
#######################################################
#                                                     #
#                        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   16 (  125),  selected   16 , name T0383TS009_2_2
# Molecule2: number of CA atoms  125 ( 1020),  selected  125 , name T0383.pdb
# PARAMETERS: T0383TS009_2_2.T0383.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    -       -      A       3           -
LGA    -       -      M       4           -
LGA    -       -      N       5           -
LGA    -       -      L       6           -
LGA    -       -      K       7           -
LGA    -       -      R       8           -
LGA    -       -      E       9           -
LGA    -       -      Q      10           -
LGA    -       -      E      11           -
LGA    -       -      F      12           -
LGA    -       -      V      13           -
LGA    -       -      S      14           -
LGA    -       -      Q      15           -
LGA    -       -      Y      16           -
LGA    -       -      H      17           -
LGA    -       -      F      18           -
LGA    -       -      D      19           -
LGA    -       -      A      20           -
LGA    -       -      R      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      E      24           -
LGA    -       -      W      25           -
LGA    -       -      E      26           -
LGA    -       -      N      27           -
LGA    -       -      E      28           -
LGA    -       -      N      29           -
LGA    -       -      G      30           -
LGA    -       -      A      31           -
LGA    -       -      P      32           -
LGA    -       -      E      33           -
LGA    -       -      T      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      D      37           -
LGA    -       -      V      38           -
LGA    -       -      N      39           -
LGA    -       -      F      40           -
LGA    -       -      Q      41           -
LGA    -       -      L      42           -
LGA    -       -      L      43           -
LGA    -       -      Q      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      Q      47           -
LGA    -       -      E      48           -
LGA    -       -      N      49           -
LGA    -       -      Q      50           -
LGA    -       -      V      51           -
LGA    -       -      T      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      I      55           -
LGA    -       -      V      56           -
LGA    -       -      I      57           -
LGA    -       -      L      58           -
LGA    -       -      S      59           -
LGA    -       -      F      60           -
LGA    -       -      M      61           -
LGA    -       -      I      62           -
LGA    -       -      V      63           -
LGA    -       -      F      64           -
LGA    -       -      D      65           -
LGA    -       -      K      66           -
LGA    -       -      F      67           -
LGA    -       -      V      68           -
LGA    -       -      I      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      T      72           -
LGA    E     112      I      73          1.973
LGA    V     113      S      74          2.139
LGA    -       -      Q      75           -
LGA    -       -      V      76           -
LGA    -       -      N      77           -
LGA    -       -      H      78           -
LGA    -       -      I      79           -
LGA    -       -      D      80           -
LGA    -       -      G      81           -
LGA    -       -      R      82           -
LGA    -       -      I      83           -
LGA    -       -      V      84           -
LGA    -       -      N      85           -
LGA    -       -      E      86           -
LGA    -       -      P      87           -
LGA    -       -      S      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    -       -      Q      92           -
LGA    -       -      E      93           -
LGA    -       -      E      94           -
LGA    -       -      V      95           -
LGA    -       -      E      96           -
LGA    -       -      T      97           -
LGA    -       -      L      98           -
