
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0347AL380_1
# Molecule2: number of CA atoms  196 ( 1574),  selected  196 , name T0347.pdb
# PARAMETERS: T0347AL380_1.T0347.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A      57      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      E       6           -
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      T      39           -
LGA    -       -      R      40           -
LGA    -       -      D      46           -
LGA    -       -      F      47           -
LGA    -       -      L      48           -
LGA    -       -      G      49           -
LGA    -       -      N      50           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      V     102           -
LGA    -       -      M     103           -
LGA    -       -      D     104           -
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -
LGA    -       -      I     109           -
LGA    -       -      Y     110           -
LGA    -       -      P     111           -
LGA    -       -      F     112           -
LGA    -       -      D     113           -
LGA    -       -      A     114           -
LGA    -       -      Q     115           -
LGA    -       -      G     116           -
LGA    -       -      L     117           -
LGA    -       -      R     118           -
LGA    -       -      R     119           -
LGA    -       -      Q     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      D     123           -
LGA    -       -      I     124           -
LGA    -       -      P     125           -
LGA    -       -      K     126           -
LGA    -       -      N     127           -
LGA    -       -      I     128           -
LGA    -       -      H     129           -
LGA    -       -      D     130           -
LGA    -       -      L     131           -
LGA    -       -      E     132           -
LGA    -       -      D     133           -
LGA    -       -      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    G      58      I     153           #
LGA    -       -      I     154           -
LGA    P      59      P     155          1.558
LGA    K      60      F     156          2.452
LGA    D      61      S     157          3.245
LGA    R      62      E     158          1.021
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    A      63      W     161          0.779
LGA    -       -      A     162           -
LGA    Y      64      D     163          2.397
LGA    L      65      F     164          1.623
LGA    I      66      L     165           #
LGA    D      67      R     166           #
LGA    H      68      R     167          4.198
LGA    H      69      R     168          3.804
LGA    H      70      I     169          4.671
LGA    L      71      D     170          2.671
LGA    V      72      -       -           -
LGA    L      73      R     171          0.992
LGA    A      74      D     172          2.293
LGA    L      75      L     173          1.718
LGA    S      76      L     174          0.951
LGA    K      77      S     175          1.951
LGA    E      78      D     176          0.721
LGA    G      79      S     177          2.658
LGA    V      80      F     178          1.624
LGA    E      81      D     179          2.972
LGA    -       -      D     180           -
LGA    -       -      A     181           -
LGA    H      82      L     182          0.513
LGA    V      83      A     183          3.188
LGA    L      84      E     184          3.222
LGA    -       -      A     185           -
LGA    -       -      M     186           -
LGA    -       -      K     187           -
LGA    T      85      L     188          1.040
LGA    -       -      A     189           -
LGA    -       -      K     190           -
LGA    S      86      S     191          2.862
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    E      87      A     194          1.831
LGA    V      88      R     195          2.455
