
#######################################################
#                                                     #
#                        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-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283AL381_3-D1.T0283_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    -       -      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    V      75      A      22          2.406
LGA    -       -      R      23           -
LGA    T      76      A      24          2.335
LGA    D      77      K      25          1.745
LGA    L      78      A      26          1.542
LGA    T      79      L      27          2.836
LGA    -       -      P      28           -
LGA    -       -      K      29           -
LGA    -       -      E      30           -
LGA    G      80      Y      31          3.185
LGA    E      81      H      32          3.726
LGA    -       -      H      33           -
LGA    -       -      A      34           -
LGA    D      82      Y      35          1.609
LGA    V      83      K      36          0.454
LGA    A      84      A      37          1.643
LGA    A      85      I      38          1.825
LGA    F      86      Q      39          1.379
LGA    C      87      K      40          1.180
LGA    D      88      Y      41          1.164
LGA    E      89      M      42          1.581
LGA    L      90      W      43          1.956
LGA    M      91      T      44          0.573
LGA    K      92      S      45          3.010
LGA    D      93      G      46          2.518
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      D      50           -
LGA    -       -      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    -       -      M      91           -
LGA    -       -      K      92           -
LGA    -       -      D      93           -
LGA    -       -      T      94           -
LGA    -       -      K      95           -
LGA    -       -      T      96           -
LGA    -       -      W      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   97    5.0     19    2.11     5.26     17.028     0.861

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.915649 * X  +  -0.218708 * Y  +  -0.337275 * Z  +  10.527247
  Y_new =  -0.400684 * X  +  -0.563867 * Y  +  -0.722154 * Z  +  46.440987
  Z_new =  -0.032237 * X  +   0.796380 * Y  +  -0.603937 * Z  +  15.936783 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.219621   -0.921971  [ DEG:   127.1749    -52.8251 ]
  Theta =   0.032243    3.109350  [ DEG:     1.8474    178.1526 ]
  Phi   =  -0.412491    2.729102  [ DEG:   -23.6340    156.3660 ]
 
# 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-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283AL381_3-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   97   5.0   19   2.11    5.26  17.028
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL381_3-D1
REMARK Aligment from pdb entry: 1qh8B
ATOM      1  N   VAL    75      24.814  16.612  -9.866  1.00  0.00              
ATOM      2  CA  VAL    75      23.446  16.867  -9.366  1.00  0.00              
ATOM      3  C   VAL    75      23.299  18.356  -9.064  1.00  0.00              
ATOM      4  O   VAL    75      22.281  18.975  -9.443  1.00  0.00              
ATOM      5  N   THR    76      24.230  18.911  -8.293  1.00  0.00              
ATOM      6  CA  THR    76      24.182  20.338  -7.959  1.00  0.00              
ATOM      7  C   THR    76      24.140  21.212  -9.216  1.00  0.00              
ATOM      8  O   THR    76      23.545  22.317  -9.224  1.00  0.00              
ATOM      9  N   ASP    77      24.946  20.886 -10.223  1.00  0.00              
ATOM     10  CA  ASP    77      24.978  21.641 -11.464  1.00  0.00              
ATOM     11  C   ASP    77      23.671  21.562 -12.226  1.00  0.00              
ATOM     12  O   ASP    77      23.173  22.583 -12.725  1.00  0.00              
ATOM     13  N   LEU    78      23.088  20.365 -12.345  1.00  0.00              
ATOM     14  CA  LEU    78      21.818  20.230 -13.053  1.00  0.00              
ATOM     15  C   LEU    78      20.732  21.061 -12.369  1.00  0.00              
ATOM     16  O   LEU    78      19.958  21.696 -13.091  1.00  0.00              
ATOM     17  N   THR    79      20.661  20.999 -11.054  1.00  0.00              
ATOM     18  CA  THR    79      19.627  21.751 -10.329  1.00  0.00              
ATOM     19  C   THR    79      19.927  23.233 -10.224  1.00  0.00              
ATOM     20  O   THR    79      19.037  24.050  -9.882  1.00  0.00              
