
#######################################################
#                                                     #
#                        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   24 (   24),  selected   24 , name T0356TS464_3-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS464_3-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    A     375      F     348          1.288
LGA    G     376      P     349          1.328
LGA    H     377      E     350          2.681
LGA    A     378      I     351          3.786
LGA    -       -      V     352           -
LGA    K     379      D     353          2.912
LGA    R     380      F     354          3.576
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     381      V     385          4.142
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    K     396      N     411          1.246
LGA    F     397      D     412          2.931
LGA    -       -      V     413           -
LGA    V     398      I     414          1.986
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    I     399      I     417          2.771
LGA    V     400      T     418          1.581
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    C     401      M     421          2.463
LGA    D     402      D     422          3.245
LGA    D     426      P     423           -
LGA    T     427      A     424           -
LGA    V     428      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     429      L     453           #
LGA    V     430      D     454          3.635
LGA    -       -      A     455           -
LGA    -       -      T     456           -
LGA    -       -      N     457           -
LGA    -       -      K     458           -
LGA    L     453      W     459          4.870
LGA    D     454      P     460          2.625
LGA    A     455      G     461          3.403
LGA    T     456      E     462          4.427
LGA    -       -      T     463           -
LGA    N     457      Q     464          4.317
LGA    -       -      R     465           -
LGA    -       -      E     466           -
LGA    -       -      W     467           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24  120    5.0     20    3.15    15.00      9.950     0.616

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.229494 * X  +  -0.032764 * Y  +  -0.972759 * Z  +  20.866295
  Y_new =  -0.128273 * X  +  -0.991734 * Y  +   0.003141 * Z  + 132.438858
  Z_new =  -0.964821 * X  +   0.124058 * Y  +  -0.231799 * Z  + 126.785286 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.650186   -0.491407  [ DEG:   151.8445    -28.1555 ]
  Theta =   1.304760    1.836833  [ DEG:    74.7572    105.2428 ]
  Phi   =  -0.509682    2.631911  [ DEG:   -29.2026    150.7974 ]
 
# 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: T0356TS464_3-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_3-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  120   5.0   20   3.15   15.00   9.950
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_3-D3
PFRMAT TS
TARGET T0356
MODEL 3
PARENT N/A
ATOM    142  CA  ALA   375      58.672  69.308  52.486  1.00  0.00
ATOM    143  CA  GLY   376      57.460  72.403  50.637  1.00  0.00
ATOM    144  CA  HIS   377      54.693  72.760  53.210  1.00  0.00
ATOM    145  CA  ALA   378      54.778  74.580  56.538  1.00  0.00
ATOM    146  CA  LYS   379      54.117  71.817  59.065  1.00  0.00
ATOM    147  CA  ARG   380      56.134  68.713  59.941  1.00  0.00
ATOM    148  CA  VAL   381      55.049  65.373  58.543  1.00  0.00
ATOM    149  CA  LYS   396      38.391  70.776  68.169  1.00  0.00
ATOM    150  CA  PHE   397      39.331  67.784  65.980  1.00  0.00
ATOM    151  CA  VAL   398      36.484  65.466  65.051  1.00  0.00
ATOM    152  CA  ILE   399      37.440  62.177  63.405  1.00  0.00
ATOM    153  CA  VAL   400      35.247  61.444  60.351  1.00  0.00
ATOM    154  CA  CYS   401      35.030  59.719  56.996  1.00  0.00
ATOM    155  CA  ASP   402      32.588  57.397  55.200  1.00  0.00
ATOM    156  CA  ASP   426      47.596  70.177  68.691  1.00  0.00
ATOM    157  CA  THR   427      48.682  68.490  65.450  1.00  0.00
ATOM    158  CA  VAL   428      46.234  66.456  63.330  1.00  0.00
ATOM    159  CA  LEU   429      47.711  63.263  61.895  1.00  0.00
ATOM    160  CA  VAL   430      46.670  61.635  58.603  1.00  0.00
ATOM    161  CA  LEU   453      38.259  66.418  40.578  1.00  0.00
ATOM    162  CA  ASP   454      37.588  66.051  44.297  1.00  0.00
ATOM    163  CA  ALA   455      36.760  62.364  43.955  1.00  0.00
ATOM    164  CA  THR   456      37.168  59.402  41.657  1.00  0.00
ATOM    165  CA  ASN   457      34.153  57.099  41.781  1.00  0.00
TER
END
