
#######################################################
#                                                     #
#                        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 T0299TS168_5-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS168_5-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79           -
LGA    E      80      E      80           -
LGA    D      81      D      81           -
LGA    F      82      F      82           -
LGA    E      83      E      83           -
LGA    A      84      A      84           -
LGA    E      85      E      85           -
LGA    L      86      L      86           -
LGA    E      87      E      87           -
LGA    N      88      N      88           -
LGA    L      89      L      89           -
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      -       -           -
LGA    T     106      -       -           -
LGA    E     107      -       -           -
LGA    G     108      -       -           -
LGA    L     109      -       -           -
LGA    D     110      L     103           #
LGA    V     111      F     104          2.053
LGA    D     112      -       -           -
LGA    Q     113      Y     105          1.545
LGA    V     114      T     106          4.755
LGA    I     115      E     107           -
LGA    A     116      -       -           -
LGA    T     117      G     108           #
LGA    V     118      L     109          1.938
LGA    E     119      D     110           -
LGA    S     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    L     123      -       -           -
LGA    K     124      V     111           #
LGA    D     125      D     112           #
LGA    E     126      -       -           -
LGA    V     127      -       -           -
LGA    L     128      Q     113          2.904
LGA    Y     129      V     114          3.131
LGA    -       -      I     115           -
LGA    F     130      A     116          3.484
LGA    G     131      T     117          3.764
LGA    K     132      V     118           #
LGA    L     133      -       -           -
LGA    G     134      -       -           -
LGA    I     135      -       -           -
LGA    F     136      E     119          3.514
LGA    W     137      S     120          4.998
LGA    G     138      L     121           -
LGA    K     139      E     122           -
LGA    F     140      L     123           -
LGA    S     141      K     124           -
LGA    E     142      D     125           -
LGA    E     143      E     126           -
LGA    S     144      V     127           -
LGA    -       -      L     128           -
LGA    Y     145      Y     129           #
LGA    S     146      F     130          3.380
LGA    K     147      G     131          0.671
LGA    T     148      K     132           #
LGA    -       -      L     133           -
LGA    A     149      G     134           #
LGA    Y     150      I     135          1.684
LGA    H     151      F     136          1.901
LGA    K     152      -       -           -
LGA    Y     153      W     137           #
LGA    L     154      G     138          1.822
LGA    L     155      K     139          2.188
LGA    K     156      F     140          2.406
LGA    V     157      S     141          3.634
LGA    P     158      E     142          3.102
LGA    F     159      E     143          2.532
LGA    Y     160      S     144          4.154
LGA    R     161      Y     145           #
LGA    H     162      S     146          5.274
LGA    I     163      K     147          1.873
LGA    T     164      T     148          3.927
LGA    I     165      A     149          0.901
LGA    R     166      Y     150          4.004
LGA    -       -      H     151           -
LGA    -       -      K     152           -
LGA    -       -      Y     153           -
LGA    N     167      L     154          1.561
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     27    3.10     3.70     18.518     0.844

