
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0360AL242_5-D1
# Molecule2: number of CA atoms   97 (  785),  selected   97 , name T0360_D1.pdb
# PARAMETERS: T0360AL242_5-D1.T0360_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      82      K      20           -
LGA    R      83      K      21           -
LGA    G      84      K      22           -
LGA    G      85      Q      23           -
LGA    K      86      T      24           -
LGA    -       -      E      25           -
LGA    -       -      M      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      D      29           -
LGA    -       -      H      30           -
LGA    -       -      I      31           -
LGA    -       -      Y      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      Y      35           -
LGA    -       -      D      36           -
LGA    -       -      V      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      R      40           -
LGA    -       -      F      41           -
LGA    -       -      K      42           -
LGA    R      87      P      43           #
LGA    F      88      L      44           #
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      G      47           -
LGA    D      89      I      48          4.397
LGA    L      90      D      49          1.936
LGA    -       -      Q      50           -
LGA    N      91      D      51          4.026
LGA    N      92      L      52          1.451
LGA    R      93      I      53          2.126
LGA    -       -      A      54           -
LGA    -       -      A      55           -
LGA    -       -      L      56           -
LGA    -       -      P      57           -
LGA    -       -      Q      58           -
LGA    -       -      Y      59           -
LGA    -       -      D      60           -
LGA    F      94      A      61          4.069
LGA    -       -      A      62           -
LGA    -       -      L      63           -
LGA    -       -      I      64           -
LGA    K      95      A      65          2.702
LGA    -       -      R      66           -
LGA    -       -      V      67           -
LGA    G      96      L      68          2.832
LGA    E      97      A      69          2.737
LGA    -       -      N      70           -
LGA    -       -      H      71           -
LGA    V      98      C      72          0.682
LGA    T      99      R      73          2.175
LGA    P     100      R      74          0.975
LGA    E     101      P      75          1.371
LGA    E     102      R      76          1.115
LGA    Q     103      Y      77          1.995
LGA    A     104      L      78          3.428
LGA    I     105      K      79          2.944
LGA    A     106      A      80          1.602
LGA    Q     107      L      81          4.235
LGA    -       -      A      82           -
LGA    -       -      R      83           -
LGA    N     108      G      84          3.658
LGA    H     109      G      85          2.375
LGA    P     110      K      86          3.150
LGA    F     111      R      87          1.687
LGA    V     112      F      88           #
LGA    -       -      D      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    Q     113      N      92           #
LGA    -       -      R      93           -
LGA    Q     114      F      94          1.686
LGA    A     115      K      95          3.837
LGA    L     116      G      96           #
LGA    -       -      E      97           -
LGA    -       -      V      98           -
LGA    -       -      T      99           -
LGA    -       -      P     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -
LGA    -       -      Q     103           -
LGA    -       -      A     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      Q     107           -
LGA    -       -      N     108           -
LGA    -       -      H     109           -
LGA    -       -      P     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      Q     113           -
LGA    -       -      Q     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   97    5.0     25    2.75     4.00     17.501     0.878

