
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0335AL333_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL333_5-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          4.128
LGA    A       8      A       8          1.561
LGA    R       9      R       9          3.059
LGA    I      10      I      10          4.100
LGA    N      11      N      11          4.889
LGA    K      16      E      12          4.182
LGA    A      17      -       -           -
LGA    K      18      -       -           -
LGA    A      19      L      13          2.731
LGA    G      20      -       -           -
LGA    V      21      -       -           -
LGA    I      22      A      14          1.617
LGA    T      23      A      15          1.635
LGA    E      24      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
LGA    E      25      T      23           #
LGA    E      26      E      24          2.679
LGA    K      27      -       -           -
LGA    A      28      E      25          1.720
LGA    E      29      E      26          2.425
LGA    Q      30      K      27          2.041
LGA    Q      31      A      28          1.672
LGA    K      32      E      29          1.300
LGA    L      33      Q      30          1.078
LGA    R      34      Q      31          1.104
LGA    Q      35      K      32          1.240
LGA    E      36      L      33          1.234
LGA    Y      37      R      34          2.570
LGA    L      38      Q      35          3.452
LGA    K      39      E      36           -
LGA    G      40      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32   36    5.0     21    2.66    33.33     43.366     0.761

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.907257 * X  +  -0.343514 * Y  +  -0.242657 * Z  +  27.576250
  Y_new =  -0.094467 * X  +   0.395777 * Y  +  -0.913475 * Z  +  40.276096
  Z_new =   0.409830 * X  +   0.851680 * Y  +   0.326621 * Z  + -147.281128 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.204592   -1.937000  [ DEG:    69.0181   -110.9819 ]
  Theta =  -0.422267   -2.719325  [ DEG:   -24.1941   -155.8059 ]
  Phi   =  -0.103750    3.037843  [ DEG:    -5.9444    174.0556 ]
 
# 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: T0335AL333_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL333_5-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32   36   5.0   21   2.66   33.33  43.366
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL333_5-D1
REMARK Aligment from pdb entry: 2irf_G
ATOM      1  N   ALA     5       8.331  -4.908 -12.432  1.00  0.00              
ATOM      2  CA  ALA     5       7.851  -4.871 -13.846  1.00  0.00              
ATOM      3  C   ALA     5       6.335  -4.671 -13.921  1.00  0.00              
ATOM      4  O   ALA     5       5.824  -4.143 -14.910  1.00  0.00              
ATOM      5  N   LYS     6      -1.588  -2.068  -7.805  1.00  0.00              
ATOM      6  CA  LYS     6      -2.452  -1.419  -6.827  1.00  0.00              
ATOM      7  C   LYS     6      -3.641  -2.298  -6.479  1.00  0.00              
ATOM      8  O   LYS     6      -4.015  -2.397  -5.315  1.00  0.00              
ATOM      9  N   ILE     7      -4.254  -2.915  -7.487  1.00  0.00              
ATOM     10  CA  ILE     7      -5.394  -3.794  -7.241  1.00  0.00              
ATOM     11  C   ILE     7      -4.967  -4.921  -6.316  1.00  0.00              
ATOM     12  O   ILE     7      -5.679  -5.263  -5.382  1.00  0.00              
ATOM     13  N   ALA     8      -3.785  -5.467  -6.573  1.00  0.00              
ATOM     14  CA  ALA     8      -3.223  -6.548  -5.774  1.00  0.00              
ATOM     15  C   ALA     8      -2.977  -6.090  -4.330  1.00  0.00              
ATOM     16  O   ALA     8      -3.134  -6.869  -3.391  1.00  0.00              
ATOM     17  N   ARG     9      -2.596  -4.823  -4.161  1.00  0.00              
ATOM     18  CA  ARG     9      -2.347  -4.247  -2.839  1.00  0.00              
ATOM     19  C   ARG     9      -3.653  -4.089  -2.078  1.00  0.00              
ATOM     20  O   ARG     9      -3.718  -4.380  -0.887  1.00  0.00              
ATOM     21  N   ILE    10      -4.689  -3.629  -2.775  1.00  0.00              
ATOM     22  CA  ILE    10      -6.004  -3.435  -2.172  1.00  0.00              
