
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0283AL381_3
# Molecule2: number of CA atoms  112 (  888),  selected  112 , name T0283
# PARAMETERS: T0283AL381_3.T0283  -4  -ie  -d:5  -o1  -sia  
# 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    -       -      S       2           -
LGA    -       -      F       3           -
LGA    -       -      I       4           -
LGA    -       -      E       5           -
LGA    -       -      K       6           -
LGA    -       -      M       7           -
LGA    -       -      I       8           -
LGA    -       -      G       9           -
LGA    -       -      S      10           -
LGA    -       -      L      11           -
LGA    -       -      N      12           -
LGA    -       -      D      13           -
LGA    -       -      K      14           -
LGA    -       -      R      15           -
LGA    -       -      E      16           -
LGA    -       -      W      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    -       -      A      22           -
LGA    -       -      R      23           -
LGA    -       -      A      24           -
LGA    -       -      K      25           -
LGA    -       -      A      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      K      29           -
LGA    -       -      E      30           -
LGA    -       -      Y      31           -
LGA    -       -      H      32           -
LGA    -       -      H      33           -
LGA    -       -      A      34           -
LGA    -       -      Y      35           -
LGA    -       -      K      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Q      39           -
LGA    -       -      K      40           -
LGA    -       -      Y      41           -
LGA    -       -      M      42           -
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    V      75      T      49          4.830
LGA    T      76      D      50          3.914
LGA    D      77      W      51           -
LGA    -       -      Q      52           -
LGA    -       -      D      53           -
LGA    -       -      T      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    -       -      I      57           -
LGA    -       -      F      58           -
LGA    -       -      G      59           -
LGA    -       -      G      60           -
LGA    -       -      I      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      L      64           -
LGA    -       -      F      65           -
LGA    -       -      E      66           -
LGA    -       -      E      67           -
LGA    -       -      G      68           -
LGA    -       -      A      69           -
LGA    -       -      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    -       -      K      73           -
LGA    -       -      K      74           -
LGA    -       -      V      75           -
LGA    -       -      T      76           -
LGA    -       -      D      77           -
LGA    -       -      L      78           -
LGA    -       -      T      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      D      82           -
LGA    -       -      V      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      F      86           -
LGA    -       -      C      87           -
LGA    -       -      D      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    L      78      M      91           #
LGA    -       -      K      92           -
LGA    -       -      D      93           -
LGA    T      79      T      94          2.427
LGA    G      80      K      95          2.195
LGA    E      81      T      96          3.373
LGA    -       -      W      97           -
LGA    -       -      M      98           -
LGA    D      82      D      99          1.087
LGA    V      83      K     100          2.637
LGA    A      84      Y     101          2.281
LGA    A      85      R     102          0.559
LGA    F      86      T     103          1.262
LGA    C      87      K     104          1.226
LGA    D      88      L     105          0.606
LGA    E      89      N     106          1.141
LGA    L      90      D     107          1.351
LGA    M      91      S     108          0.649
LGA    K      92      I     109          1.863
LGA    D      93      G     110          1.971
LGA    -       -      R     111           -
LGA    -       -      D     112           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19  112    5.0     17    2.28    11.76     13.395     0.713

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.864680 * X  +  -0.208764 * Y  +  -0.456887 * Z  +  12.041585
  Y_new =  -0.481360 * X  +  -0.604378 * Y  +  -0.634839 * Z  +  52.565693
  Z_new =  -0.143601 * X  +   0.768860 * Y  +  -0.623084 * Z  +  40.587578 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.251847   -0.889746  [ DEG:   129.0213    -50.9787 ]
  Theta =   0.144099    2.997494  [ DEG:     8.2563    171.7437 ]
  Phi   =  -0.507966    2.633627  [ DEG:   -29.1043    150.8957 ]
 
# 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: T0283AL381_3                                  
REMARK     2: T0283                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283AL381_3.T0283 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19  112   5.0   17   2.28   11.76  13.395
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL381_3
REMARK Aligment from pdb entry: 1qh8B
ATOM      1  N   VAL    75      21.078  23.748  11.474  1.00  0.00              
ATOM      2  CA  VAL    75      19.788  24.089  12.112  1.00  0.00              
ATOM      3  C   VAL    75      19.818  25.555  12.536  1.00  0.00              
ATOM      4  O   VAL    75      18.840  26.298  12.296  1.00  0.00              
ATOM      5  N   THR    76      20.860  25.955  13.259  1.00  0.00              
