
#######################################################
#                                                     #
#                        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  120 (  120),  selected  120 , name T0356AL316_4-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL316_4-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      -       -           -
LGA    P     349      -       -           -
LGA    E     350      -       -           -
LGA    I     351      -       -           -
LGA    V     352      -       -           -
LGA    D     353      -       -           -
LGA    F     354      -       -           -
LGA    Y     355      -       -           -
LGA    L     356      -       -           -
LGA    P     357      -       -           -
LGA    P     358      -       -           -
LGA    E     359      -       -           -
LGA    G     360      -       -           -
LGA    C     361      -       -           -
LGA    S     362      -       -           -
LGA    Y     363      -       -           -
LGA    R     364      -       -           -
LGA    L     365      -       -           -
LGA    A     366      -       -           -
LGA    V     367      -       -           -
LGA    V     368      -       -           -
LGA    T     369      -       -           -
LGA    I     370      -       -           -
LGA    K     371      -       -           -
LGA    K     372      -       -           -
LGA    Q     373      -       -           -
LGA    Y     374      -       -           -
LGA    A     375      -       -           -
LGA    G     376      -       -           -
LGA    H     377      -       -           -
LGA    A     378      -       -           -
LGA    K     379      -       -           -
LGA    R     380      -       -           -
LGA    V     381      -       -           -
LGA    M     382      -       -           -
LGA    M     383      -       -           -
LGA    G     384      -       -           -
LGA    V     385      -       -           -
LGA    W     386      -       -           -
LGA    S     387      -       -           -
LGA    F     388      -       -           -
LGA    L     389      -       -           -
LGA    R     390      -       -           -
LGA    Q     391      -       -           -
LGA    F     392      -       -           -
LGA    M     393      -       -           -
LGA    Y     394      -       -           -
LGA    T     395      -       -           -
LGA    K     396      -       -           -
LGA    F     397      -       -           -
LGA    V     398      -       -           -
LGA    I     399      -       -           -
LGA    V     400      -       -           -
LGA    C     401      -       -           -
LGA    D     402      -       -           -
LGA    D     403      -       -           -
LGA    D     404      -       -           -
LGA    V     405      -       -           -
LGA    N     406      -       -           -
LGA    A     407      -       -           -
LGA    R     408      -       -           -
LGA    D     409      -       -           -
LGA    W     410      -       -           -
LGA    N     411      -       -           -
LGA    D     412      F     348          1.528
LGA    V     413      -       -           -
LGA    I     414      P     349          4.998
LGA    W     415      E     350          1.902
LGA    A     416      I     351          2.350
LGA    I     417      V     352          3.803
LGA    T     418      D     353          2.300
LGA    T     419      F     354          1.849
LGA    R     420      Y     355          1.499
LGA    M     421      L     356          2.217
LGA    D     422      P     357          2.688
LGA    P     423      P     358          1.722
LGA    A     424      E     359          4.484
LGA    R     425      G     360           #
LGA    D     426      C     361          4.016
LGA    T     427      S     362           #
LGA    -       -      Y     363           -
LGA    -       -      R     364           -
LGA    -       -      L     365           -
LGA    V     428      A     366          3.400
LGA    L     429      V     367          2.910
LGA    V     430      V     368          1.980
LGA    E     431      T     369          2.054
LGA    N     432      I     370          1.715
LGA    T     433      K     371          1.507
LGA    P     434      K     372          1.144
LGA    I     435      Q     373          1.060
LGA    D     436      Y     374          0.936
LGA    Y     437      A     375          2.490
LGA    -       -      G     376           -
LGA    -       -      H     377           -
LGA    -       -      A     378           -
LGA    -       -      K     379           -
LGA    -       -      R     380           -
LGA    -       -      V     381           -
LGA    -       -      M     382           -
LGA    -       -      M     383           -
