
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0349AL242_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL242_5-D1.T0349_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    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    A      23      V      11          1.819
LGA    D      24      L      12          1.327
LGA    I      25      L      13          2.611
LGA    G      26      S      14          2.932
LGA    -       -      A      15           -
LGA    -       -      V      16           -
LGA    H      27      G      17          1.589
LGA    L      28      A      18          4.074
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    -       -      D      21           -
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    V      29      D      24          3.194
LGA    P      45      I      25           #
LGA    R      46      G      26          3.998
LGA    R      47      H      27          3.320
LGA    V      48      L      28          4.681
LGA    L      49      V      29          4.392
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    -       -      V      50           -
LGA    -       -      H      51           -
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    -       -      L      55           -
LGA    -       -      A      56           -
LGA    -       -      G      57           -
LGA    -       -      A      58           -
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    -       -      L      61           -
LGA    V      50      L      62           #
LGA    H      51      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    E      52      G      66          4.621
LGA    D      53      L      67          2.030
LGA    -       -      A      68           -
LGA    D      54      H      69          3.010
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17   57    5.0     14    3.30     0.00     15.197     0.412

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.604285 * X  +   0.578485 * Y  +   0.547901 * Z  +  -1.918303
  Y_new =   0.795940 * X  +  -0.406930 * Y  +  -0.448205 * Z  +   5.402102
  Z_new =  -0.036322 * X  +   0.706939 * Y  +  -0.706341 * Z  +   5.100802 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.355771   -0.785822  [ DEG:   134.9757    -45.0243 ]
  Theta =   0.036330    3.105262  [ DEG:     2.0816    177.9184 ]
  Phi   =   0.921427   -2.220165  [ DEG:    52.7939   -127.2061 ]
 
# 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: T0349AL242_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL242_5-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17   57   5.0   14   3.30    0.00  15.197
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL242_5-D1
REMARK Aligment from pdb entry: 1ews_A
ATOM      1  N   ALA    23      -6.898  -5.154   8.715  1.00  0.00              
ATOM      2  CA  ALA    23      -5.867  -4.690   7.748  1.00  0.00              
ATOM      3  C   ALA    23      -4.577  -4.376   8.544  1.00  0.00              
ATOM      4  O   ALA    23      -4.643  -3.622   9.497  1.00  0.00              
ATOM      5  N   ASP    24      -3.448  -4.939   8.160  1.00  0.00              
ATOM      6  CA  ASP    24      -2.137  -4.627   8.810  1.00  0.00              
ATOM      7  C   ASP    24      -1.802  -3.142   8.599  1.00  0.00              
ATOM      8  O   ASP    24      -1.282  -2.485   9.479  1.00  0.00              
ATOM      9  N   ILE    25      -2.122  -2.679   7.417  1.00  0.00              
ATOM     10  CA  ILE    25      -1.873  -1.254   7.035  1.00  0.00              
ATOM     11  C   ILE    25      -3.123  -0.433   7.423  1.00  0.00              
ATOM     12  O   ILE    25      -3.981  -0.935   8.125  1.00  0.00              
ATOM     13  N   GLY    26      -3.206   0.795   6.965  1.00  0.00              
ATOM     14  CA  GLY    26      -4.390   1.656   7.298  1.00  0.00              
ATOM     15  C   GLY    26      -4.458   2.917   6.422  1.00  0.00              
ATOM     16  O   GLY    26      -3.458   3.577   6.210  1.00  0.00              
ATOM     17  N   HIS    27      -5.643   3.214   5.945  1.00  0.00              
