
#######################################################
#                                                     #
#                        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 (  153),  selected   20 , name T0298TS022_4_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS022_4_2-D1.T0298_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      Q       3           -
LGA    -       -      P       4           -
LGA    -       -      L       5           -
LGA    -       -      N       6           -
LGA    -       -      V       7           -
LGA    -       -      A       8           -
LGA    -       -      V       9           -
LGA    -       -      V      10           -
LGA    -       -      G      11           -
LGA    -       -      A      12           -
LGA    -       -      T      13           -
LGA    -       -      G      14           -
LGA    -       -      S      15           -
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    -       -      E      18           -
LGA    -       -      A      19           -
LGA    -       -      L      20           -
LGA    -       -      V      21           -
LGA    -       -      G      22           -
LGA    -       -      L      23           -
LGA    -       -      L      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    -       -      F      29           -
LGA    -       -      P      30           -
LGA    -       -      L      31           -
LGA    -       -      H      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      H      35           -
LGA    -       -      L      36           -
LGA    -       -      L      37           -
LGA    -       -      A      38           -
LGA    -       -      S      39           -
LGA    -       -      A      40           -
LGA    -       -      E      41           -
LGA    -       -      S      42           -
LGA    -       -      A      43           -
LGA    -       -      G      44           -
LGA    -       -      Q      45           -
LGA    -       -      R      46           -
LGA    -       -      M      47           -
LGA    -       -      G      48           -
LGA    -       -      F      49           -
LGA    -       -      A      50           -
LGA    -       -      E      51           -
LGA    -       -      S      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      V      56           -
LGA    -       -      G      57           -
LGA    -       -      D      58           -
LGA    -       -      V      59           -
LGA    -       -      D      60           -
LGA    -       -      S      61           -
LGA    -       -      F      62           -
LGA    -       -      D      63           -
LGA    -       -      F      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      L      69           -
LGA    -       -      A      70           -
LGA    -       -      F      71           -
LGA    -       -      F      72           -
LGA    -       -      A      73           -
LGA    -       -      A      74           -
LGA    -       -      A      75           -
LGA    -       -      A      76           -
LGA    -       -      E      77           -
LGA    -       -      V      78           -
LGA    -       -      S      79           -
LGA    -       -      R      80           -
LGA    -       -      A      81           -
LGA    -       -      H      82           -
LGA    -       -      A      83           -
LGA    -       -      E      84           -
LGA    -       -      R      85           -
LGA    -       -      A      86           -
