
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0316AL316_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL316_5-D2.T0316_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    -       -      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    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
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    -       -      V     262           -
LGA    -       -      V     263           -
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    G     220      L     267          4.161
LGA    R     221      S     268          3.695
LGA    M     222      K     269          1.161
LGA    M     223      -       -           -
LGA    T     224      N     270          3.570
LGA    V     225      I     271          0.796
LGA    D     226      -       -           -
LGA    G     227      -       -           -
LGA    R     228      L     272          1.358
LGA    D     229      Y     273          0.999
LGA    M     230      -       -           -
LGA    G     231      -       -           -
LGA    E     232      V     274          1.330
LGA    H     233      G     275          1.620
LGA    A     234      -       -           -
LGA    G     235      -       -           -
LGA    L     236      Q     276          0.665
LGA    M     237      G     277          1.126
LGA    Y     238      F     278          2.302
LGA    Y     239      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)   20   60    5.0     12    2.23     0.00     16.957     0.514

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.712270 * X  +   0.698309 * Y  +  -0.070971 * Z  + -28.881298
  Y_new =   0.699023 * X  +  -0.714864 * Y  +  -0.018361 * Z  +  41.669720
  Z_new =  -0.063556 * X  +  -0.036533 * Y  +  -0.997309 * Z  + -19.730974 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.104977    0.036615  [ DEG:  -177.9021      2.0979 ]
  Theta =   0.063599    3.077994  [ DEG:     3.6440    176.3560 ]
  Phi   =   0.776012   -2.365581  [ DEG:    44.4622   -135.5378 ]
 
# 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: T0316AL316_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL316_5-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20   60   5.0   12   2.23    0.00  16.957
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL316_5-D2
REMARK Aligment from pdb entry: 1ni5_A
ATOM    789  N   GLY   220      48.085  13.561 -13.713  1.00  0.00              
ATOM    790  CA  GLY   220      46.698  13.220 -13.996  1.00  0.00              
ATOM    791  C   GLY   220      46.099  14.123 -15.081  1.00  0.00              
ATOM    792  O   GLY   220      44.893  14.375 -15.105  1.00  0.00              
ATOM    793  N   ARG   221      46.941  14.598 -15.988  1.00  0.00              
ATOM    794  CA  ARG   221      46.456  15.466 -17.044  1.00  0.00              
ATOM    795  C   ARG   221      45.310  14.839 -17.820  1.00  0.00              
ATOM    796  O   ARG   221      44.283  15.477 -18.049  1.00  0.00              
ATOM    797  N   MET   222      45.490  13.593 -18.235  1.00  0.00              
ATOM    798  CA  MET   222      44.459  12.915 -19.006  1.00  0.00              
ATOM    799  C   MET   222      43.133  12.808 -18.255  1.00  0.00              
ATOM    800  O   MET   222      42.069  12.749 -18.869  1.00  0.00              
ATOM    801  N   MET   223      43.198  12.787 -16.930  1.00  0.00              
ATOM    802  CA  MET   223      41.998  12.679 -16.120  1.00  0.00              
ATOM    803  C   MET   223      41.275  14.024 -16.106  1.00  0.00              
ATOM    804  O   MET   223      40.048  14.090 -16.167  1.00  0.00              
ATOM    805  N   THR   224      42.049  15.099 -16.040  1.00  0.00              
ATOM    806  CA  THR   224      41.489  16.444 -16.027  1.00  0.00              
ATOM    807  C   THR   224      40.766  16.744 -17.338  1.00  0.00              
ATOM    808  O   THR   224      39.746  17.437 -17.356  1.00  0.00              
ATOM    809  N   VAL   225      41.305  16.208 -18.429  1.00  0.00              
ATOM    810  CA  VAL   225      40.758  16.422 -19.758  1.00  0.00              
ATOM    811  C   VAL   225      39.404  15.764 -19.965  1.00  0.00              
ATOM    812  O   VAL   225      38.535  16.324 -20.632  1.00  0.00              
ATOM    813  N   ASP   226      39.225  14.579 -19.393  1.00  0.00              
ATOM    814  CA  ASP   226      37.949  13.873 -19.503  1.00  0.00              
