
#######################################################
#                                                     #
#                        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   91 (   91),  selected   91 , name T0356TS677_2-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS677_2-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      F     348          3.298
LGA    I     351      P     349          0.684
LGA    V     352      E     350          2.387
LGA    D     353      I     351          0.490
LGA    F     354      V     352          2.488
LGA    Y     355      -       -           -
LGA    L     356      D     353          1.459
LGA    P     357      F     354          5.362
LGA    P     358      Y     355          3.139
LGA    E     359      L     356           -
LGA    G     360      -       -           -
LGA    C     361      -       -           -
LGA    S     362      P     357          5.483
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      P     358          2.943
LGA    L     389      E     359          3.496
LGA    -       -      G     360           -
LGA    -       -      C     361           -
LGA    R     390      S     362          1.530
LGA    Q     391      Y     363          4.756
LGA    -       -      R     364           -
LGA    -       -      L     365           -
LGA    F     397      A     366          4.462
LGA    V     398      V     367          2.274
LGA    I     399      V     368          1.592
LGA    V     400      T     369          0.427
LGA    C     401      I     370          1.653
LGA    D     402      K     371          3.178
LGA    D     403      K     372          3.571
LGA    -       -      Q     373           -
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    D     409      G     376          4.521
LGA    W     410      H     377          2.119
LGA    N     411      A     378          0.904
LGA    D     412      K     379          1.336
LGA    V     413      R     380          1.058
LGA    I     414      V     381          0.997
LGA    W     415      M     382          1.092
LGA    A     416      M     383          1.568
LGA    I     417      G     384          1.620
LGA    T     418      V     385          1.874
LGA    T     419      W     386          2.508
LGA    R     420      S     387          2.066
LGA    M     421      F     388          4.421
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    D     422      M     393          2.450
LGA    P     423      Y     394          4.473
LGA    A     424      T     395           #
LGA    R     425      K     396          2.227
LGA    D     426      F     397          3.060
LGA    T     427      V     398          2.088
LGA    V     428      I     399          3.641
LGA    L     429      V     400          4.562
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    V     430      A     416           #
LGA    E     431      I     417          3.167
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    -       -      P     434           -
LGA    -       -      I     435           -
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    -       -      G     448           -
LGA    -       -      S     449           -
LGA    -       -      K     450           -
LGA    -       -      M     451           -
LGA    -       -      G     452           -
LGA    -       -      L     453           -
LGA    -       -      D     454           -
LGA    -       -      A     455           -
LGA    N     432      T     456          4.456
LGA    T     433      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    P     434      W     467           #
LGA    I     435      -       -           -
