
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0316AL380_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL380_3-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      G     220           -
LGA    R     221      R     221           #
LGA    M     222      -       -           -
LGA    M     223      M     222          3.160
LGA    T     224      M     223          3.372
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    V     225      G     231          4.771
LGA    D     226      E     232          2.925
LGA    G     227      H     233          3.681
LGA    R     228      -       -           -
LGA    D     229      A     234          2.606
LGA    M     230      G     235          3.712
LGA    G     231      L     236          2.438
LGA    E     232      M     237          4.329
LGA    H     233      Y     238           #
LGA    A     234      Y     239          4.415
LGA    G     235      T     240          1.019
LGA    L     236      I     241          4.344
LGA    -       -      G     242           -
LGA    M     237      Q     243          2.785
LGA    Y     238      R     244          2.456
LGA    Y     239      G     245          2.207
LGA    T     240      G     246          2.039
LGA    I     241      L     247           #
LGA    G     242      -       -           -
LGA    Q     243      G     248           #
LGA    R     244      I     249          3.725
LGA    G     245      G     250          2.340
LGA    G     246      G     251          1.851
LGA    L     247      D     256          4.888
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    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
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)   28   60    5.0     20    3.32    15.00     19.788     0.585

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.215641 * X  +   0.966772 * Y  +   0.137297 * Z  +  26.638187
  Y_new =  -0.145878 * X  +   0.107132 * Y  +  -0.983485 * Z  + -13.700243
  Z_new =  -0.965515 * X  +  -0.232109 * Y  +   0.117929 * Z  + -27.646217 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.100708    2.040884  [ DEG:   -63.0660    116.9341 ]
  Theta =   1.307413    1.834180  [ DEG:    74.9092    105.0908 ]
  Phi   =  -2.546823    0.594770  [ DEG:  -145.9222     34.0778 ]
 
# 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_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL380_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28   60   5.0   20   3.32   15.00  19.788
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL380_3-D2
REMARK Aligment from pdb entry: 1xngA
ATOM    705  N   GLY   220      36.880  18.434 -30.740  1.00  0.00              
ATOM    706  CA  GLY   220      36.879  18.062 -29.329  1.00  0.00              
ATOM    707  C   GLY   220      38.050  18.653 -28.559  1.00  0.00              
ATOM    708  O   GLY   220      37.868  19.220 -27.484  1.00  0.00              
ATOM    709  N   ARG   221      39.249  18.528 -29.119  1.00  0.00              
ATOM    710  CA  ARG   221      40.456  19.010 -28.455  1.00  0.00              
ATOM    711  C   ARG   221      40.482  20.475 -28.033  1.00  0.00              
ATOM    712  O   ARG   221      40.971  20.802 -26.952  1.00  0.00              
ATOM    713  N   MET   222      39.981  21.387 -28.877  1.00  0.00              
ATOM    714  CA  MET   222      40.008  22.784 -28.441  1.00  0.00              
ATOM    715  C   MET   222      39.185  22.969 -27.158  1.00  0.00              
ATOM    716  O   MET   222      39.574  23.720 -26.264  1.00  0.00              
ATOM    717  N   MET   223      38.059  22.265 -27.072  1.00  0.00              
ATOM    718  CA  MET   223      37.190  22.333 -25.900  1.00  0.00              
ATOM    719  C   MET   223      37.855  21.655 -24.707  1.00  0.00              
ATOM    720  O   MET   223      37.839  22.181 -23.594  1.00  0.00              
