
#######################################################
#                                                     #
#                        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   18 (  137),  selected   18 , name T0318TS469_4-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318TS469_4-D1.T0318_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     138      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    S     139      G      24          5.389
LGA    G     140      K      25          3.762
LGA    I     141      K      26          4.068
LGA    -       -      S      27           -
LGA    -       -      V      28           -
LGA    -       -      L      29           -
LGA    R     142      K      30          1.402
LGA    E     143      N      31          3.330
LGA    L     144      V      32          2.556
LGA    N     145      T      33          2.473
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    V     146      S      51           #
LGA    N     147      W      52          4.185
LGA    I     148      N      53          1.544
LGA    D     149      S      54          1.824
LGA    V     150      M      55          1.993
LGA    V     151      I      56          2.414
LGA    C     152      S      57          2.885
LGA    D     153      R      58          1.842
LGA    K     154      I      59          0.877
LGA    -       -      P      60           -
LGA    L     155      A      61          4.340
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    -       -      H      65           -
LGA    -       -      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    -       -      I      75           -
LGA    -       -      T      76           -
LGA    -       -      V      77           -
LGA    -       -      P      78           -
LGA    -       -      D      79           -
LGA    -       -      A      80           -
LGA    -       -      S      81           -
LGA    -       -      S      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      N      85           -
LGA    -       -      T      86           -
LGA    -       -      P      87           -
LGA    -       -      T      88           -
LGA    -       -      N      89           -
LGA    -       -      A      90           -
LGA    -       -      H      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      Y      94           -
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)   18  154    5.0     16    3.06     0.00      7.111     0.506

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.583622 * X  +   0.808980 * Y  +  -0.070259 * Z  +  67.732727
  Y_new =   0.313555 * X  +  -0.304327 * Y  +  -0.899483 * Z  +  32.400494
  Z_new =  -0.749045 * X  +   0.502928 * Y  +  -0.431271 * Z  +  18.291424 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.279640   -0.861952  [ DEG:   130.6138    -49.3862 ]
  Theta =   0.846619    2.294973  [ DEG:    48.5077    131.4923 ]
  Phi   =   0.493006   -2.648586  [ DEG:    28.2472   -151.7528 ]
 
# 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: T0318TS469_4-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS469_4-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  154   5.0   16   3.06    0.00   7.111
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS469_4-D1
PFRMAT TS
TARGET T0318
MODEL  4 
PARENT  n/a
ATOM      1  N   THR   138      30.830  32.753  30.032  1.00  0.00           N  
ATOM      2  CA  THR   138      29.475  32.860  29.536  1.00  0.00           C  
ATOM      3  C   THR   138      28.590  33.644  30.508  1.00  0.00           C  
ATOM      4  O   THR   138      27.541  34.179  30.138  1.00  0.00           O  