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.949881 * X  +  -0.145750 * Y  +   0.276555 * Z  +   9.888977
  Y_new =  -0.240880 * X  +  -0.222627 * Y  +  -0.944677 * Z  +  49.799583
  Z_new =   0.199255 * X  +  -0.963947 * Y  +   0.176361 * Z  +   6.258496 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.389840    1.751752  [ DEG:   -79.6320    100.3680 ]
  Theta =  -0.200598   -2.940995  [ DEG:   -11.4934   -168.5066 ]
  Phi   =  -2.893239    0.248354  [ DEG:  -165.7704     14.2296 ]
 
# 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: T0360AL242_5-D1                               
REMARK     2: T0360_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0360AL242_5-D1.T0360_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   97   5.0   25   2.75    4.00  17.501
REMARK  ---------------------------------------------------------- 
MOLECULE T0360AL242_5-D1
REMARK Aligment from pdb entry: 2auh_B
ATOM      1  N   ALA    82     -62.310  21.033 -17.994  1.00  0.00              
ATOM      2  CA  ALA    82     -61.973  21.231 -19.444  1.00  0.00              
ATOM      3  C   ALA    82     -62.165  19.919 -20.215  1.00  0.00              
ATOM      4  O   ALA    82     -62.210  19.906 -21.451  1.00  0.00              
ATOM      5  N   ARG    83     -62.273  18.827 -19.457  1.00  0.00              
ATOM      6  CA  ARG    83     -62.469  17.477 -19.983  1.00  0.00              
ATOM      7  C   ARG    83     -63.445  17.481 -21.168  1.00  0.00              
ATOM      8  O   ARG    83     -64.186  18.445 -21.368  1.00  0.00              
ATOM      9  N   GLY    84     -63.459  16.409 -21.955  1.00  0.00              
ATOM     10  CA  GLY    84     -64.331  16.372 -23.123  1.00  0.00              
ATOM     11  C   GLY    84     -65.216  15.137 -23.253  1.00  0.00              
ATOM     12  O   GLY    84     -66.434  15.251 -23.392  1.00  0.00              
ATOM     13  N   GLY    85     -64.600  13.960 -23.219  1.00  0.00              
ATOM     14  CA  GLY    85     -65.332  12.705 -23.318  1.00  0.00              
ATOM     15  C   GLY    85     -65.769  12.289 -21.928  1.00  0.00              
ATOM     16  O   GLY    85     -65.161  12.677 -20.939  1.00  0.00              
ATOM     17  N   LYS    86     -66.825  11.496 -21.848  1.00  0.00              
ATOM     18  CA  LYS    86     -67.322  11.014 -20.572  1.00  0.00              
ATOM     19  C   LYS    86     -67.632   9.537 -20.732  1.00  0.00              
ATOM     20  O   LYS    86     -67.990   9.089 -21.818  1.00  0.00              
ATOM     21  N   ARG    87     -67.495   8.769 -19.666  1.00  0.00              
ATOM     22  CA  ARG    87     -67.787   7.351 -19.767  1.00  0.00              
ATOM     23  C   ARG    87     -69.282   7.107 -19.578  1.00  0.00              
ATOM     24  O   ARG    87     -69.878   7.604 -18.631  1.00  0.00              
ATOM     25  N   PHE    88     -69.884   6.343 -20.482  1.00  0.00              
ATOM     26  CA  PHE    88     -71.303   6.026 -20.393  1.00  0.00              
ATOM     27  C   PHE    88     -71.547   4.548 -20.679  1.00  0.00              
ATOM     28  O   PHE    88     -70.617   3.802 -20.984  1.00  0.00              
ATOM     29  N   ASP    89     -72.813   4.142 -20.582  1.00  0.00              
ATOM     30  CA  ASP    89     -73.230   2.764 -20.844  1.00  0.00              
ATOM     31  C   ASP    89     -74.669   2.697 -21.344  1.00  0.00              
ATOM     32  O   ASP    89     -75.592   3.113 -20.646  1.00  0.00              
ATOM     33  N   LEU    90     -74.861   2.160 -22.546  1.00  0.00              
ATOM     34  CA  LEU    90     -76.195   2.055 -23.120  1.00  0.00              
ATOM     35  C   LEU    90     -76.814   0.658 -23.085  1.00  0.00              
ATOM     36  O   LEU    90     -77.898   0.429 -23.638  1.00  0.00              
ATOM     37  N   ASN    91     -76.115  -0.265 -22.428  1.00  0.00              
ATOM     38  CA  ASN    91     -76.565  -1.648 -22.271  1.00  0.00              
ATOM     39  C   ASN    91     -77.670  -1.635 -21.248  1.00  0.00              
