
#######################################################
#                                                     #
#                        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_1-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS599_1-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    D      81      -       -           -
LGA    F      82      E      80           #
LGA    E      83      D      81          1.859
LGA    A      84      -       -           -
LGA    E      85      F      82          4.667
LGA    L      86      E      83          1.533
LGA    E      87      A      84          4.068
LGA    N      88      E      85           #
LGA    L      89      L      86          3.388
LGA    P      90      E      87          1.947
LGA    A      91      N      88          3.780
LGA    W      92      L      89          4.189
LGA    W      93      P      90          4.281
LGA    -       -      A      91           -
LGA    -       -      W      92           -
LGA    S      94      W      93          3.249
LGA    R      95      S      94          3.374
LGA    -       -      R      95           -
LGA    D      96      D      96          3.149
LGA    L      97      L      97          1.357
LGA    A      98      A      98          3.308
LGA    R      99      R      99          1.212
LGA    K     100      K     100          1.858
LGA    D     101      D     101          1.787
LGA    F     102      F     102          1.295
LGA    L     103      L     103          3.429
LGA    F     104      F     104          1.488
LGA    Y     105      Y     105          2.979
LGA    T     106      T     106          3.226
LGA    E     107      E     107          0.462
LGA    G     108      G     108          2.896
LGA    L     109      L     109          1.141
LGA    D     110      D     110          2.977
LGA    -       -      V     111           -
LGA    V     111      D     112          5.809
LGA    D     112      Q     113           #
LGA    Q     113      -       -           -
LGA    V     114      V     114          4.188
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      I     115           #
LGA    G     134      A     116          2.553
LGA    I     135      T     117          3.160
LGA    -       -      V     118           -
LGA    F     136      E     119          3.105
LGA    W     137      S     120          2.674
LGA    G     138      L     121          4.133
LGA    K     139      E     122          2.425
LGA    F     140      L     123           #
LGA    S     141      K     124           #
LGA    E     142      -       -           -
LGA    E     143      -       -           -
LGA    S     144      D     125          1.921
LGA    Y     145      -       -           -
LGA    S     146      -       -           -
LGA    K     147      -       -           -
LGA    T     148      E     126          2.974
LGA    A     149      -       -           -
LGA    Y     150      -       -           -
LGA    H     151      -       -           -
LGA    K     152      V     127          2.819
LGA    Y     153      L     128          2.544
LGA    L     154      Y     129          2.530
LGA    L     155      -       -           -
LGA    K     156      F     130          3.852
LGA    V     157      G     131          4.477
LGA    P     158      K     132          4.794
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    F     159      I     135           #
LGA    Y     160      F     136           -
LGA    R     161      W     137           -
LGA    H     162      G     138           -
LGA    -       -      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    I     163      A     149           #
LGA    T     164      Y     150           -
LGA    I     165      H     151           -
LGA    R     166      K     152           -
LGA    N     167      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     42    3.14    40.48     26.822     1.295

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.277662 * X  +  -0.951402 * Y  +  -0.133183 * Z  +   7.654260
