
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0318AL381_5-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318AL381_5-D1.T0318_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       2           -
LGA    -       -      Q       3           -
LGA    -       -      V       4           -
LGA    -       -      L       5           -
LGA    -       -      V       6           -
LGA    -       -      R       7           -
LGA    -       -      N       8           -
LGA    -       -      G       9           -
LGA    -       -      I      10           -
LGA    -       -      Q      11           -
LGA    -       -      A      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      D      15           -
LGA    -       -      G      16           -
LGA    -       -      L      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      I      21           -
LGA    -       -      I      22           -
LGA    -       -      V      23           -
LGA    -       -      G      24           -
LGA    -       -      K      25           -
LGA    -       -      K      26           -
LGA    -       -      S      27           -
LGA    -       -      V      28           -
LGA    -       -      L      29           -
LGA    -       -      K      30           -
LGA    -       -      N      31           -
LGA    -       -      V      32           -
LGA    -       -      T      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      G      36           -
LGA    -       -      K      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      Q      43           -
LGA    -       -      K      44           -
LGA    -       -      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    -       -      D      48           -
LGA    -       -      G      49           -
LGA    -       -      D      50           -
LGA    -       -      S      51           -
LGA    -       -      W      52           -
LGA    -       -      N      53           -
LGA    -       -      S      54           -
LGA    -       -      M      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      P      60           -
LGA    -       -      A      61           -
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    K     137      H      65          3.160
LGA    T     138      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      A      72           -
LGA    -       -      H      73           -
LGA    -       -      L      74           -
LGA    S     139      I      75          5.165
LGA    G     140      T      76          1.405
LGA    I     141      V      77          2.942
LGA    R     142      P      78          1.792
LGA    -       -      D      79           -
LGA    E     143      A      80          3.540
LGA    L     144      S      81          2.578
LGA    N     145      S      82          1.813
LGA    V     146      R      83          1.814
LGA    N     147      G      84          2.482
LGA    I     148      N      85          1.230
LGA    D     149      T      86          1.333
LGA    -       -      P      87           -
LGA    -       -      T      88           -
LGA    V     150      N      89          2.048
LGA    V     151      A      90          2.615
LGA    C     152      H      91          3.132
LGA    D     153      S      92          2.240
LGA    K     154      I      93          4.316
LGA    L     155      Y      94          3.196
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      K      98           -
LGA    -       -      P      99           -
LGA    -       -      I     100           -
LGA    -       -      N     101           -
LGA    -       -      Y     102           -
LGA    -       -      P     103           -
LGA    -       -      E     104           -
LGA    -       -      D     105           -
LGA    -       -      T     106           -
LGA    -       -      K     107           -
LGA    -       -      N     108           -
LGA    -       -      V     109           -
LGA    -       -      H     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      L     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      E     116           -
LGA    -       -      Y     117           -
LGA    -       -      P     118           -
LGA    -       -      D     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      S     122           -
LGA    -       -      H     123           -
LGA    -       -      V     124           -
LGA    -       -      A     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      A     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      F     131           -
LGA    -       -      C     132           -
LGA    -       -      K     133           -
LGA    -       -      F     134           -
LGA    -       -      S     135           -
LGA    -       -      M     136           -
LGA    -       -      K     137           -
LGA    -       -      T     138           -
LGA    -       -      S     139           -
LGA    -       -      G     140           -
LGA    -       -      I     141           -
LGA    -       -      R     142           -
LGA    -       -      E     143           -
LGA    -       -      L     144           -
LGA    -       -      N     145           -
LGA    -       -      V     146           -
LGA    -       -      N     147           -
LGA    -       -      I     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      D     153           -
LGA    -       -      K     154           -
LGA    -       -      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19  154    5.0     18    2.79     0.00      9.099     0.622

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.774435 * X  +  -0.607673 * Y  +  -0.176021 * Z  +  55.746418
  Y_new =   0.029115 * X  +  -0.312165 * Y  +   0.949582 * Z  +  51.362049
  Z_new =  -0.631983 * X  +   0.730265 * Y  +   0.259444 * Z  +  34.302055 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.229431   -1.912161  [ DEG:    70.4412   -109.5588 ]
  Theta =   0.684109    2.457484  [ DEG:    39.1965    140.8035 ]
  Phi   =   3.104016   -0.037577  [ DEG:   177.8470     -2.1530 ]
 
# 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: T0318AL381_5-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318AL381_5-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19  154   5.0   18   2.79    0.00   9.099
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL381_5-D1
