
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0354AL381_4
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354AL381_4.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      E       2           -
LGA    -       -      I       3           -
LGA    -       -      Q       4           -
LGA    -       -      E       5           -
LGA    -       -      I       6           -
LGA    -       -      S       7           -
LGA    -       -      K       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      I      11           -
LGA    -       -      E      12           -
LGA    -       -      A      13           -
LGA    -       -      L      14           -
LGA    -       -      E      15           -
LGA    -       -      D      16           -
LGA    -       -      I      17           -
LGA    -       -      K      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      I      22           -
LGA    -       -      I      23           -
LGA    -       -      E      24           -
LGA    -       -      L      25           -
LGA    -       -      D      26           -
LGA    -       -      T      27           -
LGA    -       -      S      28           -
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    -       -      M      37           -
LGA    -       -      I      38           -
LGA    -       -      V      39           -
LGA    -       -      A      40           -
LGA    -       -      T      41           -
LGA    -       -      G      42           -
LGA    -       -      D      43           -
LGA    S      44      S      44          0.894
LGA    N      45      N      45          0.528
LGA    R      46      R      46          0.472
LGA    Q      47      Q      47          0.678
LGA    V      48      V      48          0.713
LGA    K      49      K      49          0.420
LGA    A      50      A      50          0.472
LGA    L      51      L      51          0.866
LGA    A      52      A      52          0.798
LGA    N      53      N      53          0.313
LGA    S      54      S      54          0.633
LGA    V      55      V      55          0.881
LGA    Q      56      Q      56          0.631
LGA    V      57      V      57          0.274
LGA    K      58      K      58          0.122
LGA    L      59      L      59          0.135
LGA    K      60      K      60          0.678
LGA    E      61      E      61          0.656
LGA    A      62      A      62          0.650
LGA    G      63      G      63          0.501
LGA    V      64      V      64          0.613
LGA    D      65      D      65          2.382
LGA    I      66      I      66          2.516
LGA    V      67      V      67          1.944
LGA    G      68      G      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    -       -      S      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      W      77           -
LGA    -       -      V      78           -
LGA    -       -      L      79           -
LGA    -       -      V      80           -
LGA    -       -      D      81           -
LGA    S      69      A      82          2.648
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    -       -      H      88           -
LGA    -       -      V      89           -
LGA    -       -      M      90           -
LGA    -       -      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    -       -      V      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      Y      97           -
LGA    -       -      Y      98           -
LGA    -       -      D      99           -
LGA    -       -      I     100           -
LGA    -       -      E     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    -       -      G     106           -
LGA    -       -      Q     107           -
LGA    -       -      K     108           -
LGA    -       -      P     109           -
LGA    -       -      S     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      V     113           -
LGA    -       -      G     114           -
LGA    -       -      A     115           -
LGA    -       -      A     116           -
LGA    -       -      K     117           -
LGA    -       -      P     118           -
LGA    -       -      W     119           -
LGA    -       -      S     120           -
LGA    -       -      A     121           -
LGA    -       -      V     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26  122    5.0     25    1.11    96.00     19.820     2.073

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.748021 * X  +  -0.333457 * Y  +   0.573821 * Z  +  60.964729
