
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0299TS599_3-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS599_3-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79           -
LGA    E      80      E      80           -
LGA    D      81      D      81           -
LGA    F      82      -       -           -
LGA    E      83      -       -           -
LGA    A      84      -       -           -
LGA    E      85      -       -           -
LGA    L      86      F      82           #
LGA    E      87      -       -           -
LGA    N      88      E      83           #
LGA    -       -      A      84           -
LGA    -       -      E      85           -
LGA    L      89      L      86          2.516
LGA    P      90      E      87          1.475
LGA    A      91      N      88          2.137
LGA    W      92      L      89          2.924
LGA    W      93      P      90          4.783
LGA    S      94      A      91          2.690
LGA    R      95      W      92          0.971
LGA    D      96      W      93           #
LGA    L      97      S      94          2.614
LGA    A      98      R      95          4.162
LGA    R      99      D      96          0.710
LGA    K     100      L      97          3.805
LGA    -       -      A      98           -
LGA    D     101      R      99          3.370
LGA    F     102      K     100          2.892
LGA    L     103      D     101          2.778
LGA    F     104      F     102          4.406
LGA    Y     105      L     103          4.861
LGA    T     106      F     104           #
LGA    E     107      Y     105           -
LGA    G     108      T     106           #
LGA    L     109      E     107           -
LGA    -       -      G     108           -
LGA    D     110      L     109          4.897
LGA    V     111      D     110          1.653
LGA    -       -      V     111           -
LGA    D     112      D     112           #
LGA    Q     113      Q     113          4.259
LGA    V     114      V     114          1.092
LGA    I     115      I     115          4.130
LGA    A     116      A     116          2.981
LGA    T     117      T     117          1.096
LGA    V     118      V     118          3.929
LGA    E     119      E     119          3.746
LGA    S     120      S     120          1.783
LGA    L     121      L     121          3.587
LGA    -       -      E     122           -
LGA    E     122      L     123           #
LGA    L     123      K     124           -
LGA    K     124      D     125           -
LGA    D     125      -       -           -
LGA    E     126      -       -           -
LGA    V     127      -       -           -
LGA    L     128      E     126          3.642
LGA    Y     129      V     127           #
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      F     130           -
LGA    -       -      G     131           -
LGA    -       -      K     132           -
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      W     137           -
LGA    -       -      G     138           -
LGA    -       -      K     139           -
LGA    F     130      F     140          2.534
LGA    G     131      S     141          1.443
LGA    K     132      E     142          4.419
LGA    L     133      E     143           -
LGA    G     134      S     144           -
LGA    I     135      Y     145           #
LGA    F     136      S     146           -
LGA    -       -      K     147           -
LGA    -       -      T     148           -
LGA    -       -      A     149           -
LGA    W     137      Y     150           #
LGA    G     138      H     151           -
LGA    -       -      K     152           -
LGA    -       -      Y     153           -
LGA    -       -      L     154           -
LGA    -       -      L     155           -
LGA    -       -      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    -       -      F     159           -
LGA    -       -      Y     160           -
LGA    -       -      R     161           -
LGA    -       -      H     162           -
LGA    K     139      I     163          4.914
LGA    F     140      T     164          3.627
LGA    S     141      I     165           -
LGA    E     142      R     166           -
LGA    E     143      N     167           -
LGA    S     144      -       -           -
LGA    Y     145      -       -           -
LGA    S     146      -       -           -
LGA    K     147      -       -           -
LGA    T     148      -       -           -
LGA    A     149      -       -           -