LGA    -       -      G     384           -
LGA    -       -      V     385           -
LGA    L     438      W     386           #
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    -       -      M     393           -
LGA    D     439      Y     394          4.415
LGA    F     440      T     395           -
LGA    A     441      K     396           -
LGA    -       -      F     397           -
LGA    -       -      V     398           -
LGA    -       -      I     399           -
LGA    -       -      V     400           -
LGA    -       -      C     401           -
LGA    -       -      D     402           -
LGA    -       -      D     403           -
LGA    -       -      D     404           -
LGA    -       -      V     405           -
LGA    -       -      N     406           -
LGA    -       -      A     407           -
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    -       -      D     412           -
LGA    -       -      V     413           -
LGA    -       -      I     414           -
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    -       -      I     417           -
LGA    -       -      T     418           -
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    -       -      M     421           -
LGA    -       -      D     422           -
LGA    -       -      P     423           -
LGA    -       -      A     424           -
LGA    -       -      R     425           -
LGA    -       -      D     426           -
LGA    -       -      T     427           -
LGA    -       -      V     428           -
LGA    -       -      L     429           -
LGA    -       -      V     430           -
LGA    -       -      E     431           -
LGA    -       -      N     432           -
LGA    -       -      T     433           -
LGA    S     442      P     434          3.660
LGA    P     443      I     435          4.006
LGA    -       -      D     436           -
LGA    -       -      Y     437           -
LGA    -       -      L     438           -
LGA    -       -      D     439           -
LGA    -       -      F     440           -
LGA    -       -      A     441           -
LGA    -       -      S     442           -
LGA    -       -      P     443           -
LGA    -       -      V     444           -
LGA    -       -      S     445           -
LGA    -       -      G     446           -
LGA    -       -      L     447           -
LGA    V     444      G     448           #
LGA    S     445      S     449          2.507
LGA    G     446      K     450          3.143
LGA    L     447      M     451          1.317
LGA    G     448      G     452          4.127
LGA    S     449      L     453          3.829
LGA    K     450      D     454          2.901
LGA    -       -      A     455           -
LGA    M     451      T     456          4.925
LGA    G     452      N     457          3.302
LGA    -       -      K     458           -
LGA    -       -      W     459           -
LGA    -       -      P     460           -
LGA    -       -      G     461           -
LGA    -       -      E     462           -
LGA    -       -      T     463           -
LGA    -       -      Q     464           -
LGA    -       -      R     465           -
LGA    L     453      E     466           #
LGA    D     454      W     467           -
LGA    A     455      -       -           -
LGA    T     456      -       -           -
LGA    N     457      -       -           -
LGA    K     458      -       -           -
LGA    W     459      -       -           -
LGA    P     460      -       -           -
LGA    G     461      -       -           -
LGA    E     462      -       -           -
LGA    T     463      -       -           -
LGA    Q     464      -       -           -
LGA    R     465      -       -           -
LGA    E     466      -       -           -
LGA    W     467      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  120  120    5.0     34    2.96    11.76     18.639     1.111

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.039838 * X  +  -0.859202 * Y  +  -0.510083 * Z  + 155.094559
  Y_new =   0.932360 * X  +  -0.151615 * Y  +   0.328204 * Z  + -189.138428
  Z_new =  -0.359330 * X  +  -0.488656 * Y  +   0.795045 * Z  + -173.183823 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.551105    2.590487  [ DEG:   -31.5760    148.4240 ]
  Theta =   0.367550    2.774043  [ DEG:    21.0591    158.9409 ]
  Phi   =   1.528094   -1.613499  [ DEG:    87.5533    -92.4467 ]
 
# 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: T0356AL316_4-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL316_4-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  120  120   5.0   34   2.96   11.76  18.639
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL316_4-D3
REMARK Aligment from pdb entry: 2cse_U
