
#######################################################
#                                                     #
#                        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   38 (  152),  selected   38 , name T0347AL381_2
# Molecule2: number of CA atoms  196 ( 1574),  selected  196 , name T0347.pdb
# PARAMETERS: T0347AL381_2.T0347.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      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    D      43      K      16          2.296
LGA    G      44      L      17          1.814
LGA    D      45      R      18          1.950
LGA    D      46      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    F      47      V      55          4.439
LGA    L      48      V      56          3.715
LGA    G      49      -       -           -
LGA    N      50      A      57          1.465
LGA    H      51      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    I      52      A      89          4.368
LGA    V      53      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    P      54      N     107          4.786
LGA    V      55      L     108          4.610
LGA    -       -      I     109           -
LGA    V      56      Y     110          3.586
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    A      57      L     131           #
LGA    G      58      E     132          4.571
LGA    -       -      D     133           -
LGA    I      66      D     134          3.950
LGA    D      67      P     135          3.791
LGA    -       -      F     136           -
LGA    H      68      R     137          3.157
LGA    H      69      S     138          1.107
LGA    H      70      L     139          1.533
LGA    L      71      A     140          2.307
LGA    V      72      G     141          1.279
LGA    L      73      A     142          1.086
LGA    A      74      L     143          1.628
LGA    L      75      R     144          0.862
LGA    S      76      M     145          1.279
LGA    K      77      A     146          1.975
LGA    E      78      G     147          2.660
LGA    -       -      G     148           -
LGA    G      79      Y     149          4.243
LGA    V      80      A     150          2.714
LGA    E      81      K     151          2.703
LGA    H      82      V     152          1.626
LGA    -       -      I     153           -
LGA    V      83      I     154          2.926
LGA    L      84      P     155          2.682
LGA    T      85      F     156          3.765
LGA    S      86      S     157           -
LGA    E      87      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    -       -      D     172           -
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    -       -      F     178           -
LGA    -       -      D     179           -
LGA    -       -      D     180           -
LGA    -       -      A     181           -
LGA    -       -      L     182           -
LGA    -       -      A     183           -
LGA    -       -      E     184           -
LGA    -       -      A     185           -
LGA    -       -      M     186           -
LGA    -       -      K     187           -
LGA    -       -      L     188           -
LGA    -       -      A     189           -
LGA    -       -      K     190           -
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    -       -      A     194           -
LGA    -       -      R     195           -
LGA    -       -      H     196           -
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)   38  196    5.0     31    2.99     0.00     10.124     1.002

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.235665 * X  +  -0.163127 * Y  +   0.958046 * Z  + -71.935349
  Y_new =   0.834640 * X  +  -0.471020 * Y  +  -0.285510 * Z  +  73.385384
  Z_new =   0.497833 * X  +   0.866908 * Y  +   0.025149 * Z  + -74.362396 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.541795   -1.599798  [ DEG:    88.3383    -91.6617 ]
  Theta =  -0.521098   -2.620494  [ DEG:   -29.8567   -150.1433 ]
  Phi   =   1.295605   -1.845988  [ DEG:    74.2327   -105.7673 ]
 