ATOM     23  C   ILE    10      -6.599  -4.782  -1.787  1.00  0.00              
ATOM     24  O   ILE    10      -7.037  -4.978  -0.652  1.00  0.00              
ATOM     25  N   ASN    11      -6.575  -5.711  -2.738  1.00  0.00              
ATOM     26  CA  ASN    11      -7.122  -7.046  -2.549  1.00  0.00              
ATOM     27  C   ASN    11      -6.431  -7.858  -1.458  1.00  0.00              
ATOM     28  O   ASN    11      -7.045  -8.751  -0.873  1.00  0.00              
ATOM     29  N   LYS    16      -5.173  -7.529  -1.168  1.00  0.00              
ATOM     30  CA  LYS    16      -4.411  -8.243  -0.147  1.00  0.00              
ATOM     31  C   LYS    16      -4.783  -7.840   1.281  1.00  0.00              
ATOM     32  O   LYS    16      -4.453  -8.550   2.230  1.00  0.00              
ATOM     33  N   ALA    17      -5.441  -6.691   1.426  1.00  0.00              
ATOM     34  CA  ALA    17      -5.856  -6.167   2.729  1.00  0.00              
ATOM     35  C   ALA    17      -4.673  -6.000   3.681  1.00  0.00              
ATOM     36  O   ALA    17      -4.848  -5.990   4.903  1.00  0.00              
ATOM     37  N   LYS    18      -3.472  -5.868   3.121  1.00  0.00              
ATOM     38  CA  LYS    18      -2.262  -5.713   3.923  1.00  0.00              
ATOM     39  C   LYS    18      -1.894  -4.252   4.203  1.00  0.00              
ATOM     40  O   LYS    18      -0.944  -3.972   4.931  1.00  0.00              
ATOM     41  N   ALA    19      -2.633  -3.323   3.605  1.00  0.00              
ATOM     42  CA  ALA    19      -2.373  -1.900   3.796  1.00  0.00              
ATOM     43  C   ALA    19      -3.521  -1.297   4.599  1.00  0.00              
ATOM     44  O   ALA    19      -4.658  -1.247   4.128  1.00  0.00              
ATOM     45  N   GLY    20      -3.233  -0.818   5.821  1.00  0.00              
ATOM     46  CA  GLY    20      -4.256  -0.217   6.686  1.00  0.00              
ATOM     47  C   GLY    20      -4.933   0.974   6.004  1.00  0.00              
ATOM     48  O   GLY    20      -4.265   1.929   5.609  1.00  0.00              
ATOM     49  N   VAL    21      -6.248   0.892   5.826  1.00  0.00              
ATOM     50  CA  VAL    21      -6.984   1.968   5.185  1.00  0.00              
ATOM     51  C   VAL    21      -7.243   1.780   3.697  1.00  0.00              
ATOM     52  O   VAL    21      -8.177   2.377   3.159  1.00  0.00              
ATOM     53  N   ILE    22      -6.417   0.973   3.029  1.00  0.00              
ATOM     54  CA  ILE    22      -6.565   0.717   1.596  1.00  0.00              
ATOM     55  C   ILE    22      -7.609  -0.368   1.349  1.00  0.00              
ATOM     56  O   ILE    22      -7.330  -1.562   1.494  1.00  0.00              
ATOM     57  N   THR    23      -8.791   0.054   0.920  1.00  0.00              
ATOM     58  CA  THR    23      -9.900  -0.863   0.678  1.00  0.00              
ATOM     59  C   THR    23     -10.828  -0.350  -0.418  1.00  0.00              
ATOM     60  O   THR    23     -10.799   0.828  -0.762  1.00  0.00              
ATOM     61  N   GLU    24      -0.343  11.713  15.291  1.00  0.00              
ATOM     62  CA  GLU    24      -1.035  10.456  15.076  1.00  0.00              
ATOM     63  C   GLU    24      -0.471   9.753  13.861  1.00  0.00              
ATOM     64  O   GLU    24      -0.718   8.566  13.652  1.00  0.00              
ATOM     65  N   GLU    25       0.273  10.493  13.044  1.00  0.00              
ATOM     66  CA  GLU    25       0.884   9.926  11.851  1.00  0.00              
ATOM     67  C   GLU    25       2.019   9.015  12.287  1.00  0.00              
ATOM     68  O   GLU    25       2.770   9.330  13.213  1.00  0.00              
ATOM     69  N   GLU    26       2.156   7.904  11.578  1.00  0.00              
ATOM     70  CA  GLU    26       3.172   6.907  11.862  1.00  0.00              
ATOM     71  C   GLU    26       3.579   6.318  10.514  1.00  0.00              
ATOM     72  O   GLU    26       2.728   6.067   9.663  1.00  0.00              
ATOM     73  N   LYS    27       4.878   6.129  10.308  1.00  0.00              
ATOM     74  CA  LYS    27       5.369   5.588   9.046  1.00  0.00              
ATOM     75  C   LYS    27       4.785   4.208   8.723  1.00  0.00              