ATOM    721  N   THR   224      38.442  20.483 -24.937  1.00  0.00              
ATOM    722  CA  THR   224      39.114  19.789 -23.850  1.00  0.00              
ATOM    723  C   THR   224      40.263  20.634 -23.294  1.00  0.00              
ATOM    724  O   THR   224      40.522  20.627 -22.090  1.00  0.00              
ATOM    725  N   VAL   225      40.955  21.368 -24.161  1.00  0.00              
ATOM    726  CA  VAL   225      42.059  22.199 -23.694  1.00  0.00              
ATOM    727  C   VAL   225      41.574  23.302 -22.749  1.00  0.00              
ATOM    728  O   VAL   225      42.212  23.577 -21.728  1.00  0.00              
ATOM    729  N   ASP   226      40.453  23.935 -23.079  1.00  0.00              
ATOM    730  CA  ASP   226      39.918  24.975 -22.207  1.00  0.00              
ATOM    731  C   ASP   226      39.413  24.383 -20.896  1.00  0.00              
ATOM    732  O   ASP   226      39.545  24.996 -19.836  1.00  0.00              
ATOM    733  N   GLY   227      38.833  23.190 -20.965  1.00  0.00              
ATOM    734  CA  GLY   227      38.341  22.529 -19.765  1.00  0.00              
ATOM    735  C   GLY   227      39.519  22.165 -18.859  1.00  0.00              
ATOM    736  O   GLY   227      39.453  22.331 -17.642  1.00  0.00              
ATOM    737  N   ARG   228      40.614  21.691 -19.446  1.00  0.00              
ATOM    738  CA  ARG   228      41.769  21.328 -18.636  1.00  0.00              
ATOM    739  C   ARG   228      42.403  22.557 -17.988  1.00  0.00              
ATOM    740  O   ARG   228      42.901  22.486 -16.863  1.00  0.00              
ATOM    741  N   ASP   229      42.378  23.683 -18.694  1.00  0.00              
ATOM    742  CA  ASP   229      42.981  24.910 -18.181  1.00  0.00              
ATOM    743  C   ASP   229      42.112  25.602 -17.141  1.00  0.00              
ATOM    744  O   ASP   229      42.615  26.115 -16.138  1.00  0.00              
ATOM    745  N   MET   230      40.808  25.596 -17.384  1.00  0.00              
ATOM    746  CA  MET   230      39.855  26.252 -16.499  1.00  0.00              
ATOM    747  C   MET   230      39.371  25.405 -15.334  1.00  0.00              
ATOM    748  O   MET   230      39.255  25.902 -14.211  1.00  0.00              
ATOM    749  N   GLY   231      39.085  24.133 -15.598  1.00  0.00              
ATOM    750  CA  GLY   231      38.571  23.244 -14.565  1.00  0.00              
ATOM    751  C   GLY   231      39.354  21.942 -14.446  1.00  0.00              
ATOM    752  O   GLY   231      38.824  20.863 -14.719  1.00  0.00              
ATOM    753  N   GLU   232      40.610  22.034 -14.030  1.00  0.00              
ATOM    754  CA  GLU   232      41.424  20.839 -13.884  1.00  0.00              
ATOM    755  C   GLU   232      41.140  20.169 -12.544  1.00  0.00              
ATOM    756  O   GLU   232      41.103  18.943 -12.452  1.00  0.00              
ATOM    757  N   HIS   233      40.933  20.981 -11.512  1.00  0.00              
ATOM    758  CA  HIS   233      40.664  20.460 -10.175  1.00  0.00              
ATOM    759  C   HIS   233      39.382  21.056  -9.595  1.00  0.00              
ATOM    760  O   HIS   233      39.189  21.073  -8.380  1.00  0.00              
ATOM    761  N   ALA   234      38.513  21.550 -10.470  1.00  0.00              
ATOM    762  CA  ALA   234      37.253  22.146 -10.046  1.00  0.00              
ATOM    763  C   ALA   234      36.145  21.710 -11.002  1.00  0.00              
ATOM    764  O   ALA   234      36.416  21.271 -12.120  1.00  0.00              
ATOM    765  N   GLY   235      34.879  21.823 -10.573  1.00  0.00              
ATOM    766  CA  GLY   235      33.745  21.430 -11.414  1.00  0.00              
ATOM    767  C   GLY   235      33.613  22.253 -12.691  1.00  0.00              
ATOM    768  O   GLY   235      33.848  23.460 -12.695  1.00  0.00              