LGA    G     448      -       -           -
LGA    S     449      -       -           -
LGA    K     450      -       -           -
LGA    M     451      -       -           -
LGA    G     452      -       -           -
LGA    L     453      -       -           -
LGA    D     454      -       -           -
LGA    A     455      -       -           -
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)   91  120    5.0     42    2.97     2.38     21.901     1.366

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.954824 * X  +   0.229755 * Y  +  -0.188477 * Z  + -66.407394
  Y_new =   0.200510 * X  +  -0.029984 * Y  +   0.979233 * Z  + 111.734779
  Z_new =   0.219332 * X  +  -0.972787 * Y  +  -0.074697 * Z  + 133.026062 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.647433    1.494160  [ DEG:   -94.3910     85.6090 ]
  Theta =  -0.221130   -2.920463  [ DEG:   -12.6698   -167.3302 ]
  Phi   =   0.206989   -2.934604  [ DEG:    11.8596   -168.1404 ]
 
# 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: T0356TS677_2-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS677_2-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   91  120   5.0   42   2.97    2.38  21.901
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS677_2-D3
PFRMAT TS
TARGET T0356
MODEL  2
PARENT 1T3T_A
ATOM    874  CA  PHE   348      59.272  72.471  55.615  1.00 90.00
ATOM    875  CA  PRO   349      62.092  72.864  53.090  1.00 99.00
ATOM    876  CA  GLU   350      59.991  71.168  50.410  1.00 99.00
ATOM    877  CA  ILE   351      57.055  73.498  51.155  1.00 99.00
ATOM    878  CA  VAL   352      54.756  70.497  51.679  1.00 99.00
ATOM    879  CA  ASP   353      53.076  71.782  54.874  1.00 99.00
ATOM    880  CA  PHE   354      50.095  74.137  55.165  1.00 99.00
ATOM    881  CA  TYR   355      50.141  74.255  58.975  1.00 99.00
ATOM    882  CA  LEU   356      51.714  72.704  62.061  1.00 34.00
ATOM    883  CA  PRO   357      50.924  72.655  65.760  1.00 43.00
ATOM    884  CA  PRO   358      52.599  70.380  68.289  1.00 31.00
ATOM    886  CA  GLU   359      51.671  69.668  74.721  1.00 21.00
ATOM    887  CA  GLY   360      49.365  70.870  77.550  1.00 22.00
ATOM    888  CA  CYS   361      45.773  69.872  76.838  1.00 24.00
ATOM    889  CA  SER   362      46.732  67.165  74.350  1.00 77.00
ATOM    890  CA  TYR   363      45.381  66.514  70.860  1.00 84.00
ATOM    891  CA  ARG   364      42.114  68.208  71.795  1.00 99.00
ATOM    892  CA  LEU   365      43.837  71.516  72.522  1.00 91.00
ATOM    893  CA  ALA   366      46.145  71.135  69.511  1.00 89.00
ATOM    894  CA  VAL   367      43.190  70.766  67.116  1.00 31.00
ATOM    895  CA  VAL   368      41.183  73.462  68.893  1.00 30.00
ATOM    896  CA  THR   369      44.004  76.002  68.735  1.00 82.00
ATOM    897  CA  ILE   370      44.580  75.266  65.031  1.00 99.00
ATOM    898  CA  LYS   371      40.833  75.797  64.513  1.00 99.00
ATOM    899  CA  LYS   372      41.032  79.123  66.387  1.00 99.00
ATOM    900  CA  GLN   373      44.025  80.346  64.363  1.00 99.00
ATOM    901  CA  TYR   374      42.458  79.326  61.048  1.00 99.00
ATOM    910  CA  ALA   375      39.059  55.432  65.947  1.00 40.00
ATOM    911  CA  GLY   376      42.660  54.430  65.160  1.00 20.00
ATOM    912  CA  HIS   377      43.941  56.064  68.371  1.00 47.00
ATOM    913  CA  ALA   378      42.593  53.404  70.725  1.00 65.00
ATOM    914  CA  LYS   379      39.327  52.452  72.404  1.00 99.00
ATOM    915  CA  ARG   380      40.063  54.881  75.239  1.00 99.00
ATOM    916  CA  VAL   381      38.910  58.170  73.679  1.00 99.00
ATOM    917  CA  MET   382      39.627  60.255  76.786  1.00 92.00
ATOM    918  CA  MET   383      43.261  59.092  76.785  1.00 70.00