  Y_new =  -0.416569 * X  +  -0.244160 * Y  +   0.875703 * Z  +  53.256317
  Z_new =  -0.865664 * X  +  -0.187670 * Y  +  -0.464118 * Z  +  -0.888403 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.757335    0.384257  [ DEG:  -157.9837     22.0163 ]
  Theta =   1.046475    2.095117  [ DEG:    59.9586    120.0414 ]
  Phi   =  -0.982878    2.158715  [ DEG:   -56.3147    123.6853 ]
 
# 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_1-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS599_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   42   3.14   40.48  26.822
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS599_1-D2
PFRMAT TS                                                                       
TARGET T0299                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM     79  CA  LEU    79      -7.040  55.756   3.908  1.00  0.00              
ATOM     80  CA  GLU    80      -8.473  59.228   4.373  1.00  0.00              
ATOM     81  CA  ASP    81      -5.384  60.754   2.879  1.00  0.00              
ATOM     82  CA  PHE    82      -5.525  58.365  -0.125  1.00  0.00              
ATOM     83  CA  GLU    83      -9.129  59.328  -0.768  1.00  0.00              
ATOM     84  CA  ALA    84      -8.136  63.021  -0.572  1.00  0.00              
ATOM     85  CA  GLU    85      -5.310  62.467  -3.035  1.00  0.00              
ATOM     86  CA  LEU    86      -7.538  60.642  -5.564  1.00  0.00              
ATOM     87  CA  GLU    87     -10.127  63.427  -5.402  1.00  0.00              
ATOM     88  CA  ASN    88      -7.585  66.175  -5.961  1.00  0.00              
ATOM     89  CA  LEU    89      -5.781  64.681  -8.967  1.00  0.00              
ATOM     90  CA  PRO    90      -2.345  66.080  -9.658  1.00  0.00              
ATOM     91  CA  ALA    91       0.158  63.415  -8.883  1.00  0.00              
ATOM     92  CA  TRP    92       1.385  61.247 -11.714  1.00  0.00              
ATOM     93  CA  TRP    93       5.178  61.688 -11.389  1.00  0.00              
ATOM     94  CA  SER    94       5.826  63.677 -14.493  1.00  0.00              
ATOM     95  CA  ARG    95       8.986  62.278 -15.781  1.00  0.00              
ATOM     96  CA  ASP    96      10.113  58.703 -15.935  1.00  0.00              
ATOM     97  CA  LEU    97      13.840  59.167 -16.246  1.00  0.00              
ATOM     98  CA  ALA    98      15.115  56.857 -13.501  1.00  0.00              
ATOM     99  CA  ARG    99      12.425  54.202 -13.611  1.00  0.00              
ATOM    100  CA  LYS   100      11.094  53.981 -10.010  1.00  0.00              
ATOM    101  CA  ASP   101       8.313  51.743  -8.949  1.00  0.00              
ATOM    102  CA  PHE   102       5.860  53.174  -6.359  1.00  0.00              
ATOM    103  CA  LEU   103       4.050  51.010  -3.815  1.00  0.00              
ATOM    104  CA  PHE   104       1.440  52.565  -1.616  1.00  0.00              
ATOM    105  CA  TYR   105       0.721  51.018   1.725  1.00  0.00              
ATOM    106  CA  THR   106      -2.353  51.841   3.520  1.00  0.00              
ATOM    107  CA  GLU   107      -2.320  50.920   7.120  1.00  0.00              
ATOM    108  CA  GLY   108      -1.743  53.847   9.387  1.00  0.00              
ATOM    109  CA  LEU   109       1.923  53.529  10.160  1.00  0.00              
ATOM    110  CA  ASP   110       2.796  54.265  13.794  1.00  0.00              
ATOM    111  CA  VAL   111       5.836  56.534  14.313  1.00  0.00              
ATOM    112  CA  ASP   112       7.530  53.718  16.239  1.00  0.00              
ATOM    113  CA  GLN   113       7.139  51.368  13.246  1.00  0.00              
ATOM    114  CA  VAL   114       8.606  53.916  10.888  1.00  0.00              
ATOM    115  CA  ILE   115      11.606  54.520  13.193  1.00  0.00              
ATOM    116  CA  ALA   116      12.245  50.814  13.449  1.00  0.00              
ATOM    117  CA  THR   117      12.048  50.379   9.672  1.00  0.00              
ATOM    118  CA  VAL   118      14.450  53.296   8.998  1.00  0.00              