# 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: T0347AL381_2                                  
REMARK     2: T0347.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL381_2.T0347.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38  196   5.0   31   2.99    0.00  10.124
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL381_2
REMARK Aligment from pdb entry: 1c30B
ATOM      1  N   ASP    43      -1.166  33.598  -8.146  1.00  0.00              
ATOM      2  CA  ASP    43      -0.908  34.953  -7.784  1.00  0.00              
ATOM      3  C   ASP    43       0.400  35.042  -6.994  1.00  0.00              
ATOM      4  O   ASP    43       0.821  34.112  -6.291  1.00  0.00              
ATOM      5  N   GLY    44       1.072  36.184  -7.178  1.00  0.00              
ATOM      6  CA  GLY    44       2.354  36.460  -6.581  1.00  0.00              
ATOM      7  C   GLY    44       2.452  36.212  -5.096  1.00  0.00              
ATOM      8  O   GLY    44       3.356  35.518  -4.663  1.00  0.00              
ATOM      9  N   ASP    45       1.521  36.789  -4.331  1.00  0.00              
ATOM     10  CA  ASP    45       1.524  36.606  -2.886  1.00  0.00              
ATOM     11  C   ASP    45       1.469  35.140  -2.513  1.00  0.00              
ATOM     12  O   ASP    45       2.249  34.649  -1.683  1.00  0.00              
ATOM     13  N   ASP    46       0.524  34.427  -3.125  1.00  0.00              
ATOM     14  CA  ASP    46       0.425  33.006  -2.865  1.00  0.00              
ATOM     15  C   ASP    46       1.721  32.313  -3.201  1.00  0.00              
ATOM     16  O   ASP    46       2.151  31.399  -2.525  1.00  0.00              
ATOM     17  N   PHE    47       2.327  32.749  -4.276  1.00  0.00              
ATOM     18  CA  PHE    47       3.572  32.169  -4.683  1.00  0.00              
ATOM     19  C   PHE    47       4.661  32.446  -3.659  1.00  0.00              
ATOM     20  O   PHE    47       5.470  31.590  -3.352  1.00  0.00              
ATOM     21  N   LEU    48       4.702  33.671  -3.118  1.00  0.00              
ATOM     22  CA  LEU    48       5.711  33.995  -2.128  1.00  0.00              
ATOM     23  C   LEU    48       5.510  33.189  -0.862  1.00  0.00              
ATOM     24  O   LEU    48       6.449  32.704  -0.237  1.00  0.00              
ATOM     25  N   GLY    49       4.263  33.073  -0.478  1.00  0.00              
ATOM     26  CA  GLY    49       3.991  32.347   0.724  1.00  0.00              
ATOM     27  C   GLY    49       4.503  30.923   0.635  1.00  0.00              
ATOM     28  O   GLY    49       5.162  30.412   1.524  1.00  0.00              
ATOM     29  N   ASN    50       4.209  30.317  -0.501  1.00  0.00              
ATOM     30  CA  ASN    50       4.608  28.961  -0.852  1.00  0.00              
ATOM     31  C   ASN    50       6.115  28.748  -0.854  1.00  0.00              
ATOM     32  O   ASN    50       6.601  27.664  -0.492  1.00  0.00              
ATOM     33  N   HIS    51       6.852  29.761  -1.292  1.00  0.00              
ATOM     34  CA  HIS    51       8.295  29.672  -1.367  1.00  0.00              
ATOM     35  C   HIS    51       8.961  30.139  -0.114  1.00  0.00              
ATOM     36  O   HIS    51      10.186  30.207  -0.046  1.00  0.00              
ATOM     37  N   ILE    52       8.091  30.491   0.836  1.00  0.00              
ATOM     38  CA  ILE    52       8.472  31.001   2.128  1.00  0.00              
ATOM     39  C   ILE    52       9.330  32.242   2.048  1.00  0.00              
ATOM     40  O   ILE    52      10.348  32.339   2.744  1.00  0.00              
ATOM     41  N   VAL    53       8.902  33.179   1.198  1.00  0.00              
ATOM     42  CA  VAL    53       9.650  34.403   1.028  1.00  0.00              
ATOM     43  C   VAL    53       9.086  35.568   1.831  1.00  0.00              
ATOM     44  O   VAL    53       7.897  35.853   1.744  1.00  0.00              
ATOM     45  N   PRO    54       9.946  36.258   2.579  1.00  0.00              
ATOM     46  CA  PRO    54       9.542  37.442   3.338  1.00  0.00              
ATOM     47  C   PRO    54       9.476  38.577   2.327  1.00  0.00              
ATOM     48  O   PRO    54      10.474  38.828   1.653  1.00  0.00              