ATOM    331  CA  PHE   348      43.227  29.483  53.136  1.00  0.00              
ATOM    332  CA  PRO   349      39.803  28.027  53.983  1.00  0.00              
ATOM    333  CA  GLU   350      22.241  48.468  54.927  1.00  0.00              
ATOM    334  CA  ILE   351      25.832  49.407  55.762  1.00  0.00              
ATOM    335  CA  VAL   352      24.811  50.013  59.358  1.00  0.00              
ATOM    336  CA  ASP   353      23.099  46.622  59.354  1.00  0.00              
ATOM    337  CA  PHE   354      26.078  44.891  57.738  1.00  0.00              
ATOM    338  CA  TYR   355      28.354  46.362  60.385  1.00  0.00              
ATOM    339  CA  LEU   356      29.928  41.728  61.453  1.00  0.00              
ATOM    340  CA  PRO   357      29.988  43.164  64.994  1.00  0.00              
ATOM    341  CA  PRO   358      29.422  39.760  66.555  1.00  0.00              
ATOM    342  CA  GLU   359      32.059  38.121  64.331  1.00  0.00              
ATOM    343  CA  GLY   360      35.613  36.916  64.909  1.00  0.00              
ATOM    344  CA  CYS   361      36.824  39.066  62.011  1.00  0.00              
ATOM    345  CA  SER   362      39.835  41.351  62.389  1.00  0.00              
ATOM    346  CA  TYR   363      39.754  42.951  58.927  1.00  0.00              
ATOM    347  CA  ARG   364      36.881  44.029  56.681  1.00  0.00              
ATOM    348  CA  LEU   365      36.968  44.944  52.983  1.00  0.00              
ATOM    349  CA  ALA   366      33.793  46.355  51.547  1.00  0.00              
ATOM    350  CA  VAL   367      28.522  54.559  32.602  1.00  0.00              
ATOM    351  CA  VAL   368      27.738  56.196  35.935  1.00  0.00              
ATOM    352  CA  THR   369      25.174  58.973  36.448  1.00  0.00              
ATOM    353  CA  ILE   370      24.672  60.374  39.959  1.00  0.00              
ATOM    354  CA  LYS   371      21.612  62.068  41.489  1.00  0.00              
ATOM    355  CA  LYS   372      22.853  64.612  44.066  1.00  0.00              
ATOM    356  CA  GLN   373      19.334  65.029  45.453  1.00  0.00              
ATOM    357  CA  TYR   374      24.323  52.399  35.754  1.00  0.00              
ATOM    358  CA  ALA   375      22.852  52.741  32.220  1.00  0.00              
ATOM    359  CA  GLY   376      24.679  49.642  30.987  1.00  0.00              
ATOM    360  CA  HIS   377      22.431  47.473  33.176  1.00  0.00              
ATOM    361  CA  ALA   378      19.527  49.823  33.768  1.00  0.00              
ATOM    362  CA  LYS   379      20.010  49.604  37.539  1.00  0.00              
ATOM    363  CA  ARG   380      30.910  57.376  61.871  1.00  0.00              
ATOM    364  CA  VAL   381      28.980  54.106  61.709  1.00  0.00              
ATOM    365  CA  MET   382      32.227  52.142  61.972  1.00  0.00              
ATOM    366  CA  MET   383      33.831  54.183  64.728  1.00  0.00              
ATOM    367  CA  GLY   384      30.747  53.820  66.920  1.00  0.00              
ATOM    368  CA  VAL   385      30.977  50.043  66.411  1.00  0.00              
ATOM    369  CA  TRP   386      34.770  49.659  66.641  1.00  0.00              
ATOM    370  CA  SER   387      43.855  53.945  46.251  1.00  0.00              
ATOM    371  CA  PHE   388      43.710  52.428  42.757  1.00  0.00              
ATOM    372  CA  LEU   389      43.270  55.268  40.240  1.00  0.00              
ATOM    373  CA  ARG   390      46.977  55.171  39.302  1.00  0.00              
ATOM    374  CA  GLN   391      48.080  51.682  40.290  1.00  0.00              
ATOM    375  CA  PHE   392      48.109  49.262  37.357  1.00  0.00              
ATOM    376  CA  MET   393      49.079  46.144  39.229  1.00  0.00              
ATOM    377  CA  TYR   394      45.511  44.900  39.020  1.00  0.00              
ATOM    378  CA  THR   395      46.007  44.531  35.257  1.00  0.00              
ATOM    379  CA  LYS   396      47.757  41.210  35.770  1.00  0.00              
ATOM    380  CA  PHE   397      44.334  39.709  36.353  1.00  0.00              
ATOM    381  CA  VAL   398      43.630  40.556  32.732  1.00  0.00              
ATOM    382  CA  ILE   399      46.838  40.166  30.768  1.00  0.00              
ATOM    383  CA  VAL   400      47.967  37.018  32.526  1.00  0.00              
ATOM    384  CA  CYS   401      44.468  35.725  31.803  1.00  0.00              
ATOM    385  CA  ASP   402      44.476  36.274  28.022  1.00  0.00              
ATOM    386  CA  ASP   403      42.161  39.263  28.279  1.00  0.00              
ATOM    387  CA  ASP   404      42.824  42.197  25.985  1.00  0.00              
ATOM    388  CA  VAL   405      42.883  45.705  27.476  1.00  0.00              
ATOM    389  CA  ASN   406      41.824  49.040  25.997  1.00  0.00              
ATOM    390  CA  ALA   407      43.366  52.366  27.004  1.00  0.00              
