
#######################################################
#                                                     #
#                        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 T0356TS168_4-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS168_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      F     348           -
LGA    P     349      P     349           -
LGA    E     350      E     350           -
LGA    I     351      I     351           -
LGA    V     352      V     352           -
LGA    D     353      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      F     354           #
LGA    A     366      Y     355          2.179
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      V     367          2.766
LGA    V     368      V     368          1.639
LGA    T     369      T     369          2.425
LGA    -       -      I     370           -
LGA    I     370      K     371          4.443
LGA    K     371      K     372          4.390
LGA    -       -      Q     373           -
LGA    K     372      Y     374          3.605
LGA    Q     373      A     375          3.809
LGA    Y     374      G     376          0.468
LGA    A     375      H     377          4.066
LGA    G     376      A     378          2.664
LGA    H     377      K     379          1.250
LGA    A     378      R     380          3.215
LGA    K     379      V     381          2.545
LGA    R     380      M     382          1.736
LGA    V     381      M     383          4.406
LGA    M     382      -       -           -
LGA    M     383      -       -           -
LGA    G     384      G     384          2.188
LGA    V     385      V     385           -
LGA    W     386      W     386           -
LGA    S     387      S     387          5.140
LGA    F     388      F     388          4.589
LGA    L     389      L     389           -
LGA    R     390      -       -           -
LGA    Q     391      -       -           -
LGA    F     392      -       -           -
LGA    M     393      -       -           -
LGA    Y     394      R     390          4.057
LGA    T     395      Q     391          2.845
LGA    K     396      F     392          5.140
LGA    F     397      M     393          3.972
LGA    -       -      Y     394           -
LGA    V     398      T     395          1.064
LGA    I     399      K     396          2.179
LGA    V     400      F     397          2.686
LGA    -       -      V     398           -
LGA    C     401      I     399          2.303
LGA    D     402      V     400          3.651
LGA    D     403      C     401           #
LGA    D     404      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    V     405      D     412           #
LGA    N     406      V     413           #
LGA    A     407      I     414           #
LGA    R     408      W     415           #
LGA    D     409      -       -           -
LGA    W     410      -       -           -
LGA    N     411      -       -           -
LGA    D     412      A     416          4.905
LGA    V     413      I     417          0.608
LGA    I     414      T     418           #
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    W     415      M     421          3.443
LGA    A     416      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    I     417      D     454          4.370
LGA    T     418      A     455          3.907
LGA    T     419      T     456          2.664
LGA    R     420      N     457          0.756
LGA    M     421      K     458          1.264
LGA    D     422      W     459          4.731
LGA    P     423      P     460           -
LGA    -       -      G     461           -
LGA    -       -      E     462           -
LGA    -       -      T     463           -
LGA    -       -      Q     464           -
LGA    -       -      R     465           -
LGA    -       -      E     466           -
LGA    A     424      W     467          1.465
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    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     38    3.27    21.05     17.553     1.126

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.732718 * X  +   0.657271 * Y  +  -0.176409 * Z  +  48.778381
  Y_new =   0.674942 * X  +   0.668700 * Y  +  -0.311919 * Z  +  76.087677
  Z_new =  -0.087051 * X  +  -0.347614 * Y  +  -0.933588 * Z  +  64.813309 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.785154    0.356439  [ DEG:  -159.5776     20.4224 ]
  Theta =   0.087161    3.054432  [ DEG:     4.9939    175.0061 ]
  Phi   =   2.397215   -0.744378  [ DEG:   137.3503    -42.6497 ]
 
# 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: T0356TS168_4-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS168_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   38   3.27   21.05  17.553
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS168_4-D3
