
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0316AL380_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL380_5-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    G     220      L     236          0.591
LGA    R     221      M     237          1.101
LGA    M     222      Y     238          1.779
LGA    M     223      Y     239          1.668
LGA    T     224      T     240          1.704
LGA    V     225      I     241          1.891
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    -       -      F     261           -
LGA    D     226      V     262          2.107
LGA    G     227      V     263          2.684
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    R     228      V     274          2.342
LGA    D     229      G     275          2.465
LGA    M     230      Q     276          4.196
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   11   60    5.0     11    2.23     9.09     15.745     0.472

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.810876 * X  +   0.521692 * Y  +  -0.265174 * Z  + 113.340668
  Y_new =   0.545969 * X  +   0.511230 * Y  +  -0.663748 * Z  + -18.441914
  Z_new =  -0.210707 * X  +  -0.682994 * Y  +  -0.699372 * Z  +  79.764519 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.368042    0.773551  [ DEG:  -135.6788     44.3212 ]
  Theta =   0.212298    2.929294  [ DEG:    12.1638    167.8362 ]
  Phi   =   2.549006   -0.592586  [ DEG:   146.0473    -33.9527 ]
 
# 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: T0316AL380_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL380_5-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   60   5.0   11   2.23    9.09  15.745
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL380_5-D2
REMARK Aligment from pdb entry: 1gpmC
ATOM    693  N   GLY   220      40.984  23.336 -14.942  1.00  0.00              
ATOM    694  CA  GLY   220      40.160  22.221 -14.469  1.00  0.00              
ATOM    695  C   GLY   220      39.858  22.267 -12.965  1.00  0.00              
ATOM    696  O   GLY   220      38.725  22.033 -12.544  1.00  0.00              
ATOM    697  N   ARG   221      40.882  22.551 -12.168  1.00  0.00              
ATOM    698  CA  ARG   221      40.747  22.627 -10.715  1.00  0.00              
ATOM    699  C   ARG   221      39.963  23.863 -10.279  1.00  0.00              
ATOM    700  O   ARG   221      39.491  23.937  -9.148  1.00  0.00              
ATOM    701  N   MET   222      39.818  24.832 -11.177  1.00  0.00              
ATOM    702  CA  MET   222      39.096  26.063 -10.861  1.00  0.00              
ATOM    703  C   MET   222      37.584  26.021 -11.102  1.00  0.00              
ATOM    704  O   MET   222      36.882  26.981 -10.790  1.00  0.00              
ATOM    705  N   MET   223      37.084  24.903 -11.629  1.00  0.00              
ATOM    706  CA  MET   223      35.648  24.735 -11.875  1.00  0.00              
ATOM    707  C   MET   223      35.130  23.540 -11.070  1.00  0.00              
ATOM    708  O   MET   223      35.892  22.615 -10.765  1.00  0.00              
ATOM    709  N   THR   224      33.840  23.553 -10.744  1.00  0.00              
ATOM    710  CA  THR   224      33.215  22.452 -10.015  1.00  0.00              
ATOM    711  C   THR   224      32.857  21.328 -10.979  1.00  0.00              
ATOM    712  O   THR   224      32.978  20.142 -10.651  1.00  0.00              
ATOM    713  N   VAL   225      32.345  21.701 -12.146  1.00  0.00              
ATOM    714  CA  VAL   225      31.967  20.723 -13.160  1.00  0.00              
ATOM    715  C   VAL   225      32.256  21.356 -14.506  1.00  0.00              
ATOM    716  O   VAL   225      32.248  22.579 -14.639  1.00  0.00              
ATOM    717  N   ASP   226      32.552  20.527 -15.494  1.00  0.00              
ATOM    718  CA  ASP   226      32.841  21.014 -16.831  1.00  0.00              
ATOM    719  C   ASP   226      32.645  19.852 -17.809  1.00  0.00              
ATOM    720  O   ASP   226      33.285  18.796 -17.692  1.00  0.00              
ATOM    721  N   GLY   227      31.730  20.043 -18.753  1.00  0.00              
ATOM    722  CA  GLY   227      31.402  19.017 -19.723  1.00  0.00              
ATOM    723  C   GLY   227      30.772  19.641 -20.945  1.00  0.00              
ATOM    724  O   GLY   227      30.392  20.812 -20.926  1.00  0.00              
ATOM    725  N   ARG   228      30.598  18.821 -21.973  1.00  0.00              
ATOM    726  CA  ARG   228      30.005  19.228 -23.235  1.00  0.00              
ATOM    727  C   ARG   228      28.624  18.564 -23.410  1.00  0.00              
ATOM    728  O   ARG   228      28.399  17.446 -22.932  1.00  0.00              
ATOM    729  N   ASP   229      27.691  19.285 -24.030  1.00  0.00              
ATOM    730  CA  ASP   229      26.350  18.776 -24.285  1.00  0.00              
ATOM    731  C   ASP   229      26.156  18.708 -25.803  1.00  0.00              
ATOM    732  O   ASP   229      26.631  19.573 -26.533  1.00  0.00              
ATOM    733  N   MET   230      25.495  17.667 -26.287  1.00  0.00              
ATOM    734  CA  MET   230      25.259  17.519 -27.718  1.00  0.00              
ATOM    735  C   MET   230      23.874  18.054 -28.081  1.00  0.00              
ATOM    736  O   MET   230      22.852  17.584 -27.566  1.00  0.00              
END
