
#######################################################
#                                                     #
#                        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   95 (   95),  selected   95 , name T0295TS168_3-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295TS168_3-D2.T0295_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     181      T     181           #
LGA    N     182      -       -           -
LGA    F     183      -       -           -
LGA    D     184      -       -           -
LGA    E     185      -       -           -
LGA    W     186      -       -           -
LGA    D     187      -       -           -
LGA    N     188      -       -           -
LGA    L     189      N     182          3.736
LGA    L     190      F     183          1.042
LGA    R     191      D     184          4.252
LGA    I     192      E     185          4.947
LGA    C     193      W     186          3.360
LGA    F     194      D     187          1.023
LGA    S     195      N     188          3.519
LGA    R     196      L     189          5.219
LGA    K     197      L     190          3.873
LGA    R     198      R     191          1.114
LGA    K     199      I     192          4.920
LGA    T     200      C     193           #
LGA    L     201      F     194          5.233
LGA    H     202      S     195          3.705
LGA    A     203      R     196           -
LGA    -       -      K     197           -
LGA    -       -      R     198           -
LGA    -       -      K     199           -
LGA    -       -      T     200           -
LGA    -       -      L     201           -
LGA    -       -      H     202           -
LGA    -       -      A     203           -
LGA    I     204      I     204           #
LGA    F     205      F     205           -
LGA    K     206      K     206           -
LGA    R     207      -       -           -
LGA    N     208      R     207           #
LGA    A     209      N     208          4.146
LGA    V     210      A     209          3.541
LGA    -       -      V     210           -
LGA    L     211      L     211          2.143
LGA    N     212      N     212          0.477
LGA    M     213      M     213          1.592
LGA    L     214      L     214          1.513
LGA    E     215      E     215          0.493
LGA    H     216      H     216          1.243
LGA    N     217      N     217          1.637
LGA    Y     218      Y     218          0.840
LGA    K     219      K     219          0.838
LGA    N     220      N     220          1.853
LGA    W     221      W     221          1.655
LGA    C     222      C     222          0.442
LGA    T     223      T     223          1.851
LGA    L     224      L     224          2.906
LGA    -       -      N     225           -
LGA    N     225      K     226          2.406
LGA    K     226      Q     227          2.903
LGA    Q     227      V     228           #
LGA    V     228      P     229           #
LGA    P     229      -       -           -
LGA    V     230      -       -           -
LGA    N     231      -       -           -
LGA    F     232      -       -           -
LGA    P     233      V     230           #
LGA    F     234      N     231           #
LGA    K     235      F     232          4.745
LGA    K     236      P     233           -
LGA    Y     237      F     234           -
LGA    C     238      K     235           #
LGA    L     239      K     236          4.021
LGA    D     240      Y     237           #
LGA    V     241      C     238          3.707
LGA    L     242      L     239          1.414
LGA    E     243      D     240          3.391
LGA    -       -      V     241           -
LGA    H     244      L     242          1.406
LGA    L     245      E     243          3.342
LGA    -       -      H     244           -
LGA    -       -      L     245           -
LGA    D     246      D     246          3.853
LGA    M     247      M     247          4.894
LGA    C     248      C     248          4.779
LGA    E     249      E     249          3.098
LGA    K     250      K     250          3.109
LGA    R     251      R     251           #
LGA    S     252      S     252          3.549
LGA    I     253      I     253          3.931
LGA    N     254      N     254          3.818
LGA    L     255      L     255          1.758
LGA    D     256      D     256          4.066
LGA    E     257      E     257          3.280
LGA    N     258      N     258          2.708
LGA    D     259      D     259          3.103
LGA    F     260      F     260          2.393
