
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0316AL242_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL242_1-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V     262      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    V     263      L     236           #
LGA    G     264      M     237          3.724
LGA    K     265      Y     238          3.853
LGA    D     266      -       -           -
LGA    L     267      -       -           -
LGA    S     268      Y     239          2.993
LGA    K     269      T     240           -
LGA    N     270      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    I     271      G     245          4.283
LGA    L     272      G     246          2.691
LGA    Y     273      L     247          5.057
LGA    V     274      G     248           #
LGA    G     275      I     249          3.499
LGA    Q     276      G     250          1.402
LGA    G     277      G     251          1.812
LGA    F     278      D     256           #
LGA    Y     279      -       -           -
LGA    H     280      N     257          2.212
LGA    D     281      A     258          1.563
LGA    S     282      P     259          3.679
LGA    L     283      W     260          2.670
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)   22   60    5.0     13    3.21     7.69     14.062     0.392

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.762054 * X  +  -0.453197 * Y  +   0.462478 * Z  +   9.511311
  Y_new =   0.122468 * X  +  -0.802224 * Y  +  -0.584327 * Z  +  45.595692
  Z_new =   0.635827 * X  +  -0.388650 * Y  +   0.666840 * Z  +  18.627224 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.527694    2.613899  [ DEG:   -30.2346    149.7654 ]
  Theta =  -0.689079   -2.452513  [ DEG:   -39.4813   -140.5187 ]
  Phi   =   2.982248   -0.159345  [ DEG:   170.8702     -9.1298 ]
 
# 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: T0316AL242_1-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL242_1-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22   60   5.0   13   3.21    7.69  14.062
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL242_1-D2
REMARK Aligment from pdb entry: 1xng_B
ATOM    709  N   VAL   262      34.775  18.387  -7.379  1.00  0.00              
ATOM    710  CA  VAL   262      36.024  18.921  -7.902  1.00  0.00              
ATOM    711  C   VAL   262      36.320  20.310  -7.364  1.00  0.00              
ATOM    712  O   VAL   262      35.408  21.036  -6.971  1.00  0.00              
ATOM    713  N   VAL   263      37.604  20.696  -7.341  1.00  0.00              
ATOM    714  CA  VAL   263      38.001  22.019  -6.856  1.00  0.00              
ATOM    715  C   VAL   263      37.812  22.994  -8.019  1.00  0.00              
ATOM    716  O   VAL   263      37.672  22.570  -9.167  1.00  0.00              
ATOM    717  N   GLY   264      37.816  24.289  -7.733  1.00  0.00              
ATOM    718  CA  GLY   264      37.626  25.275  -8.786  1.00  0.00              
ATOM    719  C   GLY   264      38.777  25.327  -9.781  1.00  0.00              
ATOM    720  O   GLY   264      38.621  25.842 -10.886  1.00  0.00              
ATOM    721  N   LYS   265      39.923  24.779  -9.398  1.00  0.00              
ATOM    722  CA  LYS   265      41.083  24.760 -10.284  1.00  0.00              
ATOM    723  C   LYS   265      40.816  23.845 -11.484  1.00  0.00              
ATOM    724  O   LYS   265      41.427  23.994 -12.548  1.00  0.00              
ATOM    725  N   ASP   266      39.904  22.896 -11.294  1.00  0.00              
ATOM    726  CA  ASP   266      39.516  21.951 -12.335  1.00  0.00              
ATOM    727  C   ASP   266      38.215  22.393 -13.004  1.00  0.00              
ATOM    728  O   ASP   266      38.033  22.231 -14.213  1.00  0.00              
ATOM    729  N   LEU   267      37.309  22.962 -12.213  1.00  0.00              
ATOM    730  CA  LEU   267      36.020  23.396 -12.734  1.00  0.00              
ATOM    731  C   LEU   267      36.069  24.638 -13.615  1.00  0.00              
ATOM    732  O   LEU   267      35.516  24.644 -14.717  1.00  0.00              
ATOM    733  N   SER   268      36.740  25.679 -13.138  1.00  0.00              
ATOM    734  CA  SER   268      36.792  26.935 -13.873  1.00  0.00              
ATOM    735  C   SER   268      37.296  26.836 -15.307  1.00  0.00              
ATOM    736  O   SER   268      36.718  27.434 -16.213  1.00  0.00              
ATOM    737  N   LYS   269      38.370  26.071 -15.544  1.00  0.00              
ATOM    738  CA  LYS   269      38.826  25.991 -16.934  1.00  0.00              
ATOM    739  C   LYS   269      37.723  25.470 -17.863  1.00  0.00              