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.316996 * X  +  -0.717426 * Y  +  -0.620334 * Z  +  14.959265
  Y_new =  -0.849130 * X  +  -0.076675 * Y  +   0.522589 * Z  +  53.760513
  Z_new =  -0.422483 * X  +   0.692403 * Y  +  -0.584882 * Z  +   8.427686 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.272213   -0.869379  [ DEG:   130.1882    -49.8118 ]
  Theta =   0.436183    2.705410  [ DEG:    24.9914    155.0086 ]
  Phi   =  -1.928092    1.213500  [ DEG:  -110.4716     69.5284 ]
 
# 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: T0299TS168_5-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS168_5-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   27   3.10    3.70  18.518
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS168_5-D2
PFRMAT TS
TARGET T0299
MODEL 5
PARENT N/A
ATOM     79  CA  LEU    79       5.181  53.411  17.965  1.00 25.00           C
ATOM     80  CA  GLU    80       3.663  51.317  20.790  1.00 25.00           C
ATOM     81  CA  ASP    81       5.036  48.119  19.190  1.00 25.00           C
ATOM     82  CA  PHE    82       8.503  49.721  18.906  1.00 25.00           C
ATOM     83  CA  GLU    83       8.353  50.759  22.589  1.00 25.00           C
ATOM     84  CA  ALA    84       7.364  47.193  23.579  1.00 25.00           C
ATOM     85  CA  GLU    85      10.284  45.790  21.536  1.00 25.00           C
ATOM     86  CA  LEU    86      12.685  48.239  23.240  1.00 25.00           C
ATOM     87  CA  GLU    87      11.358  47.189  26.676  1.00 25.00           C
ATOM     88  CA  ASN    88      11.148  49.961  29.346  1.00 25.00           C
ATOM     89  CA  LEU    89      10.746  52.528  26.559  1.00 25.00           C
ATOM     90  CA  PRO    90       7.066  53.318  26.974  1.00 25.00           C
ATOM     91  CA  ALA    91       7.208  55.929  29.719  1.00 25.00           C
ATOM     92  CA  TRP    92       8.296  58.611  27.270  1.00 25.00           C
ATOM     93  CA  TRP    93      11.629  58.354  25.503  1.00 25.00           C
ATOM     94  CA  SER    94      12.785  57.053  28.897  1.00 25.00           C
ATOM     95  CA  ARG    95      16.105  58.490  27.812  1.00 25.00           C
ATOM     96  CA  ASP    96      18.869  55.839  27.758  1.00 25.00           C
ATOM     97  CA  LEU    97      18.639  55.645  23.940  1.00 25.00           C
ATOM     98  CA  ALA    98      18.886  59.459  23.705  1.00 25.00           C
ATOM     99  CA  ARG    99      16.014  62.001  24.061  1.00 25.00           C
ATOM    100  CA  LYS   100      15.294  61.928  20.339  1.00 25.00           C
ATOM    101  CA  ASP   101      13.575  58.498  20.546  1.00 25.00           C
ATOM    102  CA  PHE   102      15.182  56.731  17.533  1.00 25.00           C
ATOM    103  CA  LEU   103      12.083  55.114  16.117  1.00 25.00           C
ATOM    104  CA  PHE   104      10.776  54.402  12.587  1.00 25.00           C
ATOM    105  CA  TYR   105       8.794  52.862   9.772  1.00 25.00           C
ATOM    106  CA  THR   106      10.226  50.460   7.220  1.00 25.00           C
ATOM    107  CA  GLU   107       6.760  48.902   6.839  1.00 25.00           C
ATOM    108  CA  GLY   108       5.160  47.234   3.777  1.00 25.00           C
ATOM    109  CA  LEU   109       1.763  49.000   3.680  1.00 25.00           C
ATOM    110  CA  ASP   110       2.167  49.912   0.006  1.00 25.00           C
ATOM    111  CA  VAL   111       4.646  52.783  -0.445  1.00 25.00           C
ATOM    112  CA  ASP   112       2.692  55.983   0.339  1.00 25.00           C
ATOM    113  CA  GLN   113       0.954  54.233   3.269  1.00 25.00           C
ATOM    114  CA  VAL   114       4.342  53.033   4.593  1.00 25.00           C
ATOM    115  CA  ILE   115       5.734  56.590   4.329  1.00 25.00           C
ATOM    116  CA  ALA   116       2.693  57.947   6.222  1.00 25.00           C
ATOM    117  CA  THR   117       3.187  55.310   8.955  1.00 25.00           C
