
#######################################################
#                                                     #
#                        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   21 (  103),  selected   21 , name T0342TS239_3_2
# Molecule2: number of CA atoms  169 ( 1343),  selected  169 , name T0342.pdb
# PARAMETERS: T0342TS239_3_2.T0342.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      E      14           -
LGA    -       -      E      15           -
LGA    -       -      S      16           -
LGA    -       -      F      17           -
LGA    -       -      L      18           -
LGA    -       -      Y      19           -
LGA    -       -      F      20           -
LGA    -       -      A      21           -
LGA    -       -      Y      22           -
LGA    -       -      G      23           -
LGA    -       -      S      24           -
LGA    -       -      N      25           -
LGA    -       -      L      26           -
LGA    -       -      L      27           -
LGA    -       -      T      28           -
LGA    -       -      E      29           -
LGA    -       -      R      30           -
LGA    -       -      I      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      S      37           -
LGA    -       -      A      38           -
LGA    -       -      A      39           -
LGA    -       -      F      40           -
LGA    -       -      F      41           -
LGA    -       -      C      42           -
LGA    -       -      V      43           -
LGA    -       -      A      44           -
LGA    -       -      R      45           -
LGA    -       -      L      46           -
LGA    -       -      Q      47           -
LGA    -       -      D      48           -
LGA    -       -      F      49           -
LGA    -       -      K      50           -
LGA    -       -      L      51           -
LGA    -       -      D      52           -
LGA    -       -      F      53           -
LGA    -       -      G      54           -
LGA    -       -      N      55           -
LGA    -       -      S      56           -
LGA    -       -      Q      57           -
LGA    -       -      G      58           -
LGA    -       -      K      59           -
LGA    -       -      T      60           -
LGA    -       -      S      61           -
LGA    -       -      Q      62           -
LGA    -       -      T      63           -
LGA    -       -      W      64           -
LGA    -       -      H      65           -
LGA    -       -      G      66           -
LGA    -       -      G      67           -
LGA    -       -      I      68           -
LGA    -       -      A      69           -
LGA    -       -      T      70           -
LGA    -       -      I      71           -
LGA    -       -      F      72           -
LGA    -       -      Q      73           -
LGA    -       -      S      74           -
LGA    -       -      P      75           -
LGA    -       -      G      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    -       -      V      79           -
LGA    -       -      W      80           -
LGA    -       -      G      81           -
LGA    -       -      V      82           -
LGA    -       -      V      83           -
LGA    -       -      W      84           -
LGA    -       -      K      85           -
LGA    -       -      M      86           -
LGA    -       -      N      87           -
LGA    -       -      K      88           -
LGA    S       1      S      89          1.054
LGA    A       2      N      90          1.138
LGA    N       3      L      91          3.872
LGA    S       4      N      92          2.449
LGA    G       5      S      93          3.626
LGA    -       -      L      94           -
LGA    -       -      D      95           -
LGA    C       6      E      96          3.294
LGA    K       7      Q      97          2.212
