
#######################################################
#                                                     #
#                        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 T0316AL257_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL257_5-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    L     355      V     369          1.140
LGA    G     356      C     370          1.482
LGA    G     357      Q     371          0.386
LGA    G     358      Y     372          0.610
LGA    L     359      I     373          0.339

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   90    5.0      5    0.91     0.00      5.468     0.496

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.583110 * X  +  -0.706238 * Y  +   0.401511 * Z  +  22.971443
  Y_new =   0.625319 * X  +  -0.705691 * Y  +  -0.333131 * Z  +   5.995211
  Z_new =   0.518612 * X  +   0.056820 * Y  +   0.853120 * Z  +  -8.130102 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.066505   -3.075088  [ DEG:     3.8104   -176.1896 ]
  Theta =  -0.545227   -2.596366  [ DEG:   -31.2392   -148.7608 ]
  Phi   =   2.321280   -0.820313  [ DEG:   132.9996    -47.0005 ]
 
# 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: T0316AL257_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL257_5-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   90   5.0    5   0.91    0.00   5.468
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL257_5-D3
REMARK Aligment from pdb entry: 1ru8_A
ATOM    877  N   LEU   355      31.117   3.884 -13.147  1.00  0.00              
ATOM    878  CA  LEU   355      32.242   4.803 -13.114  1.00  0.00              
ATOM    879  C   LEU   355      31.868   6.271 -13.157  1.00  0.00              
ATOM    880  O   LEU   355      30.806   6.649 -13.630  1.00  0.00              
ATOM    881  N   GLY   356      32.761   7.097 -12.643  1.00  0.00              
ATOM    882  CA  GLY   356      32.553   8.523 -12.659  1.00  0.00              
ATOM    883  C   GLY   356      33.801   9.121 -13.309  1.00  0.00              
ATOM    884  O   GLY   356      34.858   9.183 -12.679  1.00  0.00              
ATOM    885  N   GLY   357      33.693   9.524 -14.577  1.00  0.00              
ATOM    886  CA  GLY   357      34.841  10.107 -15.286  1.00  0.00              
ATOM    887  C   GLY   357      34.983  11.606 -14.984  1.00  0.00              
ATOM    888  O   GLY   357      35.816  12.307 -15.571  1.00  0.00              
ATOM    889  N   GLY   358      34.166  12.083 -14.050  1.00  0.00              
ATOM    890  CA  GLY   358      34.190  13.478 -13.636  1.00  0.00              
ATOM    891  C   GLY   358      35.548  13.806 -13.001  1.00  0.00              
ATOM    892  O   GLY   358      36.027  14.942 -13.075  1.00  0.00              
ATOM    893  N   LEU   359      36.162  12.792 -12.386  1.00  0.00              
ATOM    894  CA  LEU   359      37.461  12.931 -11.721  1.00  0.00              
ATOM    895  C   LEU   359      38.451  11.834 -12.104  1.00  0.00              
ATOM    896  O   LEU   359      38.133  11.056 -13.027  1.00  0.00              
END
