
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0304AL381_4
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304AL381_4.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# 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    -       -      D      16           -
LGA    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    G      96      P      28          0.732
LGA    L      97      C      29          1.795
LGA    T      98      F      30          2.527
LGA    C      99      G      31          1.144
LGA    K     100      A      32          0.765
LGA    A     101      R      33          1.575
LGA    D     102      L      34          1.850
LGA    T     103      V      35          1.610
LGA    L     104      Q      36          3.715
LGA    S     105      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    -       -      P      67           -
LGA    -       -      L      68           -
LGA    -       -      L      69           -
LGA    -       -      M      70           -
LGA    -       -      K      71           -
LGA    -       -      Q      72           -
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    -       -      L      75           -
LGA    -       -      M      76           -
LGA    -       -      L      77           -
LGA    -       -      T      78           -
LGA    -       -      S      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    S     106      P      84          5.184
LGA    C     107      R      85          2.671
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    D     108      C     107          2.211
LGA    -       -      D     108           -
LGA    Y     109      Y     109          2.003
LGA    V     110      V     110          1.029
LGA    Y     111      Y     111          2.001
LGA    L     112      L     112          1.830
LGA    A     113      A     113          1.126
LGA    V     114      V     114          1.628
LGA    Y     115      Y     115          0.935
LGA    P     116      P     116          1.226
LGA    T     117      T     117          2.710
LGA    P     118      P     118          2.733
LGA    E     119      E     119          3.486
LGA    -       -      M     120           -
LGA    -       -      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24  107    5.0     23    2.27    47.83     16.513     0.969

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.692380 * X  +   0.700775 * Y  +  -0.171825 * Z  +  23.783142
  Y_new =   0.675451 * X  +   0.545771 * Y  +  -0.495883 * Z  + 140.784119
  Z_new =  -0.253725 * X  +  -0.459399 * Y  +  -0.851220 * Z  + 236.978867 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.646696    0.494897  [ DEG:  -151.6445     28.3555 ]
  Theta =   0.256529    2.885063  [ DEG:    14.6981    165.3019 ]
  Phi   =   2.368571   -0.773022  [ DEG:   135.7091    -44.2909 ]
 
# 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: T0304AL381_4                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL381_4.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  107   5.0   23   2.27   47.83  16.513
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL381_4
REMARK Aligment from pdb entry: 2alaA
ATOM      1  N   GLY    96      37.413  23.096  31.627  1.00  0.00              
ATOM      2  CA  GLY    96      38.038  22.110  32.520  1.00  0.00              
ATOM      3  C   GLY    96      38.676  22.786  33.743  1.00  0.00              
ATOM      4  O   GLY    96      39.819  22.496  34.104  1.00  0.00              
ATOM      5  N   LEU    97      37.926  23.684  34.378  1.00  0.00              
ATOM      6  CA  LEU    97      38.414  24.399  35.556  1.00  0.00              
ATOM      7  C   LEU    97      38.378  23.503  36.793  1.00  0.00              
ATOM      8  O   LEU    97      37.312  23.040  37.206  1.00  0.00              
ATOM      9  N   THR    98      39.551  23.262  37.375  1.00  0.00              
ATOM     10  CA  THR    98      39.675  22.482  38.605  1.00  0.00              
ATOM     11  C   THR    98      40.621  23.184  39.576  1.00  0.00              
ATOM     12  O   THR    98      41.470  23.974  39.159  1.00  0.00              
ATOM     13  N   CYS    99      40.476  22.880  40.864  1.00  0.00              
ATOM     14  CA  CYS    99      41.134  23.636  41.929  1.00  0.00              
ATOM     15  C   CYS    99      41.815  22.739  42.961  1.00  0.00              
ATOM     16  O   CYS    99      41.145  22.114  43.786  1.00  0.00              
ATOM     17  N   LYS   100      43.147  22.693  42.916  1.00  0.00              
ATOM     18  CA  LYS   100      43.946  21.965  43.905  1.00  0.00              
ATOM     19  C   LYS   100      44.519  22.939  44.938  1.00  0.00              
ATOM     20  O   LYS   100      44.838  24.084  44.610  1.00  0.00              
ATOM     21  N   ALA   101      44.639  22.476  46.183  1.00  0.00              
ATOM     22  CA  ALA   101      45.219  23.265  47.269  1.00  0.00              
ATOM     23  C   ALA   101      46.538  22.629  47.700  1.00  0.00              
ATOM     24  O   ALA   101      46.558  21.489  48.165  1.00  0.00              
ATOM     25  N   ASP   102      47.633  23.370  47.542  1.00  0.00              
ATOM     26  CA  ASP   102      48.971  22.859  47.849  1.00  0.00              
ATOM     27  C   ASP   102      49.219  22.815  49.355  1.00  0.00              
ATOM     28  O   ASP   102      49.487  21.750  49.915  1.00  0.00              
