
#######################################################
#                                                     #
#                        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_1-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS393_1-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      -       -           -
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      E      83           #
LGA    F     102      A      84          2.887
LGA    L     103      E      85          2.683
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    -       -      N      88           -
LGA    F     104      L      89          2.226
LGA    Y     105      P      90          2.094
LGA    T     106      A      91           #
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      W      92          4.442
LGA    E     119      W      93           -
LGA    S     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    L     123      -       -           -
LGA    K     124      -       -           -
LGA    D     125      S      94          4.455
LGA    E     126      R      95           #
LGA    V     127      D      96           -
LGA    L     128      L      97           -
LGA    Y     129      A      98           -
LGA    F     130      R      99           -
LGA    -       -      K     100           -
LGA    G     131      D     101          3.832
LGA    K     132      F     102          3.722
LGA    L     133      L     103          4.596
LGA    G     134      F     104          2.892
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    -       -      D     125           -
LGA    -       -      E     126           -
LGA    -       -      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      I     135          2.127
LGA    F     136      F     136          1.143
LGA    W     137      W     137          4.494
LGA    G     138      G     138           #
LGA    K     139      K     139           -
LGA    F     140      -       -           -
LGA    S     141      -       -           -
LGA    E     142      -       -           -
LGA    E     143      -       -           -
LGA    S     144      -       -           -
LGA    Y     145      F     140          2.405
LGA    S     146      S     141          4.070
LGA    K     147      E     142           -
LGA    -       -      E     143           -
LGA    -       -      S     144           -
LGA    T     148      Y     145           #
LGA    A     149      S     146           -
LGA    -       -      K     147           -
LGA    Y     150      T     148          5.267
LGA    H     151      A     149          2.611
LGA    -       -      Y     150           -
LGA    K     152      H     151          3.325
LGA    Y     153      K     152          1.761
LGA    L     154      Y     153          1.538
LGA    L     155      L     154          4.128
LGA    K     156      L     155          4.530
LGA    V     157      K     156          4.184
LGA    P     158      -       -           -
LGA    F     159      V     157          4.334
LGA    Y     160      P     158          3.073
LGA    R     161      -       -           -
LGA    H     162      F     159          4.410
LGA    I     163      Y     160          3.654
LGA    -       -      R     161           -
LGA    -       -      H     162           -
LGA    T     164      I     163          2.527
LGA    I     165      T     164          2.754
LGA    R     166      I     165          2.065
LGA    N     167      R     166          2.647
LGA    -       -      N     167           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     31    3.42    19.35     18.929     0.880

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.582403 * X  +   0.249236 * Y  +   0.773749 * Z  +   2.831030
  Y_new =   0.616010 * X  +  -0.756385 * Y  +  -0.220030 * Z  +  57.402939
