
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS168_3-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      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    L      79      W      92          3.539
LGA    E      80      W      93          3.578
LGA    D      81      S      94          3.175
LGA    F      82      R      95          3.767
LGA    E      83      -       -           -
LGA    A      84      D      96          2.668
LGA    E      85      L      97          1.478
LGA    L      86      -       -           -
LGA    E      87      -       -           -
LGA    N      88      A      98          1.442
LGA    L      89      R      99          4.206
LGA    P      90      K     100           -
LGA    A      91      D     101           -
LGA    W      92      F     102           -
LGA    W      93      L     103           -
LGA    S      94      F     104           -
LGA    R      95      Y     105           -
LGA    D      96      T     106           -
LGA    L      97      E     107           -
LGA    A      98      G     108           -
LGA    R      99      L     109           -
LGA    K     100      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    D     101      K     124          2.712
LGA    F     102      D     125          0.858
LGA    L     103      E     126          0.505
LGA    F     104      V     127          2.407
LGA    Y     105      L     128          0.755
LGA    T     106      Y     129          2.096
LGA    E     107      F     130           -
LGA    G     108      -       -           -
LGA    L     109      -       -           -
LGA    D     110      -       -           -
LGA    V     111      G     131          2.711
LGA    D     112      K     132          1.615
LGA    Q     113      L     133          2.941
LGA    V     114      G     134          2.519
LGA    I     115      I     135          4.231
LGA    A     116      F     136           -
LGA    T     117      W     137           -
LGA    -       -      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    -       -      A     149           -
LGA    -       -      Y     150           -
LGA    -       -      H     151           -
LGA    -       -      K     152           -
LGA    -       -      Y     153           -
LGA    -       -      L     154           -
LGA    -       -      L     155           -
LGA    -       -      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    V     118      F     159           #
LGA    E     119      Y     160          4.481
LGA    S     120      R     161           #
LGA    L     121      H     162           #
LGA    E     122      I     163           #
LGA    -       -      T     164           -
LGA    L     123      I     165          1.357
LGA    K     124      R     166          1.484
LGA    D     125      N     167          3.545
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      -       -           -
LGA    F     136      -       -           -
LGA    W     137      -       -           -
LGA    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    A     149      -       -           -
LGA    Y     150      -       -           -
LGA    H     151      -       -           -
LGA    K     152      -       -           -
LGA    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     23    2.78     4.35     17.529     0.800

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.379840 * X  +  -0.738691 * Y  +  -0.556827 * Z  +  12.398314
  Y_new =   0.286303 * X  +   0.478509 * Y  +  -0.830096 * Z  +  66.412437
  Z_new =   0.879632 * X  +  -0.474725 * Y  +   0.029732 * Z  +  -3.688399 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.508247    1.633345  [ DEG:   -86.4162     93.5838 ]