LGA    -       -      R      87           -
LGA    -       -      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    -       -      C      91           -
LGA    -       -      S      92           -
LGA    -       -      V      93           -
LGA    -       -      I      94           -
LGA    -       -      D      95           -
LGA    V     316      L      96          3.147
LGA    -       -      S      97           -
LGA    R     317      G      98          2.421
LGA    K     318      A      99          4.109
LGA    G     319      L     100          2.642
LGA    -       -      E     101           -
LGA    -       -      P     102           -
LGA    -       -      S     103           -
LGA    -       -      V     104           -
LGA    A     320      A     105          1.786
LGA    A     321      P     106          4.603
LGA    L     322      P     107          2.282
LGA    -       -      V     108           -
LGA    -       -      M     109           -
LGA    -       -      V     110           -
LGA    -       -      S     111           -
LGA    -       -      V     112           -
LGA    -       -      N     113           -
LGA    -       -      A     114           -
LGA    -       -      E     115           -
LGA    -       -      R     116           -
LGA    -       -      L     117           -
LGA    -       -      A     118           -
LGA    -       -      S     119           -
LGA    -       -      Q     120           -
LGA    -       -      A     121           -
LGA    -       -      A     122           -
LGA    -       -      P     123           -
LGA    -       -      F     124           -
LGA    -       -      L     125           -
LGA    -       -      L     126           -
LGA    -       -      S     127           -
LGA    N     323      S     128          2.799
LGA    A     324      P     129          2.150
LGA    -       -      V     316           -
LGA    -       -      R     317           -
LGA    -       -      K     318           -
LGA    V     325      G     319          3.951
LGA    L     326      A     320          2.400
LGA    L     327      A     321          1.406
LGA    G     328      L     322          2.953
LGA    -       -      N     323           -
LGA    E     329      A     324          0.481
LGA    L     330      V     325          0.749
LGA    L     331      L     326          0.982
LGA    I     332      L     327          0.836
LGA    K     333      G     328          0.938
LGA    -       -      E     329           -
LGA    H     334      L     330          3.889
LGA    Y     335      L     331          4.805
LGA    -       -      I     332           -
LGA    -       -      K     333           -
LGA    -       -      H     334           -
LGA    -       -      Y     335           -
LGA    -       -      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20  148    5.0     20    2.79    10.00      9.435     0.693

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.148117 * X  +   0.974407 * Y  +   0.169096 * Z  +  -8.543091
  Y_new =  -0.620037 * X  +   0.224699 * Y  +  -0.751708 * Z  +  79.401970
  Z_new =  -0.770465 * X  +   0.006495 * Y  +   0.637450 * Z  +   9.325284 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.010189   -3.131404  [ DEG:     0.5838   -179.4162 ]
  Theta =   0.879570    2.262023  [ DEG:    50.3956    129.6044 ]
  Phi   =  -1.336307    1.805286  [ DEG:   -76.5647    103.4353 ]
 