LGA    L     261      L     261          1.639
LGA    K     262      K     262          1.882
LGA    L     263      L     263          1.857
LGA    L     264      L     264          1.264
LGA    L     265      L     265          1.011
LGA    E     266      E     266          1.059
LGA    F     267      F     267          0.931
LGA    N     268      N     268          1.076
LGA    K     269      K     269          0.924
LGA    K     270      K     270           #
LGA    G     271      G     271          2.608
LGA    I     272      I     272          1.374
LGA    H     273      H     273          1.480
LGA    F     274      F     274           #
LGA    F     275      F     275           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   95   95    5.0     64    2.94    65.62     43.285     2.108

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.003732 * X  +  -0.987801 * Y  +   0.155677 * Z  +  16.479494
  Y_new =  -0.586451 * X  +   0.123935 * Y  +   0.800447 * Z  +   0.613381
  Z_new =  -0.809976 * X  +  -0.094284 * Y  +  -0.578834 * Z  +  10.808290 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.980124    0.161468  [ DEG:  -170.7486      9.2514 ]
  Theta =   0.944112    2.197481  [ DEG:    54.0936    125.9064 ]
  Phi   =  -1.564433    1.577160  [ DEG:   -89.6354     90.3646 ]
 
# 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: T0295TS168_3-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS168_3-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   95   95   5.0   64   2.94   65.62  43.285
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS168_3-D2
PFRMAT TS
TARGET T0295
MODEL 3
PARENT N/A
ATOM    181  CA  THR   181      25.191  12.386  17.030  1.00 25.00           C
ATOM    182  CA  ASN   182      21.751  13.671  18.054  1.00 25.00           C
ATOM    183  CA  PHE   183      18.781  11.326  17.665  1.00 25.00           C
ATOM    184  CA  ASP   184      15.277  12.866  17.532  1.00 25.00           C
ATOM    185  CA  GLU   185      16.783  16.283  16.684  1.00 25.00           C
ATOM    186  CA  TRP   186      18.881  14.695  13.900  1.00 25.00           C
ATOM    187  CA  ASP   187      15.760  12.968  12.502  1.00 25.00           C
ATOM    188  CA  ASN   188      13.863  16.294  12.559  1.00 25.00           C
ATOM    189  CA  LEU   189      16.757  18.004  10.725  1.00 25.00           C
ATOM    190  CA  LEU   190      16.766  15.222   8.092  1.00 25.00           C
ATOM    191  CA  ARG   191      12.984  15.616   7.629  1.00 25.00           C
ATOM    192  CA  ILE   192      13.406  19.399   7.209  1.00 25.00           C
ATOM    193  CA  CYS   193      16.156  18.829   4.606  1.00 25.00           C
ATOM    194  CA  PHE   194      13.895  16.382   2.718  1.00 25.00           C
ATOM    195  CA  SER   195      11.046  18.941   2.763  1.00 25.00           C
ATOM    196  CA  ARG   196      13.411  21.637   1.424  1.00 25.00           C
ATOM    197  CA  LYS   197      14.556  19.281  -1.370  1.00 25.00           C
ATOM    198  CA  ARG   198      10.908  18.541  -2.273  1.00 25.00           C
ATOM    199  CA  LYS   199      10.147  22.293  -2.378  1.00 25.00           C
ATOM    200  CA  THR   200      13.175  22.868  -4.651  1.00 25.00           C
ATOM    201  CA  LEU   201      12.000  20.054  -6.969  1.00 25.00           C
ATOM    202  CA  HIS   202       8.496  21.595  -7.102  1.00 25.00           C
ATOM    203  CA  ALA   203      10.003  25.011  -7.951  1.00 25.00           C
ATOM    204  CA  ILE   204      12.100  23.423 -10.735  1.00 25.00           C
ATOM    205  CA  PHE   205       8.980  21.696 -12.131  1.00 25.00           C
ATOM    206  CA  LYS   206       7.084  25.022 -12.076  1.00 25.00           C
ATOM    207  CA  ARG   207       9.978  26.732 -13.910  1.00 25.00           C
ATOM    208  CA  ASN   208      12.617  28.772 -12.115  1.00 25.00           C
ATOM    209  CA  ALA   209      13.984  29.525  -8.640  1.00 25.00           C
ATOM    210  CA  VAL   210      14.711  28.139  -5.219  1.00 25.00           C
ATOM    211  CA  LEU   211      18.365  27.632  -6.253  1.00 25.00           C
ATOM    212  CA  ASN   212      18.940  31.417  -6.168  1.00 25.00           C
ATOM    213  CA  MET   213      17.374  31.602  -2.677  1.00 25.00           C
ATOM    214  CA  LEU   214      19.630  28.744  -1.488  1.00 25.00           C
ATOM    215  CA  GLU   215      22.699  30.543  -2.905  1.00 25.00           C
ATOM    216  CA  HIS   216      21.665  33.767  -1.115  1.00 25.00           C
ATOM    217  CA  ASN   217      21.241  31.840   2.166  1.00 25.00           C