ATOM     40  O   ASN    91     -77.388  -1.634 -20.052  1.00  0.00              
ATOM     41  N   ASN    92     -78.918  -1.621 -21.695  1.00  0.00              
ATOM     42  CA  ASN    92     -80.006  -1.603 -20.737  1.00  0.00              
ATOM     43  C   ASN    92     -81.045  -0.552 -21.049  1.00  0.00              
ATOM     44  O   ASN    92     -80.729   0.506 -21.594  1.00  0.00              
ATOM     45  N   ARG    93     -82.287  -0.852 -20.684  1.00  0.00              
ATOM     46  CA  ARG    93     -83.426   0.024 -20.930  1.00  0.00              
ATOM     47  C   ARG    93     -83.097   1.507 -20.815  1.00  0.00              
ATOM     48  O   ARG    93     -83.449   2.289 -21.696  1.00  0.00              
ATOM     49  N   PHE    94     -82.417   1.892 -19.742  1.00  0.00              
ATOM     50  CA  PHE    94     -82.094   3.296 -19.544  1.00  0.00              
ATOM     51  C   PHE    94     -80.641   3.693 -19.830  1.00  0.00              
ATOM     52  O   PHE    94     -79.705   2.905 -19.658  1.00  0.00              
ATOM     53  N   LYS    95     -80.473   4.937 -20.273  1.00  0.00              
ATOM     54  CA  LYS    95     -79.163   5.504 -20.579  1.00  0.00              
ATOM     55  C   LYS    95     -78.378   5.568 -19.272  1.00  0.00              
ATOM     56  O   LYS    95     -78.887   5.153 -18.239  1.00  0.00              
ATOM     57  N   GLY    96     -77.154   6.085 -19.294  1.00  0.00              
ATOM     58  CA  GLY    96     -76.383   6.158 -18.054  1.00  0.00              
ATOM     59  C   GLY    96     -74.950   6.689 -18.127  1.00  0.00              
ATOM     60  O   GLY    96     -74.109   6.133 -18.833  1.00  0.00              
ATOM     61  N   GLU    97     -74.673   7.769 -17.398  1.00  0.00              
ATOM     62  CA  GLU    97     -73.315   8.292 -17.326  1.00  0.00              
ATOM     63  C   GLU    97     -72.757   7.542 -16.124  1.00  0.00              
ATOM     64  O   GLU    97     -73.239   7.738 -15.005  1.00  0.00              
ATOM     65  N   VAL    98     -71.759   6.685 -16.354  1.00  0.00              
ATOM     66  CA  VAL    98     -71.155   5.880 -15.283  1.00  0.00              
ATOM     67  C   VAL    98     -70.754   6.722 -14.089  1.00  0.00              
ATOM     68  O   VAL    98     -69.950   7.657 -14.214  1.00  0.00              
ATOM     69  N   THR    99     -71.315   6.361 -12.936  1.00  0.00              
ATOM     70  CA  THR    99     -71.109   7.084 -11.691  1.00  0.00              
ATOM     71  C   THR    99     -69.940   6.691 -10.790  1.00  0.00              
ATOM     72  O   THR    99     -69.429   7.519 -10.050  1.00  0.00              
ATOM     73  N   PRO   100     -69.511   5.441 -10.837  1.00  0.00              
ATOM     74  CA  PRO   100     -68.409   5.032  -9.977  1.00  0.00              
ATOM     75  C   PRO   100     -67.067   5.408 -10.582  1.00  0.00              
ATOM     76  O   PRO   100     -66.747   5.008 -11.699  1.00  0.00              
ATOM     77  N   GLU   101     -66.256   6.179  -9.839  1.00  0.00              
ATOM     78  CA  GLU   101     -64.950   6.588 -10.342  1.00  0.00              
ATOM     79  C   GLU   101     -64.154   5.440 -10.931  1.00  0.00              
ATOM     80  O   GLU   101     -63.709   5.516 -12.073  1.00  0.00              
ATOM     81  N   GLU   102     -63.977   4.367 -10.166  1.00  0.00              
ATOM     82  CA  GLU   102     -63.190   3.253 -10.671  1.00  0.00              
ATOM     83  C   GLU   102     -63.802   2.519 -11.851  1.00  0.00              
ATOM     84  O   GLU   102     -63.065   2.017 -12.703  1.00  0.00              
ATOM     85  N   GLN   103     -65.132   2.451 -11.920  1.00  0.00              
ATOM     86  CA  GLN   103     -65.768   1.757 -13.052  1.00  0.00              
ATOM     87  C   GLN   103     -65.659   2.593 -14.316  1.00  0.00              
ATOM     88  O   GLN   103     -65.276   2.098 -15.365  1.00  0.00              
ATOM     89  N   ALA   104     -66.002   3.868 -14.199  1.00  0.00              
ATOM     90  CA  ALA   104     -65.945   4.788 -15.321  1.00  0.00              
