
#######################################################
#                                                     #
#                        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    9 (   76),  selected    9 , name T0316TS274_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS274_1-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    M     284      E     302          1.215
LGA    S     285      F     303          1.416
LGA    T     286      T     304          1.096
LGA    S     287      L     305          1.892
LGA    L     288      E     306          2.795
LGA    E     289      C     307          0.166
LGA    A     290      T     308          2.240
LGA    S     291      A     309          2.070
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    Q     292      S     318          0.599
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    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9   90    5.0      9    1.69    11.11      9.240     0.502

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.982493 * X  +  -0.095032 * Y  +   0.160240 * Z  +  74.665794
  Y_new =  -0.146269 * X  +   0.926183 * Y  +  -0.347550 * Z  + -10.821913
  Z_new =  -0.115383 * X  +  -0.364904 * Y  +  -0.923868 * Z  +  61.500263 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.765426    0.376166  [ DEG:  -158.4473     21.5527 ]
  Theta =   0.115641    3.025952  [ DEG:     6.6257    173.3743 ]
  Phi   =  -2.993802    0.147790  [ DEG:  -171.5322      8.4678 ]
 
# 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: T0316TS274_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS274_1-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9   90   5.0    9   1.69   11.11   9.240
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS274_1-D3
PFRMAT TS
TARGET T0316
MODEL  1
PARENT 1aab 1aac 1aaf 1aaj 1aalA
ATOM   2548  H   MET   284      26.986   0.765  10.292  1.00  1.00              
ATOM   2549  N   MET   284      27.458   0.034   9.922  1.00 28.03              
ATOM   2550  CA  MET   284      26.772  -0.799   8.907  1.00 21.73              
ATOM   2551  CB  MET   284      27.110  -2.254   9.240  1.00  3.06              
ATOM   2552  C   MET   284      25.249  -0.664   8.799  1.00 17.25              
ATOM   2553  O   MET   284      24.577  -1.691   8.672  1.00  1.00              
ATOM   2554  CG  MET   284      26.476  -3.295   8.336  1.00  2.72              
ATOM   2555  SD  MET   284      26.844  -4.964   8.918  1.00 23.71              
ATOM   2556  CE  MET   284      28.574  -5.075   8.488  1.00 30.98              
ATOM   2557  H   SER   285      25.162   1.309   8.717  1.00  1.00              
ATOM   2558  N   SER   285      24.662   0.529   8.829  1.00  9.56              
ATOM   2559  CA  SER   285      23.213   0.586   8.603  1.00  2.47              
ATOM   2560  CB  SER   285      22.612   1.877   9.184  1.00  1.00              
ATOM   2561  C   SER   285      22.909   0.424   7.119  1.00  1.00              
ATOM   2562  O   SER   285      23.805   0.591   6.287  1.00  1.00              
ATOM   2563  OG  SER   285      23.138   3.013   8.520  1.00  1.00              
ATOM   2564  H   THR   286      21.189  -0.442   7.511  1.00  1.00              
ATOM   2565  N   THR   286      21.767  -0.183   6.819  1.00  1.32              
ATOM   2566  CA  THR   286      21.517  -0.694   5.475  1.00  1.65              
ATOM   2567  CB  THR   286      21.174  -2.199   5.515  1.00  1.00              
ATOM   2568  C   THR   286      20.336   0.086   4.912  1.00  1.52              
ATOM   2569  O   THR   286      19.667  -0.350   3.973  1.00  1.00              
ATOM   2570  CG2 THR   286      22.357  -3.013   6.026  1.00  1.00              
ATOM   2571  OG1 THR   286      20.057  -2.401   6.388  1.00  1.00              
ATOM   2572  H   SER   287      20.544   1.428   6.327  1.00  1.00              
ATOM   2573  N   SER   287      19.949   1.094   5.688  1.00  1.58              
ATOM   2574  CA  SER   287      18.710   1.830   5.476  1.00  3.52              