LGA    A      89      H     196          0.789
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33  196    5.0     28    2.41    10.71     10.175     1.114

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.865684 * X  +  -0.493312 * Y  +   0.085053 * Z  +  23.598980
  Y_new =  -0.183614 * X  +   0.154847 * Y  +  -0.970726 * Z  +  75.599869
  Z_new =   0.465701 * X  +  -0.855959 * Y  +  -0.224627 * Z  +  42.045021 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.827437    1.314156  [ DEG:  -104.7044     75.2956 ]
  Theta =  -0.484426   -2.657166  [ DEG:   -27.7556   -152.2444 ]
  Phi   =  -2.932588    0.209005  [ DEG:  -168.0249     11.9751 ]
 
# 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: T0347AL380_1                                  
REMARK     2: T0347.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL380_1.T0347.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33  196   5.0   28   2.41   10.71  10.175
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL380_1
REMARK Aligment from pdb entry: 1vk1A
ATOM      1  N   ALA    57      16.856  49.818   7.342  1.00  0.00              
ATOM      2  CA  ALA    57      15.873  48.836   7.793  1.00  0.00              
ATOM      3  C   ALA    57      16.468  47.438   7.529  1.00  0.00              
ATOM      4  O   ALA    57      16.791  47.106   6.397  1.00  0.00              
ATOM      5  N   GLY    58      16.633  46.617   8.579  1.00  0.00              
ATOM      6  CA  GLY    58      17.262  45.293   8.401  1.00  0.00              
ATOM      7  C   GLY    58      16.601  44.434   7.324  1.00  0.00              
ATOM      8  O   GLY    58      15.375  44.434   7.185  1.00  0.00              
ATOM      9  N   PRO    59      17.426  43.726   6.563  1.00  0.00              
ATOM     10  CA  PRO    59      16.946  42.862   5.497  1.00  0.00              
ATOM     11  C   PRO    59      16.538  43.580   4.214  1.00  0.00              
ATOM     12  O   PRO    59      16.038  42.942   3.284  1.00  0.00              
ATOM     13  N   LYS    60      16.745  44.905   4.157  1.00  0.00              
ATOM     14  CA  LYS    60      16.419  45.691   2.979  1.00  0.00              
ATOM     15  C   LYS    60      17.563  46.595   2.638  1.00  0.00              
ATOM     16  O   LYS    60      18.490  46.770   3.425  1.00  0.00              
ATOM     17  N   ASP    61      17.462  47.232   1.477  1.00  0.00              
ATOM     18  CA  ASP    61      18.326  48.358   1.156  1.00  0.00              
ATOM     19  C   ASP    61      17.544  49.694   1.240  1.00  0.00              
ATOM     20  O   ASP    61      17.840  50.648   0.538  1.00  0.00              
ATOM     21  N   ARG    62      16.577  49.745   2.139  1.00  0.00              
ATOM     22  CA  ARG    62      15.763  50.926   2.380  1.00  0.00              
ATOM     23  C   ARG    62      16.130  51.502   3.747  1.00  0.00              
ATOM     24  O   ARG    62      16.737  50.817   4.581  1.00  0.00              
ATOM     25  N   ALA    63      15.728  52.748   3.975  1.00  0.00              
ATOM     26  CA  ALA    63      16.052  53.473   5.183  1.00  0.00              
ATOM     27  C   ALA    63      14.817  53.986   5.887  1.00  0.00              
ATOM     28  O   ALA    63      13.899  54.530   5.259  1.00  0.00              
ATOM     29  N   TYR    64      14.812  53.827   7.202  1.00  0.00              
ATOM     30  CA  TYR    64      13.935  54.556   8.086  1.00  0.00              
ATOM     31  C   TYR    64      14.348  56.006   8.114  1.00  0.00              
ATOM     32  O   TYR    64      15.500  56.311   8.370  1.00  0.00              
ATOM     33  N   LEU    65      13.394  56.912   7.886  1.00  0.00              
ATOM     34  CA  LEU    65      13.613  58.315   8.160  1.00  0.00              
ATOM     35  C   LEU    65      13.570  58.470   9.677  1.00  0.00              