# 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: T0298TS022_4_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS022_4_2-D1.T0298_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20  148   5.0   20   2.79   10.00   9.435
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS022_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1ojg_A
ATOM   1934  N   VAL   316     -12.333  73.781  -2.959  1.00  0.00
ATOM   1935  CA  VAL   316     -12.278  73.036  -4.170  1.00  0.00
ATOM   1936  C   VAL   316     -12.876  73.934  -5.193  1.00  0.00
ATOM   1937  O   VAL   316     -14.081  74.183  -5.191  1.00  0.00
ATOM   1938  CB  VAL   316     -13.071  71.721  -4.061  1.00  0.00
ATOM   1939  CG1 VAL   316     -13.022  70.959  -5.376  1.00  0.00
ATOM   1940  CG2 VAL   316     -12.489  70.836  -2.970  1.00  0.00
ATOM   1941  N   ARG   317     -12.036  74.465  -6.093  1.00  0.00
ATOM   1942  CA  ARG   317     -12.601  75.315  -7.089  1.00  0.00
ATOM   1943  C   ARG   317     -12.143  74.809  -8.412  1.00  0.00
ATOM   1944  O   ARG   317     -10.945  74.719  -8.678  1.00  0.00
ATOM   1945  CB  ARG   317     -12.136  76.759  -6.889  1.00  0.00
ATOM   1946  CG  ARG   317     -12.738  77.747  -7.874  1.00  0.00
ATOM   1947  CD  ARG   317     -12.287  79.167  -7.575  1.00  0.00
ATOM   1948  NE  ARG   317     -10.867  79.361  -7.851  1.00  0.00
ATOM   1949  CZ  ARG   317     -10.167  80.422  -7.463  1.00  0.00
ATOM   1950  NH1 ARG   317      -8.878  80.511  -7.760  1.00  0.00
ATOM   1951  NH2 ARG   317     -10.759  81.391  -6.779  1.00  0.00
ATOM   1952  N   LYS   318     -13.089  74.420  -9.279  1.00  0.00
ATOM   1953  CA  LYS   318     -12.657  74.105 -10.601  1.00  0.00
ATOM   1954  C   LYS   318     -13.171  75.246 -11.389  1.00  0.00
ATOM   1955  O   LYS   318     -14.354  75.573 -11.317  1.00  0.00
ATOM   1956  CB  LYS   318     -13.250  72.769 -11.056  1.00  0.00
ATOM   1957  CG  LYS   318     -12.746  71.568 -10.271  1.00  0.00
ATOM   1958  CD  LYS   318     -13.365  70.277 -10.781  1.00  0.00
ATOM   1959  CE  LYS   318     -12.897  69.081  -9.967  1.00  0.00
ATOM   1960  NZ  LYS   318     -13.513  67.812 -10.443  1.00  0.00
ATOM   1961  N   GLY   319     -12.296  75.892 -12.171  1.00  0.00
ATOM   1962  CA  GLY   319     -12.775  77.115 -12.716  1.00  0.00
ATOM   1963  C   GLY   319     -12.876  77.977 -11.501  1.00  0.00
ATOM   1964  O   GLY   319     -11.916  78.088 -10.739  1.00  0.00
ATOM   1965  N   ALA   320     -14.043  78.598 -11.268  1.00  0.00
ATOM   1966  CA  ALA   320     -14.157  79.416 -10.099  1.00  0.00
ATOM   1967  C   ALA   320     -15.184  78.799  -9.205  1.00  0.00
ATOM   1968  O   ALA   320     -16.231  78.353  -9.670  1.00  0.00
ATOM   1969  CB  ALA   320     -14.583  80.826 -10.479  1.00  0.00
ATOM   1970  N   ALA   321     -14.892  78.728  -7.888  1.00  0.00
ATOM   1971  CA  ALA   321     -15.874  78.196  -6.992  1.00  0.00
ATOM   1972  C   ALA   321     -15.828  78.979  -5.717  1.00  0.00
ATOM   1973  O   ALA   321     -14.785  79.082  -5.070  1.00  0.00
ATOM   1974  CB  ALA   321     -15.586  76.732  -6.700  1.00  0.00
ATOM   1975  N   LEU   322     -16.974  79.579  -5.342  1.00  0.00
ATOM   1976  CA  LEU   322     -17.098  80.280  -4.099  1.00  0.00
ATOM   1977  C   LEU   322     -17.104  79.267  -2.996  1.00  0.00
ATOM   1978  O   LEU   322     -16.578  79.507  -1.910  1.00  0.00
ATOM   1979  CB  LEU   322     -18.398  81.087  -4.066  1.00  0.00
ATOM   1980  CG  LEU   322     -18.475  82.288  -5.010  1.00  0.00
ATOM   1981  CD1 LEU   322     -19.873  82.887  -5.005  1.00  0.00
