
#######################################################
#                                                     #
#                        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 T0299TS393_2-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS393_2-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      F      82           -
LGA    E      83      E      83           -
LGA    A      84      -       -           -
LGA    E      85      -       -           -
LGA    L      86      -       -           -
LGA    E      87      -       -           -
LGA    N      88      -       -           -
LGA    L      89      -       -           -
LGA    P      90      -       -           -
LGA    A      91      -       -           -
LGA    W      92      -       -           -
LGA    W      93      -       -           -
LGA    S      94      -       -           -
LGA    R      95      -       -           -
LGA    D      96      -       -           -
LGA    L      97      -       -           -
LGA    A      98      -       -           -
LGA    R      99      -       -           -
LGA    K     100      -       -           -
LGA    D     101      A      84           #
LGA    -       -      E      85           -
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    F     102      N      88          3.744
LGA    L     103      L      89          4.035
LGA    F     104      P      90          4.636
LGA    -       -      A      91           -
LGA    Y     105      W      92           #
LGA    T     106      W      93          2.525
LGA    E     107      S      94          5.138
LGA    G     108      R      95          5.321
LGA    L     109      D      96          1.137
LGA    D     110      L      97          3.056
LGA    V     111      A      98           #
LGA    D     112      R      99           -
LGA    Q     113      K     100           -
LGA    V     114      D     101           -
LGA    -       -      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           -
LGA    -       -      V     111           -
LGA    -       -      D     112           -
LGA    -       -      Q     113           -
LGA    -       -      V     114           -
LGA    -       -      I     115           -
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    -       -      V     118           -
LGA    -       -      E     119           -
LGA    -       -      S     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      L     123           -
LGA    -       -      K     124           -
LGA    I     115      D     125          5.059
LGA    A     116      E     126          3.724
LGA    T     117      V     127          2.727
LGA    V     118      -       -           -
LGA    E     119      -       -           -
LGA    S     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    L     123      -       -           -
LGA    K     124      -       -           -
LGA    D     125      -       -           -
LGA    E     126      -       -           -
LGA    V     127      -       -           -
LGA    L     128      -       -           -
LGA    Y     129      L     128          3.659
LGA    F     130      Y     129          1.378
LGA    G     131      F     130          3.057
LGA    K     132      G     131          3.814
LGA    L     133      K     132          2.711
LGA    -       -      L     133           -
LGA    G     134      G     134          3.761
LGA    I     135      I     135          1.105
LGA    F     136      F     136          2.091
LGA    W     137      W     137          2.725
LGA    G     138      G     138          3.517
LGA    K     139      K     139          3.832
LGA    F     140      F     140          3.504
LGA    S     141      S     141          2.245
LGA    -       -      E     142           -
LGA    E     142      E     143          2.864
LGA    E     143      S     144          3.648
LGA    S     144      -       -           -
LGA    Y     145      -       -           -
LGA    S     146      -       -           -
LGA    K     147      Y     145          3.068
LGA    -       -      S     146           -
LGA    -       -      K     147           -
LGA    T     148      T     148          1.626
LGA    A     149      A     149          2.428
LGA    Y     150      Y     150          3.853
LGA    H     151      H     151          2.452
LGA    K     152      K     152           #
