
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295TS168_5-D2.T0295_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     181      -       -           -
LGA    N     182      -       -           -
LGA    F     183      -       -           -
LGA    D     184      -       -           -
LGA    E     185      -       -           -
LGA    W     186      T     181           #
LGA    D     187      -       -           -
LGA    N     188      -       -           -
LGA    L     189      N     182           #
LGA    L     190      F     183          3.028
LGA    R     191      D     184           #
LGA    I     192      E     185           #
LGA    C     193      W     186          3.076
LGA    F     194      D     187          2.225
LGA    S     195      N     188          4.264
LGA    R     196      L     189          4.571
LGA    K     197      L     190          2.680
LGA    R     198      R     191          1.847
LGA    K     199      I     192          4.382
LGA    T     200      C     193          5.390
LGA    L     201      F     194          4.595
LGA    H     202      S     195          4.081
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          3.960
LGA    F     205      F     205           -
LGA    K     206      K     206           -
LGA    R     207      R     207          4.580
LGA    N     208      N     208          3.298
LGA    A     209      A     209          1.001
LGA    V     210      V     210          1.984
LGA    L     211      L     211          1.208
LGA    N     212      N     212          0.834
LGA    M     213      M     213          1.022
LGA    L     214      L     214          0.722
LGA    E     215      E     215          0.644
LGA    H     216      H     216          0.567
LGA    N     217      N     217          0.375
LGA    Y     218      Y     218          0.423
LGA    K     219      K     219          0.403
LGA    N     220      N     220          0.290
LGA    W     221      W     221          0.497
LGA    C     222      C     222          0.553
LGA    T     223      T     223          0.281
LGA    L     224      L     224          3.467
LGA    -       -      N     225           -
LGA    N     225      K     226          0.711
LGA    K     226      Q     227          1.918
LGA    Q     227      V     228          2.242
LGA    V     228      P     229          5.647
LGA    P     229      -       -           -
LGA    V     230      -       -           -
LGA    N     231      -       -           -
LGA    F     232      -       -           -
LGA    P     233      -       -           -
LGA    F     234      -       -           -
LGA    K     235      V     230           #
LGA    K     236      N     231           -
LGA    Y     237      F     232           -
LGA    -       -      P     233           -
LGA    -       -      F     234           -
LGA    -       -      K     235           -
LGA    -       -      K     236           -
LGA    C     238      Y     237          2.888
LGA    -       -      C     238           -
LGA    L     239      L     239          5.160
LGA    D     240      D     240          2.546
LGA    V     241      V     241          2.082
LGA    L     242      L     242          5.027
LGA    E     243      E     243          3.532
LGA    H     244      H     244           #
LGA    L     245      L     245          2.438
LGA    D     246      D     246          2.143
LGA    M     247      M     247          1.307
LGA    C     248      C     248          3.618
LGA    E     249      E     249          3.349
LGA    K     250      K     250          3.020
LGA    R     251      R     251          4.085
LGA    S     252      S     252          3.638
LGA    I     253      I     253          3.906
LGA    N     254      N     254          3.058
LGA    L     255      L     255          2.507
LGA    D     256      D     256          4.198
LGA    E     257      E     257          2.622
LGA    N     258      N     258          2.403
LGA    D     259      D     259          1.420
LGA    F     260      F     260          1.515
LGA    L     261      L     261          1.995
LGA    K     262      K     262          1.167
LGA    L     263      L     263          1.341
LGA    L     264      L     264          2.364
LGA    L     265      L     265          1.733
LGA    E     266      E     266          1.077
LGA    F     267      F     267          3.041
