
#######################################################
#                                                     #
#                        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  136 (  136),  selected  136 , name T0339TS393_2-D1
# Molecule2: number of CA atoms  136 ( 1077),  selected  136 , name T0339_D1.pdb
# PARAMETERS: T0339TS393_2-D1.T0339_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E       1      E       1           -
LGA    R       2      R       2           -
LGA    K       3      K       3           -
LGA    V       4      V       4           -
LGA    Y       5      Y       5           -
LGA    M       6      M       6           -
LGA    D       7      -       -           -
LGA    Y       8      -       -           -
LGA    E     289      -       -           -
LGA    A     290      D       7           #
LGA    Y     291      Y       8          3.500
LGA    E     292      E     289           -
LGA    -       -      A     290           -
LGA    -       -      Y     291           -
LGA    A     293      E     292           #
LGA    H     294      A     293           -
LGA    M     295      H     294           -
LGA    -       -      M     295           -
LGA    -       -      R     296           -
LGA    R     296      D     297           #
LGA    D     297      V     298          1.813
LGA    V     298      R     299          4.482
LGA    R     299      -       -           -
LGA    D     300      D     300          2.079
LGA    Y     301      Y     301          1.743
LGA    L     302      L     302          3.181
LGA    E     303      E     303          2.742
LGA    E     304      E     304          2.355
LGA    R     305      R     305          3.096
LGA    L     306      L     306           #
LGA    E     307      E     307           #
LGA    A     308      -       -           -
LGA    E     309      A     308          4.257
LGA    F     310      E     309          3.351
LGA    G     311      F     310          3.302
LGA    Q     312      G     311          2.484
LGA    K     313      Q     312           #
LGA    -       -      K     313           -
LGA    -       -      R     314           -
LGA    R     314      I     315          1.083
LGA    I     315      H     316          3.106
LGA    H     316      L     317          4.443
LGA    L     317      N     318          1.391
LGA    N     318      S     319          1.913
LGA    S     319      Q     320          1.568
LGA    Q     320      F     321          3.198
LGA    -       -      P     322           -
LGA    -       -      G     323           -
LGA    -       -      T     324           -
LGA    F     321      Q     325          5.075
LGA    P     322      R     326          3.989
LGA    -       -      L     327           -
LGA    -       -      P     328           -
LGA    G     323      N     329           #
LGA    T     324      T     330          2.217
LGA    Q     325      C     331          5.027
LGA    R     326      -       -           -
LGA    L     327      -       -           -
LGA    P     328      -       -           -
LGA    N     329      -       -           -
LGA    T     330      -       -           -
LGA    C     331      -       -           -
LGA    N     332      N     332           #
LGA    F     333      F     333          4.345
LGA    S     334      S     334          3.105
LGA    I     335      I     335          2.791
LGA    R     336      R     336          2.680
LGA    G     337      G     337          1.677
LGA    -       -      P     338           -
LGA    P     338      R     339          4.659
LGA    R     339      L     340          1.710
LGA    L     340      Q     341          1.631
LGA    -       -      G     342           -
LGA    Q     341      H     343          1.911
LGA    G     342      V     344          0.980
LGA    H     343      V     345          0.460