ATOM      6  CA  THR    76      20.984  27.348  13.700  1.00  0.00              
ATOM      7  C   THR    76      20.928  28.322  12.521  1.00  0.00              
ATOM      8  O   THR    76      20.449  29.476  12.648  1.00  0.00              
ATOM      9  N   ASP    77      21.612  28.006  11.424  1.00  0.00              
ATOM     10  CA  ASP    77      21.618  28.854  10.244  1.00  0.00              
ATOM     11  C   ASP    77      20.252  28.961   9.599  1.00  0.00              
ATOM     12  O   ASP    77      19.821  30.063   9.223  1.00  0.00              
ATOM     13  N   LEU    78      19.543  27.839   9.444  1.00  0.00              
ATOM     14  CA  LEU    78      18.213  27.884   8.845  1.00  0.00              
ATOM     15  C   LEU    78      17.276  28.754   9.683  1.00  0.00              
ATOM     16  O   LEU    78      16.514  29.517   9.082  1.00  0.00              
ATOM     17  N   THR    79      17.306  28.591  10.991  1.00  0.00              
ATOM     18  CA  THR    79      16.417  29.375  11.859  1.00  0.00              
ATOM     19  C   THR    79      16.873  30.809  12.045  1.00  0.00              
ATOM     20  O   THR    79      16.101  31.674  12.525  1.00  0.00              
ATOM     21  N   GLY    80      18.098  31.153  11.671  1.00  0.00              
ATOM     22  CA  GLY    80      18.603  32.507  11.609  1.00  0.00              
ATOM     23  C   GLY    80      18.963  33.128  12.935  1.00  0.00              
ATOM     24  O   GLY    80      18.764  34.339  13.178  1.00  0.00              
ATOM     25  N   GLU    81      19.461  32.310  13.860  1.00  0.00              
ATOM     26  CA  GLU    81      19.896  32.827  15.146  1.00  0.00              
ATOM     27  C   GLU    81      20.921  33.940  14.934  1.00  0.00              
ATOM     28  O   GLU    81      21.950  33.739  14.266  1.00  0.00              
ATOM     29  N   ASP    82      20.748  35.066  15.626  1.00  0.00              
ATOM     30  CA  ASP    82      21.703  36.173  15.536  1.00  0.00              
ATOM     31  C   ASP    82      22.841  36.011  16.513  1.00  0.00              
ATOM     32  O   ASP    82      22.748  36.436  17.668  1.00  0.00              
ATOM     33  N   VAL    83      23.908  35.311  16.121  1.00  0.00              
ATOM     34  CA  VAL    83      25.021  35.005  16.984  1.00  0.00              
ATOM     35  C   VAL    83      25.582  36.210  17.713  1.00  0.00              
ATOM     36  O   VAL    83      25.820  36.177  18.926  1.00  0.00              
ATOM     37  N   ALA    84      25.918  37.264  16.977  1.00  0.00              
ATOM     38  CA  ALA    84      26.478  38.455  17.597  1.00  0.00              
ATOM     39  C   ALA    84      25.633  38.986  18.759  1.00  0.00              
ATOM     40  O   ALA    84      26.141  39.206  19.867  1.00  0.00              
ATOM     41  N   ALA    85      24.345  39.134  18.508  1.00  0.00              
ATOM     42  CA  ALA    85      23.377  39.610  19.499  1.00  0.00              
ATOM     43  C   ALA    85      23.224  38.651  20.659  1.00  0.00              
ATOM     44  O   ALA    85      23.350  39.038  21.826  1.00  0.00              
ATOM     45  N   PHE    86      23.217  37.324  20.392  1.00  0.00              
ATOM     46  CA  PHE    86      23.133  36.404  21.527  1.00  0.00              
ATOM     47  C   PHE    86      24.321  36.483  22.455  1.00  0.00              
ATOM     48  O   PHE    86      24.245  36.403  23.680  1.00  0.00              
ATOM     49  N   CYS    87      25.542  36.564  21.884  1.00  0.00              
ATOM     50  CA  CYS    87      26.774  36.633  22.636  1.00  0.00              
ATOM     51  C   CYS    87      26.870  37.946  23.433  1.00  0.00              
ATOM     52  O   CYS    87      27.135  37.831  24.629  1.00  0.00              
ATOM     53  N   ASP    88      26.396  39.029  22.824  1.00  0.00              
ATOM     54  CA  ASP    88      26.328  40.282  23.599  1.00  0.00              
ATOM     55  C   ASP    88      25.348  40.167  24.761  1.00  0.00              
ATOM     56  O   ASP    88      25.714  40.572  25.864  1.00  0.00              
ATOM     57  N   GLU    89      24.185  39.592  24.492  1.00  0.00              
ATOM     58  CA  GLU    89      23.182  39.383  25.530  1.00  0.00              
ATOM     59  C   GLU    89      23.667  38.467  26.639  1.00  0.00              
ATOM     60  O   GLU    89      23.557  38.773  27.836  1.00  0.00              
ATOM     61  N   LEU    90      24.408  37.378  26.329  1.00  0.00              
ATOM     62  CA  LEU    90      24.995  36.543  27.364  1.00  0.00              
ATOM     63  C   LEU    90      25.919  37.283  28.312  1.00  0.00              
ATOM     64  O   LEU    90      26.067  36.948  29.497  1.00  0.00              
ATOM     65  N   MET    91      26.782  38.165  27.801  1.00  0.00              
ATOM     66  CA  MET    91      27.753  38.893  28.604  1.00  0.00              
ATOM     67  C   MET    91      27.069  39.978  29.460  1.00  0.00              
ATOM     68  O   MET    91      27.334  40.119  30.647  1.00  0.00              
ATOM     69  N   LYS    92      26.086  40.613  28.847  1.00  0.00              
ATOM     70  CA  LYS    92      25.339  41.671  29.555  1.00  0.00              
ATOM     71  C   LYS    92      24.493  41.088  30.672  1.00  0.00              
ATOM     72  O   LYS    92      24.527  41.598  31.809  1.00  0.00              
ATOM     73  N   ASP    93      23.977  39.873  30.464  1.00  0.00              
ATOM     74  CA  ASP    93      23.134  39.220  31.466  1.00  0.00              
ATOM     75  C   ASP    93      23.928  38.421  32.470  1.00  0.00              
ATOM     76  O   ASP    93      23.352  37.882  33.408  1.00  0.00              
END
