
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0361AL381_5-D1
# Molecule2: number of CA atoms  158 ( 1268),  selected  158 , name T0361_D1.pdb
# PARAMETERS: T0361AL381_5-D1.T0361_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    -       -      T       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      E       6           -
LGA    -       -      D       7           -
LGA    -       -      D       8           -
LGA    -       -      V       9           -
LGA    -       -      L      10           -
LGA    -       -      E      11           -
LGA    -       -      Q      12           -
LGA    -       -      L      13           -
LGA    -       -      D      14           -
LGA    -       -      A      15           -
LGA    -       -      Q      16           -
LGA    -       -      D      17           -
LGA    -       -      N      18           -
LGA    -       -      L      19           -
LGA    -       -      F      20           -
LGA    -       -      S      21           -
LGA    -       -      F      22           -
LGA    -       -      M      23           -
LGA    -       -      K      24           -
LGA    -       -      T      25           -
LGA    -       -      A      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      I      29           -
LGA    -       -      L      30           -
LGA    -       -      L      31           -
LGA    -       -      Q      32           -
LGA    -       -      G      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    -       -      Q      36           -
LGA    -       -      F      37           -
LGA    -       -      L      38           -
LGA    -       -      P      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      F      42           -
LGA    -       -      V      43           -
LGA    -       -      D      44           -
LGA    -       -      N      45           -
LGA    -       -      D      46           -
LGA    -       -      E      47           -
LGA    -       -      E      48           -
LGA    -       -      I      49           -
LGA    -       -      V      50           -
LGA    -       -      E      51           -
LGA    -       -      Y      52           -
LGA    -       -      A      53           -
LGA    -       -      V      54           -
LGA    -       -      K      55           -
LGA    -       -      P      56           -
LGA    -       -      L      57           -
LGA    -       -      L      58           -
LGA    -       -      A      59           -
LGA    -       -      Q      60           -
LGA    -       -      S      61           -
LGA    -       -      G      62           -
LGA    -       -      P      63           -
LGA    -       -      L      64           -
LGA    -       -      D      65           -
LGA    -       -      D      66           -
LGA    -       -      I      67           -
LGA    P      39      D      68          2.374
LGA    S      40      V      69           #
LGA    L      41      -       -           -
LGA    F      42      A      70          1.378
LGA    V      43      L      71          2.987
LGA    D      44      R      72          4.780
LGA    N      45      L      73          4.564
LGA    -       -      I      74           -
LGA    D      46      Y      75          1.013
LGA    E      47      A      76           #
LGA    -       -      L      77           -
LGA    -       -      G      78           -
LGA    -       -      K      79           -
LGA    -       -      M      80           -
LGA    E      48      D      81          2.279
LGA    I      49      K      82          3.095
LGA    V      50      W      83          2.418
LGA    -       -      L      84           -
LGA    -       -      Y      85           -
LGA    -       -      A      86           -
LGA    -       -      D      87           -
LGA    -       -      I      88           -
LGA    -       -      T      89           -
LGA    -       -      H      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      Q      93           -
LGA    -       -      Y      94           -
LGA    -       -      W      95           -
LGA    -       -      H      96           -
LGA    -       -      Y      97           -
LGA    -       -      L      98           -
LGA    -       -      N      99           -
LGA    -       -      E     100           -
LGA    -       -      Q     101           -
LGA    -       -      D     102           -
LGA    -       -      E     103           -
LGA    -       -      T     104           -
LGA    -       -      P     105           -
LGA    -       -      G     106           -
LGA    -       -      F     107           -
LGA    -       -      A     108           -
LGA    -       -      D     109           -
LGA    -       -      D     110           -