  Y_new =  -0.315353 * X  +   0.939354 * Y  +   0.134788 * Z  + -17.768608
  Z_new =  -0.583966 * X  +  -0.080132 * Y  +  -0.807813 * Z  +  59.012894 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.042720    0.098873  [ DEG:  -174.3350      5.6650 ]
  Theta =   0.623606    2.517986  [ DEG:    35.7300    144.2700 ]
  Phi   =  -2.742620    0.398972  [ DEG:  -157.1406     22.8594 ]
 
# 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: T0354AL381_4                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354AL381_4.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26  122   5.0   25   1.11   96.00  19.820
REMARK  ---------------------------------------------------------- 
MOLECULE T0354AL381_4
REMARK Aligment from pdb entry: 1uvxA
ATOM      1  N   SER    44      33.325  33.227  38.326  1.00  0.00              
ATOM      2  CA  SER    44      32.781  34.338  37.558  1.00  0.00              
ATOM      3  C   SER    44      33.743  34.709  36.437  1.00  0.00              
ATOM      4  O   SER    44      34.701  33.983  36.168  1.00  0.00              
ATOM      5  N   ASN    45      33.489  35.842  35.791  1.00  0.00              
ATOM      6  CA  ASN    45      34.315  36.282  34.673  1.00  0.00              
ATOM      7  C   ASN    45      35.667  36.829  35.120  1.00  0.00              
ATOM      8  O   ASN    45      36.560  37.040  34.298  1.00  0.00              
ATOM      9  N   ARG    46      35.818  37.063  36.419  1.00  0.00              
ATOM     10  CA  ARG    46      37.103  37.493  36.959  1.00  0.00              
ATOM     11  C   ARG    46      38.101  36.338  36.918  1.00  0.00              
ATOM     12  O   ARG    46      39.268  36.527  36.580  1.00  0.00              
ATOM     13  N   GLN    47      37.630  35.142  37.257  1.00  0.00              
ATOM     14  CA  GLN    47      38.466  33.947  37.225  1.00  0.00              
ATOM     15  C   GLN    47      38.679  33.459  35.798  1.00  0.00              
ATOM     16  O   GLN    47      39.777  33.032  35.440  1.00  0.00              
ATOM     17  N   VAL    48      37.630  33.515  34.985  1.00  0.00              
ATOM     18  CA  VAL    48      37.740  33.073  33.601  1.00  0.00              
ATOM     19  C   VAL    48      38.698  33.953  32.805  1.00  0.00              
ATOM     20  O   VAL    48      39.458  33.460  31.972  1.00  0.00              
ATOM     21  N   LYS    49      38.657  35.256  33.068  1.00  0.00              
ATOM     22  CA  LYS    49      39.525  36.203  32.383  1.00  0.00              
ATOM     23  C   LYS    49      40.970  36.043  32.838  1.00  0.00              
ATOM     24  O   LYS    49      41.903  36.223  32.054  1.00  0.00              
ATOM     25  N   ALA    50      41.150  35.705  34.110  1.00  0.00              
ATOM     26  CA  ALA    50      42.483  35.452  34.639  1.00  0.00              
ATOM     27  C   ALA    50      43.091  34.243  33.934  1.00  0.00              
ATOM     28  O   ALA    50      44.224  34.295  33.450  1.00  0.00              
ATOM     29  N   LEU    51      42.327  33.156  33.873  1.00  0.00              
ATOM     30  CA  LEU    51      42.790  31.931  33.233  1.00  0.00              
ATOM     31  C   LEU    51      43.111  32.171  31.761  1.00  0.00              
ATOM     32  O   LEU    51      44.126  31.696  31.253  1.00  0.00              
ATOM     33  N   ALA    52      42.240  32.911  31.082  1.00  0.00              
ATOM     34  CA  ALA    52      42.456  33.246  29.680  1.00  0.00              
ATOM     35  C   ALA    52      43.745  34.039  29.510  1.00  0.00              
ATOM     36  O   ALA    52      44.575  33.721  28.659  1.00  0.00              
ATOM     37  N   ASN    53      43.907  35.073  30.327  1.00  0.00              
ATOM     38  CA  ASN    53      45.081  35.933  30.249  1.00  0.00              
ATOM     39  C   ASN    53      46.363  35.146  30.496  1.00  0.00              
ATOM     40  O   ASN    53      47.398  35.411  29.881  1.00  0.00              
ATOM     41  N   SER    54      46.287  34.176  31.400  1.00  0.00              
ATOM     42  CA  SER    54      47.447  33.371  31.753  1.00  0.00              
ATOM     43  C   SER    54      47.876  32.456  30.611  1.00  0.00              
ATOM     44  O   SER    54      49.068  32.224  30.405  1.00  0.00              
ATOM     45  N   VAL    55      46.902  31.936  29.872  1.00  0.00              
ATOM     46  CA  VAL    55      47.191  31.096  28.717  1.00  0.00              
ATOM     47  C   VAL    55      47.775  31.943  27.592  1.00  0.00              
ATOM     48  O   VAL    55      48.804  31.598  27.010  1.00  0.00              
