
#######################################################
#                                                     #
#                        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   10 (   40),  selected   10 , name T0356AL333_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL333_1-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    -       -      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    R     420      V     381          0.772
LGA    M     421      M     382          0.555
LGA    -       -      M     383           -
LGA    -       -      G     384           -
LGA    D     422      V     385          2.099
LGA    P     423      W     386          2.906
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    A     424      F     397          3.025
LGA    R     425      V     398          1.212
LGA    D     426      I     399          0.875
LGA    T     427      V     400          0.479
LGA    V     428      C     401          2.099
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    -       -      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    L     429      T     456          2.304
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)   10  120    5.0     10    1.87    10.00      7.712     0.507

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.327300 * X  +   0.941523 * Y  +   0.080051 * Z  + -126.786835
  Y_new =  -0.816095 * X  +   0.324365 * Y  +  -0.478305 * Z  + 158.437088
  Z_new =  -0.476301 * X  +   0.091220 * Y  +   0.874538 * Z  +  41.043964 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.103931   -3.037661  [ DEG:     5.9548   -174.0452 ]
  Theta =   0.496443    2.645149  [ DEG:    28.4441    151.5559 ]
  Phi   =  -1.189379    1.952213  [ DEG:   -68.1464    111.8536 ]
 
# 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: T0356AL333_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL333_1-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  120   5.0   10   1.87   10.00   7.712
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL333_1-D3
REMARK Aligment from pdb entry: 1lwh_A
ATOM    161  N   ARG   420      52.472  64.233  51.978  1.00  0.00              
ATOM    162  CA  ARG   420      53.495  63.509  52.732  1.00  0.00              
ATOM    163  C   ARG   420      52.938  62.918  54.026  1.00  0.00              
ATOM    164  O   ARG   420      52.672  63.640  54.981  1.00  0.00              
ATOM    165  N   MET   421      52.767  61.600  54.045  1.00  0.00              
ATOM    166  CA  MET   421      52.251  60.891  55.206  1.00  0.00              
ATOM    167  C   MET   421      53.370  60.459  56.149  1.00  0.00              
ATOM    168  O   MET   421      53.884  59.344  56.014  1.00  0.00              
ATOM    169  N   ASP   422      53.722  61.330  57.101  1.00  0.00              
ATOM    170  CA  ASP   422      54.775  61.061  58.096  1.00  0.00              
ATOM    171  C   ASP   422      54.567  59.762  58.887  1.00  0.00              
ATOM    172  O   ASP   422      53.472  59.192  58.887  1.00  0.00              
ATOM    173  N   PRO   423      55.618  59.277  59.579  1.00  0.00              
ATOM    174  CA  PRO   423      55.519  58.042  60.368  1.00  0.00              
ATOM    175  C   PRO   423      54.643  58.199  61.609  1.00  0.00              
ATOM    176  O   PRO   423      54.909  59.074  62.443  1.00  0.00              
ATOM    177  N   ALA   424      53.612  57.352  61.718  1.00  0.00              
ATOM    178  CA  ALA   424      52.689  57.347  62.865  1.00  0.00              
ATOM    179  C   ALA   424      51.850  58.621  63.026  1.00  0.00              
ATOM    180  O   ALA   424      51.528  59.013  64.151  1.00  0.00              
ATOM    181  N   ARG   425      51.477  59.235  61.904  1.00  0.00              
ATOM    182  CA  ARG   425      50.717  60.485  61.903  1.00  0.00              
ATOM    183  C   ARG   425      49.435  60.480  61.068  1.00  0.00              
ATOM    184  O   ARG   425      49.249  59.628  60.193  1.00  0.00              
ATOM    185  N   ASP   426      48.554  61.438  61.353  1.00  0.00              
ATOM    186  CA  ASP   426      47.285  61.569  60.630  1.00  0.00              
ATOM    187  C   ASP   426      47.292  62.922  59.941  1.00  0.00              
ATOM    188  O   ASP   426      47.802  63.903  60.492  1.00  0.00              
ATOM    189  N   THR   427      46.743  62.962  58.733  1.00  0.00              
ATOM    190  CA  THR   427      46.692  64.195  57.968  1.00  0.00              
ATOM    191  C   THR   427      45.310  64.344  57.369  1.00  0.00              
ATOM    192  O   THR   427      44.723  63.361  56.913  1.00  0.00              
ATOM    193  N   VAL   428      44.783  65.564  57.381  1.00  0.00              
ATOM    194  CA  VAL   428      43.475  65.826  56.788  1.00  0.00              
ATOM    195  C   VAL   428      43.643  66.941  55.748  1.00  0.00              
ATOM    196  O   VAL   428      44.471  67.834  55.920  1.00  0.00              
ATOM    197  N   LEU   429      42.880  66.876  54.659  1.00  0.00              
ATOM    198  CA  LEU   429      42.977  67.877  53.594  1.00  0.00              
ATOM    199  C   LEU   429      41.627  68.026  52.925  1.00  0.00              
ATOM    200  O   LEU   429      41.033  69.109  53.065  1.00  0.00              
END