ATOM     36  O   LEU    65      12.551  58.260  10.290  1.00  0.00              
ATOM     37  N   ILE    66      14.694  58.858  10.257  1.00  0.00              
ATOM     38  CA  ILE    66      14.779  59.145  11.693  1.00  0.00              
ATOM     39  C   ILE    66      14.343  60.596  11.891  1.00  0.00              
ATOM     40  O   ILE    66      13.491  60.882  12.695  1.00  0.00              
ATOM     41  N   ASP    67      14.951  61.501  11.131  1.00  0.00              
ATOM     42  CA  ASP    67      14.624  62.905  11.162  1.00  0.00              
ATOM     43  C   ASP    67      14.653  63.458   9.756  1.00  0.00              
ATOM     44  O   ASP    67      15.590  63.207   9.012  1.00  0.00              
ATOM     45  N   HIS    68      13.628  64.228   9.417  1.00  0.00              
ATOM     46  CA  HIS    68      13.554  64.905   8.125  1.00  0.00              
ATOM     47  C   HIS    68      12.360  64.561   7.257  1.00  0.00              
ATOM     48  O   HIS    68      12.431  64.695   6.042  1.00  0.00              
ATOM     49  N   HIS    69      11.230  64.187   7.845  1.00  0.00              
ATOM     50  CA  HIS    69      10.040  63.876   7.064  1.00  0.00              
ATOM     51  C   HIS    69       9.594  65.021   6.172  1.00  0.00              
ATOM     52  O   HIS    69       9.249  64.808   5.016  1.00  0.00              
ATOM     53  N   HIS    70       9.584  66.239   6.699  1.00  0.00              
ATOM     54  CA  HIS    70       9.118  67.377   5.924  1.00  0.00              
ATOM     55  C   HIS    70      10.095  67.742   4.827  1.00  0.00              
ATOM     56  O   HIS    70       9.668  68.139   3.727  1.00  0.00              
ATOM     57  N   LEU    71      11.389  67.595   5.098  1.00  0.00              
ATOM     58  CA  LEU    71      12.427  67.791   4.081  1.00  0.00              
ATOM     59  C   LEU    71      12.331  66.776   2.952  1.00  0.00              
ATOM     60  O   LEU    71      12.339  67.131   1.770  1.00  0.00              
ATOM     61  N   VAL    72      12.178  65.502   3.302  1.00  0.00              
ATOM     62  CA  VAL    72      11.997  64.440   2.311  1.00  0.00              
ATOM     63  C   VAL    72      10.749  64.664   1.475  1.00  0.00              
ATOM     64  O   VAL    72      10.799  64.628   0.238  1.00  0.00              
ATOM     65  N   LEU    73       9.631  64.932   2.130  1.00  0.00              
ATOM     66  CA  LEU    73       8.380  65.085   1.425  1.00  0.00              
ATOM     67  C   LEU    73       8.392  66.348   0.561  1.00  0.00              
ATOM     68  O   LEU    73       7.856  66.349  -0.549  1.00  0.00              
ATOM     69  N   ALA    74       9.001  67.425   1.058  1.00  0.00              
ATOM     70  CA  ALA    74       9.099  68.646   0.280  1.00  0.00              
ATOM     71  C   ALA    74       9.962  68.468  -0.955  1.00  0.00              
ATOM     72  O   ALA    74       9.605  68.920  -2.047  1.00  0.00              
ATOM     73  N   LEU    75      11.084  67.788  -0.798  1.00  0.00              
ATOM     74  CA  LEU    75      11.942  67.501  -1.928  1.00  0.00              
ATOM     75  C   LEU    75      11.240  66.613  -2.952  1.00  0.00              
ATOM     76  O   LEU    75      11.380  66.831  -4.156  1.00  0.00              
ATOM     77  N   SER    76      10.516  65.604  -2.494  1.00  0.00              
ATOM     78  CA  SER    76       9.762  64.766  -3.418  1.00  0.00              
ATOM     79  C   SER    76       8.728  65.592  -4.163  1.00  0.00              
ATOM     80  O   SER    76       8.589  65.459  -5.386  1.00  0.00              
ATOM     81  N   LYS    77       8.027  66.471  -3.456  1.00  0.00              
ATOM     82  CA  LYS    77       7.009  67.325  -4.091  1.00  0.00              
ATOM     83  C   LYS    77       7.634  68.232  -5.147  1.00  0.00              
ATOM     84  O   LYS    77       7.016  68.495  -6.199  1.00  0.00              