ATOM    919  CA  GLY   384      43.528  59.569  73.003  1.00 23.00
ATOM    920  CA  VAL   385      42.340  63.176  73.202  1.00 24.00
ATOM    921  CA  TRP   386      44.049  64.308  76.413  1.00  1.00
ATOM    922  CA  SER   387      47.392  62.492  76.587  1.00 17.00
ATOM    923  CA  PHE   388      50.318  64.884  76.396  1.00 39.00
ATOM    924  CA  LEU   389      52.754  62.612  74.579  1.00 88.00
ATOM    925  CA  ARG   390      55.109  64.203  72.053  1.00 71.00
ATOM    926  CA  GLN   391      54.021  64.832  68.485  1.00 79.00
ATOM    927  CA  PHE   397      51.446  67.004  66.796  1.00 96.00
ATOM    928  CA  VAL   398      49.253  67.665  63.785  1.00 67.00
ATOM    929  CA  ILE   399      50.428  68.647  60.311  1.00 24.00
ATOM    930  CA  VAL   400      48.025  69.944  57.677  1.00 38.00
ATOM    931  CA  CYS   401      48.926  69.161  54.073  1.00 48.00
ATOM    932  CA  ASP   402      47.235  69.699  50.706  1.00 33.00
ATOM    933  CA  ASP   403      44.906  66.752  49.972  1.00 61.00
ATOM    934  CA  ASP   409      46.855  65.981  46.781  1.00 92.00
ATOM    935  CA  TRP   410      50.052  65.642  48.853  1.00 94.00
ATOM    936  CA  ASN   411      48.790  63.207  51.522  1.00 99.00
ATOM    937  CA  ASP   412      50.141  60.023  49.932  1.00 99.00
ATOM    938  CA  VAL   413      53.584  61.534  49.335  1.00 78.00
ATOM    939  CA  ILE   414      53.768  63.050  52.819  1.00 70.00
ATOM    940  CA  TRP   415      52.753  59.736  54.389  1.00 80.00
ATOM    941  CA  ALA   416      55.479  58.047  52.306  1.00 53.00
ATOM    942  CA  ILE   417      58.093  60.570  53.474  1.00 58.00
ATOM    943  CA  THR   418      57.186  60.070  57.145  1.00 76.00
ATOM    944  CA  THR   419      57.466  56.293  56.646  1.00 59.00
ATOM    945  CA  ARG   420      61.010  56.737  55.257  1.00 49.00
ATOM    946  CA  MET   421      61.930  58.086  58.689  1.00 61.00
ATOM    947  CA  ASP   422      60.344  55.071  60.394  1.00 62.00
ATOM    948  CA  PRO   423      57.182  56.866  61.556  1.00 75.00
ATOM    949  CA  ALA   424      54.594  54.736  59.681  1.00 88.00
ATOM    950  CA  ARG   425      52.899  53.274  62.777  1.00 82.00
ATOM    951  CA  ASP   426      52.848  56.685  64.509  1.00 95.00
ATOM    952  CA  THR   427      51.138  58.551  61.642  1.00 99.00
ATOM    953  CA  VAL   428      47.341  58.736  61.508  1.00 99.00
ATOM    954  CA  LEU   429      45.009  60.510  59.077  1.00 99.00
ATOM    955  CA  VAL   430      42.451  62.328  61.230  1.00 99.00
ATOM    956  CA  GLU   431      40.321  64.234  58.757  1.00 88.00
ATOM    957  CA  ASN   432      40.188  67.790  57.471  1.00 72.00
ATOM    958  CA  THR   433      39.822  71.475  58.232  1.00 83.00
ATOM    959  CA  PRO   434      36.573  72.840  56.818  1.00 67.00
ATOM    960  CA  ILE   435      35.105  76.316  56.392  1.00 65.00
ATOM    961  CA  GLY   448      32.634  76.917  59.186  1.00 78.00
ATOM    962  CA  SER   449      32.220  76.820  62.943  1.00 67.00
ATOM    963  CA  LYS   450      31.936  73.094  63.703  1.00 26.00
ATOM    964  CA  MET   451      34.539  71.287  65.819  1.00 27.00
ATOM    965  CA  GLY   452      33.677  67.597  65.451  1.00 29.00
ATOM    966  CA  LEU   453      35.437  64.485  66.759  1.00 24.00
ATOM    967  CA  ASP   454      34.075  61.050  65.785  1.00 42.00
ATOM    968  CA  ALA   455      35.047  57.381  66.210  1.00 65.00
ATOM    970  CA  THR   463      29.795  56.071  63.554  1.00 81.00
ATOM    971  CA  GLN   464      29.928  57.546  67.069  1.00 99.00
ATOM    972  CA  ARG   465      30.204  61.285  67.797  1.00 84.00
ATOM    973  CA  GLU   466      32.829  61.591  70.543  1.00 64.00
ATOM    974  CA  TRP   467      32.628  65.354  70.952  1.00 59.00
TER
END