LGA    -       -      I     111           -
LGA    -       -      T     112           -
LGA    -       -      W     113           -
LGA    -       -      D     114           -
LGA    -       -      F     115           -
LGA    -       -      I     116           -
LGA    -       -      S     117           -
LGA    -       -      N     118           -
LGA    -       -      V     119           -
LGA    E      51      N     120          2.658
LGA    -       -      S     121           -
LGA    -       -      I     122           -
LGA    -       -      T     123           -
LGA    Y      52      R     124          2.573
LGA    A      53      N     125           -
LGA    V      54      A     126           -
LGA    K      55      T     127           -
LGA    P      56      L     128           -
LGA    L      57      Y     129           -
LGA    L      58      D     130           -
LGA    A      59      A     131           -
LGA    -       -      L     132           -
LGA    -       -      K     133           -
LGA    -       -      A     134           -
LGA    -       -      M     135           -
LGA    P      63      K     136          5.111
LGA    L      64      E     145          1.585
LGA    D      65      A     146          2.867
LGA    D      66      R     147          3.146
LGA    -       -      F     148           -
LGA    -       -      S     149           -
LGA    I      67      G     150          1.898
LGA    D      68      M     151          1.163
LGA    V      69      V     152          3.203
LGA    -       -      K     153           -
LGA    -       -      T     154           -
LGA    -       -      A     155           -
LGA    A      70      L     156          0.783
LGA    L      71      T     157          1.750
LGA    -       -      L     158           -
LGA    -       -      A     159           -
LGA    R      72      V     160          0.887
LGA    L      73      T     161          2.907
LGA    -       -      T     162           -
LGA    -       -      T     163           -
LGA    I      74      L     164          2.135
LGA    Y      75      K     165          3.889
LGA    -       -      E     166           -
LGA    -       -      L     167           -
LGA    -       -      T     168           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34  158    5.0     24    2.81     4.17      9.891     0.824

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.519626 * X  +  -0.574165 * Y  +  -0.632711 * Z  +  36.608219
  Y_new =   0.339651 * X  +   0.540691 * Y  +  -0.769604 * Z  +  -2.778872
  Z_new =   0.783981 * X  +  -0.614807 * Y  +  -0.085942 * Z  +  45.362091 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.709683    1.431909  [ DEG:   -97.9576     82.0424 ]
  Theta =  -0.901053   -2.240540  [ DEG:   -51.6265   -128.3735 ]
  Phi   =   2.562660   -0.578933  [ DEG:   146.8296    -33.1704 ]
 
# 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: T0361AL381_5-D1                               
REMARK     2: T0361_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0361AL381_5-D1.T0361_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  158   5.0   24   2.81    4.17   9.891
REMARK  ---------------------------------------------------------- 
MOLECULE T0361AL381_5-D1
REMARK Aligment from pdb entry: 4dcg
ATOM      1  N   PRO    39      13.067  -4.873  15.510  1.00  0.00              
ATOM      2  CA  PRO    39      12.918  -5.337  14.126  1.00  0.00              
ATOM      3  C   PRO    39      12.295  -4.181  13.343  1.00  0.00              
ATOM      4  O   PRO    39      12.754  -3.821  12.256  1.00  0.00              
ATOM      5  N   SER    40      11.279  -3.577  13.950  1.00  0.00              
ATOM      6  CA  SER    40      10.557  -2.444  13.385  1.00  0.00              
ATOM      7  C   SER    40      11.508  -1.282  13.092  1.00  0.00              
ATOM      8  O   SER    40      11.403  -0.629  12.056  1.00  0.00              
ATOM      9  N   LEU    41      12.451  -1.039  13.997  1.00  0.00              
ATOM     10  CA  LEU    41      13.417   0.042  13.828  1.00  0.00              
ATOM     11  C   LEU    41      14.624  -0.374  13.004  1.00  0.00              
ATOM     12  O   LEU    41      15.573   0.398  12.847  1.00  0.00              
ATOM     13  N   PHE    42      14.608  -1.615  12.526  1.00  0.00              
ATOM     14  CA  PHE    42      15.703  -2.122  11.718  1.00  0.00              
ATOM     15  C   PHE    42      17.001  -2.387  12.454  1.00  0.00              
ATOM     16  O   PHE    42      18.053  -2.522  11.833  1.00  0.00              
ATOM     17  N   VAL    43      16.939  -2.552  13.764  1.00  0.00              
ATOM     18  CA  VAL    43      18.166  -2.783  14.502  1.00  0.00              