  Theta =  -1.075088   -2.066505  [ DEG:   -61.5980   -118.4020 ]
  Phi   =   2.495698   -0.645894  [ DEG:   142.9930    -37.0070 ]
 
# 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_3-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS168_3-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   23   2.78    4.35  17.529
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS168_3-D2
PFRMAT TS
TARGET T0299
MODEL 3
PARENT N/A
ATOM     79  CA  LEU    79       5.843  64.835 -12.812  1.00 25.00           C
ATOM     80  CA  GLU    80       5.006  62.148 -15.408  1.00 25.00           C
ATOM     81  CA  ASP    81       8.204  62.982 -17.342  1.00 25.00           C
ATOM     82  CA  PHE    82      10.250  62.730 -14.113  1.00 25.00           C
ATOM     83  CA  GLU    83       8.659  59.333 -13.341  1.00 25.00           C
ATOM     84  CA  ALA    84       9.484  58.115 -16.876  1.00 25.00           C
ATOM     85  CA  GLU    85      13.107  59.285 -16.460  1.00 25.00           C
ATOM     86  CA  LEU    86      13.341  57.447 -13.108  1.00 25.00           C
ATOM     87  CA  GLU    87      11.956  54.266 -14.729  1.00 25.00           C
ATOM     88  CA  ASN    88      14.853  54.068 -17.200  1.00 25.00           C
ATOM     89  CA  LEU    89      16.415  51.713 -14.595  1.00 25.00           C
ATOM     90  CA  PRO    90      18.508  54.756 -13.682  1.00 25.00           C
ATOM     91  CA  ALA    91      21.313  53.392 -15.873  1.00 25.00           C
ATOM     92  CA  TRP    92      24.784  54.563 -14.960  1.00 25.00           C
ATOM     93  CA  TRP    93      23.864  55.945 -11.584  1.00 25.00           C
ATOM     94  CA  SER    94      22.120  52.689 -10.734  1.00 25.00           C
ATOM     95  CA  ARG    95      24.565  50.141  -9.413  1.00 25.00           C
ATOM     96  CA  ASP    96      27.899  51.995  -9.082  1.00 25.00           C
ATOM     97  CA  LEU    97      26.276  54.544  -6.729  1.00 25.00           C
ATOM     98  CA  ALA    98      24.822  51.702  -4.613  1.00 25.00           C
ATOM     99  CA  ARG    99      21.086  50.973  -4.075  1.00 25.00           C
ATOM    100  CA  LYS   100      20.739  54.615  -2.913  1.00 25.00           C
ATOM    101  CA  ASP   101      22.200  57.296  -5.182  1.00 25.00           C
ATOM    102  CA  PHE   102      21.161  59.031  -8.436  1.00 25.00           C
ATOM    103  CA  LEU   103      17.389  59.553  -8.292  1.00 25.00           C
ATOM    104  CA  PHE   104      13.974  59.641  -6.684  1.00 25.00           C
ATOM    105  CA  TYR   105      11.179  60.943  -4.372  1.00 25.00           C
ATOM    106  CA  THR   106       7.500  61.876  -4.233  1.00 25.00           C
ATOM    107  CA  GLU   107       6.237  59.778  -7.148  1.00 25.00           C
ATOM    108  CA  GLY   108       2.539  59.166  -8.044  1.00 25.00           C
ATOM    109  CA  LEU   109       1.132  56.387  -5.847  1.00 25.00           C
ATOM    110  CA  ASP   110      -1.294  58.138  -3.526  1.00 25.00           C
ATOM    111  CA  VAL   111       1.495  60.639  -2.949  1.00 25.00           C
ATOM    112  CA  ASP   112       0.833  60.158   0.792  1.00 25.00           C
ATOM    113  CA  GLN   113       2.287  56.619   0.618  1.00 25.00           C
ATOM    114  CA  VAL   114       5.393  57.956  -1.178  1.00 25.00           C
ATOM    115  CA  ILE   115       5.811  60.658   1.504  1.00 25.00           C
ATOM    116  CA  ALA   116       5.510  58.009   4.254  1.00 25.00           C
ATOM    117  CA  THR   117       8.148  55.854   2.502  1.00 25.00           C
ATOM    118  CA  VAL   118       8.105  53.101  -0.104  1.00 25.00           C
ATOM    119  CA  GLU   119       8.219  50.838   2.924  1.00 25.00           C
ATOM    120  CA  SER   120      11.953  50.077   3.036  1.00 25.00           C