ATOM     49  N   VAL    55       8.307  39.214   2.158  1.00  0.00              
ATOM     50  CA  VAL    55       8.191  40.302   1.198  1.00  0.00              
ATOM     51  C   VAL    55       7.457  41.495   1.796  1.00  0.00              
ATOM     52  O   VAL    55       6.601  41.384   2.675  1.00  0.00              
ATOM     53  N   VAL    56       7.774  42.664   1.286  1.00  0.00              
ATOM     54  CA  VAL    56       7.129  43.847   1.781  1.00  0.00              
ATOM     55  C   VAL    56       6.635  44.677   0.606  1.00  0.00              
ATOM     56  O   VAL    56       7.276  44.768  -0.446  1.00  0.00              
ATOM     57  N   ALA    57       5.469  45.272   0.763  1.00  0.00              
ATOM     58  CA  ALA    57       4.931  46.121  -0.290  1.00  0.00              
ATOM     59  C   ALA    57       4.568  47.443   0.330  1.00  0.00              
ATOM     60  O   ALA    57       4.615  47.569   1.561  1.00  0.00              
ATOM     61  N   GLY    58       4.227  48.420  -0.504  1.00  0.00              
ATOM     62  CA  GLY    58       3.786  49.731  -0.054  1.00  0.00              
ATOM     63  C   GLY    58       4.814  50.700   0.496  1.00  0.00              
ATOM     64  O   GLY    58       4.464  51.619   1.240  1.00  0.00              
ATOM     65  N   ILE    66       6.065  50.537   0.104  1.00  0.00              
ATOM     66  CA  ILE    66       7.106  51.417   0.536  1.00  0.00              
ATOM     67  C   ILE    66       7.615  52.295  -0.618  1.00  0.00              
ATOM     68  O   ILE    66       7.460  51.995  -1.795  1.00  0.00              
ATOM     69  N   ASP    67       8.224  53.405  -0.243  1.00  0.00              
ATOM     70  CA  ASP    67       8.787  54.328  -1.194  1.00  0.00              
ATOM     71  C   ASP    67      10.035  53.713  -1.840  1.00  0.00              
ATOM     72  O   ASP    67      11.188  53.984  -1.478  1.00  0.00              
ATOM     73  N   HIS    68       9.798  52.878  -2.818  1.00  0.00              
ATOM     74  CA  HIS    68      10.909  52.257  -3.517  1.00  0.00              
ATOM     75  C   HIS    68      11.839  53.211  -4.239  1.00  0.00              
ATOM     76  O   HIS    68      13.032  52.915  -4.433  1.00  0.00              
ATOM     77  N   HIS    69      11.323  54.345  -4.641  1.00  0.00              
ATOM     78  CA  HIS    69      12.177  55.275  -5.342  1.00  0.00              
ATOM     79  C   HIS    69      13.178  55.888  -4.377  1.00  0.00              
ATOM     80  O   HIS    69      14.343  56.153  -4.687  1.00  0.00              
ATOM     81  N   HIS    70      12.708  56.095  -3.164  1.00  0.00              
ATOM     82  CA  HIS    70      13.564  56.665  -2.130  1.00  0.00              
ATOM     83  C   HIS    70      14.701  55.699  -1.876  1.00  0.00              
ATOM     84  O   HIS    70      15.885  56.073  -1.859  1.00  0.00              
ATOM     85  N   LEU    71      14.276  54.442  -1.705  1.00  0.00              
ATOM     86  CA  LEU    71      15.172  53.318  -1.487  1.00  0.00              
ATOM     87  C   LEU    71      16.228  53.245  -2.594  1.00  0.00              
ATOM     88  O   LEU    71      17.434  53.238  -2.348  1.00  0.00              
ATOM     89  N   VAL    72      15.769  53.225  -3.833  1.00  0.00              
ATOM     90  CA  VAL    72      16.639  53.193  -5.002  1.00  0.00              
ATOM     91  C   VAL    72      17.628  54.344  -5.018  1.00  0.00              
ATOM     92  O   VAL    72      18.800  54.168  -5.299  1.00  0.00              
ATOM     93  N   LEU    73      17.162  55.551  -4.744  1.00  0.00              
ATOM     94  CA  LEU    73      18.044  56.694  -4.780  1.00  0.00              
ATOM     95  C   LEU    73      19.111  56.629  -3.706  1.00  0.00              
ATOM     96  O   LEU    73      20.211  57.151  -3.832  1.00  0.00              
ATOM     97  N   ALA    74      18.767  55.983  -2.627  1.00  0.00              
ATOM     98  CA  ALA    74      19.682  55.825  -1.520  1.00  0.00              
ATOM     99  C   ALA    74      20.853  54.883  -1.862  1.00  0.00              
ATOM    100  O   ALA    74      22.023  55.179  -1.605  1.00  0.00              