LGA    Y     153      Y     153           -
LGA    L     154      L     154           -
LGA    L     155      L     155           #
LGA    K     156      K     156           -
LGA    V     157      V     157           -
LGA    P     158      P     158           -
LGA    F     159      F     159           -
LGA    Y     160      Y     160           -
LGA    R     161      R     161           -
LGA    H     162      H     162           -
LGA    I     163      -       -           -
LGA    T     164      I     163           #
LGA    I     165      T     164          2.977
LGA    R     166      I     165          2.847
LGA    N     167      R     166          1.602
LGA    -       -      N     167           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     34    3.29    41.18     21.465     1.003

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.872650 * X  +  -0.016235 * Y  +   0.488076 * Z  +   3.795102
  Y_new =  -0.483058 * X  +   0.117989 * Y  +   0.867602 * Z  +  57.972584
  Z_new =  -0.071673 * X  +  -0.992882 * Y  +   0.095121 * Z  +  -7.543178 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.475285    1.666307  [ DEG:   -84.5276     95.4724 ]
  Theta =   0.071734    3.069859  [ DEG:     4.1101    175.8899 ]
  Phi   =  -0.505567    2.636026  [ DEG:   -28.9669    151.0331 ]
 
# 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: T0299TS393_2-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS393_2-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   34   3.29   41.18  21.465
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS393_2-D2
PFRMAT TS
TARGET T0299
MODEL 2
PARENT N/A
ATOM     79  CA  LEU    79       9.094  64.916 -17.283  1.00 25.00           C
ATOM     80  CA  GLU    80       7.642  67.485 -19.725  1.00 25.00           C
ATOM     81  CA  ASP    81       4.931  64.992 -20.774  1.00 25.00           C
ATOM     82  CA  PHE    82       4.078  64.336 -17.099  1.00 25.00           C
ATOM     83  CA  GLU    83       3.838  68.104 -16.457  1.00 25.00           C
ATOM     84  CA  ALA    84       1.528  68.498 -19.486  1.00 25.00           C
ATOM     85  CA  GLU    85      -0.678  65.640 -18.206  1.00 25.00           C
ATOM     86  CA  LEU    86      -0.848  67.286 -14.752  1.00 25.00           C
ATOM     87  CA  GLU    87      -1.832  70.619 -16.361  1.00 25.00           C
ATOM     88  CA  ASN    88      -3.310  69.839 -19.748  1.00 25.00           C
ATOM     89  CA  LEU    89      -1.019  72.741 -20.830  1.00 25.00           C
ATOM     90  CA  PRO    90      -0.358  75.179 -18.003  1.00 25.00           C
ATOM     91  CA  ALA    91      -2.384  77.909 -16.215  1.00 25.00           C
ATOM     92  CA  TRP    92      -4.499  75.729 -13.857  1.00 25.00           C
ATOM     93  CA  TRP    93      -2.382  73.622 -11.556  1.00 25.00           C
ATOM     94  CA  SER    94      -1.253  76.983 -10.104  1.00 25.00           C
ATOM     95  CA  ARG    95      -2.100  79.598  -7.524  1.00 25.00           C
ATOM     96  CA  ASP    96      -5.187  77.892  -6.031  1.00 25.00           C
ATOM     97  CA  LEU    97      -3.405  74.504  -6.155  1.00 25.00           C
ATOM     98  CA  ALA    98      -0.350  76.021  -4.413  1.00 25.00           C
ATOM     99  CA  ARG    99       0.116  75.038  -0.786  1.00 25.00           C
ATOM    100  CA  LYS   100      -0.925  71.399  -1.308  1.00 25.00           C
ATOM    101  CA  ASP   101      -0.666  70.184  -4.937  1.00 25.00           C
ATOM    102  CA  PHE   102       1.671  67.470  -3.581  1.00 25.00           C
ATOM    103  CA  LEU   103       3.955  67.026  -6.595  1.00 25.00           C
ATOM    104  CA  PHE   104       3.395  63.312  -5.896  1.00 25.00           C
ATOM    105  CA  TYR   105       4.766  62.116  -9.302  1.00 25.00           C
ATOM    106  CA  THR   106       7.263  59.595 -10.718  1.00 25.00           C
ATOM    107  CA  GLU   107       7.007  57.127 -13.625  1.00 25.00           C
ATOM    108  CA  GLY   108       9.927  56.578 -15.999  1.00 25.00           C
ATOM    109  CA  LEU   109      12.170  58.156 -18.634  1.00 25.00           C
ATOM    110  CA  ASP   110      15.459  59.559 -17.430  1.00 25.00           C
ATOM    111  CA  VAL   111      13.543  61.277 -14.688  1.00 25.00           C
ATOM    112  CA  ASP   112      17.033  62.496 -13.684  1.00 25.00           C