PFRMAT TS
TARGET T0356
MODEL 4
PARENT N/A
ATOM    348  CA  PHE   348      52.318  56.763  56.281  1.00 25.00           C
ATOM    349  CA  PRO   349      52.361  60.069  58.108  1.00 25.00           C
ATOM    350  CA  GLU   350      53.462  59.587  61.770  1.00 25.00           C
ATOM    351  CA  ILE   351      54.610  62.064  64.423  1.00 25.00           C
ATOM    352  CA  VAL   352      52.369  64.124  66.660  1.00 25.00           C
ATOM    353  CA  ASP   353      48.997  64.523  68.381  1.00 25.00           C
ATOM    354  CA  PHE   354      46.179  66.451  66.838  1.00 25.00           C
ATOM    355  CA  TYR   355      44.447  68.796  69.307  1.00 25.00           C
ATOM    356  CA  LEU   356      44.227  70.255  72.775  1.00 25.00           C
ATOM    357  CA  PRO   357      41.469  67.723  73.352  1.00 25.00           C
ATOM    358  CA  PRO   358      40.018  64.276  74.266  1.00 25.00           C
ATOM    359  CA  GLU   359      38.183  61.482  72.394  1.00 25.00           C
ATOM    360  CA  GLY   360      40.901  61.116  69.742  1.00 25.00           C
ATOM    361  CA  CYS   361      43.658  63.687  70.443  1.00 25.00           C
ATOM    362  CA  SER   362      46.755  63.913  72.633  1.00 25.00           C
ATOM    363  CA  TYR   363      47.921  67.577  72.879  1.00 25.00           C
ATOM    364  CA  ARG   364      49.392  71.049  73.549  1.00 25.00           C
ATOM    365  CA  LEU   365      50.857  70.115  70.237  1.00 25.00           C
ATOM    366  CA  ALA   366      50.591  68.677  66.699  1.00 25.00           C
ATOM    367  CA  VAL   367      49.165  68.274  63.234  1.00 25.00           C
ATOM    368  CA  VAL   368      48.507  67.325  59.607  1.00 25.00           C
ATOM    369  CA  THR   369      47.600  68.558  56.164  1.00 25.00           C
ATOM    370  CA  ILE   370      47.788  68.384  52.381  1.00 25.00           C
ATOM    371  CA  LYS   371      50.073  67.409  49.558  1.00 25.00           C
ATOM    372  CA  LYS   372      49.114  66.307  46.077  1.00 25.00           C
ATOM    373  CA  GLN   373      48.149  63.060  44.354  1.00 25.00           C
ATOM    374  CA  TYR   374      46.090  61.246  46.981  1.00 25.00           C
ATOM    375  CA  ALA   375      45.226  63.190  50.183  1.00 25.00           C
ATOM    376  CA  GLY   376      46.623  61.122  53.089  1.00 25.00           C
ATOM    377  CA  HIS   377      48.900  59.216  50.670  1.00 25.00           C
ATOM    378  CA  ALA   378      50.137  62.524  49.188  1.00 25.00           C
ATOM    379  CA  LYS   379      50.854  63.859  52.705  1.00 25.00           C
ATOM    380  CA  ARG   380      52.792  60.666  53.549  1.00 25.00           C
ATOM    381  CA  VAL   381      54.825  61.017  50.323  1.00 25.00           C
ATOM    382  CA  MET   382      55.605  64.667  51.183  1.00 25.00           C
ATOM    383  CA  MET   383      56.725  63.626  54.695  1.00 25.00           C
ATOM    384  CA  GLY   384      58.980  60.915  53.198  1.00 25.00           C
ATOM    385  CA  VAL   385      60.500  63.476  50.790  1.00 25.00           C
ATOM    386  CA  TRP   386      61.141  65.874  53.706  1.00 25.00           C
ATOM    387  CA  SER   387      62.822  63.059  55.686  1.00 25.00           C
ATOM    388  CA  PHE   388      65.021  62.217  52.666  1.00 25.00           C
ATOM    389  CA  LEU   389      65.805  58.594  51.865  1.00 25.00           C
ATOM    390  CA  ARG   390      65.544  57.706  55.544  1.00 25.00           C
ATOM    391  CA  GLN   391      67.783  57.327  58.607  1.00 25.00           C
ATOM    392  CA  PHE   392      69.084  60.845  59.376  1.00 25.00           C
ATOM    393  CA  MET   393      70.234  62.944  62.375  1.00 25.00           C
ATOM    394  CA  TYR   394      68.036  60.805  64.543  1.00 25.00           C
ATOM    395  CA  THR   395      64.806  58.942  65.054  1.00 25.00           C
ATOM    396  CA  LYS   396      62.192  56.381  66.025  1.00 25.00           C
ATOM    397  CA  PHE   397      58.452  57.083  65.767  1.00 25.00           C
ATOM    398  CA  VAL   398      54.768  56.355  65.244  1.00 25.00           C
ATOM    399  CA  ILE   399      51.142  56.208  64.190  1.00 25.00           C
ATOM    400  CA  VAL   400      48.643  57.519  61.615  1.00 25.00           C
ATOM    401  CA  CYS   401      48.076  60.706  59.606  1.00 25.00           C
ATOM    402  CA  ASP   402      46.437  63.754  61.137  1.00 25.00           C
ATOM    403  CA  ASP   403      44.263  62.658  64.058  1.00 25.00           C
ATOM    404  CA  ASP   404      41.702  65.551  63.945  1.00 25.00           C
ATOM    405  CA  VAL   405      39.143  64.169  66.440  1.00 25.00           C
ATOM    406  CA  ASN   406      35.357  64.365  66.429  1.00 25.00           C