LGA    -       -      A      99           -
LGA    T     114      R     100           #
LGA    E     115      P     101          3.417
LGA    I     116      C     102          3.452
LGA    A     117      L     103          2.038
LGA    -       -      N     104           -
LGA    L     118      M     105          1.171
LGA    -       -      L     106           -
LGA    -       -      N     107           -
LGA    D     119      R     108          0.563
LGA    L     120      L     109          0.321
LGA    P     121      T     110          0.602
LGA    G     122      Y     111          1.245
LGA    -       -      E     112           -
LGA    -       -      V     113           -
LGA    -       -      T     114           -
LGA    -       -      E     115           -
LGA    -       -      I     116           -
LGA    -       -      A     117           -
LGA    -       -      L     118           -
LGA    -       -      D     119           -
LGA    -       -      L     120           -
LGA    -       -      P     121           -
LGA    -       -      G     122           -
LGA    I     123      I     123          1.981
LGA    N     124      N     124          1.958
LGA    L     125      L     125          2.640
LGA    E     126      E     126           -
LGA    F     127      F     127           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16  125    5.0     13    2.05    30.77      8.386     0.605

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.375587 * X  +   0.278847 * Y  +  -0.883843 * Z  +   7.468011
  Y_new =   0.093916 * X  +   0.937303 * Y  +   0.335623 * Z  +  41.192863
  Z_new =   0.922017 * X  +  -0.209063 * Y  +   0.325850 * Z  +   1.758018 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.570441    2.571152  [ DEG:   -32.6839    147.3161 ]
  Theta =  -1.173257   -1.968336  [ DEG:   -67.2227   -112.7773 ]
  Phi   =   0.245027   -2.896565  [ DEG:    14.0390   -165.9610 ]
 
# 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: T0383TS009_2_2                                
REMARK     2: T0383.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0383TS009_2_2.T0383.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  125   5.0   13   2.05   30.77   8.386
REMARK  ---------------------------------------------------------- 
MOLECULE T0383TS009_2_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0383                                                                    
PARENT N/A                                                                      
ATOM    910  N   GLU   112      10.021  26.267  12.009  1.00  0.00              
ATOM    911  CA  GLU   112       8.959  27.023  11.354  1.00  0.00              
ATOM    912  C   GLU   112       9.352  28.486  11.175  1.00  0.00              
ATOM    913  O   GLU   112       9.214  29.047  10.089  1.00  0.00              
ATOM    914  CB  GLU   112       8.619  26.400   9.998  1.00  0.00              
ATOM    915  CG  GLU   112       7.129  26.240   9.746  1.00  0.00              
ATOM    916  CD  GLU   112       6.823  25.140   8.747  1.00  0.00              
ATOM    917  OE1 GLU   112       6.150  24.160   9.132  1.00  0.00              
ATOM    918  OE2 GLU   112       7.255  25.258   7.582  1.00  0.00              
ATOM    919  N   VAL   113       9.842  29.096  12.250  1.00  0.00              
ATOM    920  CA  VAL   113      10.264  30.526  12.213  1.00  0.00              
ATOM    921  C   VAL   113      11.500  30.714  11.341  1.00  0.00              
ATOM    922  O   VAL   113      12.527  31.213  11.801  1.00  0.00              
ATOM    923  CB  VAL   113       9.136  31.434  11.691  1.00  0.00              
ATOM    924  CG1 VAL   113       8.441  32.140  12.845  1.00  0.00              
ATOM    925  CG2 VAL   113       8.138  30.629  10.872  1.00  0.00              
ATOM    926  N   THR   114      11.395  30.309  10.079  1.00  0.00              
ATOM    927  CA  THR   114      12.529  30.435   9.119  1.00  0.00              
ATOM    928  C   THR   114      13.856  30.600   9.852  1.00  0.00              
ATOM    929  O   THR   114      14.891  30.848   9.233  1.00  0.00              
ATOM    930  CB  THR   114      12.617  29.212   8.187  1.00  0.00              