ATOM    391  CA  ARG   408      39.965  54.096  27.052  1.00  0.00              
ATOM    392  CA  ASP   409      38.097  51.380  28.965  1.00  0.00              
ATOM    393  CA  TRP   410      40.705  51.544  31.732  1.00  0.00              
ATOM    394  CA  ASN   411      40.486  55.311  32.252  1.00  0.00              
ATOM    395  CA  ASP   412      58.211  68.155  51.532  1.00  0.00              
ATOM    396  CA  VAL   413      56.593  67.934  48.104  1.00  0.00              
ATOM    397  CA  ILE   414      53.467  69.420  49.703  1.00  0.00              
ATOM    398  CA  TRP   415      52.878  73.200  49.979  1.00  0.00              
ATOM    399  CA  ALA   416      52.647  73.254  53.818  1.00  0.00              
ATOM    400  CA  ILE   417      53.182  70.797  56.695  1.00  0.00              
ATOM    401  CA  THR   418      53.462  71.185  60.495  1.00  0.00              
ATOM    402  CA  THR   419      54.502  68.545  63.036  1.00  0.00              
ATOM    403  CA  ARG   420      53.490  68.995  66.688  1.00  0.00              
ATOM    404  CA  MET   421      53.393  66.800  69.783  1.00  0.00              
ATOM    405  CA  ASP   422      51.439  67.309  73.033  1.00  0.00              
ATOM    406  CA  PRO   423      53.398  65.205  75.552  1.00  0.00              
ATOM    407  CA  ALA   424      50.631  65.667  78.151  1.00  0.00              
ATOM    408  CA  ARG   425      48.031  63.931  75.938  1.00  0.00              
ATOM    409  CA  ASP   426      50.457  61.947  73.769  1.00  0.00              
ATOM    410  CA  THR   427      48.746  63.331  70.664  1.00  0.00              
ATOM    411  CA  VAL   428      50.509  64.545  67.521  1.00  0.00              
ATOM    412  CA  LEU   429      48.938  67.246  65.391  1.00  0.00              
ATOM    413  CA  VAL   430      49.643  67.561  61.674  1.00  0.00              
ATOM    414  CA  GLU   431      48.559  70.751  59.917  1.00  0.00              
ATOM    415  CA  ASN   432      48.703  70.648  56.129  1.00  0.00              
ATOM    416  CA  THR   433      47.602  72.215  52.854  1.00  0.00              
ATOM    417  CA  PRO   434      47.532  70.177  49.637  1.00  0.00              
ATOM    418  CA  ILE   435      48.003  71.239  46.003  1.00  0.00              
ATOM    419  CA  ASP   436      46.717  68.046  44.376  1.00  0.00              
ATOM    420  CA  TYR   437      43.438  66.254  45.038  1.00  0.00              
ATOM    421  CA  LEU   438      58.435  53.459  65.580  1.00  0.00              
ATOM    422  CA  ASP   439      61.573  52.437  67.432  1.00  0.00              
ATOM    423  CA  PHE   440      65.187  53.506  66.858  1.00  0.00              
ATOM    424  CA  ALA   441      65.309  50.766  64.194  1.00  0.00              
ATOM    425  CA  SER   442      62.127  52.220  62.639  1.00  0.00              
ATOM    426  CA  PRO   443      59.333  49.664  62.120  1.00  0.00              
ATOM    427  CA  VAL   444      56.651  50.578  59.508  1.00  0.00              
ATOM    428  CA  SER   445      53.086  50.433  60.842  1.00  0.00              
ATOM    429  CA  GLY   446      50.185  51.456  58.668  1.00  0.00              
ATOM    430  CA  LEU   447      47.474  53.877  59.706  1.00  0.00              
ATOM    431  CA  GLY   448      44.535  54.626  57.439  1.00  0.00              
ATOM    432  CA  SER   449      44.287  57.099  54.594  1.00  0.00              
ATOM    433  CA  LYS   450      42.311  60.268  54.004  1.00  0.00              
ATOM    434  CA  MET   451      40.689  61.963  51.057  1.00  0.00              
ATOM    435  CA  GLY   452      41.216  65.482  49.746  1.00  0.00              
ATOM    436  CA  LEU   453      33.521  72.955  39.947  1.00  0.00              
ATOM    437  CA  ASP   454      31.260  76.013  39.735  1.00  0.00              
ATOM    438  CA  ALA   455      31.687  78.357  36.780  1.00  0.00              
ATOM    439  CA  THR   456      29.981  81.375  35.197  1.00  0.00              
ATOM    440  CA  ASN   457      30.302  83.529  32.091  1.00  0.00              
ATOM    441  CA  LYS   458      29.355  87.211  32.469  1.00  0.00              
ATOM    442  CA  TRP   459      28.761  88.994  29.167  1.00  0.00              
ATOM    443  CA  PRO   460      28.711  92.797  28.552  1.00  0.00              
ATOM    444  CA  GLY   461      25.720  94.756  27.208  1.00  0.00              
ATOM    445  CA  GLU   462      27.367  95.568  23.865  1.00  0.00              
ATOM    446  CA  THR   463      29.255  93.008  21.757  1.00  0.00              
ATOM    447  CA  GLN   464      32.446  93.574  19.774  1.00  0.00              
ATOM    448  CA  ARG   465      41.468  74.527  37.158  1.00  0.00              
ATOM    449  CA  GLU   466      43.084  75.212  33.774  1.00  0.00              
ATOM    450  CA  TRP   467      40.605  76.091  31.038  1.00  0.00              
END