LGA    D       8      E      98           #
LGA    I     176      G      99           -
LGA    -       -      V     100           -
LGA    -       -      K     101           -
LGA    -       -      S     102           -
LGA    -       -      G     103           -
LGA    -       -      M     104           -
LGA    -       -      Y     105           -
LGA    -       -      V     106           -
LGA    -       -      V     107           -
LGA    -       -      I     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      K     111           -
LGA    -       -      V     112           -
LGA    -       -      A     113           -
LGA    -       -      T     114           -
LGA    -       -      Q     115           -
LGA    -       -      E     116           -
LGA    -       -      G     117           -
LGA    -       -      K     118           -
LGA    -       -      E     119           -
LGA    -       -      I     120           -
LGA    -       -      T     121           -
LGA    -       -      C     122           -
LGA    -       -      R     123           -
LGA    -       -      S     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      M     127           -
LGA    -       -      T     128           -
LGA    -       -      N     129           -
LGA    -       -      Y     130           -
LGA    -       -      E     131           -
LGA    -       -      S     132           -
LGA    E     177      A     133           #
LGA    D     178      -       -           -
LGA    I     179      -       -           -
LGA    I     180      P     134           #
LGA    -       -      P     135           -
LGA    -       -      S     136           -
LGA    -       -      P     137           -
LGA    -       -      Q     138           -
LGA    -       -      Y     139           -
LGA    -       -      K     140           -
LGA    -       -      K     141           -
LGA    -       -      I     142           -
LGA    -       -      I     143           -
LGA    -       -      C     144           -
LGA    -       -      M     145           -
LGA    -       -      G     146           -
LGA    -       -      A     147           -
LGA    -       -      K     148           -
LGA    -       -      E     149           -
LGA    -       -      N     150           -
LGA    -       -      G     151           -
LGA    -       -      L     152           -
LGA    -       -      P     153           -
LGA    -       -      L     154           -
LGA    -       -      E     155           -
LGA    -       -      Y     156           -
LGA    -       -      Q     157           -
LGA    -       -      E     158           -
LGA    -       -      K     159           -
LGA    -       -      L     160           -
LGA    -       -      K     161           -
LGA    -       -      A     162           -
LGA    -       -      I     163           -
LGA    K     181      E     164          4.755
LGA    K     182      P     165          1.090
LGA    G     183      N     166          3.784
LGA    E     184      D     167          1.823
LGA    T     185      Y     168          2.643
LGA    Q     186      T     169          2.927
LGA    T     187      G     170          4.162
LGA    L     188      K     171          3.256
LGA    -       -      V     172           -
LGA    -       -      S     173           -
LGA    -       -      E     174           -
LGA    -       -      E     175           -
LGA    -       -      I     176           -
LGA    -       -      E     177           -
LGA    -       -      D     178           -
LGA    -       -      I     179           -
LGA    -       -      I     180           -
LGA    -       -      K     181           -
LGA    -       -      K     182           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  169    5.0     15    3.02     6.67      5.715     0.480