ATOM    931  OG1 THR   114      12.136  28.049   8.872  1.00  0.00              
ATOM    932  CG2 THR   114      11.784  29.437   6.934  1.00  0.00              
ATOM    933  N   GLU   115      13.818  30.460  11.172  1.00  0.00              
ATOM    934  CA  GLU   115      15.017  30.594  11.991  1.00  0.00              
ATOM    935  C   GLU   115      16.241  30.898  11.133  1.00  0.00              
ATOM    936  O   GLU   115      16.735  30.032  10.411  1.00  0.00              
ATOM    937  CB  GLU   115      14.829  31.688  13.044  1.00  0.00              
ATOM    938  CG  GLU   115      14.691  31.165  14.465  1.00  0.00              
ATOM    939  CD  GLU   115      14.351  32.259  15.458  1.00  0.00              
ATOM    940  OE1 GLU   115      13.190  32.718  15.460  1.00  0.00              
ATOM    941  OE2 GLU   115      15.246  32.655  16.233  1.00  0.00              
ATOM    942  N   ILE   116      16.723  32.134  11.217  1.00  0.00              
ATOM    943  CA  ILE   116      17.914  32.564  10.430  1.00  0.00              
ATOM    944  C   ILE   116      17.729  32.276   8.944  1.00  0.00              
ATOM    945  O   ILE   116      18.690  31.983   8.234  1.00  0.00              
ATOM    946  CB  ILE   116      18.205  34.064  10.621  1.00  0.00              
ATOM    947  CG2 ILE   116      19.241  34.272  11.715  1.00  0.00              
ATOM    948  CG1 ILE   116      16.915  34.819  10.948  1.00  0.00              
ATOM    949  CD1 ILE   116      17.059  35.810  12.083  1.00  0.00              
ATOM    950  N   ALA   117      16.486  32.363   8.482  1.00  0.00              
ATOM    951  CA  ALA   117      16.172  32.113   7.080  1.00  0.00              
ATOM    952  C   ALA   117      17.003  30.960   6.526  1.00  0.00              
ATOM    953  O   ALA   117      17.294  30.911   5.331  1.00  0.00              
ATOM    954  CB  ALA   117      14.689  31.817   6.913  1.00  0.00              
ATOM    955  N   LEU   118      17.380  30.035   7.401  1.00  0.00              
ATOM    956  CA  LEU   118      18.178  28.882   7.002  1.00  0.00              
ATOM    957  C   LEU   118      18.743  29.063   5.597  1.00  0.00              
ATOM    958  O   LEU   118      18.932  30.187   5.133  1.00  0.00              
ATOM    959  CB  LEU   118      19.314  28.645   7.999  1.00  0.00              
ATOM    960  CG  LEU   118      19.095  27.530   9.024  1.00  0.00              
ATOM    961  CD1 LEU   118      20.399  27.176   9.721  1.00  0.00              
ATOM    962  CD2 LEU   118      18.485  26.304   8.363  1.00  0.00              
ATOM    963  N   ASP   119      19.009  27.948   4.924  1.00  0.00              
ATOM    964  CA  ASP   119      19.552  27.981   3.571  1.00  0.00              
ATOM    965  C   ASP   119      18.697  27.159   2.613  1.00  0.00              
ATOM    966  O   ASP   119      18.766  27.334   1.397  1.00  0.00              
ATOM    967  CB  ASP   119      19.663  29.423   3.073  1.00  0.00              
ATOM    968  CG  ASP   119      21.027  29.735   2.489  1.00  0.00              
ATOM    969  OD1 ASP   119      21.128  30.696   1.698  1.00  0.00              
ATOM    970  OD2 ASP   119      21.993  29.019   2.823  1.00  0.00              
ATOM    971  N   LEU   120      17.889  26.262   3.169  1.00  0.00              
ATOM    972  CA  LEU   120      17.018  25.412   2.367  1.00  0.00              
ATOM    973  C   LEU   120      16.665  26.080   1.041  1.00  0.00              
ATOM    974  O   LEU   120      16.241  25.422   0.091  1.00  0.00              
ATOM    975  CB  LEU   120      17.680  24.056   2.113  1.00  0.00              
ATOM    976  CG  LEU   120      16.772  22.829   2.216  1.00  0.00              
ATOM    977  CD1 LEU   120      17.327  21.678   1.391  1.00  0.00              
ATOM    978  CD2 LEU   120      15.354  23.171   1.782  1.00  0.00              
ATOM    979  N   PRO   121      16.839  27.407   0.965  1.00  0.00              
ATOM    980  CA  PRO   121      16.539  28.175  -0.247  1.00  0.00              
ATOM    981  C   PRO   121      17.809  28.675  -0.928  1.00  0.00              
ATOM    982  O   PRO   121      17.747  29.391  -1.928  1.00  0.00              