ATOM    119  CA  GLU   119      16.947  51.917  11.538  1.00  0.00              
ATOM    120  CA  SER   120      16.783  48.437  10.048  1.00  0.00              
ATOM    121  CA  LEU   121      17.333  49.223   6.321  1.00  0.00              
ATOM    122  CA  GLU   122      19.631  52.165   6.419  1.00  0.00              
ATOM    123  CA  LEU   123      23.159  50.938   6.021  1.00  0.00              
ATOM    124  CA  LYS   124      24.005  51.528   2.526  1.00  0.00              
ATOM    125  CA  ASP   125      23.271  55.127   1.935  1.00  0.00              
ATOM    126  CA  GLU   126      24.069  56.405   5.396  1.00  0.00              
ATOM    127  CA  VAL   127      20.915  56.917   7.397  1.00  0.00              
ATOM    128  CA  LEU   128      20.612  59.802   9.948  1.00  0.00              
ATOM    129  CA  TYR   129      17.776  59.822  12.451  1.00  0.00              
ATOM    130  CA  PHE   130      16.415  63.080  13.709  1.00  0.00              
ATOM    131  CA  GLY   131      13.432  62.938  15.968  1.00  0.00              
ATOM    132  CA  LYS   132       9.973  64.141  15.173  1.00  0.00              
ATOM    133  CA  LEU   133       9.056  62.059  12.190  1.00  0.00              
ATOM    134  CA  GLY   134      12.243  62.940  10.247  1.00  0.00              
ATOM    135  CA  ILE   135      14.694  60.589   8.556  1.00  0.00              
ATOM    136  CA  PHE   136      17.720  62.123   6.888  1.00  0.00              
ATOM    137  CA  TRP   137      19.341  60.169   4.063  1.00  0.00              
ATOM    138  CA  GLY   138      22.790  61.098   2.916  1.00  0.00              
ATOM    139  CA  LYS   139      23.789  60.333  -0.590  1.00  0.00              
ATOM    140  CA  PHE   140      27.252  61.079  -1.822  1.00  0.00              
ATOM    141  CA  SER   141      27.627  62.160  -5.275  1.00  0.00              
ATOM    142  CA  GLU   142      26.190  65.072  -7.180  1.00  0.00              
ATOM    143  CA  GLU   143      25.209  62.953 -10.098  1.00  0.00              
ATOM    144  CA  SER   144      22.943  60.416  -8.635  1.00  0.00              
ATOM    145  CA  TYR   145      20.427  62.945  -7.248  1.00  0.00              
ATOM    146  CA  SER   146      20.159  64.758 -10.582  1.00  0.00              
ATOM    147  CA  LYS   147      19.001  61.687 -12.460  1.00  0.00              
ATOM    148  CA  THR   148      16.093  60.428 -10.380  1.00  0.00              
ATOM    149  CA  ALA   149      14.221  63.559  -9.484  1.00  0.00              
ATOM    150  CA  TYR   150      10.646  62.418  -9.631  1.00  0.00              
ATOM    151  CA  HIS   151      10.891  59.055  -7.794  1.00  0.00              
ATOM    152  CA  LYS   152      12.885  60.578  -5.017  1.00  0.00              
ATOM    153  CA  TYR   153      10.534  63.467  -4.482  1.00  0.00              
ATOM    154  CA  LEU   154       7.425  61.358  -4.343  1.00  0.00              
ATOM    155  CA  LEU   155       9.074  58.963  -1.864  1.00  0.00              
ATOM    156  CA  LYS   156      10.346  61.697   0.460  1.00  0.00              
ATOM    157  CA  VAL   157       6.903  63.338   0.590  1.00  0.00              
ATOM    158  CA  PRO   158       4.598  60.412   1.498  1.00  0.00              
ATOM    159  CA  PHE   159       7.174  59.113   3.993  1.00  0.00              
ATOM    160  CA  TYR   160       8.873  62.110   5.626  1.00  0.00              
ATOM    161  CA  ARG   161      12.351  61.439   4.335  1.00  0.00              
ATOM    162  CA  HIS   162      14.965  64.106   3.779  1.00  0.00              
ATOM    163  CA  ILE   163      17.512  63.460   1.114  1.00  0.00              
ATOM    164  CA  THR   164      20.830  65.267   1.094  1.00  0.00              
ATOM    165  CA  ILE   165      23.043  64.900  -1.787  1.00  0.00              
ATOM    166  CA  ARG   166      26.282  66.762  -1.701  1.00  0.00              
ATOM    167  CA  ASN   167      25.975  67.808   1.983  1.00  0.00              
TER                                                                             
END