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.149426 * X  +   0.186352 * Y  +  -0.971053 * Z  +  -1.830745
  Y_new =  -0.738838 * X  +   0.673703 * Y  +   0.015596 * Z  +  90.365234
  Z_new =   0.657108 * X  +   0.715121 * Y  +   0.238353 * Z  + -13.072777 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.249072   -1.892521  [ DEG:    71.5666   -108.4334 ]
  Theta =  -0.716975   -2.424618  [ DEG:   -41.0796   -138.9203 ]
  Phi   =  -1.371244    1.770349  [ DEG:   -78.5665    101.4335 ]
 
# 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: T0342TS239_3_2                                
REMARK     2: T0342.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0342TS239_3_2.T0342.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21  169   5.0   15   3.02    6.67   5.715
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0342
PARENT 1kdg_A
ATOM      1  N   SER     1      -5.449  81.096 -10.510  1.00  9.99
ATOM      2  CA  SER     1      -6.607  80.557  -9.731  1.00  9.99
ATOM      3  C   SER     1      -6.648  81.132  -8.302  1.00  9.99
ATOM      4  O   SER     1      -7.544  80.790  -7.508  1.00  9.99
ATOM      5  CB  SER     1      -6.612  79.046  -9.665  1.00  9.99
ATOM      6  N   ALA     2      -5.655  81.928  -7.934  1.00  9.99
ATOM      7  CA  ALA     2      -5.641  82.479  -6.575  1.00  9.99
ATOM      8  C   ALA     2      -6.843  83.363  -6.355  1.00  9.99
ATOM      9  O   ALA     2      -7.206  84.105  -7.283  1.00  9.99
ATOM     10  CB  ALA     2      -4.375  83.240  -6.268  1.00  9.99
ATOM     11  N   ASN     3      -7.443  83.356  -5.159  1.00  9.99
ATOM     12  CA  ASN     3      -8.602  84.210  -4.835  1.00  9.99
ATOM     13  C   ASN     3      -8.141  85.304  -3.872  1.00  9.99
ATOM     14  O   ASN     3      -7.692  85.034  -2.774  1.00  9.99
ATOM     15  CB  ASN     3      -9.690  83.390  -4.182  1.00  9.99
ATOM     16  N   SER     4      -8.234  86.538  -4.310  1.00  9.99
ATOM     17  CA  SER     4      -7.820  87.682  -3.553  1.00  9.99
ATOM     18  C   SER     4      -8.907  88.128  -2.614  1.00  9.99
ATOM     19  O   SER     4      -9.899  88.701  -3.039  1.00  9.99
ATOM     20  CB  SER     4      -7.462  88.850  -4.510  1.00  9.99
ATOM     21  N   GLY     5      -8.704  87.808  -1.346  1.00  9.99
ATOM     22  CA  GLY     5      -9.619  88.157  -0.279  1.00  9.99
ATOM     23  C   GLY     5      -8.824  88.683   0.903  1.00  9.99
ATOM     24  O   GLY     5      -7.656  88.312   1.097  1.00  9.99
ATOM     25  N   CYS     6      -9.446  89.505   1.711  1.00  9.99
ATOM     26  CA  CYS     6      -8.746  90.118   2.872  1.00  9.99
ATOM     27  C   CYS     6      -8.503  89.238   4.089  1.00  9.99
ATOM     28  O   CYS     6      -8.825  89.592   5.236  1.00  9.99
ATOM     29  CB  CYS     6      -9.656  91.304   3.198  1.00  9.99
ATOM     30  N   LYS     7      -8.007  88.048   3.814  1.00  9.99
ATOM     31  CA  LYS     7      -7.693  87.076   4.870  1.00  9.99
ATOM     32  C   LYS     7      -6.571  87.574   5.783  1.00  9.99
ATOM     33  O   LYS     7      -5.487  87.873   5.308  1.00  9.99
ATOM     34  CB  LYS     7      -7.285  85.722   4.231  1.00  9.99
ATOM     35  N   ASP     8      -6.833  87.682   7.068  1.00  9.99
ATOM     36  CA  ASP     8      -5.873  88.168   8.024  1.00  9.99
ATOM     37  C   ASP     8      -6.036  89.700   8.219  1.00  9.99
ATOM     38  O   ASP     8      -5.546  90.240   9.211  1.00  9.99
ATOM     39  CB  ASP     8      -4.461  87.793   7.542  1.00  9.99
ATOM    851  N   ILE   176       0.600 103.712  30.003  1.00  9.99
ATOM    852  CA  ILE   176       0.118 103.260  28.708  1.00  9.99
ATOM    853  C   ILE   176       1.175 103.468  27.627  1.00  9.99
ATOM    854  O   ILE   176       1.373 102.620  26.759  1.00  9.99
ATOM    855  CB  ILE   176      -1.248 103.896  28.335  1.00  9.99
ATOM    856  N   GLU   177       1.896 104.600  27.705  1.00  9.99