LGA    Y     150      -       -           -
LGA    H     151      -       -           -
LGA    K     152      -       -           -
LGA    Y     153      -       -           -
LGA    L     154      -       -           -
LGA    L     155      -       -           -
LGA    K     156      -       -           -
LGA    V     157      -       -           -
LGA    P     158      -       -           -
LGA    F     159      -       -           -
LGA    Y     160      -       -           -
LGA    R     161      -       -           -
LGA    H     162      -       -           -
LGA    I     163      -       -           -
LGA    T     164      -       -           -
LGA    I     165      -       -           -
LGA    R     166      -       -           -
LGA    N     167      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     33    3.30    36.36     22.688     0.970

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.394724 * X  +  -0.532346 * Y  +   0.748866 * Z  +   8.664809
  Y_new =  -0.774687 * X  +  -0.631061 * Y  +  -0.040268 * Z  +  55.760567
  Z_new =   0.494016 * X  +  -0.564242 * Y  +  -0.661497 * Z  +  -4.099689 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.435373    0.706220  [ DEG:  -139.5366     40.4634 ]
  Theta =  -0.516703   -2.624889  [ DEG:   -29.6049   -150.3951 ]
  Phi   =  -1.099556    2.042037  [ DEG:   -62.9999    117.0001 ]
 
# 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: T0299TS599_3-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS599_3-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89   89   5.0   33   3.30   36.36  22.688
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS599_3-D2
PFRMAT TS                                                                       
TARGET T0299                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM     79  CA  LEU    79       4.770  52.230 -18.634  1.00  0.00              
ATOM     80  CA  GLU    80       1.095  52.761 -19.649  1.00  0.00              
ATOM     81  CA  ASP    81      -0.020  52.939 -16.062  1.00  0.00              
ATOM     82  CA  PHE    82       2.853  55.366 -15.210  1.00  0.00              
ATOM     83  CA  GLU    83       1.597  57.712 -17.942  1.00  0.00              
ATOM     84  CA  ALA    84      -1.885  57.466 -16.590  1.00  0.00              
ATOM     85  CA  GLU    85      -0.584  58.232 -13.048  1.00  0.00              
ATOM     86  CA  LEU    86       1.457  61.207 -14.167  1.00  0.00              
ATOM     87  CA  GLU    87      -1.411  62.670 -16.099  1.00  0.00              
ATOM     88  CA  ASN    88      -3.834  62.395 -13.126  1.00  0.00              
ATOM     89  CA  LEU    89      -1.612  63.648 -10.366  1.00  0.00              
ATOM     90  CA  PRO    90      -2.286  66.869  -8.593  1.00  0.00              
ATOM     91  CA  ALA    91       1.273  67.887  -7.873  1.00  0.00              
ATOM     92  CA  TRP    92       3.725  66.325 -10.400  1.00  0.00              
ATOM     93  CA  TRP    93       5.496  69.089 -12.316  1.00  0.00              
ATOM     94  CA  SER    94       9.015  67.797 -12.442  1.00  0.00              
ATOM     95  CA  ARG    95       8.558  64.295 -13.670  1.00  0.00              
ATOM     96  CA  ASP    96       9.823  63.345 -17.067  1.00  0.00              
ATOM     97  CA  LEU    97       6.837  61.369 -18.431  1.00  0.00              
ATOM     98  CA  ALA    98       8.774  59.457 -21.096  1.00  0.00              
ATOM     99  CA  ARG    99      11.559  58.003 -18.870  1.00  0.00              
ATOM    100  CA  LYS   100       9.696  56.945 -15.854  1.00  0.00              
ATOM    101  CA  ASP   101       9.835  53.497 -14.262  1.00  0.00              
ATOM    102  CA  PHE   102       7.689  53.061 -11.082  1.00  0.00              
ATOM    103  CA  LEU   103       8.669  50.537  -8.428  1.00  0.00              
ATOM    104  CA  PHE   104       6.435  49.893  -5.493  1.00  0.00              
ATOM    105  CA  TYR   105       8.053  48.563  -2.404  1.00  0.00              
ATOM    106  CA  THR   106       6.106  47.013   0.282  1.00  0.00              
ATOM    107  CA  GLU   107       7.470  47.477   3.630  1.00  0.00              
ATOM    108  CA  GLY   108       5.185  47.245   6.596  1.00  0.00              
ATOM    109  CA  LEU   109       6.410  50.502   8.054  1.00  0.00              
ATOM    110  CA  ASP   110       6.488  51.256  11.724  1.00  0.00              
ATOM    111  CA  VAL   111       5.492  54.926  12.326  1.00  0.00              
ATOM    112  CA  ASP   112       8.755  55.649  14.031  1.00  0.00              