LGA    N     268      N     268          3.240
LGA    K     269      K     269          1.423
LGA    K     270      K     270          3.811
LGA    G     271      G     271          2.885
LGA    I     272      I     272          1.511
LGA    H     273      H     273          2.160
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     69    2.86    78.26     47.558     2.333

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.501201 * X  +   0.835768 * Y  +  -0.224254 * Z  +   9.694062
  Y_new =   0.184538 * X  +   0.356425 * Y  +   0.915919 * Z  +   0.787445
  Z_new =   0.845425 * X  +   0.417676 * Y  +  -0.332871 * Z  +   7.908100 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.243682   -0.897911  [ DEG:   128.5535    -51.4465 ]
  Theta =  -1.007361   -2.134232  [ DEG:   -57.7175   -122.2825 ]
  Phi   =   2.788804   -0.352789  [ DEG:   159.7867    -20.2133 ]
 
# 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_5-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS168_5-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   69   2.86   78.26  47.558
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS168_5-D2
PFRMAT TS
TARGET T0295
MODEL 5
PARENT N/A
ATOM    181  CA  THR   181      19.802   9.743  18.672  1.00 25.00           C
ATOM    182  CA  ASN   182      16.813  11.463  20.313  1.00 25.00           C
ATOM    183  CA  PHE   183      14.197   9.826  18.017  1.00 25.00           C
ATOM    184  CA  ASP   184      11.516  12.542  17.697  1.00 25.00           C
ATOM    185  CA  GLU   185      14.203  15.124  16.809  1.00 25.00           C
ATOM    186  CA  TRP   186      15.636  12.758  14.161  1.00 25.00           C
ATOM    187  CA  ASP   187      12.137  12.246  12.690  1.00 25.00           C
ATOM    188  CA  ASN   188      11.604  16.037  12.572  1.00 25.00           C
ATOM    189  CA  LEU   189      14.973  16.479  10.806  1.00 25.00           C
ATOM    190  CA  LEU   190      14.020  13.782   8.260  1.00 25.00           C
ATOM    191  CA  ARG   191      10.668  15.523   7.633  1.00 25.00           C
ATOM    192  CA  ILE   192      12.470  18.863   7.120  1.00 25.00           C
ATOM    193  CA  CYS   193      14.882  17.209   4.647  1.00 25.00           C
ATOM    194  CA  PHE   194      11.927  15.690   2.741  1.00 25.00           C
ATOM    195  CA  SER   195      10.227  19.119   2.598  1.00 25.00           C
ATOM    196  CA  ARG   196      13.457  20.694   1.275  1.00 25.00           C
ATOM    197  CA  LYS   197      13.721  17.966  -1.399  1.00 25.00           C
ATOM    198  CA  ARG   198      10.083  18.585  -2.425  1.00 25.00           C
ATOM    199  CA  LYS   199      10.768  22.346  -2.671  1.00 25.00           C
ATOM    200  CA  THR   200      13.853  21.667  -4.838  1.00 25.00           C
ATOM    201  CA  LEU   201      11.782  19.390  -7.117  1.00 25.00           C
ATOM    202  CA  HIS   202       9.101  22.106  -7.437  1.00 25.00           C
ATOM    203  CA  ALA   203      11.788  24.687  -8.324  1.00 25.00           C
ATOM    204  CA  ILE   204      13.221  22.322 -10.973  1.00 25.00           C
ATOM    205  CA  PHE   205       9.722  21.810 -12.443  1.00 25.00           C
ATOM    206  CA  LYS   206       9.189  25.601 -12.561  1.00 25.00           C
ATOM    207  CA  ARG   207      12.559  26.044 -14.328  1.00 25.00           C
ATOM    208  CA  ASN   208      14.147  28.556 -12.023  1.00 25.00           C
ATOM    209  CA  ALA   209      14.113  30.425  -8.764  1.00 25.00           C
ATOM    210  CA  VAL   210      15.357  28.044  -6.014  1.00 25.00           C
ATOM    211  CA  LEU   211      18.852  28.988  -7.263  1.00 25.00           C
ATOM    212  CA  ASN   212      18.468  32.491  -5.765  1.00 25.00           C
ATOM    213  CA  MET   213      17.378  30.970  -2.423  1.00 25.00           C
ATOM    214  CA  LEU   214      20.413  28.634  -2.470  1.00 25.00           C
ATOM    215  CA  GLU   215      22.721  31.607  -3.181  1.00 25.00           C
ATOM    216  CA  HIS   216      21.157  33.549  -0.276  1.00 25.00           C
ATOM    217  CA  ASN   217      21.664  30.541   2.041  1.00 25.00           C
ATOM    218  CA  TYR   218      25.323  30.283   0.943  1.00 25.00           C
ATOM    219  CA  LYS   219      25.817  34.019   1.621  1.00 25.00           C
ATOM    220  CA  ASN   220      24.257  33.620   5.096  1.00 25.00           C