ATOM     29  N   THR   103      49.139  23.978  49.997  1.00  0.00              
ATOM     30  CA  THR   103      49.301  24.090  51.447  1.00  0.00              
ATOM     31  C   THR   103      48.346  25.143  51.999  1.00  0.00              
ATOM     32  O   THR   103      47.824  25.973  51.252  1.00  0.00              
ATOM     33  N   LEU   104      48.127  25.103  53.310  1.00  0.00              
ATOM     34  CA  LEU   104      47.145  25.973  53.952  1.00  0.00              
ATOM     35  C   LEU   104      47.318  26.026  55.474  1.00  0.00              
ATOM     36  O   LEU   104      47.705  25.036  56.098  1.00  0.00              
ATOM     37  N   SER   105      45.574  32.345  59.584  1.00  0.00              
ATOM     38  CA  SER   105      46.659  33.285  59.303  1.00  0.00              
ATOM     39  C   SER   105      46.145  34.450  58.456  1.00  0.00              
ATOM     40  O   SER   105      44.958  34.506  58.120  1.00  0.00              
ATOM     41  N   SER   106      47.038  35.380  58.122  1.00  0.00              
ATOM     42  CA  SER   106      46.687  36.503  57.253  1.00  0.00              
ATOM     43  C   SER   106      46.363  35.980  55.852  1.00  0.00              
ATOM     44  O   SER   106      45.300  36.277  55.313  1.00  0.00              
ATOM     45  N   CYS   107      47.285  35.203  55.278  1.00  0.00              
ATOM     46  CA  CYS   107      47.074  34.532  53.985  1.00  0.00              
ATOM     47  C   CYS   107      47.835  33.202  53.934  1.00  0.00              
ATOM     48  O   CYS   107      48.821  33.065  53.206  1.00  0.00              
ATOM     49  N   ASP   108      47.369  32.228  54.711  1.00  0.00              
ATOM     50  CA  ASP   108      48.030  30.926  54.799  1.00  0.00              
ATOM     51  C   ASP   108      47.820  30.030  53.589  1.00  0.00              
ATOM     52  O   ASP   108      48.658  29.177  53.292  1.00  0.00              
ATOM     53  N   TYR   109      46.706  30.227  52.888  1.00  0.00              
ATOM     54  CA  TYR   109      46.311  29.346  51.791  1.00  0.00              
ATOM     55  C   TYR   109      47.154  29.466  50.531  1.00  0.00              
ATOM     56  O   TYR   109      47.589  30.561  50.166  1.00  0.00              
ATOM     57  N   VAL   110      47.380  28.328  49.873  1.00  0.00              
ATOM     58  CA  VAL   110      48.091  28.275  48.591  1.00  0.00              
ATOM     59  C   VAL   110      47.411  27.263  47.659  1.00  0.00              
ATOM     60  O   VAL   110      47.669  26.059  47.746  1.00  0.00              
ATOM     61  N   TYR   111      46.545  27.760  46.774  1.00  0.00              
ATOM     62  CA  TYR   111      45.829  26.914  45.814  1.00  0.00              
ATOM     63  C   TYR   111      46.254  27.217  44.380  1.00  0.00              
ATOM     64  O   TYR   111      46.743  28.309  44.088  1.00  0.00              
ATOM     65  N   LEU   112      46.052  26.241  43.494  1.00  0.00              
ATOM     66  CA  LEU   112      46.344  26.389  42.065  1.00  0.00              
ATOM     67  C   LEU   112      45.169  25.875  41.228  1.00  0.00              
ATOM     68  O   LEU   112      44.487  24.923  41.620  1.00  0.00              
ATOM     69  N   ALA   113      44.942  26.509  40.079  1.00  0.00              
ATOM     70  CA  ALA   113      43.841  26.145  39.191  1.00  0.00              
ATOM     71  C   ALA   113      44.351  25.649  37.843  1.00  0.00              
ATOM     72  O   ALA   113      45.069  26.366  37.145  1.00  0.00              
ATOM     73  N   VAL   114      43.981  24.420  37.486  1.00  0.00              
ATOM     74  CA  VAL   114      44.240  23.892  36.147  1.00  0.00              
ATOM     75  C   VAL   114      43.017  24.136  35.268  1.00  0.00              
ATOM     76  O   VAL   114      41.881  24.115  35.748  1.00  0.00              
ATOM     77  N   TYR   115      43.263  24.369  33.981  1.00  0.00              
ATOM     78  CA  TYR   115      42.218  24.771  33.040  1.00  0.00              
ATOM     79  C   TYR   115      42.725  24.710  31.595  1.00  0.00              
ATOM     80  O   TYR   115      43.873  24.338  31.342  1.00  0.00              
ATOM     81  N   PRO   116      41.851  25.069  30.660  1.00  0.00              
ATOM     82  CA  PRO   116      42.229  25.309  29.269  1.00  0.00              
ATOM     83  C   PRO   116      41.557  26.594  28.797  1.00  0.00              
ATOM     84  O   PRO   116      40.396  26.837  29.116  1.00  0.00              
ATOM     85  N   THR   117      42.285  27.411  28.042  1.00  0.00              
ATOM     86  CA  THR   117      41.732  28.646  27.488  1.00  0.00              
ATOM     87  C   THR   117      42.185  28.857  26.044  1.00  0.00              
ATOM     88  O   THR   117      43.295  28.474  25.669  1.00  0.00              
ATOM     89  N   PRO   118      41.314  29.465  25.243  1.00  0.00              
ATOM     90  CA  PRO   118      41.595  29.702  23.822  1.00  0.00              
ATOM     91  C   PRO   118      42.707  30.729  23.574  1.00  0.00              
ATOM     92  O   PRO   118      43.401  30.648  22.559  1.00  0.00              
ATOM     93  N   GLU   119      42.869  31.684  24.489  1.00  0.00              
ATOM     94  CA  GLU   119      43.968  32.660  24.410  1.00  0.00              
ATOM     95  C   GLU   119      44.200  33.396  25.737  1.00  0.00              
ATOM     96  O   GLU   119      43.415  33.258  26.678  1.00  0.00              
END
