
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS599_4-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           -
LGA    E      80      D      81           #
LGA    D      81      F      82          1.505
LGA    F      82      -       -           -
LGA    E      83      E      83          4.771
LGA    A      84      A      84          3.540
LGA    E      85      E      85          1.620
LGA    L      86      L      86          2.264
LGA    E      87      E      87          3.311
LGA    N      88      N      88          4.705
LGA    L      89      L      89          4.791
LGA    P      90      P      90           #
LGA    A      91      A      91           -
LGA    W      92      W      92           -
LGA    W      93      W      93           -
LGA    S      94      S      94           -
LGA    R      95      R      95           -
LGA    D      96      D      96           -
LGA    L      97      L      97           -
LGA    A      98      A      98           -
LGA    R      99      R      99           -
LGA    K     100      K     100           -
LGA    D     101      D     101           -
LGA    F     102      F     102           -
LGA    L     103      -       -           -
LGA    F     104      -       -           -
LGA    Y     105      L     103           #
LGA    T     106      F     104          3.218
LGA    E     107      Y     105          3.039
LGA    G     108      T     106          2.456
LGA    L     109      E     107          3.482
LGA    D     110      G     108          1.587
LGA    V     111      L     109          4.003
LGA    D     112      D     110          2.397
LGA    Q     113      -       -           -
LGA    V     114      V     111          1.876
LGA    I     115      D     112          2.609
LGA    A     116      Q     113          2.490
LGA    T     117      V     114          1.512
LGA    V     118      I     115          0.868
LGA    E     119      A     116          0.938
LGA    S     120      T     117          1.278
LGA    L     121      V     118          0.895
LGA    E     122      E     119          2.536
LGA    L     123      S     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    K     124      L     123           #
LGA    -       -      K     124           -
LGA    -       -      D     125           -
LGA    -       -      E     126           -
LGA    D     125      V     127           #
LGA    E     126      L     128          2.470
LGA    V     127      Y     129          3.573
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      F     130          2.703
LGA    G     138      G     131          3.040
LGA    -       -      K     132           -
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    K     139      I     135          1.246
LGA    F     140      F     136          3.994
LGA    S     141      W     137           #
LGA    E     142      G     138           -
LGA    E     143      K     139           -
LGA    -       -      F     140           -
LGA    -       -      S     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
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    S     144      L     154           #
LGA    Y     145      L     155           -
LGA    S     146      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    K     147      F     159           #
LGA    T     148      Y     160          2.501
LGA    -       -      R     161           -
LGA    A     149      H     162          3.405
LGA    Y     150      I     163           -
LGA    H     151      T     164           -
LGA    K     152      I     165           -
LGA    Y     153      R     166           -
LGA    L     154      N     167           -
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     32    2.87    37.50     23.801     1.078

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.843156 * X  +   0.054908 * Y  +   0.534859 * Z  +  10.412724
  Y_new =  -0.534480 * X  +  -0.193798 * Y  +  -0.822663 * Z  +  55.216499