  Z_new =   0.530413 * X  +   0.604783 * Y  +  -0.594053 * Z  +  -5.919651 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.347244   -0.794349  [ DEG:   134.4872    -45.5128 ]
  Theta =  -0.559088   -2.582505  [ DEG:   -32.0334   -147.9666 ]
  Phi   =   0.813434   -2.328159  [ DEG:    46.6063   -133.3937 ]
 
# 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_1-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS393_1-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   31   3.42   19.35  18.929
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS393_1-D2
PFRMAT TS
TARGET T0299
MODEL 1
PARENT N/A
ATOM     79  CA  LEU    79       1.951  49.576 -16.921  1.00 25.00           C
ATOM     80  CA  GLU    80       2.031  50.832 -20.539  1.00 25.00           C
ATOM     81  CA  ASP    81      -1.789  50.620 -20.722  1.00 25.00           C
ATOM     82  CA  PHE    82      -2.079  52.579 -17.444  1.00 25.00           C
ATOM     83  CA  GLU    83       0.303  55.252 -18.802  1.00 25.00           C
ATOM     84  CA  ALA    84      -1.772  55.506 -22.011  1.00 25.00           C
ATOM     85  CA  GLU    85      -4.971  55.887 -19.941  1.00 25.00           C
ATOM     86  CA  LEU    86      -3.323  58.642 -17.854  1.00 25.00           C
ATOM     87  CA  GLU    87      -2.233  60.446 -21.052  1.00 25.00           C
ATOM     88  CA  ASN    88      -5.312  59.759 -23.120  1.00 25.00           C
ATOM     89  CA  LEU    89      -8.595  59.223 -21.195  1.00 25.00           C
ATOM     90  CA  PRO    90      -8.110  62.080 -18.680  1.00 25.00           C
ATOM     91  CA  ALA    91     -11.001  63.704 -20.546  1.00 25.00           C
ATOM     92  CA  TRP    92     -13.352  60.840 -19.568  1.00 25.00           C
ATOM     93  CA  TRP    93     -12.836  59.650 -15.986  1.00 25.00           C
ATOM     94  CA  SER    94     -15.282  62.415 -15.196  1.00 25.00           C
ATOM     95  CA  ARG    95     -14.678  66.149 -15.930  1.00 25.00           C
ATOM     96  CA  ASP    96     -14.063  67.095 -12.270  1.00 25.00           C
ATOM     97  CA  LEU    97     -11.001  64.798 -12.165  1.00 25.00           C
ATOM     98  CA  ALA    98      -9.660  66.396 -15.376  1.00 25.00           C
ATOM     99  CA  ARG    99      -8.765  69.571 -13.495  1.00 25.00           C
ATOM    100  CA  LYS   100      -5.942  69.235 -10.961  1.00 25.00           C
ATOM    101  CA  ASP   101      -7.081  67.060  -7.990  1.00 25.00           C
ATOM    102  CA  PHE   102      -4.450  65.028  -6.128  1.00 25.00           C
ATOM    103  CA  LEU   103      -0.882  63.871  -5.609  1.00 25.00           C
ATOM    104  CA  PHE   104       2.077  62.586  -7.597  1.00 25.00           C
ATOM    105  CA  TYR   105       5.043  63.474  -9.786  1.00 25.00           C
ATOM    106  CA  THR   106       6.343  60.481 -11.697  1.00 25.00           C
ATOM    107  CA  GLU   107       6.023  57.114 -13.459  1.00 25.00           C
ATOM    108  CA  GLY   108       6.716  54.904 -16.442  1.00 25.00           C
ATOM    109  CA  LEU   109      10.246  54.191 -15.075  1.00 25.00           C
ATOM    110  CA  ASP   110      11.455  53.229 -18.537  1.00 25.00           C
ATOM    111  CA  VAL   111      11.594  56.968 -19.403  1.00 25.00           C
ATOM    112  CA  ASP   112      14.453  58.376 -17.278  1.00 25.00           C
ATOM    113  CA  GLN   113      13.256  61.944 -17.987  1.00 25.00           C
ATOM    114  CA  VAL   114       9.690  60.974 -16.982  1.00 25.00           C
ATOM    115  CA  ILE   115      11.002  59.420 -13.737  1.00 25.00           C
ATOM    116  CA  ALA   116      12.989  62.607 -12.985  1.00 25.00           C
ATOM    117  CA  THR   117       9.863  64.731 -13.606  1.00 25.00           C
ATOM    118  CA  VAL   118       8.813  67.222 -16.340  1.00 25.00           C
ATOM    119  CA  GLU   119       8.689  70.197 -18.655  1.00 25.00           C