ATOM   1982  CD2 LEU   322     -17.493  83.370  -4.584  1.00  0.00
ATOM   1983  N   ASN   323     -17.711  78.092  -3.250  1.00  0.00
ATOM   1984  CA  ASN   323     -17.754  77.063  -2.253  1.00  0.00
ATOM   1985  C   ASN   323     -16.361  76.637  -1.966  1.00  0.00
ATOM   1986  O   ASN   323     -15.511  76.632  -2.853  1.00  0.00
ATOM   1987  CB  ASN   323     -18.563  75.865  -2.755  1.00  0.00
ATOM   1988  CG  ASN   323     -17.850  75.097  -3.851  1.00  0.00
ATOM   1989  OD1 ASN   323     -16.870  74.398  -3.594  1.00  0.00
ATOM   1990  ND2 ASN   323     -18.343  75.225  -5.077  1.00  0.00
ATOM   1991  N   ALA   324     -16.092  76.268  -0.701  1.00  0.00
ATOM   1992  CA  ALA   324     -14.797  75.773  -0.350  1.00  0.00
ATOM   1993  C   ALA   324     -15.032  74.412   0.203  1.00  0.00
ATOM   1994  O   ALA   324     -16.094  74.158   0.769  1.00  0.00
ATOM   1995  CB  ALA   324     -14.146  76.679   0.684  1.00  0.00
ATOM   1996  N   VAL   325     -14.054  73.502   0.008  1.00  0.00
ATOM   1997  CA  VAL   325     -14.112  72.139   0.459  1.00  0.00
ATOM   1998  C   VAL   325     -14.763  71.354  -0.624  1.00  0.00
ATOM   1999  O   VAL   325     -15.563  71.895  -1.386  1.00  0.00
ATOM   2000  CB  VAL   325     -14.927  72.011   1.760  1.00  0.00
ATOM   2001  CG1 VAL   325     -15.065  70.549   2.159  1.00  0.00
ATOM   2002  CG2 VAL   325     -14.240  72.755   2.895  1.00  0.00
ATOM   2003  N   LEU   326     -14.410  70.061  -0.756  1.00  0.00
ATOM   2004  CA  LEU   326     -15.077  69.280  -1.753  1.00  0.00
ATOM   2005  C   LEU   326     -16.492  69.220  -1.297  1.00  0.00
ATOM   2006  O   LEU   326     -17.426  69.463  -2.056  1.00  0.00
ATOM   2007  CB  LEU   326     -14.459  67.883  -1.843  1.00  0.00
ATOM   2008  CG  LEU   326     -15.084  66.930  -2.863  1.00  0.00
ATOM   2009  CD1 LEU   326     -14.959  67.491  -4.271  1.00  0.00
ATOM   2010  CD2 LEU   326     -14.390  65.576  -2.828  1.00  0.00
ATOM   2011  N   LEU   327     -16.673  68.922   0.001  1.00  0.00
ATOM   2012  CA  LEU   327     -17.992  68.864   0.533  1.00  0.00
ATOM   2013  C   LEU   327     -18.433  70.284   0.631  1.00  0.00
ATOM   2014  O   LEU   327     -17.606  71.193   0.673  1.00  0.00
ATOM   2015  CB  LEU   327     -17.986  68.192   1.908  1.00  0.00
ATOM   2016  CG  LEU   327     -17.549  66.726   1.943  1.00  0.00
ATOM   2017  CD1 LEU   327     -17.468  66.223   3.376  1.00  0.00
ATOM   2018  CD2 LEU   327     -18.539  65.852   1.189  1.00  0.00
ATOM   2019  N   GLY   328     -19.756  70.515   0.623  1.00  0.00
ATOM   2020  CA  GLY   328     -20.257  71.856   0.715  1.00  0.00
ATOM   2021  C   GLY   328     -20.575  72.319  -0.668  1.00  0.00
ATOM   2022  O   GLY   328     -21.316  73.281  -0.864  1.00  0.00
ATOM   2023  N   GLU   329     -20.022  71.629  -1.679  1.00  0.00
ATOM   2024  CA  GLU   329     -20.325  72.008  -3.025  1.00  0.00
ATOM   2025  C   GLU   329     -21.792  71.800  -3.198  1.00  0.00
ATOM   2026  O   GLU   329     -22.489  72.625  -3.788  1.00  0.00
ATOM   2027  CB  GLU   329     -19.539  71.145  -4.015  1.00  0.00
ATOM   2028  CG  GLU   329     -19.753  71.521  -5.472  1.00  0.00
ATOM   2029  CD  GLU   329     -18.915  70.684  -6.418  1.00  0.00
ATOM   2030  OE1 GLU   329     -18.153  69.822  -5.933  1.00  0.00
ATOM   2031  OE2 GLU   329     -19.021  70.890  -7.645  1.00  0.00
ATOM   2032  N   LEU   330     -22.294  70.675  -2.660  1.00  0.00
ATOM   2033  CA  LEU   330     -23.674  70.322  -2.793  1.00  0.00
ATOM   2034  C   LEU   330     -24.501  71.340  -2.085  1.00  0.00