ATOM     19  C   VAL    43      18.423  -4.213  14.960  1.00  0.00              
ATOM     20  O   VAL    43      19.451  -4.504  15.568  1.00  0.00              
ATOM     21  N   ASP    44      17.520  -5.119  14.605  1.00  0.00              
ATOM     22  CA  ASP    44      17.665  -6.519  14.997  1.00  0.00              
ATOM     23  C   ASP    44      18.554  -7.353  14.050  1.00  0.00              
ATOM     24  O   ASP    44      19.476  -8.045  14.490  1.00  0.00              
ATOM     25  N   ASN    45      18.278  -7.263  12.750  1.00  0.00              
ATOM     26  CA  ASN    45      19.021  -8.036  11.753  1.00  0.00              
ATOM     27  C   ASN    45      20.518  -7.796  11.829  1.00  0.00              
ATOM     28  O   ASN    45      20.974  -6.655  11.828  1.00  0.00              
ATOM     29  N   ASP    46      21.268  -8.886  11.922  1.00  0.00              
ATOM     30  CA  ASP    46      22.711  -8.804  11.989  1.00  0.00              
ATOM     31  C   ASP    46      23.274  -8.608  13.383  1.00  0.00              
ATOM     32  O   ASP    46      24.486  -8.544  13.547  1.00  0.00              
ATOM     33  N   GLU    47      22.420  -8.512  14.392  1.00  0.00              
ATOM     34  CA  GLU    47      22.907  -8.317  15.755  1.00  0.00              
ATOM     35  C   GLU    47      23.226  -9.612  16.476  1.00  0.00              
ATOM     36  O   GLU    47      22.866 -10.702  16.010  1.00  0.00              
ATOM     37  N   GLU    48      23.970  -9.493  17.575  1.00  0.00              
ATOM     38  CA  GLU    48      24.276 -10.630  18.440  1.00  0.00              
ATOM     39  C   GLU    48      23.540 -10.322  19.742  1.00  0.00              
ATOM     40  O   GLU    48      23.730  -9.243  20.322  1.00  0.00              
ATOM     41  N   ILE    49      22.616 -11.191  20.144  1.00  0.00              
ATOM     42  CA  ILE    49      21.892 -10.982  21.387  1.00  0.00              
ATOM     43  C   ILE    49      22.688 -11.647  22.515  1.00  0.00              
ATOM     44  O   ILE    49      22.904 -12.862  22.505  1.00  0.00              
ATOM     45  N   VAL    50      23.193 -10.839  23.445  1.00  0.00              
ATOM     46  CA  VAL    50      23.924 -11.361  24.594  1.00  0.00              
ATOM     47  C   VAL    50      22.903 -11.385  25.752  1.00  0.00              
ATOM     48  O   VAL    50      22.408 -10.333  26.178  1.00  0.00              
ATOM     49  N   GLU    51      22.526 -12.588  26.188  1.00  0.00              
ATOM     50  CA  GLU    51      21.541 -12.774  27.247  1.00  0.00              
ATOM     51  C   GLU    51      22.294 -13.305  28.452  1.00  0.00              
ATOM     52  O   GLU    51      22.841 -14.421  28.412  1.00  0.00              
ATOM     53  N   TYR    52      22.359 -12.486  29.504  1.00  0.00              
ATOM     54  CA  TYR    52      23.039 -12.838  30.753  1.00  0.00              
ATOM     55  C   TYR    52      21.977 -13.193  31.794  1.00  0.00              
ATOM     56  O   TYR    52      21.043 -12.411  32.059  1.00  0.00              
ATOM     57  N   ALA    53      27.316  -3.771  32.412  1.00  0.00              
ATOM     58  CA  ALA    53      27.050  -4.583  31.222  1.00  0.00              
ATOM     59  C   ALA    53      26.895  -3.628  30.040  1.00  0.00              
ATOM     60  O   ALA    53      27.442  -3.854  28.961  1.00  0.00              
ATOM     61  N   VAL    54      26.131  -2.560  30.254  1.00  0.00              
ATOM     62  CA  VAL    54      25.896  -1.552  29.222  1.00  0.00              
ATOM     63  C   VAL    54      27.162  -0.743  28.901  1.00  0.00              
ATOM     64  O   VAL    54      27.526  -0.577  27.731  1.00  0.00              
ATOM     65  N   LYS    55      27.867  -0.301  29.942  1.00  0.00              
ATOM     66  CA  LYS    55      29.084   0.483  29.742  1.00  0.00              
ATOM     67  C   LYS    55      30.188  -0.272  29.029  1.00  0.00              
ATOM     68  O   LYS    55      30.871   0.293  28.183  1.00  0.00              
ATOM     69  N   PRO    56      30.374  -1.541  29.382  1.00  0.00              
ATOM     70  CA  PRO    56      31.417  -2.352  28.745  1.00  0.00              
ATOM     71  C   PRO    56      31.005  -2.930  27.380  1.00  0.00              
ATOM     72  O   PRO    56      31.767  -2.870  26.422  1.00  0.00              
ATOM     73  N   LEU    57      29.792  -3.460  27.282  1.00  0.00              
ATOM     74  CA  LEU    57      29.343  -4.047  26.023  1.00  0.00              
ATOM     75  C   LEU    57      28.945  -3.004  24.995  1.00  0.00              
ATOM     76  O   LEU    57      29.059  -3.239  23.792  1.00  0.00              
ATOM     77  N   LEU    58      28.472  -1.851  25.459  1.00  0.00              