ATOM     91  C   ALA   104     -64.549   4.841 -15.906  1.00  0.00              
ATOM     92  O   ALA   104     -64.364   4.954 -17.109  1.00  0.00              
ATOM     93  N   ILE   105     -63.557   4.758 -15.043  1.00  0.00              
ATOM     94  CA  ILE   105     -62.183   4.820 -15.504  1.00  0.00              
ATOM     95  C   ILE   105     -61.785   3.563 -16.265  1.00  0.00              
ATOM     96  O   ILE   105     -60.764   3.546 -16.953  1.00  0.00              
ATOM     97  N   ALA   106     -62.595   2.518 -16.141  1.00  0.00              
ATOM     98  CA  ALA   106     -62.321   1.249 -16.812  1.00  0.00              
ATOM     99  C   ALA   106     -62.827   1.254 -18.239  1.00  0.00              
ATOM    100  O   ALA   106     -62.218   0.651 -19.117  1.00  0.00              
ATOM    101  N   GLN   107     -63.944   1.939 -18.463  1.00  0.00              
ATOM    102  CA  GLN   107     -64.565   2.018 -19.779  1.00  0.00              
ATOM    103  C   GLN   107     -63.566   2.189 -20.919  1.00  0.00              
ATOM    104  O   GLN   107     -63.622   1.477 -21.920  1.00  0.00              
ATOM    105  N   ASN   108     -62.654   3.136 -20.763  1.00  0.00              
ATOM    106  CA  ASN   108     -61.638   3.390 -21.777  1.00  0.00              
ATOM    107  C   ASN   108     -61.090   2.095 -22.408  1.00  0.00              
ATOM    108  O   ASN   108     -61.441   1.735 -23.537  1.00  0.00              
ATOM    109  N   HIS   109     -60.229   1.406 -21.667  1.00  0.00              
ATOM    110  CA  HIS   109     -59.606   0.172 -22.132  1.00  0.00              
ATOM    111  C   HIS   109     -60.572  -0.797 -22.782  1.00  0.00              
ATOM    112  O   HIS   109     -60.266  -1.394 -23.815  1.00  0.00              
ATOM    113  N   PRO   110     -61.737  -0.947 -22.161  1.00  0.00              
ATOM    114  CA  PRO   110     -62.763  -1.861 -22.640  1.00  0.00              
ATOM    115  C   PRO   110     -63.379  -1.468 -23.985  1.00  0.00              
ATOM    116  O   PRO   110     -63.555  -2.323 -24.854  1.00  0.00              
ATOM    117  N   PHE   111     -63.705  -0.189 -24.170  1.00  0.00              
ATOM    118  CA  PHE   111     -64.296   0.239 -25.435  1.00  0.00              
ATOM    119  C   PHE   111     -63.294  -0.107 -26.518  1.00  0.00              
ATOM    120  O   PHE   111     -63.659  -0.355 -27.661  1.00  0.00              
ATOM    121  N   VAL   112     -62.023  -0.129 -26.139  1.00  0.00              
ATOM    122  CA  VAL   112     -60.966  -0.437 -27.084  1.00  0.00              
ATOM    123  C   VAL   112     -60.982  -1.883 -27.524  1.00  0.00              
ATOM    124  O   VAL   112     -61.054  -2.170 -28.717  1.00  0.00              
ATOM    125  N   GLN   113     -60.900  -2.795 -26.560  1.00  0.00              
ATOM    126  CA  GLN   113     -60.926  -4.226 -26.853  1.00  0.00              
ATOM    127  C   GLN   113     -62.200  -4.550 -27.633  1.00  0.00              
ATOM    128  O   GLN   113     -62.155  -5.140 -28.715  1.00  0.00              
ATOM    129  N   GLN   114     -63.332  -4.151 -27.059  1.00  0.00              
ATOM    130  CA  GLN   114     -64.640  -4.370 -27.654  1.00  0.00              
ATOM    131  C   GLN   114     -64.658  -4.047 -29.145  1.00  0.00              
ATOM    132  O   GLN   114     -65.416  -4.651 -29.904  1.00  0.00              
ATOM    133  N   ALA   115     -63.829  -3.095 -29.564  1.00  0.00              
ATOM    134  CA  ALA   115     -63.758  -2.730 -30.973  1.00  0.00              
ATOM    135  C   ALA   115     -62.829  -3.682 -31.725  1.00  0.00              
ATOM    136  O   ALA   115     -63.110  -4.053 -32.866  1.00  0.00              
ATOM    137  N   LEU   116     -61.727  -4.072 -31.087  1.00  0.00              
ATOM    138  CA  LEU   116     -60.772  -4.998 -31.695  1.00  0.00              
ATOM    139  C   LEU   116     -61.578  -6.121 -32.345  1.00  0.00              
ATOM    140  O   LEU   116     -61.325  -6.501 -33.490  1.00  0.00              
END
