
#######################################################
#                                                     #
#                        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 (    5),  selected    5 , name T0301TS464_3_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301TS464_3_2-D2.T0301_D2.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    -       -      D     187           -
LGA    -       -      G     188           -
LGA    -       -      G     189           -
LGA    -       -      A     190           -
LGA    -       -      I     191           -
LGA    -       -      F     192           -
LGA    -       -      P     193           -
LGA    -       -      T     194           -
LGA    -       -      G     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      V     198           -
LGA    -       -      D     199           -
LGA    -       -      D     200           -
LGA    -       -      L     201           -
LGA    -       -      E     202           -
LGA    -       -      V     203           -
LGA    -       -      P     204           -
LGA    -       -      G     205           -
LGA    -       -      V     206           -
LGA    -       -      G     207           -
LGA    -       -      T     208           -
LGA    -       -      F     209           -
LGA    -       -      K     210           -
LGA    -       -      A     211           -
LGA    -       -      T     212           -
LGA    -       -      M     213           -
LGA    -       -      I     214           -
LGA    -       -      N     215           -
LGA    -       -      A     216           -
LGA    -       -      G     217           -
LGA    -       -      I     218           -
LGA    -       -      P     219           -
LGA    -       -      T     220           -
LGA    -       -      V     221           -
LGA    -       -      F     222           -
LGA    -       -      V     223           -
LGA    -       -      N     224           -
LGA    -       -      A     225           -
LGA    -       -      E     226           -
LGA    -       -      E     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      Y     230           -
LGA    -       -      R     231           -
LGA    -       -      G     232           -
LGA    -       -      T     233           -
LGA    -       -      E     234           -
LGA    -       -      L     235           -
LGA    -       -      R     236           -
LGA    -       -      E     237           -
LGA    -       -      E     238           -
LGA    -       -      I     239           -
LGA    -       -      N     240           -
LGA    -       -      G     241           -
LGA    -       -      D     242           -
LGA    -       -      P     243           -
LGA    -       -      Q     244           -
LGA    -       -      Q     245           -
LGA    -       -      L     246           -
LGA    -       -      A     247           -
LGA    -       -      R     248           -
LGA    -       -      F     249           -
LGA    -       -      E     250           -
LGA    -       -      R     251           -
LGA    -       -      I     252           -
LGA    -       -      R     253           -
LGA    -       -      V     254           -
LGA    -       -      A     255           -
LGA    -       -      G     256           -
LGA    -       -      A     257           -
LGA    -       -      L     258           -
LGA    -       -      R     259           -
LGA    -       -      M     260           -
LGA    -       -      G     261           -
LGA    -       -      L     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      P     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      A     269           -
LGA    -       -      A     270           -
LGA    -       -      T     271           -
LGA    -       -      R     272           -
LGA    -       -      Q     273           -
LGA    -       -      H     274           -
LGA    -       -      T     275           -
LGA    -       -      P     276           -
LGA    -       -      K     277           -
LGA    -       -      I     278           -
LGA    -       -      A     279           -
LGA    -       -      F     280           -
LGA    -       -      V     281           -
LGA    -       -      A     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      R     285           -
LGA    -       -      D     286           -
LGA    -       -      Y     287           -
LGA    -       -      R     288           -
LGA    -       -      T     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      G     292           -
LGA    -       -      K     293           -
LGA    -       -      L     294           -
LGA    -       -      V     295           -
LGA    -       -      A     296           -
LGA    -       -      A     297           -
LGA    -       -      G     298           -
LGA    -       -      D     299           -
LGA    -       -      I     300           -
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    -       -      L     303           -
LGA    -       -      V     304           -
LGA    -       -      R     305           -
LGA    -       -      A     306           -
LGA    -       -      L     307           -
LGA    -       -      S     308           -
LGA    -       -      M     309           -
LGA    -       -      G     310           -
LGA    -       -      K     311           -
LGA    -       -      L     312           -
LGA    -       -      H     313           -
LGA    -       -      H     314           -
LGA    -       -      A     315           -
LGA    -       -      M     316           -
LGA    -       -      M     317           -
LGA    -       -      G     318           -
LGA    -       -      T     319           -
LGA    -       -      A     320           -
LGA    -       -      A     321           -
LGA    -       -      V     322           -
LGA    -       -      A     323           -
LGA    -       -      I     324           -
LGA    -       -      G     325           -
LGA    -       -      T     326           -
LGA    -       -      A     327           -
LGA    -       -      A     328           -
LGA    -       -      A     329           -
LGA    -       -      I     330           -
LGA    -       -      P     331           -
LGA    T     319      G     332          0.687
LGA    A     320      T     333          0.881
LGA    A     321      L     334          1.132
LGA    -       -      V     335           -
LGA    -       -      N     336           -
LGA    V     322      L     337          1.172
LGA    A     323      A     338          0.750
LGA    -       -      A     339           -
LGA    -       -      G     340           -
LGA    -       -      G     341           -
LGA    -       -      G     342           -
LGA    -       -      E     343           -
LGA    -       -      R     344           -
LGA    -       -      S     345           -
LGA    -       -      A     346           -
LGA    -       -      V     347           -
LGA    -       -      R     348           -
LGA    -       -      F     349           -
LGA    -       -      G     350           -
LGA    -       -      H     351           -
LGA    -       -      P     352           -
LGA    -       -      S     353           -
LGA    -       -      G     354           -
LGA    -       -      T     355           -
LGA    -       -      L     356           -
LGA    -       -      R     357           -
LGA    -       -      V     358           -
LGA    -       -      G     359           -
LGA    -       -      A     360           -
LGA    -       -      E     361           -
LGA    -       -      A     362           -
LGA    -       -      S     363           -
LGA    -       -      Q     364           -
LGA    -       -      A     365           -
LGA    -       -      N     366           -
LGA    -       -      G     367           -
LGA    -       -      E     368           -
LGA    -       -      W     369           -
LGA    -       -      T     370           -
LGA    -       -      V     371           -
LGA    -       -      T     372           -
LGA    -       -      K     373           -
LGA    -       -      A     374           -
LGA    -       -      I     375           -
LGA    -       -      M     376           -
LGA    -       -      S     377           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  191    5.0      5    0.95    20.00      2.576     0.478

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.834401 * X  +   0.318603 * Y  +   0.449741 * Z  +  13.248140
  Y_new =   0.361263 * X  +  -0.932414 * Y  +  -0.009712 * Z  +  48.261261
  Z_new =   0.416250 * X  +   0.170579 * Y  +  -0.893106 * Z  +  66.672501 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.952871   -0.188722  [ DEG:   169.1870    -10.8130 ]
  Theta =  -0.429317   -2.712275  [ DEG:   -24.5981   -155.4019 ]
  Phi   =   0.408594   -2.732999  [ DEG:    23.4107   -156.5893 ]
 
# 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: T0301TS464_3_2-D2                             
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_2-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  191   5.0    5   0.95   20.00   2.576
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM     29  CA  THR   319      93.453  -6.644  10.691  1.00  0.00
ATOM     30  CA  ALA   320      95.635  -3.553  10.736  1.00  0.00
ATOM     31  CA  ALA   321      96.375  -2.977  14.412  1.00  0.00
ATOM     32  CA  VAL   322      95.378  -4.806  17.601  1.00  0.00
ATOM     33  CA  ALA   323      94.890  -2.458  20.545  1.00  0.00
TER
END