ATOM     49  N   GLN    56      47.112  33.053  27.291  1.00  0.00              
ATOM     50  CA  GLN    56      47.615  33.992  26.297  1.00  0.00              
ATOM     51  C   GLN    56      49.073  34.337  26.591  1.00  0.00              
ATOM     52  O   GLN    56      49.944  34.174  25.737  1.00  0.00              
ATOM     53  N   VAL    57      49.326  34.813  27.806  1.00  0.00              
ATOM     54  CA  VAL    57      50.678  35.136  28.244  1.00  0.00              
ATOM     55  C   VAL    57      51.609  33.942  28.063  1.00  0.00              
ATOM     56  O   VAL    57      52.744  34.093  27.611  1.00  0.00              
ATOM     57  N   LYS    58      51.126  32.755  28.421  1.00  0.00              
ATOM     58  CA  LYS    58      51.902  31.530  28.260  1.00  0.00              
ATOM     59  C   LYS    58      52.365  31.354  26.818  1.00  0.00              
ATOM     60  O   LYS    58      53.562  31.231  26.549  1.00  0.00              
ATOM     61  N   LEU    59      51.409  31.337  25.897  1.00  0.00              
ATOM     62  CA  LEU    59      51.707  31.133  24.484  1.00  0.00              
ATOM     63  C   LEU    59      52.623  32.222  23.937  1.00  0.00              
ATOM     64  O   LEU    59      53.545  31.943  23.169  1.00  0.00              
ATOM     65  N   LYS    60      52.363  33.464  24.331  1.00  0.00              
ATOM     66  CA  LYS    60      53.177  34.585  23.880  1.00  0.00              
ATOM     67  C   LYS    60      54.639  34.366  24.251  1.00  0.00              
ATOM     68  O   LYS    60      55.541  34.686  23.480  1.00  0.00              
ATOM     69  N   GLU    61      54.862  33.811  25.438  1.00  0.00              
ATOM     70  CA  GLU    61      56.213  33.584  25.935  1.00  0.00              
ATOM     71  C   GLU    61      56.844  32.339  25.319  1.00  0.00              
ATOM     72  O   GLU    61      58.057  32.145  25.392  1.00  0.00              
ATOM     73  N   ALA    62      56.011  31.501  24.710  1.00  0.00              
ATOM     74  CA  ALA    62      56.484  30.277  24.076  1.00  0.00              
ATOM     75  C   ALA    62      56.728  30.483  22.584  1.00  0.00              
ATOM     76  O   ALA    62      57.085  29.546  21.868  1.00  0.00              
ATOM     77  N   GLY    63      56.533  31.715  22.124  1.00  0.00              
ATOM     78  CA  GLY    63      56.915  32.101  20.778  1.00  0.00              
ATOM     79  C   GLY    63      55.866  31.837  19.716  1.00  0.00              
ATOM     80  O   GLY    63      56.186  31.731  18.531  1.00  0.00              
ATOM     81  N   VAL    64      54.609  31.735  20.137  1.00  0.00              
ATOM     82  CA  VAL    64      53.516  31.432  19.222  1.00  0.00              
ATOM     83  C   VAL    64      53.089  32.663  18.432  1.00  0.00              
ATOM     84  O   VAL    64      52.870  33.730  19.004  1.00  0.00              
ATOM     85  N   ASP    65      52.975  32.512  17.116  1.00  0.00              
ATOM     86  CA  ASP    65      52.432  33.571  16.258  1.00  0.00              
ATOM     87  C   ASP    65      51.148  34.141  16.847  1.00  0.00              
ATOM     88  O   ASP    65      50.299  33.380  17.312  1.00  0.00              
ATOM     89  N   ILE    66      51.004  35.462  16.819  1.00  0.00              
ATOM     90  CA  ILE    66      49.842  36.129  17.416  1.00  0.00              
ATOM     91  C   ILE    66      48.531  35.616  16.828  1.00  0.00              
ATOM     92  O   ILE    66      47.539  35.506  17.549  1.00  0.00              
ATOM     93  N   VAL    67      48.531  35.310  15.535  1.00  0.00              
ATOM     94  CA  VAL    67      47.331  34.815  14.871  1.00  0.00              
ATOM     95  C   VAL    67      46.948  33.447  15.423  1.00  0.00              
ATOM     96  O   VAL    67      45.768  33.110  15.506  1.00  0.00              
ATOM     97  N   GLY    68      47.953  32.666  15.803  1.00  0.00              
ATOM     98  CA  GLY    68      47.721  31.362  16.411  1.00  0.00              
ATOM     99  C   GLY    68      47.185  31.518  17.829  1.00  0.00              
ATOM    100  O   GLY    68      46.359  30.725  18.282  1.00  0.00              
ATOM    101  N   SER    69      47.660  32.542  18.528  1.00  0.00              
ATOM    102  CA  SER    69      47.165  32.834  19.867  1.00  0.00              
ATOM    103  C   SER    69      45.698  33.247  19.787  1.00  0.00              
ATOM    104  O   SER    69      44.909  32.977  20.694  1.00  0.00              
END