LGA    V     344      L     346          1.401
LGA    V     345      A     347          0.911
LGA    L     346      Q     348          0.908
LGA    A     347      C     349          1.842
LGA    Q     348      -       -           -
LGA    C     349      -       -           -
LGA    R     350      R     350          1.714
LGA    V     351      V     351          3.095
LGA    L     352      L     352          3.135
LGA    M     353      M     353          0.310
LGA    A     354      A     354          1.591
LGA    S     355      S     355          2.548
LGA    V     356      V     356           #
LGA    G     357      -       -           -
LGA    A     358      -       -           -
LGA    A     359      -       -           -
LGA    C     360      G     357           #
LGA    H     361      A     358          4.850
LGA    S     362      A     359          3.220
LGA    D     363      C     360          2.567
LGA    H     364      H     361           #
LGA    G     365      S     362          2.929
LGA    D     366      D     363          2.728
LGA    Q     367      H     364          1.752
LGA    -       -      G     365           -
LGA    P     368      D     366           #
LGA    S     369      Q     367          1.866
LGA    P     370      P     368          4.692
LGA    V     371      S     369          3.027
LGA    L     372      -       -           -
LGA    L     373      -       -           -
LGA    S     374      P     370          2.630
LGA    Y     375      V     371          2.409
LGA    -       -      L     372           -
LGA    -       -      L     373           -
LGA    G     376      S     374          1.736
LGA    V     377      Y     375          3.404
LGA    P     378      G     376          3.311
LGA    -       -      V     377           -
LGA    F     379      P     378          2.988
LGA    D     380      F     379          3.020
LGA    -       -      D     380           -
LGA    V     381      V     381          0.286
LGA    A     382      A     382          1.303
LGA    R     383      R     383          1.865
LGA    -       -      N     384           -
LGA    N     384      A     385          3.025
LGA    A     385      L     386          4.988
LGA    L     386      R     387          4.691
LGA    R     387      L     388           -
LGA    L     388      -       -           -
LGA    S     389      S     389           #
LGA    V     390      V     390           #
LGA    G     391      -       -           -
LGA    R     392      G     391           #
LGA    S     393      R     392          1.733
LGA    T     394      S     393          1.427
LGA    T     395      T     394          1.977
LGA    R     396      T     395          1.877
LGA    -       -      R     396           -
LGA    A     397      A     397          1.580
LGA    E     398      E     398          1.995
LGA    V     399      V     399          2.279
LGA    D     400      D     400          1.323
LGA    L     401      L     401          0.300
LGA    V     402      V     402          1.186
LGA    V     403      V     403          1.032
LGA    Q     404      Q     404          0.758
LGA    D     405      D     405          0.909
LGA    L     406      L     406          0.097
LGA    K     407      K     407          1.391
LGA    Q     408      Q     408          1.975
LGA    A     409      A     409          1.747
LGA    V     410      V     410          1.997
LGA    A     411      A     411          2.890
LGA    Q     412      Q     412          3.211
LGA    L     413      L     413          3.088
LGA    E     414      E     414          3.497
LGA    D     415      D     415          3.672
LGA    Q     416      Q     416           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  136  136    5.0     90    2.72    48.89     40.295     3.186

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.277512 * X  +  -0.858424 * Y  +   0.431387 * Z  + -15.670535