ATOM   2035  O   LEU   330     -25.535  71.772  -2.595  1.00  0.00
ATOM   2036  CB  LEU   330     -23.937  68.945  -2.181  1.00  0.00
ATOM   2037  CG  LEU   330     -23.337  67.749  -2.923  1.00  0.00
ATOM   2038  CD1 LEU   330     -23.516  66.471  -2.118  1.00  0.00
ATOM   2039  CD2 LEU   330     -24.012  67.558  -4.273  1.00  0.00
ATOM   2040  N   LEU   331     -24.058  71.765  -0.886  1.00  0.00
ATOM   2041  CA  LEU   331     -24.865  72.677  -0.139  1.00  0.00
ATOM   2042  C   LEU   331     -25.020  73.911  -0.953  1.00  0.00
ATOM   2043  O   LEU   331     -26.134  74.383  -1.177  1.00  0.00
ATOM   2044  CB  LEU   331     -24.197  73.013   1.196  1.00  0.00
ATOM   2045  CG  LEU   331     -24.945  73.998   2.098  1.00  0.00
ATOM   2046  CD1 LEU   331     -26.301  73.437   2.498  1.00  0.00
ATOM   2047  CD2 LEU   331     -24.153  74.274   3.366  1.00  0.00
ATOM   2048  N   ILE   332     -23.905  74.459  -1.460  1.00  0.00
ATOM   2049  CA  ILE   332     -24.104  75.634  -2.241  1.00  0.00
ATOM   2050  C   ILE   332     -24.073  75.178  -3.657  1.00  0.00
ATOM   2051  O   ILE   332     -23.200  75.557  -4.435  1.00  0.00
ATOM   2052  CB  ILE   332     -22.999  76.676  -1.985  1.00  0.00
ATOM   2053  CG1 ILE   332     -22.993  77.098  -0.515  1.00  0.00
ATOM   2054  CG2 ILE   332     -23.225  77.913  -2.841  1.00  0.00
ATOM   2055  CD1 ILE   332     -21.744  77.843  -0.097  1.00  0.00
ATOM   2056  N   LYS   333     -25.076  74.356  -4.015  1.00  0.00
ATOM   2057  CA  LYS   333     -25.214  73.807  -5.325  1.00  0.00
ATOM   2058  C   LYS   333     -25.502  74.947  -6.231  1.00  0.00
ATOM   2059  O   LYS   333     -25.068  74.987  -7.381  1.00  0.00
ATOM   2060  CB  LYS   333     -26.358  72.791  -5.363  1.00  0.00
ATOM   2061  CG  LYS   333     -26.529  72.098  -6.704  1.00  0.00
ATOM   2062  CD  LYS   333     -27.613  71.034  -6.642  1.00  0.00
ATOM   2063  CE  LYS   333     -27.781  70.337  -7.983  1.00  0.00
ATOM   2064  NZ  LYS   333     -28.829  69.281  -7.932  1.00  0.00
ATOM   2065  N   HIS   334     -26.238  75.929  -5.693  1.00  0.00
ATOM   2066  CA  HIS   334     -26.626  77.060  -6.469  1.00  0.00
ATOM   2067  C   HIS   334     -25.409  77.903  -6.628  1.00  0.00
ATOM   2068  O   HIS   334     -24.407  77.720  -5.940  1.00  0.00
ATOM   2069  CB  HIS   334     -27.730  77.844  -5.758  1.00  0.00
ATOM   2070  CG  HIS   334     -29.018  77.091  -5.626  1.00  0.00
ATOM   2071  ND1 HIS   334     -29.851  76.849  -6.696  1.00  0.00
ATOM   2072  CD2 HIS   334     -29.740  76.453  -4.535  1.00  0.00
ATOM   2073  CE1 HIS   334     -30.921  76.156  -6.269  1.00  0.00
ATOM   2074  NE2 HIS   334     -30.862  75.915  -4.975  1.00  0.00
ATOM   2075  N   TYR   335     -25.464  78.839  -7.587  1.00  0.00
ATOM   2076  CA  TYR   335     -24.346  79.698  -7.813  1.00  0.00
ATOM   2077  C   TYR   335     -24.332  80.693  -6.660  1.00  0.00
ATOM   2078  O   TYR   335     -23.805  80.336  -5.573  1.00  0.00
ATOM   2079  CB  TYR   335     -24.491  80.427  -9.150  1.00  0.00
ATOM   2080  CG  TYR   335     -24.374  79.522 -10.356  1.00  0.00
ATOM   2081  CD1 TYR   335     -25.506  78.972 -10.946  1.00  0.00
ATOM   2082  CD2 TYR   335     -23.132  79.220 -10.902  1.00  0.00
ATOM   2083  CE1 TYR   335     -25.408  78.145 -12.048  1.00  0.00
ATOM   2084  CE2 TYR   335     -23.017  78.394 -12.003  1.00  0.00
ATOM   2085  CZ  TYR   335     -24.168  77.856 -12.576  1.00  0.00
ATOM   2086  OH  TYR   335     -24.070  77.033 -13.673  1.00  0.00
TER
END