ATOM     18  CA  HIS    27      -5.847   4.417   5.081  1.00  0.00              
ATOM     19  C   HIS    27      -6.173   5.665   5.919  1.00  0.00              
ATOM     20  O   HIS    27      -7.155   5.693   6.636  1.00  0.00              
ATOM     21  N   LEU    28      -5.327   6.657   5.793  1.00  0.00              
ATOM     22  CA  LEU    28      -5.491   7.950   6.534  1.00  0.00              
ATOM     23  C   LEU    28      -4.943   9.102   5.672  1.00  0.00              
ATOM     24  O   LEU    28      -4.126   8.879   4.801  1.00  0.00              
ATOM     25  N   VAL    29      -5.411  10.300   5.939  1.00  0.00              
ATOM     26  CA  VAL    29      -4.937  11.498   5.164  1.00  0.00              
ATOM     27  C   VAL    29      -3.456  11.714   5.509  1.00  0.00              
ATOM     28  O   VAL    29      -2.660  12.110   4.681  1.00  0.00              
ATOM     89  N   PRO    45      -7.260   9.173  -5.065  1.00  0.00              
ATOM     90  CA  PRO    45      -5.976   8.988  -4.306  1.00  0.00              
ATOM     91  C   PRO    45      -5.755  10.110  -3.271  1.00  0.00              
ATOM     92  O   PRO    45      -4.646  10.344  -2.825  1.00  0.00              
ATOM     93  N   ARG    46      -6.836  10.764  -2.923  1.00  0.00              
ATOM     94  CA  ARG    46      -6.803  11.882  -1.931  1.00  0.00              
ATOM     95  C   ARG    46      -6.255  11.411  -0.575  1.00  0.00              
ATOM     96  O   ARG    46      -5.521  12.125   0.079  1.00  0.00              
ATOM     97  N   ARG    47      -6.637  10.214  -0.207  1.00  0.00              
ATOM     98  CA  ARG    47      -6.179   9.626   1.089  1.00  0.00              
ATOM     99  C   ARG    47      -4.867   8.868   0.831  1.00  0.00              
ATOM    100  O   ARG    47      -4.493   8.650  -0.307  1.00  0.00              
ATOM    101  N   VAL    48      -4.210   8.487   1.900  1.00  0.00              
ATOM    102  CA  VAL    48      -2.912   7.743   1.792  1.00  0.00              
ATOM    103  C   VAL    48      -2.949   6.385   2.483  1.00  0.00              
ATOM    104  O   VAL    48      -3.527   6.247   3.542  1.00  0.00              
ATOM    105  N   LEU    49      -2.317   5.424   1.857  1.00  0.00              
ATOM    106  CA  LEU    49      -2.266   4.041   2.420  1.00  0.00              
ATOM    107  C   LEU    49      -1.036   4.049   3.313  1.00  0.00              
ATOM    108  O   LEU    49       0.069   3.804   2.873  1.00  0.00              
ATOM    109  N   VAL    50      -1.289   4.342   4.556  1.00  0.00              
ATOM    110  CA  VAL    50      -0.182   4.389   5.547  1.00  0.00              
ATOM    111  C   VAL    50      -0.046   3.056   6.289  1.00  0.00              
ATOM    112  O   VAL    50      -0.977   2.611   6.932  1.00  0.00              
ATOM    113  N   HIS    51       1.118   2.464   6.172  1.00  0.00              
ATOM    114  CA  HIS    51       1.391   1.153   6.843  1.00  0.00              
ATOM    115  C   HIS    51       2.412   1.310   7.980  1.00  0.00              
ATOM    116  O   HIS    51       3.242   2.200   7.958  1.00  0.00              
ATOM    117  N   GLU    52       2.305   0.421   8.937  1.00  0.00              
ATOM    118  CA  GLU    52       3.212   0.412  10.133  1.00  0.00              
ATOM    119  C   GLU    52       4.713   0.456   9.795  1.00  0.00              
ATOM    120  O   GLU    52       5.139  -0.028   8.764  1.00  0.00              
ATOM    121  N   ASP    53       5.456   1.047  10.696  1.00  0.00              
ATOM    122  CA  ASP    53       6.936   1.173  10.527  1.00  0.00              
ATOM    123  C   ASP    53       7.597  -0.088  11.109  1.00  0.00              
ATOM    124  O   ASP    53       8.009  -0.111  12.253  1.00  0.00              
ATOM    125  N   ASP    54       7.668  -1.103  10.283  1.00  0.00              
ATOM    126  CA  ASP    54       8.283  -2.406  10.699  1.00  0.00              
ATOM    127  C   ASP    54       9.434  -2.795   9.750  1.00  0.00              
ATOM    128  O   ASP    54       9.402  -2.337   8.617  1.00  0.00              
END