ATOM    983  CB  PRO   121      15.833  27.151  -1.137  1.00  0.00              
ATOM    984  CG  PRO   121      16.117  25.836  -0.492  1.00  0.00              
ATOM    985  CD  PRO   121      17.342  28.258   2.059  1.00  0.00              
ATOM    986  N   GLY   122      18.958  28.294  -0.381  1.00  0.00              
ATOM    987  CA  GLY   122      20.224  28.715  -0.951  1.00  0.00              
ATOM    988  C   GLY   122      20.061  29.831  -1.964  1.00  0.00              
ATOM    989  O   GLY   122      20.882  30.746  -2.032  1.00  0.00              
ATOM    990  N   ILE   123      18.996  29.759  -2.757  1.00  0.00              
ATOM    991  CA  ILE   123      18.722  30.794  -3.794  1.00  0.00              
ATOM    992  C   ILE   123      18.783  32.199  -3.203  1.00  0.00              
ATOM    993  O   ILE   123      18.510  33.183  -3.888  1.00  0.00              
ATOM    994  CB  ILE   123      19.716  30.697  -4.966  1.00  0.00              
ATOM    995  CG2 ILE   123      19.228  29.692  -5.998  1.00  0.00              
ATOM    996  CG1 ILE   123      21.107  30.315  -4.455  1.00  0.00              
ATOM    997  CD1 ILE   123      21.869  29.400  -5.388  1.00  0.00              
ATOM    998  N   ASN   124      19.144  32.282  -1.927  1.00  0.00              
ATOM    999  CA  ASN   124      19.242  33.564  -1.241  1.00  0.00              
ATOM   1000  C   ASN   124      18.323  34.602  -1.878  1.00  0.00              
ATOM   1001  O   ASN   124      17.121  34.623  -1.616  1.00  0.00              
ATOM   1002  CB  ASN   124      18.907  33.405   0.244  1.00  0.00              
ATOM   1003  CG  ASN   124      19.804  34.241   1.136  1.00  0.00              
ATOM   1004  OD1 ASN   124      19.541  34.392   2.329  1.00  0.00              
ATOM   1005  ND2 ASN   124      20.868  34.786   0.560  1.00  0.00              
ATOM   1006  N   LEU   125      18.898  35.461  -2.713  1.00  0.00              
ATOM   1007  CA  LEU   125      18.133  36.502  -3.388  1.00  0.00              
ATOM   1008  C   LEU   125      17.139  35.902  -4.377  1.00  0.00              
ATOM   1009  O   LEU   125      16.087  36.484  -4.645  1.00  0.00              
ATOM   1010  CB  LEU   125      17.397  37.374  -2.367  1.00  0.00              
ATOM   1011  CG  LEU   125      17.371  38.877  -2.654  1.00  0.00              
ATOM   1012  CD1 LEU   125      16.144  39.522  -2.028  1.00  0.00              
ATOM   1013  CD2 LEU   125      17.417  39.139  -4.152  1.00  0.00              
ATOM   1014  N   GLU   126      17.479  34.736  -4.916  1.00  0.00              
ATOM   1015  CA  GLU   126      16.618  34.056  -5.877  1.00  0.00              
ATOM   1016  C   GLU   126      15.992  32.807  -5.267  1.00  0.00              
ATOM   1017  O   GLU   126      15.344  32.872  -4.222  1.00  0.00              
ATOM   1018  CB  GLU   126      15.525  35.001  -6.380  1.00  0.00              
ATOM   1019  CG  GLU   126      15.126  34.773  -7.829  1.00  0.00              
ATOM   1020  CD  GLU   126      14.542  36.014  -8.475  1.00  0.00              
ATOM   1021  OE1 GLU   126      15.190  36.571  -9.385  1.00  0.00              
ATOM   1022  OE2 GLU   126      13.436  36.429  -8.070  1.00  0.00              
ATOM   1023  N   PHE   127      16.188  31.670  -5.925  1.00  0.00              
ATOM   1024  CA  PHE   127      15.643  30.404  -5.449  1.00  0.00              
ATOM   1025  C   PHE   127      16.431  29.878  -4.255  1.00  0.00              
ATOM   1026  O   PHE   127      15.985  28.861  -3.684  1.00  0.00              
ATOM   1027  CB  PHE   127      14.168  30.562  -5.078  1.00  0.00              
ATOM   1028  CG  PHE   127      13.229  29.832  -5.995  1.00  0.00              
ATOM   1029  CD1 PHE   127      13.702  29.200  -7.132  1.00  0.00              
ATOM   1030  CD2 PHE   127      11.874  29.777  -5.722  1.00  0.00              
ATOM   1031  CE1 PHE   127      12.839  28.528  -7.977  1.00  0.00              
ATOM   1032  CE2 PHE   127      11.010  29.104  -6.566  1.00  0.00              
ATOM   1033  CZ  PHE   127      11.487  28.482  -7.690  1.00  0.00              
ATOM   1034  OXT PHE   127      17.465  30.504  -3.938  1.00  0.00              
TER
END