ATOM    857  CA  GLU   177       2.891 104.891  26.658  1.00  9.99
ATOM    858  C   GLU   177       4.123 103.977  26.721  1.00  9.99
ATOM    859  O   GLU   177       4.793 103.709  25.722  1.00  9.99
ATOM    860  CB  GLU   177       3.298 106.372  26.671  1.00  9.99
ATOM    861  N   ASP   178       4.432 103.525  27.922  1.00  9.99
ATOM    862  CA  ASP   178       5.568 102.647  28.142  1.00  9.99
ATOM    863  C   ASP   178       5.179 101.159  28.002  1.00  9.99
ATOM    864  O   ASP   178       6.040 100.284  28.021  1.00  9.99
ATOM    865  CB  ASP   178       6.111 102.914  29.482  1.00  9.99
ATOM    866  N   ILE   179       3.870 100.903  27.851  1.00  9.99
ATOM    867  CA  ILE   179       3.364  99.523  27.827  1.00  9.99
ATOM    868  C   ILE   179       3.802  98.792  26.541  1.00  9.99
ATOM    869  O   ILE   179       3.788  99.316  25.439  1.00  9.99
ATOM    870  CB  ILE   179       1.851  99.549  27.954  1.00  9.99
ATOM    871  N   ILE   180       4.210  97.555  26.684  1.00  9.99
ATOM    872  CA  ILE   180       4.622  96.774  25.528  1.00  9.99
ATOM    873  C   ILE   180       3.361  96.423  24.770  1.00  9.99
ATOM    874  O   ILE   180       2.504  95.752  25.324  1.00  9.99
ATOM    875  CB  ILE   180       5.352  95.524  26.005  1.00  9.99
ATOM    876  N   LYS   181       3.209  96.880  23.545  1.00  9.99
ATOM    877  CA  LYS   181       1.961  96.612  22.812  1.00  9.99
ATOM    878  C   LYS   181       1.566  95.161  22.787  1.00  9.99
ATOM    879  O   LYS   181       0.390  94.844  22.963  1.00  9.99
ATOM    880  CB  LYS   181       2.267  97.122  21.422  1.00  9.99
ATOM    881  N   LYS   182       2.532  94.292  22.619  1.00  9.99
ATOM    882  CA  LYS   182       2.275  92.879  22.509  1.00  9.99
ATOM    883  C   LYS   182       1.617  92.332  23.762  1.00  9.99
ATOM    884  O   LYS   182       0.826  91.354  23.727  1.00  9.99
ATOM    885  CB  LYS   182       3.547  92.120  22.165  1.00  9.99
ATOM    886  N   GLY   183       1.867  92.969  24.898  1.00  9.99
ATOM    887  CA  GLY   183       1.284  92.500  26.143  1.00  9.99
ATOM    888  C   GLY   183      -0.161  92.960  26.322  1.00  9.99
ATOM    889  O   GLY   183      -0.817  92.539  27.281  1.00  9.99
ATOM    890  N   GLU   184      -0.652  93.783  25.384  1.00  9.99
ATOM    891  CA  GLU   184      -2.059  94.224  25.390  1.00  9.99
ATOM    892  C   GLU   184      -2.983  93.126  24.837  1.00  9.99
ATOM    893  O   GLU   184      -4.196  93.261  24.869  1.00  9.99
ATOM    894  CB  GLU   184      -2.248  95.496  24.598  1.00  9.99
ATOM    895  N   THR   185      -2.394  92.116  24.214  1.00  9.99
ATOM    896  CA  THR   185      -3.134  91.009  23.619  1.00  9.99
ATOM    897  C   THR   185      -4.057  90.397  24.656  1.00  9.99
ATOM    898  O   THR   185      -3.636  89.976  25.738  1.00  9.99
ATOM    899  CB  THR   185      -2.107  89.968  23.141  1.00  9.99
ATOM    900  N   GLN   186      -5.317  90.332  24.302  1.00  9.99
ATOM    901  CA  GLN   186      -6.358  89.777  25.134  1.00  9.99
ATOM    902  C   GLN   186      -6.744  88.358  24.719  1.00  9.99
ATOM    903  O   GLN   186      -7.604  87.734  25.345  1.00  9.99
ATOM    904  CB  GLN   186      -7.571  90.655  25.001  1.00  9.99
ATOM    905  N   THR   187      -6.113  87.851  23.678  1.00  9.99
ATOM    906  CA  THR   187      -6.387  86.506  23.144  1.00  9.99
ATOM    907  C   THR   187      -7.814  86.367  22.648  1.00  9.99
ATOM    908  O   THR   187      -8.372  85.259  22.674  1.00  9.99
ATOM    909  CB  THR   187      -6.112  85.429  24.170  1.00  9.99
ATOM    910  N   LEU   188      -8.368  87.472  22.154  1.00  9.99
ATOM    911  CA  LEU   188      -9.755  87.489  21.667  1.00  9.99
ATOM    912  C   LEU   188      -9.885  87.761  20.174  1.00  9.99
ATOM    913  O   LEU   188     -10.851  88.389  19.732  1.00  9.99
ATOM    914  CB  LEU   188     -10.515  88.585  22.423  1.00  9.99
TER
END