ATOM     21  N   GLY    80      21.143  23.671 -10.525  1.00  0.00              
ATOM     22  CA  GLY    80      21.521  25.061 -10.656  1.00  0.00              
ATOM     23  C   GLY    80      21.700  25.812  -9.361  1.00  0.00              
ATOM     24  O   GLY    80      21.367  27.011  -9.236  1.00  0.00              
ATOM     25  N   GLU    81      22.189  25.119  -8.335  1.00  0.00              
ATOM     26  CA  GLU    81      22.456  25.771  -7.063  1.00  0.00              
ATOM     27  C   GLU    81      23.387  26.963  -7.283  1.00  0.00              
ATOM     28  O   GLU    81      24.486  26.819  -7.845  1.00  0.00              
ATOM     29  N   ASP    82      23.046  28.114  -6.702  1.00  0.00              
ATOM     30  CA  ASP    82      23.897  29.302  -6.805  1.00  0.00              
ATOM     31  C   ASP    82      24.953  29.329  -5.727  1.00  0.00              
ATOM     32  O   ASP    82      24.717  29.826  -4.623  1.00  0.00              
ATOM     33  N   VAL    83      26.112  28.713  -5.972  1.00  0.00              
ATOM     34  CA  VAL    83      27.168  28.586  -4.998  1.00  0.00              
ATOM     35  C   VAL    83      27.545  29.893  -4.327  1.00  0.00              
ATOM     36  O   VAL    83      27.675  29.974  -3.101  1.00  0.00              
ATOM     37  N   ALA    84      27.844  30.918  -5.118  1.00  0.00              
ATOM     38  CA  ALA    84      28.232  32.202  -4.555  1.00  0.00              
ATOM     39  C   ALA    84      27.240  32.729  -3.513  1.00  0.00              
ATOM     40  O   ALA    84      27.623  33.081  -2.389  1.00  0.00              
ATOM     41  N   ALA    85      25.971  32.727  -3.880  1.00  0.00              
ATOM     42  CA  ALA    85      24.877  33.174  -3.014  1.00  0.00              
ATOM     43  C   ALA    85      24.713  32.294  -1.795  1.00  0.00              
ATOM     44  O   ALA    85      24.696  32.776  -0.659  1.00  0.00              
ATOM     45  N   PHE    86      24.855  30.956  -1.953  1.00  0.00              
ATOM     46  CA  PHE    86      24.757  30.120  -0.756  1.00  0.00              
ATOM     47  C   PHE    86      25.844  30.386   0.256  1.00  0.00              
ATOM     48  O   PHE    86      25.667  30.390   1.473  1.00  0.00              
ATOM     49  N   CYS    87      27.098  30.549  -0.218  1.00  0.00              
ATOM     50  CA  CYS    87      28.246  30.797   0.624  1.00  0.00              
ATOM     51  C   CYS    87      28.146  32.168   1.316  1.00  0.00              
ATOM     52  O   CYS    87      28.312  32.170   2.534  1.00  0.00              
ATOM     53  N   ASP    88      27.628  33.149   0.583  1.00  0.00              
ATOM     54  CA  ASP    88      27.373  34.443   1.244  1.00  0.00              
ATOM     55  C   ASP    88      26.308  34.316   2.327  1.00  0.00              
ATOM     56  O   ASP    88      26.534  34.836   3.419  1.00  0.00              
ATOM     57  N   GLU    89      25.234  33.607   2.013  1.00  0.00              
ATOM     58  CA  GLU    89      24.166  33.376   2.978  1.00  0.00              
ATOM     59  C   GLU    89      24.634  32.598   4.195  1.00  0.00              
ATOM     60  O   GLU    89      24.388  32.979   5.350  1.00  0.00              
ATOM     61  N   LEU    90      25.499  31.570   4.038  1.00  0.00              
ATOM     62  CA  LEU    90      26.067  30.878   5.182  1.00  0.00              
ATOM     63  C   LEU    90      26.829  31.775   6.139  1.00  0.00              
ATOM     64  O   LEU    90      26.901  31.545   7.355  1.00  0.00              
ATOM     65  N   MET    91      27.647  32.700   5.629  1.00  0.00              
ATOM     66  CA  MET    91      28.469  33.580   6.446  1.00  0.00              
ATOM     67  C   MET    91      27.612  34.651   7.151  1.00  0.00              
ATOM     68  O   MET    91      27.755  34.904   8.340  1.00  0.00              
ATOM     69  N   LYS    92      26.632  35.135   6.409  1.00  0.00              
ATOM     70  CA  LYS    92      25.729  36.162   6.964  1.00  0.00              
ATOM     71  C   LYS    92      24.844  35.580   8.053  1.00  0.00              
ATOM     72  O   LYS    92      24.728  36.174   9.143  1.00  0.00              
ATOM     73  N   ASP    93      24.466  34.307   7.904  1.00  0.00              
ATOM     74  CA  ASP    93      23.602  33.648   8.884  1.00  0.00              
ATOM     75  C   ASP    93      24.375  33.010  10.012  1.00  0.00              
ATOM     76  O   ASP    93      23.771  32.486  10.940  1.00  0.00              
END
