
#######################################################
#                                                     #
#                        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_4-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_4-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    -       -      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    P     349      A     424          2.865
LGA    E     350      R     425          3.161
LGA    I     351      D     426          1.443
LGA    D     353      T     427          0.307
LGA    Y     355      V     428          1.227
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    2.09     0.00      3.496     0.228

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.450416 * X  +  -0.359749 * Y  +   0.817132 * Z  +  72.641716
  Y_new =  -0.363811 * X  +  -0.761842 * Y  +  -0.535946 * Z  + 187.639465
  Z_new =   0.815332 * X  +  -0.538681 * Y  +   0.212265 * Z  +  30.711323 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.195433    1.946160  [ DEG:   -68.4933    111.5067 ]
  Theta =  -0.953302   -2.188290  [ DEG:   -54.6202   -125.3798 ]
  Phi   =  -2.462161    0.679432  [ DEG:  -141.0714     38.9286 ]
 
# 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_4-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_4-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   2.09    0.00   3.496
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_4-D3
REMARK Aligment from pdb entry: 1yw6_A
ATOM    137  N   PRO   349      39.811  51.987  55.193  1.00  0.00              
ATOM    138  CA  PRO   349      40.805  52.094  54.127  1.00  0.00              
ATOM    139  C   PRO   349      40.124  52.493  52.831  1.00  0.00              
ATOM    140  O   PRO   349      40.728  53.118  51.964  1.00  0.00              
ATOM    141  N   GLU   350      36.522  53.872  52.538  1.00  0.00              
ATOM    142  CA  GLU   350      35.721  55.065  52.743  1.00  0.00              
ATOM    143  C   GLU   350      36.436  56.271  53.295  1.00  0.00              
ATOM    144  O   GLU   350      35.845  57.340  53.331  1.00  0.00              
ATOM    145  N   ILE   351      40.280  56.152  53.111  1.00  0.00              
ATOM    146  CA  ILE   351      41.658  55.995  52.682  1.00  0.00              
ATOM    147  C   ILE   351      42.612  55.914  53.851  1.00  0.00              
ATOM    148  O   ILE   351      43.708  56.486  53.817  1.00  0.00              
ATOM    149  N   ASP   353      42.183  55.206  54.891  1.00  0.00              
ATOM    150  CA  ASP   353      42.978  55.052  56.092  1.00  0.00              
ATOM    151  C   ASP   353      43.976  53.965  55.849  1.00  0.00              
ATOM    152  O   ASP   353      43.684  53.000  55.148  1.00  0.00              
ATOM    153  N   TYR   355      45.174  54.135  56.385  1.00  0.00              
ATOM    154  CA  TYR   355      46.176  53.097  56.230  1.00  0.00              
ATOM    155  C   TYR   355      45.766  52.107  57.304  1.00  0.00              
ATOM    156  O   TYR   355      46.285  52.137  58.406  1.00  0.00              
END
