + -44.397419
  Z_new =  -0.012351 * X  +  -0.850718 * Y  +  -0.525477 * Z  + -16.080978 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.124119    1.017473  [ DEG:  -121.7031     58.2969 ]
  Theta =   0.012351    3.129241  [ DEG:     0.7077    179.2923 ]
  Phi   =   0.759933   -2.381660  [ DEG:    43.5409   -136.4591 ]
 
# 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_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_5-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   36   5.0   14   2.80   21.43  29.509
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_5-D1
REMARK Aligment from pdb entry: 1qw7A
ATOM      1  N   GLU    26      -8.368   3.816  12.415  1.00  0.00              
ATOM      2  CA  GLU    26      -7.514   4.346  13.459  1.00  0.00              
ATOM      3  C   GLU    26      -6.069   3.936  13.403  1.00  0.00              
ATOM      4  O   GLU    26      -5.399   3.971  14.422  1.00  0.00              
ATOM      5  N   LYS    27      -5.557   3.587  12.226  1.00  0.00              
ATOM      6  CA  LYS    27      -4.164   3.171  12.130  1.00  0.00              
ATOM      7  C   LYS    27      -3.291   4.052  11.274  1.00  0.00              
ATOM      8  O   LYS    27      -2.380   3.569  10.631  1.00  0.00              
ATOM      9  N   ALA    28      -3.552   5.353  11.261  1.00  0.00              
ATOM     10  CA  ALA    28      -2.744   6.240  10.429  1.00  0.00              
ATOM     11  C   ALA    28      -1.258   6.073  10.679  1.00  0.00              
ATOM     12  O   ALA    28      -0.480   6.138   9.754  1.00  0.00              
ATOM     13  N   GLU    29      -0.863   5.824  11.926  1.00  0.00              
ATOM     14  CA  GLU    29       0.555   5.672  12.269  1.00  0.00              
ATOM     15  C   GLU    29       1.229   4.419  11.726  1.00  0.00              
ATOM     16  O   GLU    29       2.459   4.336  11.727  1.00  0.00              
ATOM     17  N   GLN    30       0.424   3.473  11.241  1.00  0.00              
ATOM     18  CA  GLN    30       0.912   2.177  10.759  1.00  0.00              
ATOM     19  C   GLN    30       1.038   2.087   9.255  1.00  0.00              
ATOM     20  O   GLN    30       1.452   1.061   8.740  1.00  0.00              
ATOM     21  N   GLN    31       0.642   3.138   8.565  1.00  0.00              
ATOM     22  CA  GLN    31       0.655   3.129   7.100  1.00  0.00              
ATOM     23  C   GLN    31       1.911   3.703   6.469  1.00  0.00              
ATOM     24  O   GLN    31       2.418   4.727   6.921  1.00  0.00              
ATOM     25  N   LYS    32       2.404   3.034   5.423  1.00  0.00              
ATOM     26  CA  LYS    32       3.557   3.512   4.657  1.00  0.00              
ATOM     27  C   LYS    32       3.070   3.415   3.200  1.00  0.00              
ATOM     28  O   LYS    32       2.467   2.426   2.791  1.00  0.00              
ATOM     29  N   LEU    33       3.319   4.456   2.425  1.00  0.00              
ATOM     30  CA  LEU    33       2.820   4.486   1.065  1.00  0.00              
ATOM     31  C   LEU    33       3.938   4.577   0.054  1.00  0.00              
ATOM     32  O   LEU    33       4.957   5.233   0.305  1.00  0.00              
ATOM     33  N   ARG    34       3.756   3.938  -1.100  1.00  0.00              
ATOM     34  CA  ARG    34       4.772   4.017  -2.144  1.00  0.00              
ATOM     35  C   ARG    34       4.203   3.663  -3.525  1.00  0.00              
ATOM     36  O   ARG    34       3.004   3.409  -3.638  1.00  0.00              
ATOM     37  N   GLN    35       5.051   3.676  -4.555  1.00  0.00              
ATOM     38  CA  GLN    35       4.634   3.429  -5.949  1.00  0.00              
ATOM     39  C   GLN    35       5.173   2.104  -6.448  1.00  0.00              
ATOM     40  O   GLN    35       4.664   1.559  -7.417  1.00  0.00              
ATOM     41  N   GLU    36       6.224   1.589  -5.813  1.00  0.00              
ATOM     42  CA  GLU    36       6.841   0.352  -6.297  1.00  0.00              
ATOM     43  C   GLU    36       7.144   0.557  -7.790  1.00  0.00              
ATOM     44  O   GLU    36       6.808  -0.270  -8.636  1.00  0.00              
ATOM     45  N   TYR    37       7.768   1.693  -8.093  1.00  0.00              
ATOM     46  CA  TYR    37       8.152   2.041  -9.449  1.00  0.00              
ATOM     47  C   TYR    37       9.618   1.666  -9.739  1.00  0.00              
ATOM     48  O   TYR    37      10.329   1.163  -8.882  1.00  0.00              
ATOM     49  N   LEU    38      10.051   1.917 -10.967  1.00  0.00              
ATOM     50  CA  LEU    38      11.418   1.643 -11.398  1.00  0.00              
ATOM     51  C   LEU    38      11.647   2.373 -12.721  1.00  0.00              
ATOM     52  O   LEU    38      10.708   2.951 -13.284  1.00  0.00              
ATOM     53  N   LYS    39      12.882   2.357 -13.203  1.00  0.00              
ATOM     54  CA  LYS    39      13.220   3.077 -14.416  1.00  0.00              
ATOM     55  C   LYS    39      13.794   2.118 -15.432  1.00  0.00              
ATOM     56  O   LYS    39      13.968   2.462 -16.595  1.00  0.00              
ATOM     57  N   GLY    40      14.045   0.897 -14.964  1.00  0.00              
ATOM     58  CA  GLY    40      14.543  -0.188 -15.804  1.00  0.00              
ATOM     59  C   GLY    40      13.915  -1.454 -15.222  1.00  0.00              
ATOM     60  O   GLY    40      13.822  -1.560 -14.000  1.00  0.00              
END