ATOM      5  CB  THR   138      28.897  31.448  29.299  1.00  0.00           C  
ATOM      6  OG1 THR   138      29.640  30.780  28.290  1.00  0.00           O  
ATOM      7  CG2 THR   138      27.429  31.567  28.857  1.00  0.00           C  
ATOM      8  N   SER   139      28.966  33.706  31.780  1.00  0.00           N  
ATOM      9  CA  SER   139      28.260  34.466  32.780  1.00  0.00           C  
ATOM     10  C   SER   139      29.251  34.692  33.897  1.00  0.00           C  
ATOM     11  O   SER   139      29.946  33.773  34.334  1.00  0.00           O  
ATOM     12  CB  SER   139      27.031  33.682  33.267  1.00  0.00           C  
ATOM     13  OG  SER   139      26.370  34.403  34.297  1.00  0.00           O  
ATOM     14  N   GLY   140      29.342  35.921  34.388  1.00  0.00           N  
ATOM     15  CA  GLY   140      30.295  36.249  35.432  1.00  0.00           C  
ATOM     16  C   GLY   140      31.552  36.716  34.742  1.00  0.00           C  
ATOM     17  O   GLY   140      31.495  37.374  33.700  1.00  0.00           O  
ATOM     18  N   ILE   141      32.727  36.395  35.283  1.00  0.00           N  
ATOM     19  CA  ILE   141      33.950  36.828  34.627  1.00  0.00           C  
ATOM     20  C   ILE   141      34.766  35.579  34.295  1.00  0.00           C  
ATOM     21  O   ILE   141      35.225  35.384  33.166  1.00  0.00           O  
ATOM     22  CB  ILE   141      35.181  37.605  35.145  1.00  0.00           C  
ATOM     23  CG1 ILE   141      34.833  38.984  35.729  1.00  0.00           C  
ATOM     24  CG2 ILE   141      36.233  37.882  34.058  1.00  0.00           C  
ATOM     25  CD1 ILE   141      34.229  39.946  34.706  1.00  0.00           C  
ATOM     26  N   ARG   142      34.956  34.715  35.288  1.00  0.00           N  
ATOM     27  CA  ARG   142      35.711  33.486  35.081  1.00  0.00           C  
ATOM     28  C   ARG   142      35.350  32.834  33.744  1.00  0.00           C  
ATOM     29  O   ARG   142      36.208  32.324  33.020  1.00  0.00           O  
ATOM     30  CB  ARG   142      35.551  32.271  35.998  1.00  0.00           C  
ATOM     31  CG  ARG   142      36.480  31.109  35.640  1.00  0.00           C  
ATOM     32  CD  ARG   142      36.422  29.950  36.638  1.00  0.00           C  
ATOM     33  NE  ARG   142      37.276  28.853  36.100  1.00  0.00           N  
ATOM     34  CZ  ARG   142      37.529  27.749  36.862  1.00  0.00           C  
ATOM     35  NH1 ARG   142      36.887  27.911  38.055  1.00  0.00           N  
ATOM     36  NH2 ARG   142      38.326  26.916  36.133  1.00  0.00           N  
ATOM     37  N   GLU   143      34.063  32.845  33.404  1.00  0.00           N  
ATOM     38  CA  GLU   143      33.590  32.258  32.148  1.00  0.00           C  
ATOM     39  C   GLU   143      34.647  32.345  31.057  1.00  0.00           C  
ATOM     40  O   GLU   143      34.890  31.399  30.302  1.00  0.00           O  
ATOM     41  CB  GLU   143      32.372  32.882  31.460  1.00  0.00           C  
ATOM     42  CG  GLU   143      31.833  32.046  30.298  1.00  0.00           C  
ATOM     43  CD  GLU   143      31.378  30.704  30.855  1.00  0.00           C  
ATOM     44  OE1 GLU   143      30.612  30.709  31.856  1.00  0.00           O  
ATOM     45  OE2 GLU   143      31.791  29.657  30.288  1.00  0.00           O  
ATOM     46  N   LEU   144      35.293  33.506  30.966  1.00  0.00           N  
ATOM     47  CA  LEU   144      36.331  33.737  29.967  1.00  0.00           C  
ATOM     48  C   LEU   144      37.665  33.183  30.438  1.00  0.00           C  