  Y_new =  -0.690796 * X  +  -0.490352 * Y  +  -0.531371 * Z  + -12.751871
  Z_new =   0.667673 * X  +  -0.150539 * Y  +  -0.729075 * Z  +  17.317091 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.937975    0.203618  [ DEG:  -168.3335     11.6665 ]
  Theta =  -0.731079   -2.410513  [ DEG:   -41.8878   -138.1122 ]
  Phi   =  -1.188802    1.952791  [ DEG:   -68.1133    111.8867 ]
 
# 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: T0339TS393_2-D1                               
REMARK     2: T0339_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0339TS393_2-D1.T0339_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  136  136   5.0   90   2.72   48.89  40.295
REMARK  ---------------------------------------------------------- 
MOLECULE T0339TS393_2-D1
PFRMAT TS
TARGET T0339
MODEL 2
PARENT N/A
ATOM      1  CA  GLU     1       2.190 -26.536  26.117  1.00 25.00           C
ATOM      2  CA  ARG     2      -0.600 -25.475  28.482  1.00 25.00           C
ATOM      3  CA  LYS     3      -4.065 -26.725  29.543  1.00 25.00           C
ATOM      4  CA  VAL     4      -6.916 -25.278  27.521  1.00 25.00           C
ATOM      5  CA  TYR     5     -10.176 -27.246  27.600  1.00 25.00           C
ATOM      6  CA  MET     6     -13.101 -25.642  25.722  1.00 25.00           C
ATOM      7  CA  ASP     7     -13.281 -23.337  22.708  1.00 25.00           C
ATOM      8  CA  TYR     8     -16.871 -22.505  23.789  1.00 25.00           C
ATOM    289  CA  GLU   289      -5.372 -24.345  15.186  1.00 25.00           C
ATOM    290  CA  ALA   290      -3.131 -27.451  15.117  1.00 25.00           C
ATOM    291  CA  TYR   291      -6.175 -29.660  14.391  1.00 25.00           C
ATOM    292  CA  GLU   292      -7.224 -27.321  11.546  1.00 25.00           C
ATOM    293  CA  ALA   293      -3.683 -27.459  10.095  1.00 25.00           C
ATOM    294  CA  HIS   294      -3.729 -31.283  10.277  1.00 25.00           C
ATOM    295  CA  MET   295      -7.120 -31.352   8.499  1.00 25.00           C
ATOM    296  CA  ARG   296      -5.762 -29.038   5.767  1.00 25.00           C
ATOM    297  CA  ASP   297      -2.709 -31.307   5.328  1.00 25.00           C
ATOM    298  CA  VAL   298      -4.994 -34.367   5.046  1.00 25.00           C
ATOM    299  CA  ARG   299      -7.120 -32.569   2.417  1.00 25.00           C
ATOM    300  CA  ASP   300      -3.963 -31.667   0.446  1.00 25.00           C
ATOM    301  CA  TYR   301      -2.799 -35.312   0.592  1.00 25.00           C
ATOM    302  CA  LEU   302      -6.227 -36.483  -0.654  1.00 25.00           C
ATOM    303  CA  GLU   303      -6.066 -33.964  -3.534  1.00 25.00           C
ATOM    304  CA  GLU   304      -2.561 -35.203  -4.454  1.00 25.00           C
ATOM    305  CA  ARG   305      -3.805 -38.825  -4.420  1.00 25.00           C
ATOM    306  CA  LEU   306      -6.745 -37.862  -6.678  1.00 25.00           C
ATOM    307  CA  GLU   307      -4.345 -36.108  -9.095  1.00 25.00           C
ATOM    308  CA  ALA   308      -2.106 -39.215  -9.164  1.00 25.00           C
ATOM    309  CA  GLU   309      -5.148 -41.423  -9.890  1.00 25.00           C
ATOM    310  CA  PHE   310      -7.643 -42.819  -7.361  1.00 25.00           C
ATOM    311  CA  GLY   311     -10.673 -40.668  -8.279  1.00 25.00           C
ATOM    312  CA  GLN   312     -13.637 -38.450  -7.246  1.00 25.00           C
ATOM    313  CA  LYS   313     -14.972 -37.444  -3.824  1.00 25.00           C
ATOM    314  CA  ARG   314     -15.541 -33.807  -4.756  1.00 25.00           C
ATOM    315  CA  ILE   315     -14.938 -30.762  -2.522  1.00 25.00           C
ATOM    316  CA  HIS   316     -17.709 -28.280  -1.865  1.00 25.00           C
ATOM    317  CA  LEU   317     -16.640 -24.786  -0.820  1.00 25.00           C
ATOM    318  CA  ASN   318     -13.648 -22.448  -1.138  1.00 25.00           C