ATOM    101  N   LEU    75      20.504  53.744  -2.471  1.00  0.00              
ATOM    102  CA  LEU    75      21.419  52.713  -2.924  1.00  0.00              
ATOM    103  C   LEU    75      22.348  53.270  -4.005  1.00  0.00              
ATOM    104  O   LEU    75      23.550  52.997  -4.074  1.00  0.00              
ATOM    105  N   SER    76      21.776  54.065  -4.903  1.00  0.00              
ATOM    106  CA  SER    76      22.541  54.641  -5.980  1.00  0.00              
ATOM    107  C   SER    76      23.565  55.623  -5.451  1.00  0.00              
ATOM    108  O   SER    76      24.758  55.575  -5.693  1.00  0.00              
ATOM    109  N   LYS    77      23.051  56.524  -4.674  1.00  0.00              
ATOM    110  CA  LYS    77      23.889  57.522  -4.109  1.00  0.00              
ATOM    111  C   LYS    77      24.867  56.990  -3.102  1.00  0.00              
ATOM    112  O   LYS    77      26.041  57.276  -3.159  1.00  0.00              
ATOM    113  N   GLU    78      24.366  56.251  -2.150  1.00  0.00              
ATOM    114  CA  GLU    78      25.245  55.762  -1.125  1.00  0.00              
ATOM    115  C   GLU    78      25.797  54.328  -1.244  1.00  0.00              
ATOM    116  O   GLU    78      26.523  53.860  -0.377  1.00  0.00              
ATOM    117  N   GLY    79      25.479  53.630  -2.335  1.00  0.00              
ATOM    118  CA  GLY    79      25.925  52.260  -2.588  1.00  0.00              
ATOM    119  C   GLY    79      25.081  51.191  -1.899  1.00  0.00              
ATOM    120  O   GLY    79      24.274  51.498  -1.034  1.00  0.00              
ATOM    121  N   VAL    80      25.287  49.920  -2.277  1.00  0.00              
ATOM    122  CA  VAL    80      24.593  48.783  -1.684  1.00  0.00              
ATOM    123  C   VAL    80      24.731  48.807  -0.172  1.00  0.00              
ATOM    124  O   VAL    80      25.714  49.298   0.375  1.00  0.00              
ATOM    125  N   GLU    81      23.711  48.282   0.489  1.00  0.00              
ATOM    126  CA  GLU    81      23.671  48.237   1.909  1.00  0.00              
ATOM    127  C   GLU    81      22.964  46.974   2.264  1.00  0.00              
ATOM    128  O   GLU    81      22.152  46.498   1.492  1.00  0.00              
ATOM    129  N   HIS    82      23.279  46.444   3.419  1.00  0.00              
ATOM    130  CA  HIS    82      22.682  45.233   3.897  1.00  0.00              
ATOM    131  C   HIS    82      21.418  45.607   4.611  1.00  0.00              
ATOM    132  O   HIS    82      21.318  46.703   5.176  1.00  0.00              
ATOM    133  N   VAL    83      20.469  44.688   4.604  1.00  0.00              
ATOM    134  CA  VAL    83      19.265  45.053   5.267  1.00  0.00              
ATOM    135  C   VAL    83      18.485  43.902   5.842  1.00  0.00              
ATOM    136  O   VAL    83      18.836  42.729   5.703  1.00  0.00              
ATOM    137  N   LEU    84      17.404  44.283   6.496  1.00  0.00              
ATOM    138  CA  LEU    84      16.560  43.302   7.078  1.00  0.00              
ATOM    139  C   LEU    84      15.117  43.684   6.923  1.00  0.00              
ATOM    140  O   LEU    84      14.717  44.825   7.116  1.00  0.00              
ATOM    141  N   THR    85      14.340  42.689   6.549  1.00  0.00              
ATOM    142  CA  THR    85      12.934  42.907   6.408  1.00  0.00              
ATOM    143  C   THR    85      12.295  42.053   7.479  1.00  0.00              
ATOM    144  O   THR    85      12.649  40.885   7.604  1.00  0.00              
ATOM    145  N   SER    86      11.379  42.627   8.266  1.00  0.00              
ATOM    146  CA  SER    86      10.680  41.862   9.266  1.00  0.00              
ATOM    147  C   SER    86       9.198  41.957   9.025  1.00  0.00              
ATOM    148  O   SER    86       8.601  43.036   9.080  1.00  0.00              
ATOM    149  N   GLU    87       8.601  40.812   8.787  1.00  0.00              
ATOM    150  CA  GLU    87       7.185  40.785   8.530  1.00  0.00              
ATOM    151  C   GLU    87       6.455  40.046   9.642  1.00  0.00              
ATOM    152  O   GLU    87       6.633  38.845   9.815  1.00  0.00              
END