ATOM    113  CA  GLN   113      15.477  65.286 -11.572  1.00 25.00           C
ATOM    114  CA  VAL   114      13.173  62.744  -9.867  1.00 25.00           C
ATOM    115  CA  ILE   115      16.174  60.483  -9.128  1.00 25.00           C
ATOM    116  CA  ALA   116      18.080  63.455  -7.646  1.00 25.00           C
ATOM    117  CA  THR   117      15.063  64.330  -5.456  1.00 25.00           C
ATOM    118  CA  VAL   118      13.758  67.908  -6.037  1.00 25.00           C
ATOM    119  CA  GLU   119      16.525  69.801  -4.329  1.00 25.00           C
ATOM    120  CA  SER   120      15.015  72.778  -6.145  1.00 25.00           C
ATOM    121  CA  LEU   121      15.946  71.360  -9.566  1.00 25.00           C
ATOM    122  CA  GLU   122      16.173  74.726 -11.171  1.00 25.00           C
ATOM    123  CA  LEU   123      15.407  72.975 -14.432  1.00 25.00           C
ATOM    124  CA  LYS   124      11.884  72.944 -15.805  1.00 25.00           C
ATOM    125  CA  ASP   125      11.764  69.528 -14.068  1.00 25.00           C
ATOM    126  CA  GLU   126       8.615  68.438 -12.256  1.00 25.00           C
ATOM    127  CA  VAL   127       9.823  64.839 -12.001  1.00 25.00           C
ATOM    128  CA  LEU   128       8.847  65.023  -8.385  1.00 25.00           C
ATOM    129  CA  TYR   129       8.821  61.965  -6.206  1.00 25.00           C
ATOM    130  CA  PHE   130       8.404  61.952  -2.428  1.00 25.00           C
ATOM    131  CA  GLY   131       6.090  64.893  -1.765  1.00 25.00           C
ATOM    132  CA  LYS   132       3.495  65.134   1.022  1.00 25.00           C
ATOM    133  CA  LEU   133       1.628  62.583  -0.990  1.00 25.00           C
ATOM    134  CA  GLY   134       4.298  60.096  -2.032  1.00 25.00           C
ATOM    135  CA  ILE   135       6.941  57.352  -2.521  1.00 25.00           C
ATOM    136  CA  PHE   136       6.457  57.027  -6.323  1.00 25.00           C
ATOM    137  CA  TRP   137       9.735  55.116  -6.078  1.00 25.00           C
ATOM    138  CA  GLY   138      10.711  54.954  -9.747  1.00 25.00           C
ATOM    139  CA  LYS   139      13.907  53.564 -11.196  1.00 25.00           C
ATOM    140  CA  PHE   140      17.099  55.060 -12.603  1.00 25.00           C
ATOM    141  CA  SER   141      20.641  54.423 -13.827  1.00 25.00           C
ATOM    142  CA  GLU   142      24.148  55.863 -13.899  1.00 25.00           C
ATOM    143  CA  GLU   143      27.001  56.901 -11.624  1.00 25.00           C
ATOM    144  CA  SER   144      25.588  58.010  -8.221  1.00 25.00           C
ATOM    145  CA  TYR   145      23.649  58.372  -4.939  1.00 25.00           C
ATOM    146  CA  SER   146      20.342  58.433  -6.870  1.00 25.00           C
ATOM    147  CA  LYS   147      21.372  55.279  -8.781  1.00 25.00           C
ATOM    148  CA  THR   148      22.265  53.543  -5.486  1.00 25.00           C
ATOM    149  CA  ALA   149      18.867  54.530  -4.018  1.00 25.00           C
ATOM    150  CA  TYR   150      17.098  53.153  -7.123  1.00 25.00           C
ATOM    151  CA  HIS   151      19.052  49.874  -6.812  1.00 25.00           C
ATOM    152  CA  LYS   152      19.794  47.070  -9.271  1.00 25.00           C
ATOM    153  CA  TYR   153      19.974  43.281  -9.679  1.00 25.00           C
ATOM    154  CA  LEU   154      16.257  43.150  -8.981  1.00 25.00           C
ATOM    155  CA  LEU   155      16.270  40.384  -6.330  1.00 25.00           C
ATOM    156  CA  LYS   156      17.157  36.939  -4.982  1.00 25.00           C
ATOM    157  CA  VAL   157      14.521  34.293  -5.643  1.00 25.00           C
ATOM    158  CA  PRO   158      10.981  33.090  -5.790  1.00 25.00           C
ATOM    159  CA  PHE   159       7.627  34.852  -5.839  1.00 25.00           C
ATOM    160  CA  TYR   160       5.546  34.626  -2.707  1.00 25.00           C
ATOM    161  CA  ARG   161       2.417  36.285  -1.158  1.00 25.00           C
ATOM    162  CA  HIS   162      -0.398  38.796  -1.202  1.00 25.00           C
ATOM    163  CA  ILE   163       1.367  41.607  -2.944  1.00 25.00           C
ATOM    164  CA  THR   164       3.156  44.437  -4.840  1.00 25.00           C
ATOM    165  CA  ILE   165       4.599  47.715  -3.515  1.00 25.00           C
ATOM    166  CA  ARG   166       5.155  51.398  -4.469  1.00 25.00           C
ATOM    167  CA  ASN   167       5.466  50.288  -8.050  1.00 25.00           C
TER
END