ATOM     85  N   GLU    78       8.854  68.701  -4.896  1.00  0.00              
ATOM     86  CA  GLU    78       9.570  69.561  -5.841  1.00  0.00              
ATOM     87  C   GLU    78      10.156  68.801  -7.033  1.00  0.00              
ATOM     88  O   GLU    78      10.634  69.417  -7.992  1.00  0.00              
ATOM     89  N   GLY    79      10.139  67.480  -6.981  1.00  0.00              
ATOM     90  CA  GLY    79      10.674  66.644  -8.048  1.00  0.00              
ATOM     91  C   GLY    79      12.155  66.310  -7.932  1.00  0.00              
ATOM     92  O   GLY    79      12.750  65.868  -8.900  1.00  0.00              
ATOM     93  N   VAL    80      12.747  66.464  -6.741  1.00  0.00              
ATOM     94  CA  VAL    80      14.136  66.131  -6.541  1.00  0.00              
ATOM     95  C   VAL    80      14.318  64.622  -6.481  1.00  0.00              
ATOM     96  O   VAL    80      13.336  63.874  -6.388  1.00  0.00              
ATOM     97  N   GLU    81      15.570  64.196  -6.501  1.00  0.00              
ATOM     98  CA  GLU    81      15.928  62.790  -6.530  1.00  0.00              
ATOM     99  C   GLU    81      16.665  62.283  -5.311  1.00  0.00              
ATOM    100  O   GLU    81      16.552  61.114  -4.995  1.00  0.00              
ATOM    101  N   HIS    82      17.454  63.137  -4.656  1.00  0.00              
ATOM    102  CA  HIS    82      18.336  62.690  -3.595  1.00  0.00              
ATOM    103  C   HIS    82      18.408  63.737  -2.503  1.00  0.00              
ATOM    104  O   HIS    82      18.024  64.889  -2.722  1.00  0.00              
ATOM    105  N   VAL    83      18.907  63.339  -1.335  1.00  0.00              
ATOM    106  CA  VAL    83      19.173  64.301  -0.285  1.00  0.00              
ATOM    107  C   VAL    83      20.404  63.878   0.497  1.00  0.00              
ATOM    108  O   VAL    83      20.620  62.690   0.743  1.00  0.00              
ATOM    109  N   LEU    84      21.210  64.849   0.942  1.00  0.00              
ATOM    110  CA  LEU    84      22.323  64.549   1.837  1.00  0.00              
ATOM    111  C   LEU    84      21.827  64.020   3.178  1.00  0.00              
ATOM    112  O   LEU    84      20.895  64.581   3.752  1.00  0.00              
ATOM    113  N   THR    85      22.461  62.954   3.637  1.00  0.00              
ATOM    114  CA  THR    85      21.990  62.162   4.740  1.00  0.00              
ATOM    115  C   THR    85      23.135  61.694   5.640  1.00  0.00              
ATOM    116  O   THR    85      24.244  61.441   5.190  1.00  0.00              
ATOM    117  N   SER    86      22.811  61.538   6.912  1.00  0.00              
ATOM    118  CA  SER    86      23.689  60.904   7.880  1.00  0.00              
ATOM    119  C   SER    86      23.042  59.576   8.211  1.00  0.00              
ATOM    120  O   SER    86      21.872  59.541   8.579  1.00  0.00              
ATOM    121  N   GLU    87      23.800  58.494   8.089  1.00  0.00              
ATOM    122  CA  GLU    87      23.314  57.149   8.340  1.00  0.00              
ATOM    123  C   GLU    87      23.719  56.723   9.764  1.00  0.00              
ATOM    124  O   GLU    87      24.899  56.722  10.095  1.00  0.00              
ATOM    125  N   VAL    88      22.733  56.398  10.581  1.00  0.00              
ATOM    126  CA  VAL    88      22.873  56.051  11.983  1.00  0.00              
ATOM    127  C   VAL    88      22.654  54.555  12.180  1.00  0.00              
ATOM    128  O   VAL    88      21.955  53.905  11.388  1.00  0.00              
ATOM    129  N   ALA    89      23.237  54.009  13.250  1.00  0.00              
ATOM    130  CA  ALA    89      22.813  52.718  13.778  1.00  0.00              
ATOM    131  C   ALA    89      21.697  53.032  14.765  1.00  0.00              
ATOM    132  O   ALA    89      21.956  53.556  15.836  1.00  0.00              
END
