
#######################################################
#                                                     #
#                        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    5 (   20),  selected    5 , name T0356AL044_5-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_5-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    P     349      G     360          0.918
LGA    E     350      C     361          2.633
LGA    I     351      S     362          0.697
LGA    D     353      Y     363          1.713
LGA    -       -      R     364           -
LGA    Y     355      L     365          1.275
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           -
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    -       -      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)    5  120    5.0      5    1.60     0.00      3.914     0.294

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.717130 * X  +  -0.653568 * Y  +   0.242018 * Z  +  55.042366
  Y_new =   0.271324 * X  +  -0.581673 * Y  +  -0.766837 * Z  + 136.803345
  Z_new =   0.641956 * X  +  -0.484257 * Y  +   0.594464 * Z  + -21.159435 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.683587    2.458006  [ DEG:   -39.1666    140.8334 ]
  Theta =  -0.697046   -2.444546  [ DEG:   -39.9378   -140.0622 ]
  Phi   =   2.779891   -0.361702  [ DEG:   159.2760    -20.7240 ]
 
# 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: T0356AL044_5-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_5-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  120   5.0    5   1.60    0.00   3.914
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_5-D3
REMARK Aligment from pdb entry: 1yw4_A
ATOM    125  N   PRO   349      51.467  58.881  72.212  1.00  0.00              
ATOM    126  CA  PRO   349      51.308  60.266  71.785  1.00  0.00              
ATOM    127  C   PRO   349      51.758  61.249  72.871  1.00  0.00              
ATOM    128  O   PRO   349      52.462  62.214  72.585  1.00  0.00              
ATOM    129  N   GLU   350      53.334  60.417  76.263  1.00  0.00              
ATOM    130  CA  GLU   350      54.591  60.068  76.908  1.00  0.00              
ATOM    131  C   GLU   350      55.765  60.053  75.945  1.00  0.00              
ATOM    132  O   GLU   350      56.844  60.536  76.275  1.00  0.00              
ATOM    133  N   ILE   351      55.467  61.370  72.959  1.00  0.00              
ATOM    134  CA  ILE   351      55.146  62.485  72.081  1.00  0.00              
ATOM    135  C   ILE   351      55.275  62.109  70.611  1.00  0.00              
ATOM    136  O   ILE   351      55.931  62.792  69.831  1.00  0.00              
ATOM    137  N   ASP   353      54.638  61.006  70.233  1.00  0.00              
ATOM    138  CA  ASP   353      54.678  60.565  68.847  1.00  0.00              
ATOM    139  C   ASP   353      53.316  60.770  68.203  1.00  0.00              
ATOM    140  O   ASP   353      52.339  61.085  68.882  1.00  0.00              
ATOM    141  N   TYR   355      53.260  60.619  66.887  1.00  0.00              
ATOM    142  CA  TYR   355      52.002  60.752  66.167  1.00  0.00              
ATOM    143  C   TYR   355      51.377  59.369  66.220  1.00  0.00              
ATOM    144  O   TYR   355      51.693  58.499  65.418  1.00  0.00              
END