ATOM    319  CA  SER   319     -11.414 -24.392  -3.547  1.00 25.00           C
ATOM    320  CA  GLN   320      -9.011 -21.782  -4.844  1.00 25.00           C
ATOM    321  CA  PHE   321      -8.850 -20.462  -1.330  1.00 25.00           C
ATOM    322  CA  PRO   322      -5.299 -21.265  -0.358  1.00 25.00           C
ATOM    323  CA  GLY   323      -6.823 -24.438   1.023  1.00 25.00           C
ATOM    324  CA  THR   324      -8.912 -25.935   3.800  1.00 25.00           C
ATOM    325  CA  GLN   325     -10.157 -25.078   7.321  1.00 25.00           C
ATOM    326  CA  ARG   326     -11.107 -21.946   9.178  1.00 25.00           C
ATOM    327  CA  LEU   327      -8.795 -19.707  11.128  1.00 25.00           C
ATOM    328  CA  PRO   328      -9.771 -22.374  13.602  1.00 25.00           C
ATOM    329  CA  ASN   329     -12.087 -25.195  14.690  1.00 25.00           C
ATOM    330  CA  THR   330     -12.254 -27.337  11.547  1.00 25.00           C
ATOM    331  CA  CYS   331     -15.043 -26.510   9.152  1.00 25.00           C
ATOM    332  CA  ASN   332     -16.862 -29.447   7.708  1.00 25.00           C
ATOM    333  CA  PHE   333     -15.493 -30.682   4.416  1.00 25.00           C
ATOM    334  CA  SER   334     -18.102 -31.720   1.827  1.00 25.00           C
ATOM    335  CA  ILE   335     -19.366 -34.477  -0.378  1.00 25.00           C
ATOM    336  CA  ARG   336     -21.744 -34.377  -3.355  1.00 25.00           C
ATOM    337  CA  GLY   337     -24.126 -37.292  -3.559  1.00 25.00           C
ATOM    338  CA  PRO   338     -22.412 -39.128  -0.763  1.00 25.00           C
ATOM    339  CA  ARG   339     -25.355 -37.894   1.279  1.00 25.00           C
ATOM    340  CA  LEU   340     -23.787 -35.141   3.417  1.00 25.00           C
ATOM    341  CA  GLN   341     -25.214 -35.707   6.925  1.00 25.00           C
ATOM    342  CA  GLY   342     -25.298 -39.486   6.309  1.00 25.00           C
ATOM    343  CA  HIS   343     -21.659 -39.397   5.120  1.00 25.00           C
ATOM    344  CA  VAL   344     -20.657 -37.438   8.254  1.00 25.00           C
ATOM    345  CA  VAL   345     -22.462 -39.996  10.460  1.00 25.00           C
ATOM    346  CA  LEU   346     -20.654 -42.856   8.665  1.00 25.00           C
ATOM    347  CA  ALA   347     -17.294 -41.093   9.188  1.00 25.00           C
ATOM    348  CA  GLN   348     -18.086 -40.635  12.908  1.00 25.00           C
ATOM    349  CA  CYS   349     -18.989 -44.346  13.199  1.00 25.00           C
ATOM    350  CA  ARG   350     -15.239 -45.179  13.414  1.00 25.00           C
ATOM    351  CA  VAL   351     -12.691 -42.745  14.772  1.00 25.00           C
ATOM    352  CA  LEU   352     -11.168 -39.548  13.468  1.00 25.00           C
ATOM    353  CA  MET   353     -14.068 -37.073  13.460  1.00 25.00           C
ATOM    354  CA  ALA   354     -15.270 -33.510  13.005  1.00 25.00           C
ATOM    355  CA  SER   355     -16.823 -30.068  12.879  1.00 25.00           C
ATOM    356  CA  VAL   356     -20.500 -30.437  13.900  1.00 25.00           C
ATOM    357  CA  GLY   357     -20.057 -28.018  16.772  1.00 25.00           C
ATOM    358  CA  ALA   358     -20.049 -25.592  19.683  1.00 25.00           C
ATOM    359  CA  ALA   359     -18.663 -22.410  18.210  1.00 25.00           C
ATOM    360  CA  CYS   360     -22.056 -20.873  18.951  1.00 25.00           C
ATOM    361  CA  HIS   361     -22.877 -21.715  15.367  1.00 25.00           C
ATOM    362  CA  SER   362     -21.108 -24.356  13.344  1.00 25.00           C
ATOM    363  CA  ASP   363     -24.145 -26.688  13.072  1.00 25.00           C
ATOM    364  CA  HIS   364     -26.811 -23.928  13.113  1.00 25.00           C
ATOM    365  CA  GLY   365     -28.286 -26.710  15.203  1.00 25.00           C
ATOM    366  CA  ASP   366     -27.672 -29.923  13.357  1.00 25.00           C
ATOM    367  CA  GLN   367     -29.665 -28.482  10.472  1.00 25.00           C