ATOM    121  CA  LEU   121      11.273  47.793   0.105  1.00 25.00           C
ATOM    122  CA  GLU   122       8.976  45.393  -1.846  1.00 25.00           C
ATOM    123  CA  LEU   123       7.286  48.564  -3.053  1.00 25.00           C
ATOM    124  CA  LYS   124       6.156  49.006  -6.698  1.00 25.00           C
ATOM    125  CA  ASP   125       6.503  52.729  -7.596  1.00 25.00           C
ATOM    126  CA  GLU   126       9.267  55.069  -6.543  1.00 25.00           C
ATOM    127  CA  VAL   127      13.053  54.725  -6.058  1.00 25.00           C
ATOM    128  CA  LEU   128      12.771  56.485  -2.736  1.00 25.00           C
ATOM    129  CA  TYR   129      14.292  58.582   0.026  1.00 25.00           C
ATOM    130  CA  PHE   130      15.565  57.672   3.512  1.00 25.00           C
ATOM    131  CA  GLY   131      13.586  60.808   4.492  1.00 25.00           C
ATOM    132  CA  LYS   132      16.994  61.626   6.036  1.00 25.00           C
ATOM    133  CA  LEU   133      17.913  64.666   3.935  1.00 25.00           C
ATOM    134  CA  GLY   134      16.383  63.096   0.807  1.00 25.00           C
ATOM    135  CA  ILE   135      12.572  63.612   0.456  1.00 25.00           C
ATOM    136  CA  PHE   136      10.284  66.581  -0.278  1.00 25.00           C
ATOM    137  CA  TRP   137       8.778  68.827   2.423  1.00 25.00           C
ATOM    138  CA  GLY   138       4.974  68.794   2.390  1.00 25.00           C
ATOM    139  CA  LYS   139       5.321  67.735   6.026  1.00 25.00           C
ATOM    140  CA  PHE   140       3.649  64.705   7.531  1.00 25.00           C
ATOM    141  CA  SER   141       1.220  63.890  10.284  1.00 25.00           C
ATOM    142  CA  GLU   142      -1.728  62.982  12.592  1.00 25.00           C
ATOM    143  CA  GLU   143      -4.590  61.528  10.631  1.00 25.00           C
ATOM    144  CA  SER   144      -5.042  61.933   6.880  1.00 25.00           C
ATOM    145  CA  TYR   145      -2.912  65.114   6.821  1.00 25.00           C
ATOM    146  CA  SER   146      -0.489  63.477   4.348  1.00 25.00           C
ATOM    147  CA  LYS   147      -3.426  62.442   2.118  1.00 25.00           C
ATOM    148  CA  THR   148      -4.794  66.018   2.219  1.00 25.00           C
ATOM    149  CA  ALA   149      -1.348  67.389   1.266  1.00 25.00           C
ATOM    150  CA  TYR   150      -1.143  64.916  -1.650  1.00 25.00           C
ATOM    151  CA  HIS   151      -4.626  65.982  -2.832  1.00 25.00           C
ATOM    152  CA  LYS   152      -8.421  66.388  -2.708  1.00 25.00           C
ATOM    153  CA  TYR   153     -10.165  69.587  -3.533  1.00 25.00           C
ATOM    154  CA  LEU   154      -7.140  71.853  -3.602  1.00 25.00           C
ATOM    155  CA  LEU   155      -6.298  74.698  -5.947  1.00 25.00           C
ATOM    156  CA  LYS   156      -8.060  77.419  -7.995  1.00 25.00           C
ATOM    157  CA  VAL   157      -8.131  79.548 -11.133  1.00 25.00           C
ATOM    158  CA  PRO   158      -5.303  82.084 -11.348  1.00 25.00           C
ATOM    159  CA  PHE   159      -1.565  82.269 -11.134  1.00 25.00           C
ATOM    160  CA  TYR   160       0.727  85.049 -10.070  1.00 25.00           C
ATOM    161  CA  ARG   161       4.380  86.101 -10.061  1.00 25.00           C
ATOM    162  CA  HIS   162       7.465  85.633  -7.891  1.00 25.00           C
ATOM    163  CA  ILE   163       8.815  82.347  -6.501  1.00 25.00           C
ATOM    164  CA  THR   164       8.728  78.793  -5.315  1.00 25.00           C
ATOM    165  CA  ILE   165       8.250  75.930  -2.873  1.00 25.00           C
ATOM    166  CA  ARG   166       8.061  72.599  -4.777  1.00 25.00           C
ATOM    167  CA  ASN   167       7.617  70.874  -8.187  1.00 25.00           C
TER
END