ATOM    221  CA  TRP   221      26.578  30.661   5.824  1.00 25.00           C
ATOM    222  CA  CYS   222      29.603  32.728   4.709  1.00 25.00           C
ATOM    223  CA  THR   223      28.504  35.608   6.981  1.00 25.00           C
ATOM    224  CA  LEU   224      30.215  35.077  10.347  1.00 25.00           C
ATOM    225  CA  ASN   225      33.355  33.923   8.537  1.00 25.00           C
ATOM    226  CA  LYS   226      35.783  32.812   5.849  1.00 25.00           C
ATOM    227  CA  GLN   227      35.687  35.879   3.591  1.00 25.00           C
ATOM    228  CA  VAL   228      37.788  34.664   0.718  1.00 25.00           C
ATOM    229  CA  PRO   229      41.345  34.139   1.773  1.00 25.00           C
ATOM    230  CA  VAL   230      43.647  31.149   1.350  1.00 25.00           C
ATOM    231  CA  ASN   231      42.444  27.603   2.231  1.00 25.00           C
ATOM    232  CA  PHE   232      40.976  26.644  -1.126  1.00 25.00           C
ATOM    233  CA  PRO   233      37.759  24.624  -1.453  1.00 25.00           C
ATOM    234  CA  PHE   234      34.086  25.125  -2.291  1.00 25.00           C
ATOM    235  CA  LYS   235      33.872  26.773  -5.742  1.00 25.00           C
ATOM    236  CA  LYS   236      35.587  23.736  -7.325  1.00 25.00           C
ATOM    237  CA  TYR   237      33.122  21.395  -5.562  1.00 25.00           C
ATOM    238  CA  CYS   238      30.182  23.497  -6.829  1.00 25.00           C
ATOM    239  CA  LEU   239      31.586  23.360 -10.390  1.00 25.00           C
ATOM    240  CA  ASP   240      31.957  19.558 -10.124  1.00 25.00           C
ATOM    241  CA  VAL   241      28.342  19.266  -8.893  1.00 25.00           C
ATOM    242  CA  LEU   242      27.145  21.422 -11.823  1.00 25.00           C
ATOM    243  CA  GLU   243      29.092  19.216 -14.274  1.00 25.00           C
ATOM    244  CA  HIS   244      27.531  16.078 -12.730  1.00 25.00           C
ATOM    245  CA  LEU   245      28.951  13.554 -10.263  1.00 25.00           C
ATOM    246  CA  ASP   246      28.188  10.059 -11.387  1.00 25.00           C
ATOM    247  CA  MET   247      24.708  11.578 -11.681  1.00 25.00           C
ATOM    248  CA  CYS   248      24.183  12.221 -15.440  1.00 25.00           C
ATOM    249  CA  GLU   249      21.681   9.773 -16.815  1.00 25.00           C
ATOM    250  CA  LYS   250      21.344   7.843 -13.577  1.00 25.00           C
ATOM    251  CA  ARG   251      17.587   7.463 -14.001  1.00 25.00           C
ATOM    252  CA  SER   252      15.581   8.424 -10.945  1.00 25.00           C
ATOM    253  CA  ILE   253      15.064   4.849  -9.999  1.00 25.00           C
ATOM    254  CA  ASN   254      18.639   4.070  -9.079  1.00 25.00           C
ATOM    255  CA  LEU   255      20.093   5.302  -5.786  1.00 25.00           C
ATOM    256  CA  ASP   256      21.738   2.865  -3.337  1.00 25.00           C
ATOM    257  CA  GLU   257      21.473   5.518  -0.567  1.00 25.00           C
ATOM    258  CA  ASN   258      25.187   5.929  -1.404  1.00 25.00           C
ATOM    259  CA  ASP   259      24.385   8.982  -3.573  1.00 25.00           C
ATOM    260  CA  PHE   260      22.325  10.497  -0.722  1.00 25.00           C
ATOM    261  CA  LEU   261      25.218   9.905   1.717  1.00 25.00           C
ATOM    262  CA  LYS   262      27.648  11.582  -0.721  1.00 25.00           C
ATOM    263  CA  LEU   263      25.287  14.578  -1.053  1.00 25.00           C
ATOM    264  CA  LEU   264      25.052  14.846   2.760  1.00 25.00           C
ATOM    265  CA  LEU   265      28.870  14.744   3.028  1.00 25.00           C
ATOM    266  CA  GLU   266      29.154  17.498   0.383  1.00 25.00           C
ATOM    267  CA  PHE   267      26.612  19.631   2.293  1.00 25.00           C
ATOM    268  CA  ASN   268      28.585  19.122   5.536  1.00 25.00           C
ATOM    269  CA  LYS   269      31.818  20.152   3.759  1.00 25.00           C
ATOM    270  CA  LYS   270      30.087  23.527   4.035  1.00 25.00           C
ATOM    271  CA  GLY   271      26.328  24.119   4.108  1.00 25.00           C
ATOM    272  CA  ILE   272      24.110  24.218   1.027  1.00 25.00           C
ATOM    273  CA  HIS   273      21.807  21.959   3.081  1.00 25.00           C
ATOM    274  CA  PHE   274      22.524  19.289   5.649  1.00 25.00           C
ATOM    275  CA  PHE   275      21.130  18.314   9.067  1.00 25.00           C
TER
END
