
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0356TS383_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS383_2-D1.T0356_D1.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    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    D     314      G      20          1.188
LGA    G     323      E      21          3.299
LGA    -       -      L      22           -
LGA    R     324      K      23          1.450
LGA    P     325      R      24          1.114
LGA    P     326      I      25          2.161
LGA    D     327      T      26          1.720
LGA    E     328      L      27          3.385
LGA    P     329      P      28          1.735
LGA    A     330      V      29          2.099
LGA    V     331      D      30          3.241
LGA    L     332      P      31          2.768
LGA    G     333      H      32          3.467
LGA    V     334      L      33          3.823
LGA    A     335      E      34          4.418
LGA    L     336      I      35          3.629
LGA    N     337      T      36          1.362
LGA    -       -      E      37           -
LGA    E     338      I      38          2.891
LGA    V     339      A      39          2.984
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18  124    5.0     18    2.78     5.56      9.538     0.626

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.379679 * X  +  -0.887046 * Y  +   0.262665 * Z  +  56.289291
  Y_new =  -0.856135 * X  +   0.444490 * Y  +   0.263556 * Z  +  78.132706
  Z_new =  -0.350539 * X  +  -0.124810 * Y  +  -0.928195 * Z  + 181.076111 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.007929    0.133663  [ DEG:  -172.3417      7.6583 ]
  Theta =   0.358146    2.783447  [ DEG:    20.5203    159.4797 ]
  Phi   =  -1.988215    1.153377  [ DEG:  -113.9164     66.0836 ]
 
# 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: T0356TS383_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_2-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  124   5.0   18   2.78    5.56   9.538
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_2-D1
PFRMAT TS
TARGET t0356
MODEL 2
PARENT 1i0rA
ATOM    537  N   ASP   314      61.134  84.333  87.909  1.00  0.00
ATOM    538  CA  ASP   314      59.794  84.482  88.434  1.00  0.00
ATOM    539  C   ASP   314      59.295  83.178  89.092  1.00  0.00
ATOM    540  O   ASP   314      58.150  83.092  89.562  1.00  0.00
ATOM    541  N   GLY   323      60.165  82.176  89.152  1.00  0.00
ATOM    542  CA  GLY   323      59.830  80.863  89.691  1.00  0.00
ATOM    543  C   GLY   323      59.549  80.800  91.181  1.00  0.00
ATOM    544  O   GLY   323      59.949  81.684  91.939  1.00  0.00
ATOM    545  N   ARG   324      58.859  79.736  91.585  1.00  0.00
ATOM    546  CA  ARG   324      58.563  79.494  92.989  1.00  0.00
ATOM    547  C   ARG   324      59.869  79.022  93.619  1.00  0.00
ATOM    548  O   ARG   324      60.757  78.472  92.931  1.00  0.00
ATOM    549  N   PRO   325      60.004  79.262  94.917  1.00  0.00
ATOM    550  CA  PRO   325      61.197  78.824  95.622  1.00  0.00
ATOM    551  C   PRO   325      60.994  77.415  96.150  1.00  0.00
ATOM    552  O   PRO   325      59.865  76.936  96.279  1.00  0.00
ATOM    553  N   PRO   326      62.097  76.746  96.435  1.00  0.00
ATOM    554  CA  PRO   326      62.065  75.394  96.977  1.00  0.00
ATOM    555  C   PRO   326      62.143  75.499  98.479  1.00  0.00
ATOM    556  O   PRO   326      63.067  76.119  99.001  1.00  0.00