ATOM     49  O   LEU   144      38.732  33.528  29.925  1.00  0.00           O  
ATOM     50  CB  LEU   144      36.763  35.153  29.576  1.00  0.00           C  
ATOM     51  CG  LEU   144      35.635  35.991  28.971  1.00  0.00           C  
ATOM     52  CD1 LEU   144      35.992  37.449  28.691  1.00  0.00           C  
ATOM     53  CD2 LEU   144      35.108  35.490  27.627  1.00  0.00           C  
ATOM     54  N   ASN   145      37.613  32.306  31.434  1.00  0.00           N  
ATOM     55  CA  ASN   145      38.813  31.687  31.977  1.00  0.00           C  
ATOM     56  C   ASN   145      39.965  32.691  32.044  1.00  0.00           C  
ATOM     57  O   ASN   145      40.724  32.869  31.088  1.00  0.00           O  
ATOM     58  CB  ASN   145      39.317  30.485  31.173  1.00  0.00           C  
ATOM     59  CG  ASN   145      38.281  29.376  31.288  1.00  0.00           C  
ATOM     60  OD1 ASN   145      37.566  29.277  32.283  1.00  0.00           O  
ATOM     61  ND2 ASN   145      38.144  28.480  30.273  1.00  0.00           N  
ATOM     62  N   VAL   146      40.112  33.365  33.185  1.00  0.00           N  
ATOM     63  CA  VAL   146      41.173  34.359  33.364  1.00  0.00           C  
ATOM     64  C   VAL   146      41.830  34.276  34.741  1.00  0.00           C  
ATOM     65  O   VAL   146      41.164  34.130  35.770  1.00  0.00           O  
ATOM     66  CB  VAL   146      41.406  35.876  33.524  1.00  0.00           C  
ATOM     67  CG1 VAL   146      42.877  36.251  33.719  1.00  0.00           C  
ATOM     68  CG2 VAL   146      40.940  36.695  32.318  1.00  0.00           C  
ATOM     69  N   ASN   147      43.156  34.369  34.772  1.00  0.00           N  
ATOM     70  CA  ASN   147      43.903  34.307  36.026  1.00  0.00           C  
ATOM     71  C   ASN   147      43.877  35.685  36.674  1.00  0.00           C  
ATOM     72  O   ASN   147      44.909  36.271  37.014  1.00  0.00           O  
ATOM     73  CB  ASN   147      45.371  33.892  35.877  1.00  0.00           C  
ATOM     74  CG  ASN   147      45.918  33.594  37.266  1.00  0.00           C  
ATOM     75  OD1 ASN   147      45.173  33.242  38.179  1.00  0.00           O  
ATOM     76  ND2 ASN   147      47.251  33.718  37.501  1.00  0.00           N  
ATOM     77  N   ILE   148      42.671  36.215  36.851  1.00  0.00           N  
ATOM     78  CA  ILE   148      42.477  37.540  37.427  1.00  0.00           C  
ATOM     79  C   ILE   148      41.580  37.503  38.650  1.00  0.00           C  
ATOM     80  O   ILE   148      40.482  36.937  38.615  1.00  0.00           O  
ATOM     81  CB  ILE   148      41.756  38.791  36.877  1.00  0.00           C  
ATOM     82  CG1 ILE   148      42.366  39.325  35.570  1.00  0.00           C  
ATOM     83  CG2 ILE   148      41.776  39.985  37.847  1.00  0.00           C  
ATOM     84  CD1 ILE   148      41.525  40.413  34.905  1.00  0.00           C  
ATOM     85  N   ASP   149      41.986  38.065  39.705  1.00  0.00           N  
ATOM     86  CA  ASP   149      41.195  38.317  40.905  1.00  0.00           C  
ATOM     87  C   ASP   149      40.665  39.747  40.940  1.00  0.00           C  
ATOM     88  O   ASP   149      39.607  40.031  41.506  1.00  0.00           O  
ATOM     89  CB  ASP   149      41.915  38.162  42.247  1.00  0.00           C  
ATOM     90  CG  ASP   149      42.337  36.707  42.389  1.00  0.00           C  
ATOM     91  OD1 ASP   149      41.450  35.819  42.275  1.00  0.00           O  
ATOM     92  OD2 ASP   149      43.552  36.464  42.613  1.00  0.00           O  
ATOM     93  N   VAL   150      41.401  40.673  40.330  1.00  0.00           N  