REMARK Aligment from pdb entry: 1t4mA
ATOM      1  N   LYS   137      39.911  46.705  33.886  1.00  0.00              
ATOM      2  CA  LYS   137      38.599  46.512  34.567  1.00  0.00              
ATOM      3  C   LYS   137      38.280  45.025  34.694  1.00  0.00              
ATOM      4  O   LYS   137      38.629  44.235  33.815  1.00  0.00              
ATOM      5  N   THR   138      37.631  44.638  35.789  1.00  0.00              
ATOM      6  CA  THR   138      37.234  43.246  35.944  1.00  0.00              
ATOM      7  C   THR   138      36.059  43.094  34.985  1.00  0.00              
ATOM      8  O   THR   138      35.438  44.088  34.594  1.00  0.00              
ATOM      9  N   SER   139      35.750  41.857  34.573  1.00  0.00              
ATOM     10  CA  SER   139      34.609  41.713  33.669  1.00  0.00              
ATOM     11  C   SER   139      33.377  42.113  34.483  1.00  0.00              
ATOM     12  O   SER   139      33.374  41.992  35.709  1.00  0.00              
ATOM     13  N   GLY   140      32.347  42.600  33.812  1.00  0.00              
ATOM     14  CA  GLY   140      31.131  43.004  34.507  1.00  0.00              
ATOM     15  C   GLY   140      30.013  42.010  34.238  1.00  0.00              
ATOM     16  O   GLY   140      29.744  41.655  33.084  1.00  0.00              
ATOM     17  N   ILE   141      29.391  41.539  35.313  1.00  0.00              
ATOM     18  CA  ILE   141      28.277  40.607  35.215  1.00  0.00              
ATOM     19  C   ILE   141      26.984  41.361  35.567  1.00  0.00              
ATOM     20  O   ILE   141      26.852  41.925  36.661  1.00  0.00              
ATOM     21  N   ARG   142      26.039  41.371  34.633  1.00  0.00              
ATOM     22  CA  ARG   142      24.776  42.073  34.837  1.00  0.00              
ATOM     23  C   ARG   142      23.631  41.116  35.118  1.00  0.00              
ATOM     24  O   ARG   142      23.431  40.142  34.401  1.00  0.00              
ATOM     25  N   GLU   143      22.886  41.420  36.180  1.00  0.00              
ATOM     26  CA  GLU   143      21.797  40.576  36.659  1.00  0.00              
ATOM     27  C   GLU   143      20.417  41.229  36.625  1.00  0.00              
ATOM     28  O   GLU   143      20.155  42.184  37.359  1.00  0.00              
ATOM     29  N   LEU   144      19.529  40.678  35.798  1.00  0.00              
ATOM     30  CA  LEU   144      18.176  41.207  35.653  1.00  0.00              
ATOM     31  C   LEU   144      17.214  40.811  36.765  1.00  0.00              
ATOM     32  O   LEU   144      17.508  39.956  37.598  1.00  0.00              
ATOM     33  N   ASN   145      16.052  41.451  36.766  1.00  0.00              
ATOM     34  CA  ASN   145      15.058  41.158  37.776  1.00  0.00              
ATOM     35  C   ASN   145      13.961  40.255  37.256  1.00  0.00              
ATOM     36  O   ASN   145      14.099  39.616  36.206  1.00  0.00              
ATOM     37  N   VAL   146      12.866  40.213  38.005  1.00  0.00              
ATOM     38  CA  VAL   146      11.706  39.396  37.680  1.00  0.00              
ATOM     39  C   VAL   146      11.136  39.748  36.311  1.00  0.00              
ATOM     40  O   VAL   146      10.895  40.920  36.002  1.00  0.00              
ATOM     41  N   ASN   147      10.928  38.716  35.499  1.00  0.00              
ATOM     42  CA  ASN   147      10.388  38.897  34.163  1.00  0.00              
ATOM     43  C   ASN   147      11.333  39.620  33.222  1.00  0.00              
ATOM     44  O   ASN   147      10.945  39.993  32.116  1.00  0.00              
ATOM     45  N   ILE   148      12.575  39.808  33.659  1.00  0.00              
ATOM     46  CA  ILE   148      13.558  40.497  32.839  1.00  0.00              
ATOM     47  C   ILE   148      14.409  39.591  31.962  1.00  0.00              
ATOM     48  O   ILE   148      14.200  38.381  31.878  1.00  0.00              
ATOM     49  N   ASP   149      15.392  40.187  31.306  1.00  0.00              
ATOM     50  CA  ASP   149      16.266  39.433  30.418  1.00  0.00              
ATOM     51  C   ASP   149      17.603  40.130  30.300  1.00  0.00              
ATOM     52  O   ASP   149      17.748  41.299  30.686  1.00  0.00              
ATOM     53  N   VAL   150      18.580  39.413  29.761  1.00  0.00              
ATOM     54  CA  VAL   150      19.909  39.979  29.578  1.00  0.00              
ATOM     55  C   VAL   150      19.793  41.246  28.723  1.00  0.00              
ATOM     56  O   VAL   150      20.549  42.199  28.909  1.00  0.00              
ATOM     57  N   VAL   151      18.832  41.238  27.797  1.00  0.00              
ATOM     58  CA  VAL   151      18.577  42.361  26.890  1.00  0.00              
ATOM     59  C   VAL   151      18.332  43.680  27.609  1.00  0.00              
ATOM     60  O   VAL   151      18.578  44.750  27.054  1.00  0.00              
ATOM     61  N   CYS   152      17.845  43.595  28.841  1.00  0.00              
ATOM     62  CA  CYS   152      17.549  44.778  29.642  1.00  0.00              
ATOM     63  C   CYS   152      18.768  45.658  29.847  1.00  0.00              
ATOM     64  O   CYS   152      18.647  46.849  30.162  1.00  0.00              
ATOM     65  N   ASP   153      19.944  45.073  29.661  1.00  0.00              
ATOM     66  CA  ASP   153      21.177  45.806  29.877  1.00  0.00              
ATOM     67  C   ASP   153      21.849  46.428  28.667  1.00  0.00              
ATOM     68  O   ASP   153      23.017  46.800  28.737  1.00  0.00              
ATOM     69  N   LYS   154      21.112  46.561  27.568  1.00  0.00              
ATOM     70  CA  LYS   154      21.674  47.153  26.352  1.00  0.00              
ATOM     71  C   LYS   154      22.211  48.558  26.620  1.00  0.00              
ATOM     72  O   LYS   154      23.329  48.895  26.225  1.00  0.00              
ATOM     73  N   LEU   155      21.414  49.375  27.295  1.00  0.00              
ATOM     74  CA  LEU   155      21.839  50.730  27.596  1.00  0.00              
ATOM     75  C   LEU   155      23.102  50.800  28.442  1.00  0.00              
ATOM     76  O   LEU   155      24.047  51.504  28.101  1.00  0.00              
END