ATOM    557  N   ASP   327      61.197  74.913  99.197  1.00  0.00
ATOM    558  CA  ASP   327      61.300  74.956 100.653  1.00  0.00
ATOM    559  C   ASP   327      61.952  73.671 101.147  1.00  0.00
ATOM    560  O   ASP   327      62.052  72.676 100.417  1.00  0.00
ATOM    561  N   GLU   328      62.425  73.680 102.384  1.00  0.00
ATOM    562  CA  GLU   328      63.054  72.494 102.949  1.00  0.00
ATOM    563  C   GLU   328      62.000  71.376 103.045  1.00  0.00
ATOM    564  O   GLU   328      62.289  70.206 102.795  1.00  0.00
ATOM    565  N   PRO   329      60.775  71.745 103.410  1.00  0.00
ATOM    566  CA  PRO   329      59.684  70.773 103.496  1.00  0.00
ATOM    567  C   PRO   329      59.468  70.147 102.107  1.00  0.00
ATOM    568  O   PRO   329      59.228  68.933 102.012  1.00  0.00
ATOM    569  N   ALA   330      61.946  67.546 101.382  1.00  0.00
ATOM    570  CA  ALA   330      61.698  66.287 102.058  1.00  0.00
ATOM    571  C   ALA   330      60.663  65.439 101.337  1.00  0.00
ATOM    572  O   ALA   330      60.733  64.203 101.386  1.00  0.00
ATOM    573  N   VAL   331      59.734  66.091 100.642  1.00  0.00
ATOM    574  CA  VAL   331      58.743  65.357  99.878  1.00  0.00
ATOM    575  C   VAL   331      59.509  64.766  98.697  1.00  0.00
ATOM    576  O   VAL   331      59.246  63.637  98.277  1.00  0.00
ATOM    577  N   LEU   332      60.483  65.516  98.179  1.00  0.00
ATOM    578  CA  LEU   332      61.282  65.019  97.063  1.00  0.00
ATOM    579  C   LEU   332      62.074  63.790  97.493  1.00  0.00
ATOM    580  O   LEU   332      62.179  62.822  96.736  1.00  0.00
ATOM    581  N   GLY   333      62.641  63.825  98.696  1.00  0.00
ATOM    582  CA  GLY   333      63.401  62.680  99.195  1.00  0.00
ATOM    583  C   GLY   333      62.524  61.430  99.180  1.00  0.00
ATOM    584  O   GLY   333      62.989  60.340  98.855  1.00  0.00
ATOM    585  N   VAL   334      61.256  61.603  99.542  1.00  0.00
ATOM    586  CA  VAL   334      60.307  60.496  99.581  1.00  0.00
ATOM    587  C   VAL   334      59.814  60.088  98.193  1.00  0.00
ATOM    588  O   VAL   334      58.926  59.244  98.069  1.00  0.00
ATOM    589  N   ALA   335      60.378  60.693  97.152  1.00  0.00
ATOM    590  CA  ALA   335      59.993  60.327  95.799  1.00  0.00
ATOM    591  C   ALA   335      59.037  61.219  95.029  1.00  0.00
ATOM    592  O   ALA   335      58.883  61.048  93.818  1.00  0.00
ATOM    593  N   LEU   336      58.386  62.158  95.706  1.00  0.00
ATOM    594  CA  LEU   336      57.453  63.053  95.030  1.00  0.00
ATOM    595  C   LEU   336      58.224  63.966  94.071  1.00  0.00
ATOM    596  O   LEU   336      59.447  64.081  94.146  1.00  0.00
ATOM    597  N   ASN   337      57.505  64.607  93.161  1.00  0.00
ATOM    598  CA  ASN   337      58.134  65.517  92.214  1.00  0.00
ATOM    599  C   ASN   337      57.167  66.672  91.941  1.00  0.00
ATOM    600  O   ASN   337      55.974  66.459  91.729  1.00  0.00
ATOM    601  N   GLU   338      57.671  67.914  91.966  1.00  0.00
ATOM    602  CA  GLU   338      56.845  69.104  91.725  1.00  0.00
ATOM    603  C   GLU   338      56.218  69.095  90.335  1.00  0.00
ATOM    604  O   GLU   338      56.818  68.596  89.385  1.00  0.00
ATOM    605  N   VAL   339      55.011  69.636  90.217  1.00  0.00
ATOM    606  CA  VAL   339      54.358  69.702  88.919  1.00  0.00
ATOM    607  C   VAL   339      53.874  71.112  88.621  1.00  0.00
ATOM    608  O   VAL   339      53.159  71.717  89.421  1.00  0.00
TER
END