ATOM     76  O   LYS    27       4.367   3.959   7.590  1.00  0.00              
ATOM     77  N   ALA    28       4.682   3.353   9.743  1.00  0.00              
ATOM     78  CA  ALA    28       4.151   1.994   9.586  1.00  0.00              
ATOM     79  C   ALA    28       2.655   1.933   9.312  1.00  0.00              
ATOM     80  O   ALA    28       2.181   1.031   8.623  1.00  0.00              
ATOM     81  N   GLU    29       1.913   2.889   9.860  1.00  0.00              
ATOM     82  CA  GLU    29       0.471   2.933   9.682  1.00  0.00              
ATOM     83  C   GLU    29       0.008   3.729   8.471  1.00  0.00              
ATOM     84  O   GLU    29      -0.931   3.328   7.783  1.00  0.00              
ATOM     85  N   GLN    30       0.698   4.827   8.177  1.00  0.00              
ATOM     86  CA  GLN    30       0.293   5.699   7.079  1.00  0.00              
ATOM     87  C   GLN    30       1.088   5.664   5.775  1.00  0.00              
ATOM     88  O   GLN    30       0.570   6.052   4.727  1.00  0.00              
ATOM     89  N   GLN    31       2.328   5.191   5.820  1.00  0.00              
ATOM     90  CA  GLN    31       3.137   5.134   4.606  1.00  0.00              
ATOM     91  C   GLN    31       3.468   3.760   4.002  1.00  0.00              
ATOM     92  O   GLN    31       4.183   3.705   3.003  1.00  0.00              
ATOM     93  N   LYS    32       2.929   2.644   4.552  1.00  0.00              
ATOM     94  CA  LYS    32       3.269   1.339   3.958  1.00  0.00              
ATOM     95  C   LYS    32       3.016   1.204   2.454  1.00  0.00              
ATOM     96  O   LYS    32       3.808   0.597   1.751  1.00  0.00              
ATOM     97  N   LEU    33       1.929   1.787   1.960  1.00  0.00              
ATOM     98  CA  LEU    33       1.613   1.717   0.536  1.00  0.00              
ATOM     99  C   LEU    33       2.629   2.487  -0.306  1.00  0.00              
ATOM    100  O   LEU    33       3.007   2.049  -1.395  1.00  0.00              
ATOM    101  N   ARG    34       3.051   3.643   0.197  1.00  0.00              
ATOM    102  CA  ARG    34       4.016   4.486  -0.501  1.00  0.00              
ATOM    103  C   ARG    34       5.382   3.821  -0.482  1.00  0.00              
ATOM    104  O   ARG    34       6.105   3.856  -1.472  1.00  0.00              
ATOM    105  N   GLN    35       5.712   3.190   0.641  1.00  0.00              
ATOM    106  CA  GLN    35       6.978   2.486   0.795  1.00  0.00              
ATOM    107  C   GLN    35       7.016   1.287  -0.166  1.00  0.00              
ATOM    108  O   GLN    35       8.019   1.059  -0.843  1.00  0.00              
ATOM    109  N   GLU    36       5.907   0.548  -0.232  1.00  0.00              
ATOM    110  CA  GLU    36       5.781  -0.623  -1.098  1.00  0.00              
ATOM    111  C   GLU    36       6.006  -0.285  -2.558  1.00  0.00              
ATOM    112  O   GLU    36       6.609  -1.066  -3.288  1.00  0.00              
ATOM    113  N   TYR    37       5.487   0.860  -2.993  1.00  0.00              
ATOM    114  CA  TYR    37       5.661   1.287  -4.378  1.00  0.00              
ATOM    115  C   TYR    37       7.130   1.628  -4.624  1.00  0.00              
ATOM    116  O   TYR    37       7.683   1.312  -5.672  1.00  0.00              
ATOM    117  N   LEU    38       7.759   2.239  -3.627  1.00  0.00              
ATOM    118  CA  LEU    38       9.161   2.619  -3.712  1.00  0.00              
ATOM    119  C   LEU    38      10.056   1.388  -3.770  1.00  0.00              
ATOM    120  O   LEU    38      11.057   1.369  -4.483  1.00  0.00              
ATOM    121  N   LYS    39       8.222  11.269   2.634  1.00  0.00              
ATOM    122  CA  LYS    39       7.815  12.432   1.852  1.00  0.00              
ATOM    123  C   LYS    39       7.950  12.187   0.359  1.00  0.00              
ATOM    124  O   LYS    39       7.042  12.506  -0.407  1.00  0.00              
ATOM    125  N   GLY    40       9.076  11.606  -0.047  1.00  0.00              
ATOM    126  CA  GLY    40       9.319  11.300  -1.457  1.00  0.00              
ATOM    127  C   GLY    40       8.463  10.123  -1.903  1.00  0.00              
ATOM    128  O   GLY    40       7.903  10.145  -2.998  1.00  0.00              
END