ATOM    113  CA  GLN   113      10.837  54.134  11.286  1.00  0.00              
ATOM    114  CA  VAL   114       9.002  56.034   8.620  1.00  0.00              
ATOM    115  CA  ILE   115       9.474  59.331  10.466  1.00  0.00              
ATOM    116  CA  ALA   116      13.184  58.591  10.918  1.00  0.00              
ATOM    117  CA  THR   117      13.662  57.740   7.253  1.00  0.00              
ATOM    118  CA  VAL   118      11.924  60.861   6.108  1.00  0.00              
ATOM    119  CA  GLU   119      14.067  63.005   8.153  1.00  0.00              
ATOM    120  CA  SER   120      17.489  61.613   7.349  1.00  0.00              
ATOM    121  CA  LEU   121      17.376  61.324   3.518  1.00  0.00              
ATOM    122  CA  GLU   122      14.751  64.021   2.721  1.00  0.00              
ATOM    123  CA  LEU   123      12.308  62.614   0.213  1.00  0.00              
ATOM    124  CA  LYS   124       8.966  62.836   2.069  1.00  0.00              
ATOM    125  CA  ASP   125       7.850  59.363   0.844  1.00  0.00              
ATOM    126  CA  GLU   126       8.930  59.188  -2.749  1.00  0.00              
ATOM    127  CA  VAL   127      12.471  58.052  -3.561  1.00  0.00              
ATOM    128  CA  LEU   128      14.112  58.999  -6.910  1.00  0.00              
ATOM    129  CA  TYR   129      16.669  56.663  -8.522  1.00  0.00              
ATOM    130  CA  PHE   130      18.726  57.848 -11.392  1.00  0.00              
ATOM    131  CA  GLY   131      19.925  55.242 -13.918  1.00  0.00              
ATOM    132  CA  LYS   132      19.122  55.945 -17.540  1.00  0.00              
ATOM    133  CA  LEU   133      15.340  56.117 -17.970  1.00  0.00              
ATOM    134  CA  GLY   134      14.233  57.414 -14.494  1.00  0.00              
ATOM    135  CA  ILE   135      13.208  54.997 -11.751  1.00  0.00              
ATOM    136  CA  PHE   136      10.657  56.101  -9.179  1.00  0.00              
ATOM    137  CA  TRP   137      10.447  54.099  -5.915  1.00  0.00              
ATOM    138  CA  GLY   138       7.261  54.209  -3.883  1.00  0.00              
ATOM    139  CA  LYS   139       7.075  52.789  -0.403  1.00  0.00              
ATOM    140  CA  PHE   140       3.881  51.398   0.679  1.00  0.00              
ATOM    141  CA  SER   141       3.241  50.817   4.267  1.00  0.00              
ATOM    142  CA  GLU   142      -0.319  49.465   4.388  1.00  0.00              
ATOM    143  CA  GLU   143      -2.014  52.283   6.386  1.00  0.00              
ATOM    144  CA  SER   144      -0.560  55.013   4.246  1.00  0.00              
ATOM    145  CA  TYR   145      -3.154  54.990   1.417  1.00  0.00              
ATOM    146  CA  SER   146      -6.031  55.884   3.752  1.00  0.00              
ATOM    147  CA  LYS   147      -4.162  58.799   5.352  1.00  0.00              
ATOM    148  CA  THR   148      -3.045  60.354   2.050  1.00  0.00              
ATOM    149  CA  ALA   149      -6.075  60.639  -0.169  1.00  0.00              
ATOM    150  CA  TYR   150      -8.127  62.273   2.599  1.00  0.00              
ATOM    151  CA  HIS   151      -5.442  64.842   3.539  1.00  0.00              
ATOM    152  CA  LYS   152      -4.998  65.837  -0.118  1.00  0.00              
ATOM    153  CA  TYR   153      -8.760  66.251  -0.604  1.00  0.00              
ATOM    154  CA  LEU   154      -9.031  68.287   2.637  1.00  0.00              
ATOM    155  CA  LEU   155      -6.116  70.461   1.618  1.00  0.00              
ATOM    156  CA  LYS   156      -7.534  71.179  -1.846  1.00  0.00              
ATOM    157  CA  VAL   157     -10.897  72.077  -0.273  1.00  0.00              
ATOM    158  CA  PRO   158      -9.656  74.312   2.601  1.00  0.00              
ATOM    159  CA  PHE   159      -7.507  76.313   0.249  1.00  0.00              
ATOM    160  CA  TYR   160      -9.893  76.726  -2.717  1.00  0.00              
ATOM    161  CA  ARG   161      -7.167  76.333  -5.291  1.00  0.00              
ATOM    162  CA  HIS   162      -7.533  75.357  -8.913  1.00  0.00              
ATOM    163  CA  ILE   163      -4.088  73.796  -9.513  1.00  0.00              
ATOM    164  CA  THR   164      -2.630  73.018 -12.890  1.00  0.00              
ATOM    165  CA  ILE   165      -0.525  69.869 -13.362  1.00  0.00              
ATOM    166  CA  ARG   166       2.761  71.409 -14.500  1.00  0.00              
ATOM    167  CA  ASN   167       2.608  74.200 -11.911  1.00  0.00              
TER                                                                             
END