ATOM    815  C   ASP   226      36.942  14.691 -18.714  1.00  0.00              
ATOM    816  O   ASP   226      35.769  14.782 -19.074  1.00  0.00              
ATOM    817  N   GLY   227      37.427  15.290 -17.634  1.00  0.00              
ATOM    818  CA  GLY   227      36.601  16.123 -16.784  1.00  0.00              
ATOM    819  C   GLY   227      36.098  17.292 -17.619  1.00  0.00              
ATOM    820  O   GLY   227      34.904  17.596 -17.611  1.00  0.00              
ATOM    821  N   ARG   228      36.999  17.947 -18.347  1.00  0.00              
ATOM    822  CA  ARG   228      36.584  19.062 -19.188  1.00  0.00              
ATOM    823  C   ARG   228      35.628  18.572 -20.270  1.00  0.00              
ATOM    824  O   ARG   228      34.590  19.187 -20.521  1.00  0.00              
ATOM    825  N   ASP   229      35.973  17.468 -20.921  1.00  0.00              
ATOM    826  CA  ASP   229      35.107  16.945 -21.960  1.00  0.00              
ATOM    827  C   ASP   229      33.718  16.788 -21.371  1.00  0.00              
ATOM    828  O   ASP   229      32.735  17.258 -21.940  1.00  0.00              
ATOM    829  N   MET   230      33.648  16.147 -20.210  1.00  0.00              
ATOM    830  CA  MET   230      32.375  15.901 -19.557  1.00  0.00              
ATOM    831  C   MET   230      31.606  17.171 -19.287  1.00  0.00              
ATOM    832  O   MET   230      30.384  17.204 -19.436  1.00  0.00              
ATOM    833  N   GLY   231      32.309  18.221 -18.882  1.00  0.00              
ATOM    834  CA  GLY   231      31.642  19.485 -18.585  1.00  0.00              
ATOM    835  C   GLY   231      31.101  20.153 -19.848  1.00  0.00              
ATOM    836  O   GLY   231      30.044  20.785 -19.820  1.00  0.00              
ATOM    837  N   GLU   232      31.825  20.013 -20.954  1.00  0.00              
ATOM    838  CA  GLU   232      31.375  20.588 -22.200  1.00  0.00              
ATOM    839  C   GLU   232      30.093  19.888 -22.576  1.00  0.00              
ATOM    840  O   GLU   232      29.132  20.519 -23.019  1.00  0.00              
ATOM    841  N   HIS   233      30.079  18.574 -22.396  1.00  0.00              
ATOM    842  CA  HIS   233      28.900  17.789 -22.709  1.00  0.00              
ATOM    843  C   HIS   233      27.720  18.236 -21.841  1.00  0.00              
ATOM    844  O   HIS   233      26.627  18.464 -22.353  1.00  0.00              
ATOM    845  N   ALA   234      27.933  18.381 -20.538  1.00  0.00              
ATOM    846  CA  ALA   234      26.848  18.810 -19.671  1.00  0.00              
ATOM    847  C   ALA   234      26.229  20.110 -20.155  1.00  0.00              
ATOM    848  O   ALA   234      25.017  20.289 -20.104  1.00  0.00              
ATOM    849  N   GLY   235      27.063  21.024 -20.625  1.00  0.00              
ATOM    850  CA  GLY   235      26.563  22.307 -21.098  1.00  0.00              
ATOM    851  C   GLY   235      25.768  22.168 -22.392  1.00  0.00              
ATOM    852  O   GLY   235      24.742  22.822 -22.568  1.00  0.00              
ATOM    853  N   LEU   236      26.240  21.321 -23.304  1.00  0.00              
ATOM    854  CA  LEU   236      25.529  21.138 -24.567  1.00  0.00              
ATOM    855  C   LEU   236      24.163  20.534 -24.285  1.00  0.00              
ATOM    856  O   LEU   236      23.193  20.837 -24.970  1.00  0.00              
ATOM    857  N   MET   237      24.080  19.690 -23.267  1.00  0.00              
ATOM    858  CA  MET   237      22.805  19.081 -22.941  1.00  0.00              
ATOM    859  C   MET   237      21.946  20.123 -22.248  1.00  0.00              
ATOM    860  O   MET   237      20.723  20.075 -22.339  1.00  0.00              
ATOM    861  N   TYR   238      22.587  21.065 -21.556  1.00  0.00              
ATOM    862  CA  TYR   238      21.843  22.125 -20.883  1.00  0.00              
ATOM    863  C   TYR   238      21.162  22.913 -21.993  1.00  0.00              
ATOM    864  O   TYR   238      19.975  23.223 -21.906  1.00  0.00              
ATOM    865  N   TYR   239      21.913  23.227 -23.044  1.00  0.00              
ATOM    866  CA  TYR   239      21.342  23.950 -24.166  1.00  0.00              
ATOM    867  C   TYR   239      20.254  23.112 -24.802  1.00  0.00              
ATOM    868  O   TYR   239      19.224  23.646 -25.203  1.00  0.00              
END