ATOM     94  CA  VAL   150      40.969  42.066  40.292  1.00  0.00           C  
ATOM     95  C   VAL   150      39.622  42.176  39.584  1.00  0.00           C  
ATOM     96  O   VAL   150      38.706  42.869  40.034  1.00  0.00           O  
ATOM     97  CB  VAL   150      41.279  43.427  39.634  1.00  0.00           C  
ATOM     98  CG1 VAL   150      40.236  44.505  39.940  1.00  0.00           C  
ATOM     99  CG2 VAL   150      42.616  44.027  40.072  1.00  0.00           C  
ATOM    100  N   VAL   151      39.488  41.486  38.456  1.00  0.00           N  
ATOM    101  CA  VAL   151      38.245  41.508  37.697  1.00  0.00           C  
ATOM    102  C   VAL   151      37.062  41.047  38.551  1.00  0.00           C  
ATOM    103  O   VAL   151      36.186  41.833  38.922  1.00  0.00           O  
ATOM    104  CB  VAL   151      37.502  40.793  36.547  1.00  0.00           C  
ATOM    105  CG1 VAL   151      36.062  41.275  36.357  1.00  0.00           C  
ATOM    106  CG2 VAL   151      38.169  40.978  35.183  1.00  0.00           C  
ATOM    107  N   CYS   152      37.027  39.757  38.873  1.00  0.00           N  
ATOM    108  CA  CYS   152      35.938  39.213  39.680  1.00  0.00           C  
ATOM    109  C   CYS   152      35.546  40.133  40.825  1.00  0.00           C  
ATOM    110  O   CYS   152      34.367  40.429  41.042  1.00  0.00           O  
ATOM    111  CB  CYS   152      36.001  37.948  40.540  1.00  0.00           C  
ATOM    112  SG  CYS   152      36.397  36.805  39.797  1.00  0.00           S  
ATOM    113  N   ASP   153      36.531  40.603  41.578  1.00  0.00           N  
ATOM    114  CA  ASP   153      36.238  41.494  42.692  1.00  0.00           C  
ATOM    115  C   ASP   153      35.413  42.684  42.213  1.00  0.00           C  
ATOM    116  O   ASP   153      34.845  43.442  43.004  1.00  0.00           O  
ATOM    117  CB  ASP   153      37.434  42.129  43.408  1.00  0.00           C  
ATOM    118  CG  ASP   153      38.115  41.048  44.235  1.00  0.00           C  
ATOM    119  OD1 ASP   153      37.517  39.949  44.380  1.00  0.00           O  
ATOM    120  OD2 ASP   153      39.243  41.308  44.733  1.00  0.00           O  
ATOM    121  N   LYS   154      35.338  42.863  40.897  1.00  0.00           N  
ATOM    122  CA  LYS   154      34.576  43.969  40.326  1.00  0.00           C  
ATOM    123  C   LYS   154      33.285  43.498  39.668  1.00  0.00           C  
ATOM    124  O   LYS   154      32.185  43.961  39.984  1.00  0.00           O  
ATOM    125  CB  LYS   154      35.147  44.818  39.186  1.00  0.00           C  
ATOM    126  CG  LYS   154      36.473  45.497  39.535  1.00  0.00           C  
ATOM    127  CD  LYS   154      36.335  46.610  40.577  1.00  0.00           C  
ATOM    128  CE  LYS   154      37.653  47.321  40.891  1.00  0.00           C  
ATOM    129  NZ  LYS   154      37.442  48.333  41.950  1.00  0.00           N  
ATOM    130  N   LEU   155      33.412  42.551  38.726  1.00  0.00           N  
ATOM    131  CA  LEU   155      32.246  42.026  38.036  1.00  0.00           C  
ATOM    132  C   LEU   155      30.997  41.934  38.908  1.00  0.00           C  
ATOM    133  O   LEU   155      29.880  42.210  38.462  1.00  0.00           O  
ATOM    134  CB  LEU   155      32.245  40.598  37.480  1.00  0.00           C  
ATOM    135  CG  LEU   155      32.637  39.541  38.514  1.00  0.00           C  
ATOM    136  CD1 LEU   155      31.501  39.070  39.419  1.00  0.00           C  
ATOM    137  CD2 LEU   155      33.188  38.241  37.930  1.00  0.00           C  
TER
END