ATOM    407  CA  ALA   407      32.487  65.559  64.204  1.00 25.00           C
ATOM    408  CA  ARG   408      30.934  62.254  65.124  1.00 25.00           C
ATOM    409  CA  ASP   409      33.620  59.694  64.475  1.00 25.00           C
ATOM    410  CA  TRP   410      36.395  58.877  61.983  1.00 25.00           C
ATOM    411  CA  ASN   411      35.559  59.289  58.269  1.00 25.00           C
ATOM    412  CA  ASP   412      35.048  63.051  58.776  1.00 25.00           C
ATOM    413  CA  VAL   413      38.417  63.290  60.580  1.00 25.00           C
ATOM    414  CA  ILE   414      40.115  61.405  57.711  1.00 25.00           C
ATOM    415  CA  TRP   415      38.512  63.778  55.170  1.00 25.00           C
ATOM    416  CA  ALA   416      39.726  66.799  57.186  1.00 25.00           C
ATOM    417  CA  ILE   417      43.264  65.334  57.293  1.00 25.00           C
ATOM    418  CA  THR   418      43.177  64.782  53.504  1.00 25.00           C
ATOM    419  CA  THR   419      42.025  68.396  52.979  1.00 25.00           C
ATOM    420  CA  ARG   420      38.544  67.678  51.598  1.00 25.00           C
ATOM    421  CA  MET   421      39.411  64.391  49.887  1.00 25.00           C
ATOM    422  CA  ASP   422      35.828  64.636  48.577  1.00 25.00           C
ATOM    423  CA  PRO   423      32.296  64.686  49.791  1.00 25.00           C
ATOM    424  CA  ALA   424      32.194  68.520  49.913  1.00 25.00           C
ATOM    425  CA  ARG   425      34.914  70.705  51.341  1.00 25.00           C
ATOM    426  CA  ASP   426      36.641  73.633  53.011  1.00 25.00           C
ATOM    427  CA  THR   427      38.496  73.612  56.258  1.00 25.00           C
ATOM    428  CA  VAL   428      38.449  76.302  58.986  1.00 25.00           C
ATOM    429  CA  LEU   429      41.060  77.557  61.508  1.00 25.00           C
ATOM    430  CA  VAL   430      40.023  78.677  64.942  1.00 25.00           C
ATOM    431  CA  GLU   431      39.399  82.483  64.941  1.00 25.00           C
ATOM    432  CA  ASN   432      38.230  82.238  68.549  1.00 25.00           C
ATOM    433  CA  THR   433      40.006  82.136  71.937  1.00 25.00           C
ATOM    434  CA  PRO   434      41.125  85.676  70.975  1.00 25.00           C
ATOM    435  CA  ILE   435      44.242  83.959  69.689  1.00 25.00           C
ATOM    436  CA  ASP   436      47.321  81.768  68.989  1.00 25.00           C
ATOM    437  CA  TYR   437      48.193  81.973  65.316  1.00 25.00           C
ATOM    438  CA  LEU   438      50.976  82.329  62.779  1.00 25.00           C
ATOM    439  CA  ASP   439      51.345  85.986  63.694  1.00 25.00           C
ATOM    440  CA  PHE   440      52.446  86.840  67.220  1.00 25.00           C
ATOM    441  CA  ALA   441      55.133  87.354  69.833  1.00 25.00           C
ATOM    442  CA  SER   442      57.529  89.306  67.642  1.00 25.00           C
ATOM    443  CA  PRO   443      59.706  90.920  70.362  1.00 25.00           C
ATOM    444  CA  VAL   444      60.892  93.139  67.475  1.00 25.00           C
ATOM    445  CA  SER   445      61.871  91.684  64.058  1.00 25.00           C
ATOM    446  CA  GLY   446      63.460  88.479  65.330  1.00 25.00           C
ATOM    447  CA  LEU   447      60.509  86.179  64.982  1.00 25.00           C
ATOM    448  CA  GLY   448      57.635  83.723  64.941  1.00 25.00           C
ATOM    449  CA  SER   449      57.692  80.175  63.607  1.00 25.00           C
ATOM    450  CA  LYS   450      56.086  77.934  60.971  1.00 25.00           C
ATOM    451  CA  MET   451      57.296  75.362  63.444  1.00 25.00           C
ATOM    452  CA  GLY   452      57.762  73.909  66.949  1.00 25.00           C
ATOM    453  CA  LEU   453      56.063  73.735  70.384  1.00 25.00           C
ATOM    454  CA  ASP   454      54.991  71.617  73.303  1.00 25.00           C
ATOM    455  CA  ALA   455      53.290  72.708  76.537  1.00 25.00           C
ATOM    456  CA  THR   456      55.139  73.329  79.798  1.00 25.00           C
ATOM    457  CA  ASN   457      54.723  76.809  81.278  1.00 25.00           C
ATOM    458  CA  LYS   458      54.436  79.024  84.353  1.00 25.00           C
ATOM    459  CA  TRP   459      51.911  80.752  86.525  1.00 25.00           C
ATOM    460  CA  PRO   460      49.049  82.980  87.734  1.00 25.00           C
ATOM    461  CA  GLY   461      48.207  86.467  86.533  1.00 25.00           C
ATOM    462  CA  GLU   462      49.955  89.075  84.330  1.00 25.00           C
ATOM    463  CA  THR   463      46.877  91.339  84.507  1.00 25.00           C
ATOM    464  CA  GLN   464      43.104  91.468  84.449  1.00 25.00           C
ATOM    465  CA  ARG   465      43.061  94.654  82.354  1.00 25.00           C
ATOM    466  CA  GLU   466      44.842  96.757  79.712  1.00 25.00           C
ATOM    467  CA  TRP   467      43.940  94.995  76.471  1.00 25.00           C
TER
END