ATOM    118  CA  VAL   118       0.520  52.518   8.977  1.00 25.00           C
ATOM    119  CA  GLU   119      -3.034  53.463   7.941  1.00 25.00           C
ATOM    120  CA  SER   120      -4.792  50.829  10.083  1.00 25.00           C
ATOM    121  CA  LEU   121      -3.392  51.939  13.441  1.00 25.00           C
ATOM    122  CA  GLU   122      -5.234  55.005  14.732  1.00 25.00           C
ATOM    123  CA  LEU   123      -2.057  56.935  15.378  1.00 25.00           C
ATOM    124  CA  LYS   124       0.415  58.182  17.922  1.00 25.00           C
ATOM    125  CA  ASP   125       2.435  60.559  15.660  1.00 25.00           C
ATOM    126  CA  GLU   126       5.835  58.950  15.662  1.00 25.00           C
ATOM    127  CA  VAL   127       9.256  60.134  16.816  1.00 25.00           C
ATOM    128  CA  LEU   128      10.502  59.510  13.260  1.00 25.00           C
ATOM    129  CA  TYR   129      10.821  58.495   9.680  1.00 25.00           C
ATOM    130  CA  PHE   130      12.855  58.310   6.500  1.00 25.00           C
ATOM    131  CA  GLY   131      12.612  54.537   6.500  1.00 25.00           C
ATOM    132  CA  LYS   132      12.295  52.725   3.135  1.00 25.00           C
ATOM    133  CA  LEU   133      14.951  50.764   5.002  1.00 25.00           C
ATOM    134  CA  GLY   134      17.910  52.770   6.303  1.00 25.00           C
ATOM    135  CA  ILE   135      17.643  56.447   6.983  1.00 25.00           C
ATOM    136  CA  PHE   136      17.095  60.130   7.485  1.00 25.00           C
ATOM    137  CA  TRP   137      14.603  62.800   8.540  1.00 25.00           C
ATOM    138  CA  GLY   138      11.816  64.376  10.588  1.00 25.00           C
ATOM    139  CA  LYS   139      10.828  66.746   7.767  1.00 25.00           C
ATOM    140  CA  PHE   140       7.141  66.353   7.227  1.00 25.00           C
ATOM    141  CA  SER   141       4.633  68.987   6.143  1.00 25.00           C
ATOM    142  CA  GLU   142       1.707  69.943   3.845  1.00 25.00           C
ATOM    143  CA  GLU   143       0.210  68.982   0.433  1.00 25.00           C
ATOM    144  CA  SER   144       1.850  65.620   1.117  1.00 25.00           C
ATOM    145  CA  TYR   145       5.286  64.496   2.380  1.00 25.00           C
ATOM    146  CA  SER   146       4.304  60.831   1.869  1.00 25.00           C
ATOM    147  CA  LYS   147       3.128  61.617  -1.690  1.00 25.00           C
ATOM    148  CA  THR   148       6.439  63.400  -2.416  1.00 25.00           C
ATOM    149  CA  ALA   149       8.384  60.384  -1.078  1.00 25.00           C
ATOM    150  CA  TYR   150       6.318  58.038  -3.291  1.00 25.00           C
ATOM    151  CA  HIS   151       7.010  60.258  -6.333  1.00 25.00           C
ATOM    152  CA  LYS   152       6.620  57.323  -8.715  1.00 25.00           C
ATOM    153  CA  TYR   153       7.742  58.808 -12.000  1.00 25.00           C
ATOM    154  CA  LEU   154      11.207  58.341 -10.525  1.00 25.00           C
ATOM    155  CA  LEU   155      14.657  57.515 -11.893  1.00 25.00           C
ATOM    156  CA  LYS   156      16.546  56.950 -15.130  1.00 25.00           C
ATOM    157  CA  VAL   157      18.489  57.045 -18.388  1.00 25.00           C
ATOM    158  CA  PRO   158      20.991  54.167 -17.886  1.00 25.00           C
ATOM    159  CA  PHE   159      22.003  52.492 -14.625  1.00 25.00           C
ATOM    160  CA  TYR   160      25.814  52.330 -14.622  1.00 25.00           C
ATOM    161  CA  ARG   161      27.679  52.244 -11.330  1.00 25.00           C
ATOM    162  CA  HIS   162      27.953  52.797  -7.550  1.00 25.00           C
ATOM    163  CA  ILE   163      25.321  53.048  -4.814  1.00 25.00           C
ATOM    164  CA  THR   164      22.184  52.168  -2.870  1.00 25.00           C
ATOM    165  CA  ILE   165      20.087  54.747  -1.154  1.00 25.00           C
ATOM    166  CA  ARG   166      17.177  53.220   0.732  1.00 25.00           C
ATOM    167  CA  ASN   167      15.197  50.143  -0.161  1.00 25.00           C
TER
END