ATOM   2575  CB  SER   287      17.538   1.051   6.078  1.00  1.00              
ATOM   2576  C   SER   287      18.805   3.179   6.161  1.00  4.42              
ATOM   2577  O   SER   287      19.825   3.492   6.782  1.00  1.00              
ATOM   2578  OG  SER   287      17.679   0.962   7.487  1.00  1.00              
ATOM   2579  H   LEU   288      17.110   3.761   5.397  1.00  1.00              
ATOM   2580  N   LEU   288      17.955   4.065   5.698  1.00 10.85              
ATOM   2581  CA  LEU   288      18.121   5.482   5.913  1.00 11.58              
ATOM   2582  CB  LEU   288      19.515   5.934   5.464  1.00  3.46              
ATOM   2583  C   LEU   288      17.054   6.171   5.077  1.00  8.37              
ATOM   2584  O   LEU   288      16.601   5.547   4.111  1.00  1.00              
ATOM   2585  CG  LEU   288      20.405   6.654   6.482  1.00  3.45              
ATOM   2586  CD1 LEU   288      21.502   7.410   5.747  1.00 17.92              
ATOM   2587  CD2 LEU   288      19.594   7.607   7.352  1.00 14.71              
ATOM   2588  H   GLU   289      17.447   7.970   5.783  1.00  1.00              
ATOM   2589  N   GLU   289      17.020   7.491   5.087  1.00  4.53              
ATOM   2590  CA  GLU   289      16.514   8.203   3.920  1.00  1.00              
ATOM   2591  CB  GLU   289      15.207   8.932   4.245  1.00  1.00              
ATOM   2592  C   GLU   289      17.541   9.192   3.357  1.00  1.00              
ATOM   2593  O   GLU   289      18.085  10.011   4.101  1.00  1.00              
ATOM   2594  CG  GLU   289      14.043   8.007   4.572  1.00  1.00              
ATOM   2595  CD  GLU   289      12.772   8.754   4.937  1.00  1.00              
ATOM   2596  OE1 GLU   289      12.815  10.003   5.011  1.00  1.00              
ATOM   2597  OE2 GLU   289      11.713   8.104   5.077  1.00  1.00              
ATOM   2598  H   ALA   290      17.292   8.555   1.511  1.00  1.00              
ATOM   2599  N   ALA   290      17.740   9.186   2.034  1.00  1.05              
ATOM   2600  CA  ALA   290      18.626  10.151   1.372  1.00  1.00              
ATOM   2601  CB  ALA   290      19.082   9.612   0.018  1.00  1.00              
ATOM   2602  C   ALA   290      17.937  11.502   1.203  1.00  4.58              
ATOM   2603  O   ALA   290      16.707  11.559   1.113  1.00  1.00              
ATOM   2604  H   SER   291      19.636  12.513   1.134  1.00  1.00              
ATOM   2605  N   SER   291      18.705  12.591   1.121  1.00 10.13              
ATOM   2606  CA  SER   291      18.099  13.895   0.865  1.00 10.38              
ATOM   2607  CB  SER   291      18.961  15.002   1.482  1.00  1.26              
ATOM   2608  C   SER   291      17.981  14.120  -0.635  1.00  9.19              
ATOM   2609  O   SER   291      17.891  15.282  -1.041  1.00  1.00              
ATOM   2610  OG  SER   291      20.285  14.938   0.980  1.00  1.25              
ATOM   2611  H   GLN   292      17.621  12.269  -1.102  1.00  1.00              
ATOM   2612  N   GLN   292      17.314  13.139  -1.235  1.00  5.34              
ATOM   2613  CA  GLN   292      16.400  13.370  -2.343  1.00  1.00              
ATOM   2614  CB  GLN   292      16.898  12.617  -3.580  1.00  1.00              
ATOM   2615  C   GLN   292      15.006  12.863  -1.985  1.00  1.00              
ATOM   2616  O   GLN   292      14.013  13.466  -2.439  1.00  1.00              
ATOM   2617  OXT GLN   292      14.916  11.823  -1.301  1.00  1.00              
ATOM   2618  CG  GLN   292      18.236  13.112  -4.114  1.00  1.00              
ATOM   2619  CD  GLN   292      18.173  14.549  -4.595  1.00  1.00              
ATOM   2620  NE2 GLN   292      19.142  15.358  -4.178  1.00  1.00              
ATOM   2621 HE21 GLN   292      19.806  15.007  -3.608  1.00  1.00              
ATOM   2622 HE22 GLN   292      19.163  16.252  -4.477  1.00  1.00              
ATOM   2623  OE1 GLN   292      17.365  14.884  -5.466  1.00  1.00              
TER
END