ATOM    368  CA  PRO   368     -26.344 -27.872   8.777  1.00 25.00           C
ATOM    369  CA  SER   369     -28.257 -27.505   5.480  1.00 25.00           C
ATOM    370  CA  PRO   370     -30.065 -24.417   6.844  1.00 25.00           C
ATOM    371  CA  VAL   371     -26.717 -22.905   7.926  1.00 25.00           C
ATOM    372  CA  LEU   372     -25.265 -23.566   4.444  1.00 25.00           C
ATOM    373  CA  LEU   373     -28.311 -21.897   2.830  1.00 25.00           C
ATOM    374  CA  SER   374     -27.897 -18.863   5.130  1.00 25.00           C
ATOM    375  CA  TYR   375     -24.189 -18.635   4.204  1.00 25.00           C
ATOM    376  CA  GLY   376     -25.351 -17.317   0.839  1.00 25.00           C
ATOM    377  CA  VAL   377     -23.204 -20.165  -0.535  1.00 25.00           C
ATOM    378  CA  PRO   378     -24.434 -21.828  -3.757  1.00 25.00           C
ATOM    379  CA  PHE   379     -26.220 -25.053  -2.627  1.00 25.00           C
ATOM    380  CA  ASP   380     -26.646 -28.814  -3.218  1.00 25.00           C
ATOM    381  CA  VAL   381     -22.845 -29.234  -3.444  1.00 25.00           C
ATOM    382  CA  ALA   382     -22.413 -27.292  -0.171  1.00 25.00           C
ATOM    383  CA  ARG   383     -24.351 -29.739   2.007  1.00 25.00           C
ATOM    384  CA  ASN   384     -21.644 -28.827   4.563  1.00 25.00           C
ATOM    385  CA  ALA   385     -18.560 -26.727   3.831  1.00 25.00           C
ATOM    386  CA  LEU   386     -15.109 -25.218   4.318  1.00 25.00           C
ATOM    387  CA  ARG   387     -12.675 -22.276   3.983  1.00 25.00           C
ATOM    388  CA  LEU   388      -9.083 -21.363   4.582  1.00 25.00           C
ATOM    389  CA  SER   389      -6.470 -22.354   7.123  1.00 25.00           C
ATOM    390  CA  VAL   390      -3.944 -22.382  10.001  1.00 25.00           C
ATOM    391  CA  GLY   391      -1.181 -23.671  12.312  1.00 25.00           C
ATOM    392  CA  ARG   392       1.569 -25.718  13.933  1.00 25.00           C
ATOM    393  CA  SER   393       1.545 -29.419  14.591  1.00 25.00           C
ATOM    394  CA  THR   394      -0.209 -32.718  13.692  1.00 25.00           C
ATOM    395  CA  THR   395      -0.794 -35.897  11.640  1.00 25.00           C
ATOM    396  CA  ARG   396      -0.533 -37.981   8.482  1.00 25.00           C
ATOM    397  CA  ALA   397      -1.131 -41.762   8.594  1.00 25.00           C
ATOM    398  CA  GLU   398      -4.369 -41.217  10.564  1.00 25.00           C
ATOM    399  CA  VAL   399      -5.522 -38.620   7.997  1.00 25.00           C
ATOM    400  CA  ASP   400      -4.760 -41.061   5.147  1.00 25.00           C
ATOM    401  CA  LEU   401      -6.747 -43.805   6.933  1.00 25.00           C
ATOM    402  CA  VAL   402      -9.696 -41.405   7.392  1.00 25.00           C
ATOM    403  CA  VAL   403      -9.561 -40.489   3.675  1.00 25.00           C
ATOM    404  CA  GLN   404      -9.534 -44.202   2.736  1.00 25.00           C
ATOM    405  CA  ASP   405     -12.555 -44.823   5.007  1.00 25.00           C
ATOM    406  CA  LEU   406     -14.408 -41.889   3.386  1.00 25.00           C
ATOM    407  CA  LYS   407     -13.620 -43.282  -0.092  1.00 25.00           C
ATOM    408  CA  GLN   408     -14.917 -46.726   0.965  1.00 25.00           C
ATOM    409  CA  ALA   409     -18.130 -45.132   2.306  1.00 25.00           C
ATOM    410  CA  VAL   410     -18.593 -43.235  -0.989  1.00 25.00           C
ATOM    411  CA  ALA   411     -18.095 -46.483  -2.957  1.00 25.00           C
ATOM    412  CA  GLN   412     -20.681 -48.246  -0.750  1.00 25.00           C
ATOM    413  CA  LEU   413     -23.157 -45.381  -1.320  1.00 25.00           C
ATOM    414  CA  GLU   414     -22.587 -45.607  -5.099  1.00 25.00           C
ATOM    415  CA  ASP   415     -23.185 -49.388  -4.988  1.00 25.00           C
ATOM    416  CA  GLN   416     -20.003 -51.423  -5.373  1.00 25.00           C
TER
END