  Z_new =   0.058484 * X  +  -0.979504 * Y  +   0.192749 * Z  +  14.324882 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.376496    1.765096  [ DEG:   -78.8674    101.1326 ]
  Theta =  -0.058517   -3.083076  [ DEG:    -3.3528   -176.6472 ]
  Phi   =  -2.576616    0.564977  [ DEG:  -147.6292     32.3708 ]
 
# 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_4-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS599_4-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   32   2.87   37.50  23.801
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS599_4-D2
PFRMAT TS                                                                       
TARGET T0299                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM     79  CA  LEU    79      -3.423  53.784  -4.305  1.00  0.00              
ATOM     80  CA  GLU    80      -6.576  55.290  -5.848  1.00  0.00              
ATOM     81  CA  ASP    81      -6.375  58.325  -3.646  1.00  0.00              
ATOM     82  CA  PHE    82      -2.644  58.695  -4.634  1.00  0.00              
ATOM     83  CA  GLU    83      -3.683  58.828  -8.243  1.00  0.00              
ATOM     84  CA  ALA    84      -6.171  61.566  -7.259  1.00  0.00              
ATOM     85  CA  GLU    85      -3.374  63.484  -5.455  1.00  0.00              
ATOM     86  CA  LEU    86      -1.019  63.134  -8.455  1.00  0.00              
ATOM     87  CA  GLU    87      -3.736  64.348 -10.838  1.00  0.00              
ATOM     88  CA  ASN    88      -4.256  67.429  -8.647  1.00  0.00              
ATOM     89  CA  LEU    89      -0.603  68.174  -8.115  1.00  0.00              
ATOM     90  CA  PRO    90       0.553  71.749  -7.881  1.00  0.00              
ATOM     91  CA  ALA    91       2.329  71.545  -4.497  1.00  0.00              
ATOM     92  CA  TRP    92      -0.083  73.090  -2.030  1.00  0.00              
ATOM     93  CA  TRP    93       1.566  76.213  -0.560  1.00  0.00              
ATOM     94  CA  SER    94      -1.371  78.602  -0.939  1.00  0.00              
ATOM     95  CA  ARG    95      -1.205  80.585   2.212  1.00  0.00              
ATOM     96  CA  ASP    96      -1.351  79.524   5.815  1.00  0.00              
ATOM     97  CA  LEU    97       2.199  80.335   6.976  1.00  0.00              
ATOM     98  CA  ALA    98       2.561  77.752   9.710  1.00  0.00              
ATOM     99  CA  ARG    99       5.773  75.896   8.725  1.00  0.00              
ATOM    100  CA  LYS   100       4.527  72.371   8.521  1.00  0.00              
ATOM    101  CA  ASP   101       6.006  69.311   6.911  1.00  0.00              
ATOM    102  CA  PHE   102       3.637  66.894   5.231  1.00  0.00              
ATOM    103  CA  LEU   103       4.556  63.382   4.405  1.00  0.00              
ATOM    104  CA  PHE   104       2.521  61.398   2.057  1.00  0.00              
ATOM    105  CA  TYR   105       2.826  57.684   1.915  1.00  0.00              
ATOM    106  CA  THR   106       1.043  55.607  -0.614  1.00  0.00              
ATOM    107  CA  GLU   107       0.243  52.262   0.874  1.00  0.00              
ATOM    108  CA  GLY   108      -1.823  51.493   4.019  1.00  0.00              
ATOM    109  CA  LEU   109       0.521  52.341   6.683  1.00  0.00              
ATOM    110  CA  ASP   110       0.311  52.335  10.433  1.00  0.00              
ATOM    111  CA  VAL   111       1.246  55.703  11.913  1.00  0.00              
ATOM    112  CA  ASP   112       4.356  54.517  13.648  1.00  0.00              
ATOM    113  CA  GLN   113       5.743  52.821  10.624  1.00  0.00              
ATOM    114  CA  VAL   114       5.177  55.908   8.550  1.00  0.00              
ATOM    115  CA  ILE   115       7.140  58.111  10.914  1.00  0.00              
ATOM    116  CA  ALA   116      10.091  55.755  10.931  1.00  0.00              
ATOM    117  CA  THR   117      10.212  55.484   7.124  1.00  0.00              
ATOM    118  CA  VAL   118       9.968  59.236   6.600  1.00  0.00              
ATOM    119  CA  GLU   119      12.952  59.902   8.824  1.00  0.00              