ATOM    769  N   LEU   236      33.231  21.590 -13.776  1.00  0.00              
ATOM    770  CA  LEU   236      33.067  22.262 -15.057  1.00  0.00              
ATOM    771  C   LEU   236      31.855  23.196 -15.060  1.00  0.00              
ATOM    772  O   LEU   236      30.774  22.828 -14.599  1.00  0.00              
ATOM    773  N   MET   237      32.052  24.410 -15.568  1.00  0.00              
ATOM    774  CA  MET   237      30.982  25.402 -15.655  1.00  0.00              
ATOM    775  C   MET   237      30.581  25.509 -17.120  1.00  0.00              
ATOM    776  O   MET   237      31.233  26.199 -17.905  1.00  0.00              
ATOM    777  N   TYR   238      29.507  24.816 -17.484  1.00  0.00              
ATOM    778  CA  TYR   238      29.032  24.811 -18.860  1.00  0.00              
ATOM    779  C   TYR   238      28.675  26.199 -19.373  1.00  0.00              
ATOM    780  O   TYR   238      28.756  26.466 -20.572  1.00  0.00              
ATOM    781  N   TYR   239      28.281  27.083 -18.463  1.00  0.00              
ATOM    782  CA  TYR   239      27.914  28.437 -18.846  1.00  0.00              
ATOM    783  C   TYR   239      29.153  29.199 -19.301  1.00  0.00              
ATOM    784  O   TYR   239      29.105  29.958 -20.267  1.00  0.00              
ATOM    785  N   THR   240      30.264  28.988 -18.602  1.00  0.00              
ATOM    786  CA  THR   240      31.515  29.648 -18.950  1.00  0.00              
ATOM    787  C   THR   240      31.961  29.172 -20.327  1.00  0.00              
ATOM    788  O   THR   240      32.403  29.966 -21.155  1.00  0.00              
ATOM    789  N   ILE   241      31.837  27.871 -20.569  1.00  0.00              
ATOM    790  CA  ILE   241      32.225  27.297 -21.852  1.00  0.00              
ATOM    791  C   ILE   241      31.321  27.835 -22.959  1.00  0.00              
ATOM    792  O   ILE   241      31.758  28.028 -24.095  1.00  0.00              
ATOM    793  N   GLY   242      30.061  28.082 -22.614  1.00  0.00              
ATOM    794  CA  GLY   242      29.093  28.606 -23.569  1.00  0.00              
ATOM    795  C   GLY   242      29.514  30.001 -24.019  1.00  0.00              
ATOM    796  O   GLY   242      29.378  30.356 -25.190  1.00  0.00              
ATOM    797  N   GLN   243      30.031  30.786 -23.081  1.00  0.00              
ATOM    798  CA  GLN   243      30.474  32.143 -23.370  1.00  0.00              
ATOM    799  C   GLN   243      31.699  32.156 -24.277  1.00  0.00              
ATOM    800  O   GLN   243      31.938  33.128 -24.994  1.00  0.00              
ATOM    801  N   ARG   244      32.475  31.078 -24.242  1.00  0.00              
ATOM    802  CA  ARG   244      33.669  30.983 -25.071  1.00  0.00              
ATOM    803  C   ARG   244      33.306  30.738 -26.529  1.00  0.00              
ATOM    804  O   ARG   244      34.173  30.757 -27.405  1.00  0.00              
ATOM    805  N   GLY   245      32.023  30.501 -26.783  1.00  0.00              
ATOM    806  CA  GLY   245      31.569  30.273 -28.142  1.00  0.00              
ATOM    807  C   GLY   245      31.400  28.820 -28.541  1.00  0.00              
ATOM    808  O   GLY   245      31.298  28.517 -29.729  1.00  0.00              
ATOM    809  N   GLY   246      31.371  27.918 -27.564  1.00  0.00              
ATOM    810  CA  GLY   246      31.208  26.499 -27.863  1.00  0.00              
ATOM    811  C   GLY   246      29.742  26.107 -27.977  1.00  0.00              
ATOM    812  O   GLY   246      28.896  26.612 -27.242  1.00  0.00              
ATOM    813  N   LEU   247      29.457  25.202 -28.906  1.00  0.00              
ATOM    814  CA  LEU   247      28.101  24.714 -29.138  1.00  0.00              
ATOM    815  C   LEU   247      27.521  24.137 -27.853  1.00  0.00              
ATOM    816  O   LEU   247      28.192  23.388 -27.143  1.00  0.00              
END