ATOM    740  O   LYS   269      37.561  25.952 -18.991  1.00  0.00              
ATOM    741  N   ASN   270      36.946  24.499 -17.382  1.00  0.00              
ATOM    742  CA  ASN   270      35.867  23.940 -18.181  1.00  0.00              
ATOM    743  C   ASN   270      34.740  24.946 -18.378  1.00  0.00              
ATOM    744  O   ASN   270      34.177  25.043 -19.464  1.00  0.00              
ATOM    745  N   ILE   271      34.412  25.703 -17.332  1.00  0.00              
ATOM    746  CA  ILE   271      33.346  26.690 -17.444  1.00  0.00              
ATOM    747  C   ILE   271      33.720  27.766 -18.455  1.00  0.00              
ATOM    748  O   ILE   271      32.870  28.237 -19.214  1.00  0.00              
ATOM    749  N   LEU   272      34.991  28.156 -18.472  1.00  0.00              
ATOM    750  CA  LEU   272      35.432  29.177 -19.409  1.00  0.00              
ATOM    751  C   LEU   272      35.278  28.697 -20.851  1.00  0.00              
ATOM    752  O   LEU   272      34.926  29.484 -21.727  1.00  0.00              
ATOM    753  N   TYR   273      35.535  27.416 -21.109  1.00  0.00              
ATOM    754  CA  TYR   273      35.376  26.902 -22.471  1.00  0.00              
ATOM    755  C   TYR   273      33.896  26.827 -22.833  1.00  0.00              
ATOM    756  O   TYR   273      33.505  27.123 -23.962  1.00  0.00              
ATOM    757  N   VAL   274      33.068  26.431 -21.872  1.00  0.00              
ATOM    758  CA  VAL   274      31.634  26.346 -22.107  1.00  0.00              
ATOM    759  C   VAL   274      31.100  27.735 -22.453  1.00  0.00              
ATOM    760  O   VAL   274      30.231  27.877 -23.311  1.00  0.00              
ATOM    761  N   GLY   275      31.634  28.753 -21.792  1.00  0.00              
ATOM    762  CA  GLY   275      31.227  30.130 -22.048  1.00  0.00              
ATOM    763  C   GLY   275      31.623  30.573 -23.453  1.00  0.00              
ATOM    764  O   GLY   275      30.896  31.317 -24.111  1.00  0.00              
ATOM    765  N   GLN   276      32.780  30.111 -23.913  1.00  0.00              
ATOM    766  CA  GLN   276      33.266  30.485 -25.234  1.00  0.00              
ATOM    767  C   GLN   276      32.650  29.667 -26.364  1.00  0.00              
ATOM    768  O   GLN   276      32.389  30.190 -27.446  1.00  0.00              
ATOM    769  N   GLY   277      32.406  28.387 -26.107  1.00  0.00              
ATOM    770  CA  GLY   277      31.854  27.499 -27.122  1.00  0.00              
ATOM    771  C   GLY   277      30.340  27.493 -27.232  1.00  0.00              
ATOM    772  O   GLY   277      29.793  27.408 -28.330  1.00  0.00              
ATOM    773  N   PHE   278      29.661  27.577 -26.094  1.00  0.00              
ATOM    774  CA  PHE   278      28.208  27.532 -26.092  1.00  0.00              
ATOM    775  C   PHE   278      27.585  28.749 -25.436  1.00  0.00              
ATOM    776  O   PHE   278      27.840  29.039 -24.269  1.00  0.00              
ATOM    777  N   TYR   279      26.765  29.456 -26.198  1.00  0.00              
ATOM    778  CA  TYR   279      26.089  30.644 -25.704  1.00  0.00              
ATOM    779  C   TYR   279      24.894  30.923 -26.603  1.00  0.00              
ATOM    780  O   TYR   279      23.955  31.614 -26.212  1.00  0.00              
ATOM    781  N   HIS   280      24.942  30.368 -27.809  1.00  0.00              
ATOM    782  CA  HIS   280      23.872  30.527 -28.784  1.00  0.00              
ATOM    783  C   HIS   280      23.273  29.152 -29.048  1.00  0.00              
ATOM    784  O   HIS   280      22.221  29.025 -29.676  1.00  0.00              
ATOM    785  N   ASP   281      23.960  28.121 -28.563  1.00  0.00              
ATOM    786  CA  ASP   281      23.515  26.745 -28.733  1.00  0.00              
ATOM    787  C   ASP   281      23.790  25.948 -27.461  1.00  0.00              
ATOM    788  O   ASP   281      24.644  26.321 -26.656  1.00  0.00              
ATOM    789  N   SER   282      23.069  24.836 -27.264  1.00  0.00              
ATOM    790  CA  SER   282      23.263  24.008 -26.072  1.00  0.00              
ATOM    791  C   SER   282      24.644  23.352 -26.000  1.00  0.00              
ATOM    792  O   SER   282      25.322  23.183 -27.014  1.00  0.00              
ATOM    793  N   LEU   283      25.048  22.989 -24.790  1.00  0.00              
ATOM    794  CA  LEU   283      26.338  22.351 -24.556  1.00  0.00              
ATOM    795  C   LEU   283      26.449  21.034 -25.323  1.00  0.00              
ATOM    796  O   LEU   283      25.514  20.236 -25.346  1.00  0.00              
END