ATOM    218  CA  TYR   218      24.710  30.276   1.724  1.00 25.00           C
ATOM    219  CA  LYS   219      26.216  33.739   1.083  1.00 25.00           C
ATOM    220  CA  ASN   220      24.511  35.091   4.235  1.00 25.00           C
ATOM    221  CA  TRP   221      25.884  32.151   6.268  1.00 25.00           C
ATOM    222  CA  CYS   222      29.398  32.811   4.897  1.00 25.00           C
ATOM    223  CA  THR   223      29.091  36.514   5.826  1.00 25.00           C
ATOM    224  CA  LEU   224      29.291  35.197   9.329  1.00 25.00           C
ATOM    225  CA  ASN   225      32.816  36.132  10.384  1.00 25.00           C
ATOM    226  CA  LYS   226      34.919  34.237   7.779  1.00 25.00           C
ATOM    227  CA  GLN   227      38.121  35.831   6.531  1.00 25.00           C
ATOM    228  CA  VAL   228      37.218  34.062   3.275  1.00 25.00           C
ATOM    229  CA  PRO   229      40.897  34.593   2.480  1.00 25.00           C
ATOM    230  CA  VAL   230      43.505  33.408  -0.024  1.00 25.00           C
ATOM    231  CA  ASN   231      43.380  30.392  -2.247  1.00 25.00           C
ATOM    232  CA  PHE   232      39.887  30.298  -3.763  1.00 25.00           C
ATOM    233  CA  PRO   233      38.860  26.663  -3.022  1.00 25.00           C
ATOM    234  CA  PHE   234      35.347  27.935  -2.594  1.00 25.00           C
ATOM    235  CA  LYS   235      35.184  28.752  -6.332  1.00 25.00           C
ATOM    236  CA  LYS   236      36.462  25.244  -7.180  1.00 25.00           C
ATOM    237  CA  TYR   237      33.816  23.698  -4.882  1.00 25.00           C
ATOM    238  CA  CYS   238      31.092  25.796  -6.567  1.00 25.00           C
ATOM    239  CA  LEU   239      32.319  24.666 -10.015  1.00 25.00           C
ATOM    240  CA  ASP   240      32.252  21.012  -8.868  1.00 25.00           C
ATOM    241  CA  VAL   241      28.683  21.464  -7.555  1.00 25.00           C
ATOM    242  CA  LEU   242      27.624  23.014 -10.893  1.00 25.00           C
ATOM    243  CA  GLU   243      29.196  20.077 -12.782  1.00 25.00           C
ATOM    244  CA  HIS   244      27.344  17.600 -10.524  1.00 25.00           C
ATOM    245  CA  LEU   245      28.504  14.000 -10.371  1.00 25.00           C
ATOM    246  CA  ASP   246      25.343  13.315 -12.368  1.00 25.00           C
ATOM    247  CA  MET   247      22.684  15.094 -14.381  1.00 25.00           C
ATOM    248  CA  CYS   248      22.970  13.759 -17.858  1.00 25.00           C
ATOM    249  CA  GLU   249      20.294  11.173 -17.228  1.00 25.00           C
ATOM    250  CA  LYS   250      21.170   8.320 -14.870  1.00 25.00           C
ATOM    251  CA  ARG   251      19.595   6.492 -11.901  1.00 25.00           C
ATOM    252  CA  SER   252      16.502   8.081 -10.258  1.00 25.00           C
ATOM    253  CA  ILE   253      14.606   4.791 -10.480  1.00 25.00           C
ATOM    254  CA  ASN   254      16.831   2.429  -8.493  1.00 25.00           C
ATOM    255  CA  LEU   255      18.668   5.209  -6.671  1.00 25.00           C
ATOM    256  CA  ASP   256      21.974   4.248  -5.006  1.00 25.00           C
ATOM    257  CA  GLU   257      21.895   5.671  -1.512  1.00 25.00           C
ATOM    258  CA  ASN   258      25.664   5.771  -0.842  1.00 25.00           C
ATOM    259  CA  ASP   259      26.142   8.217  -3.750  1.00 25.00           C
ATOM    260  CA  PHE   260      23.341  10.436  -2.376  1.00 25.00           C
ATOM    261  CA  LEU   261      24.970  10.389   1.089  1.00 25.00           C
ATOM    262  CA  LYS   262      28.339  11.354  -0.453  1.00 25.00           C
ATOM    263  CA  LEU   263      26.674  14.235  -2.348  1.00 25.00           C
ATOM    264  CA  LEU   264      25.016  15.438   0.888  1.00 25.00           C
ATOM    265  CA  LEU   265      28.391  15.307   2.694  1.00 25.00           C
ATOM    266  CA  GLU   266      30.010  17.319  -0.135  1.00 25.00           C
ATOM    267  CA  PHE   267      27.206  19.920   0.076  1.00 25.00           C
ATOM    268  CA  ASN   268      27.695  20.174   3.867  1.00 25.00           C
ATOM    269  CA  LYS   269      31.462  20.654   3.374  1.00 25.00           C
ATOM    270  CA  LYS   270      31.205  23.548   5.811  1.00 25.00           C
ATOM    271  CA  GLY   271      27.937  25.460   5.400  1.00 25.00           C
ATOM    272  CA  ILE   272      26.246  24.814   2.012  1.00 25.00           C
ATOM    273  CA  HIS   273      23.605  23.157   4.124  1.00 25.00           C
ATOM    274  CA  PHE   274      23.652  20.646   6.974  1.00 25.00           C
ATOM    275  CA  PHE   275      25.814  17.968   8.673  1.00 25.00           C
TER
END