ATOM    120  CA  SER   120      15.203  57.388   7.134  1.00  0.00              
ATOM    121  CA  LEU   121      14.361  57.986   3.466  1.00  0.00              
ATOM    122  CA  GLU   122      13.364  61.604   3.351  1.00  0.00              
ATOM    123  CA  LEU   123      15.501  62.868   0.540  1.00  0.00              
ATOM    124  CA  LYS   124      14.788  60.107  -2.048  1.00  0.00              
ATOM    125  CA  ASP   125      11.050  60.180  -1.808  1.00  0.00              
ATOM    126  CA  GLU   126      10.004  62.944  -4.089  1.00  0.00              
ATOM    127  CA  VAL   127      10.188  66.310  -2.402  1.00  0.00              
ATOM    128  CA  LEU   128       7.763  69.083  -3.258  1.00  0.00              
ATOM    129  CA  TYR   129       8.445  72.592  -2.143  1.00  0.00              
ATOM    130  CA  PHE   130       5.650  75.005  -1.680  1.00  0.00              
ATOM    131  CA  GLY   131       6.486  78.578  -0.825  1.00  0.00              
ATOM    132  CA  LYS   132       6.235  79.982   2.659  1.00  0.00              
ATOM    133  CA  LEU   133       8.014  77.411   4.762  1.00  0.00              
ATOM    134  CA  GLY   134       6.012  74.453   3.377  1.00  0.00              
ATOM    135  CA  ILE   135       7.698  71.165   2.524  1.00  0.00              
ATOM    136  CA  PHE   136       5.808  68.294   1.038  1.00  0.00              
ATOM    137  CA  TRP   137       7.346  64.805   0.984  1.00  0.00              
ATOM    138  CA  GLY   138       6.049  62.135  -1.253  1.00  0.00              
ATOM    139  CA  LYS   139       7.114  58.597  -0.679  1.00  0.00              
ATOM    140  CA  PHE   140       5.722  55.914  -2.901  1.00  0.00              
ATOM    141  CA  SER   141       7.971  53.118  -3.949  1.00  0.00              
ATOM    142  CA  GLU   142       5.605  50.111  -3.842  1.00  0.00              
ATOM    143  CA  GLU   143       8.239  47.771  -2.469  1.00  0.00              
ATOM    144  CA  SER   144       8.940  49.806   0.615  1.00  0.00              
ATOM    145  CA  TYR   145       5.717  49.174   2.616  1.00  0.00              
ATOM    146  CA  SER   146       5.944  45.434   1.949  1.00  0.00              
ATOM    147  CA  LYS   147       9.600  45.003   3.001  1.00  0.00              
ATOM    148  CA  THR   148       9.267  46.798   6.325  1.00  0.00              
ATOM    149  CA  ALA   149       6.358  45.069   8.107  1.00  0.00              
ATOM    150  CA  TYR   150       7.925  41.714   7.339  1.00  0.00              
ATOM    151  CA  HIS   151      11.397  42.625   8.617  1.00  0.00              
ATOM    152  CA  LYS   152       9.947  43.968  11.842  1.00  0.00              
ATOM    153  CA  TYR   153       7.882  40.804  12.400  1.00  0.00              
ATOM    154  CA  LEU   154      10.973  38.624  11.788  1.00  0.00              
ATOM    155  CA  LEU   155      13.054  40.755  14.113  1.00  0.00              
ATOM    156  CA  LYS   156      10.433  40.543  16.877  1.00  0.00              
ATOM    157  CA  VAL   157      10.282  36.756  16.474  1.00  0.00              
ATOM    158  CA  PRO   158      13.995  35.902  16.136  1.00  0.00              
ATOM    159  CA  PHE   159      14.819  37.966  19.213  1.00  0.00              
ATOM    160  CA  TYR   160      12.081  37.020  21.591  1.00  0.00              
ATOM    161  CA  ARG   161      10.483  40.075  23.034  1.00  0.00              
ATOM    162  CA  HIS   162       9.490  40.238  26.541  1.00  0.00              
ATOM    163  CA  ILE   163       7.165  42.990  27.548  1.00  0.00              
ATOM    164  CA  THR   164       6.260  43.511  31.155  1.00  0.00              
ATOM    165  CA  ILE   165       4.020  46.297  32.123  1.00  0.00              
ATOM    166  CA  ARG   166       4.033  46.736  35.849  1.00  0.00              
ATOM    167  CA  ASN   167       6.229  43.732  36.797  1.00  0.00              
TER                                                                             
END