ATOM     78  CA  LEU    58      28.046  -0.782  24.560  1.00  0.00              
ATOM     79  C   LEU    58      27.038  -1.292  23.501  1.00  0.00              
ATOM     80  O   LEU    58      27.266  -1.199  22.287  1.00  0.00              
ATOM     81  N   ALA    59      25.885  -1.795  23.959  1.00  0.00              
ATOM     82  CA  ALA    59      24.832  -2.330  23.095  1.00  0.00              
ATOM     83  C   ALA    59      24.012  -1.289  22.360  1.00  0.00              
ATOM     84  O   ALA    59      23.935  -0.140  22.796  1.00  0.00              
ATOM     85  N   PRO    63       4.263 -12.514  38.721  1.00  0.00              
ATOM     86  CA  PRO    63       3.564 -13.069  39.888  1.00  0.00              
ATOM     87  C   PRO    63       2.480 -12.074  40.325  1.00  0.00              
ATOM     88  O   PRO    63       2.591 -10.881  40.066  1.00  0.00              
ATOM     89  N   LEU    64       1.433 -12.583  40.964  1.00  0.00              
ATOM     90  CA  LEU    64       0.293 -11.785  41.401  1.00  0.00              
ATOM     91  C   LEU    64       0.589 -10.409  42.004  1.00  0.00              
ATOM     92  O   LEU    64      -0.063  -9.421  41.654  1.00  0.00              
ATOM     93  N   ASP    65       1.580 -10.333  42.883  1.00  0.00              
ATOM     94  CA  ASP    65       1.916  -9.070  43.517  1.00  0.00              
ATOM     95  C   ASP    65       3.309  -8.543  43.243  1.00  0.00              
ATOM     96  O   ASP    65       3.804  -7.662  43.955  1.00  0.00              
ATOM     97  N   ASP    66       3.921  -9.018  42.165  1.00  0.00              
ATOM     98  CA  ASP    66       5.249  -8.571  41.792  1.00  0.00              
ATOM     99  C   ASP    66       5.275  -7.094  41.338  1.00  0.00              
ATOM    100  O   ASP    66       4.383  -6.618  40.616  1.00  0.00              
ATOM    101  N   ILE    67       6.321  -6.379  41.747  1.00  0.00              
ATOM    102  CA  ILE    67       6.484  -4.977  41.366  1.00  0.00              
ATOM    103  C   ILE    67       7.554  -4.878  40.282  1.00  0.00              
ATOM    104  O   ILE    67       8.017  -3.793  39.942  1.00  0.00              
ATOM    105  N   ASP    68       7.930  -6.025  39.713  1.00  0.00              
ATOM    106  CA  ASP    68       8.962  -6.099  38.665  1.00  0.00              
ATOM    107  C   ASP    68       8.473  -5.685  37.277  1.00  0.00              
ATOM    108  O   ASP    68       7.344  -5.988  36.890  1.00  0.00              
ATOM    109  N   VAL    69       9.332  -5.009  36.522  1.00  0.00              
ATOM    110  CA  VAL    69       9.019  -4.597  35.153  1.00  0.00              
ATOM    111  C   VAL    69      10.302  -4.750  34.334  1.00  0.00              
ATOM    112  O   VAL    69      11.310  -5.248  34.853  1.00  0.00              
ATOM    113  N   ALA    70      10.265  -4.407  33.048  1.00  0.00              
ATOM    114  CA  ALA    70      11.468  -4.512  32.224  1.00  0.00              
ATOM    115  C   ALA    70      11.812  -3.147  31.634  1.00  0.00              
ATOM    116  O   ALA    70      10.983  -2.501  30.994  1.00  0.00              
ATOM    117  N   LEU    71      13.057  -2.733  31.828  1.00  0.00              
ATOM    118  CA  LEU    71      13.552  -1.444  31.341  1.00  0.00              
ATOM    119  C   LEU    71      14.081  -1.662  29.918  1.00  0.00              
ATOM    120  O   LEU    71      15.048  -2.393  29.722  1.00  0.00              
ATOM    121  N   ARG    72      13.413  -1.046  28.940  1.00  0.00              
ATOM    122  CA  ARG    72      13.763  -1.163  27.525  1.00  0.00              
ATOM    123  C   ARG    72      14.413   0.121  27.019  1.00  0.00              
ATOM    124  O   ARG    72      13.757   1.155  26.978  1.00  0.00              
ATOM    125  N   LEU    73      15.660   0.037  26.563  1.00  0.00              
ATOM    126  CA  LEU    73      16.395   1.209  26.071  1.00  0.00              
ATOM    127  C   LEU    73      17.038   0.994  24.698  1.00  0.00              
ATOM    128  O   LEU    73      17.492  -0.106  24.372  1.00  0.00              
ATOM    129  N   ILE    74      17.081   2.055  23.901  1.00  0.00              
ATOM    130  CA  ILE    74      17.703   2.033  22.578  1.00  0.00              
ATOM    131  C   ILE    74      18.756   3.132  22.622  1.00  0.00              
ATOM    132  O   ILE    74      18.455   4.284  22.945  1.00  0.00              
ATOM    133  N   TYR    75      19.990   2.774  22.308  1.00  0.00              
ATOM    134  CA  TYR    75      21.078   3.722  22.376  1.00  0.00              
ATOM    135  C   TYR    75      21.441   4.420  21.084  1.00  0.00              
ATOM    136  O   TYR    75      21.665   3.782  20.062  1.00  0.00              
END