ATOM    120  CA  SER   120       5.489  71.643 -17.122  1.00 25.00           C
ATOM    121  CA  LEU   121       3.277  69.394 -19.189  1.00 25.00           C
ATOM    122  CA  GLU   122       4.935  68.605 -22.501  1.00 25.00           C
ATOM    123  CA  LEU   123       3.310  65.552 -24.122  1.00 25.00           C
ATOM    124  CA  LYS   124       2.344  61.992 -23.071  1.00 25.00           C
ATOM    125  CA  ASP   125       5.051  62.335 -20.384  1.00 25.00           C
ATOM    126  CA  GLU   126       3.664  62.812 -16.870  1.00 25.00           C
ATOM    127  CA  VAL   127       0.318  63.980 -15.444  1.00 25.00           C
ATOM    128  CA  LEU   128       1.073  61.190 -12.883  1.00 25.00           C
ATOM    129  CA  TYR   129       2.188  58.469 -10.445  1.00 25.00           C
ATOM    130  CA  PHE   130       2.264  57.085  -6.882  1.00 25.00           C
ATOM    131  CA  GLY   131       5.553  55.751  -8.248  1.00 25.00           C
ATOM    132  CA  LYS   132       4.349  52.146  -8.372  1.00 25.00           C
ATOM    133  CA  LEU   133       2.697  52.680  -5.022  1.00 25.00           C
ATOM    134  CA  GLY   134       2.114  55.187  -2.281  1.00 25.00           C
ATOM    135  CA  ILE   135       5.483  56.884  -3.059  1.00 25.00           C
ATOM    136  CA  PHE   136       8.029  59.172  -4.617  1.00 25.00           C
ATOM    137  CA  TRP   137       9.365  61.618  -7.200  1.00 25.00           C
ATOM    138  CA  GLY   138      11.740  64.557  -6.646  1.00 25.00           C
ATOM    139  CA  LYS   139      14.060  63.989  -3.773  1.00 25.00           C
ATOM    140  CA  PHE   140      16.767  63.972  -6.410  1.00 25.00           C
ATOM    141  CA  SER   141      18.769  65.210  -9.371  1.00 25.00           C
ATOM    142  CA  GLU   142      22.292  64.803 -10.829  1.00 25.00           C
ATOM    143  CA  GLU   143      24.363  61.802 -11.872  1.00 25.00           C
ATOM    144  CA  SER   144      21.194  59.707 -12.057  1.00 25.00           C
ATOM    145  CA  TYR   145      17.409  59.879 -11.499  1.00 25.00           C
ATOM    146  CA  SER   146      17.143  56.088 -11.970  1.00 25.00           C
ATOM    147  CA  LYS   147      19.977  55.552  -9.451  1.00 25.00           C
ATOM    148  CA  THR   148      18.216  57.848  -6.943  1.00 25.00           C
ATOM    149  CA  ALA   149      14.951  55.906  -7.419  1.00 25.00           C
ATOM    150  CA  TYR   150      16.804  52.603  -6.849  1.00 25.00           C
ATOM    151  CA  HIS   151      18.383  54.011  -3.657  1.00 25.00           C
ATOM    152  CA  LYS   152      21.683  52.388  -4.393  1.00 25.00           C
ATOM    153  CA  TYR   153      23.172  51.301  -1.120  1.00 25.00           C
ATOM    154  CA  LEU   154      19.563  50.769  -0.048  1.00 25.00           C
ATOM    155  CA  LEU   155      18.995  47.114   0.828  1.00 25.00           C
ATOM    156  CA  LYS   156      20.804  46.791   4.171  1.00 25.00           C
ATOM    157  CA  VAL   157      20.671  45.390   7.644  1.00 25.00           C
ATOM    158  CA  PRO   158      19.730  47.730  10.479  1.00 25.00           C
ATOM    159  CA  PHE   159      16.383  49.599  10.729  1.00 25.00           C
ATOM    160  CA  TYR   160      13.669  46.934  11.307  1.00 25.00           C
ATOM    161  CA  ARG   161      11.153  44.154  11.941  1.00 25.00           C
ATOM    162  CA  HIS   162       9.055  46.054   9.406  1.00 25.00           C
ATOM    163  CA  ILE   163       7.553  46.957   6.063  1.00 25.00           C
ATOM    164  CA  THR   164       7.631  49.825   3.580  1.00 25.00           C
ATOM    165  CA  ILE   165       6.071  49.523   0.125  1.00 25.00           C
ATOM    166  CA  ARG   166       7.560  50.251  -3.284  1.00 25.00           C
ATOM    167  CA  ASN   167       5.253  47.759  -4.976  1.00 25.00           C
TER
END
