
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0312AL381_4
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312AL381_4.T0312.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      V       3           -
LGA    -       -      F       4           -
LGA    -       -      E       5           -
LGA    -       -      F       6           -
LGA    -       -      E       7           -
LGA    -       -      V       8           -
LGA    -       -      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      L      16           -
LGA    -       -      D      17           -
LGA    -       -      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      R      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      E      27           -
LGA    -       -      E      28           -
LGA    -       -      F      29           -
LGA    -       -      L      30           -
LGA    -       -      E      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      G      34           -
LGA    -       -      I      35           -
LGA    -       -      H      36           -
LGA    -       -      A      37           -
LGA    -       -      A      38           -
LGA    -       -      H      39           -
LGA    -       -      I      40           -
LGA    -       -      S      41           -
LGA    -       -      A      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      A      45           -
LGA    -       -      V      46           -
LGA    R      47      R      47          4.233
LGA    S      48      S      48          2.697
LGA    A      49      A      49          0.723
LGA    V      50      V      50          1.522
LGA    I      51      I      51          1.807
LGA    G      52      G      52          2.747
LGA    Y      53      Y      53          1.623
LGA    Y      54      Y      54          0.767
LGA    D      55      D      55          1.365
LGA    Q      56      Q      56          2.343
LGA    E      57      E      57          3.191
LGA    K      58      K      58          1.824
LGA    K      59      K      59          0.963
LGA    E      60      E      60          0.907
LGA    Y      61      Y      61          0.731
LGA    V      62      V      62          1.355
LGA    K      63      K      63          1.427
LGA    K      64      K      64          1.043
LGA    E      65      E      65          2.490
LGA    L      66      L      66          4.573
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    M      67      P      69          5.719
LGA    -       -      L      70           -
LGA    -       -      E      71           -
LGA    -       -      I      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      G      77           -
LGA    -       -      N      78           -
LGA    -       -      V      79           -
LGA    -       -      S      80           -
LGA    -       -      M      81           -
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    -       -      P      86           -
LGA    -       -      F      87           -
LGA    -       -      C      88           -
LGA    -       -      H      89           -
LGA    -       -      I      90           -
LGA    -       -      H      91           -
LGA    -       -      V      92           -
LGA    -       -      L      93           -
LGA    E      68      L      94          2.707
LGA    P      69      G      95          0.978
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      G      98           -
LGA    -       -      E      99           -
LGA    -       -      V     100           -
LGA    -       -      Y     101           -
LGA    -       -      G     102           -
LGA    -       -      G     103           -
LGA    -       -      H     104           -
LGA    -       -      L     105           -
LGA    -       -      F     106           -
LGA    -       -      S     107           -
LGA    -       -      A     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      C     113           -
LGA    -       -      E     114           -
LGA    -       -      V     115           -
LGA    -       -      F     116           -
LGA    -       -      V     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      L     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      E     123           -
LGA    -       -      A     124           -
LGA    -       -      P     125           -
LGA    -       -      E     126           -
LGA    -       -      R     127           -
LGA    -       -      A     128           -
LGA    -       -      F     129           -
LGA    -       -      D     130           -
LGA    -       -      E     131           -
LGA    -       -      Q     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      L     135           -
LGA    -       -      F     136           -
LGA    -       -      L     137           -
LGA    -       -      W     138           -
LGA    -       -      L     139           -
LGA    -       -      E     140           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  140    5.0     23    2.45    86.96     13.340     0.901

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.161544 * X  +  -0.762843 * Y  +   0.626078 * Z  +  51.380371
  Y_new =  -0.720975 * X  +  -0.341971 * Y  +  -0.602703 * Z  +  -4.208223
  Z_new =   0.673869 * X  +  -0.548749 * Y  +  -0.494748 * Z  +  17.421825 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.304490    0.837103  [ DEG:  -132.0375     47.9625 ]
  Theta =  -0.739432   -2.402160  [ DEG:   -42.3664   -137.6337 ]
  Phi   =  -1.791219    1.350374  [ DEG:  -102.6293     77.3707 ]
 
# 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: T0312AL381_4                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312AL381_4.T0312.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  140   5.0   23   2.45   86.96  13.340
REMARK  ---------------------------------------------------------- 
MOLECULE T0312AL381_4
REMARK Aligment from pdb entry: 1bf0
ATOM      1  N   ARG    47      43.298   6.688   3.756  1.00  0.00              
ATOM      2  CA  ARG    47      44.736   6.615   3.613  1.00  0.00              
ATOM      3  C   ARG    47      45.146   5.626   4.688  1.00  0.00              
ATOM      4  O   ARG    47      44.544   5.637   5.754  1.00  0.00              
ATOM      5  N   SER    48      46.132   4.716   4.483  1.00  0.00              
ATOM      6  CA  SER    48      46.600   3.760   5.480  1.00  0.00              
ATOM      7  C   SER    48      48.121   3.924   5.608  1.00  0.00              
ATOM      8  O   SER    48      48.824   3.989   4.605  1.00  0.00              
ATOM      9  N   ALA    49      48.672   3.979   6.846  1.00  0.00              
ATOM     10  CA  ALA    49      50.089   4.072   7.201  1.00  0.00              
ATOM     11  C   ALA    49      50.562   2.714   7.769  1.00  0.00              
ATOM     12  O   ALA    49      49.770   2.041   8.422  1.00  0.00              
ATOM     13  N   VAL    50      51.834   2.247   7.559  1.00  0.00              
ATOM     14  CA  VAL    50      52.319   0.913   8.000  1.00  0.00              
ATOM     15  C   VAL    50      52.514   0.680   9.508  1.00  0.00              
ATOM     16  O   VAL    50      53.012   1.531  10.246  1.00  0.00              
ATOM     17  N   ILE    51      52.065  -0.512   9.984  1.00  0.00              
ATOM     18  CA  ILE    51      52.085  -0.908  11.387  1.00  0.00              
ATOM     19  C   ILE    51      52.335  -2.386  11.600  1.00  0.00              
ATOM     20  O   ILE    51      52.076  -3.220  10.735  1.00  0.00              
ATOM     21  N   GLY    52      52.745  -2.715  12.836  1.00  0.00              
ATOM     22  CA  GLY    52      52.998  -4.065  13.327  1.00  0.00              
ATOM     23  C   GLY    52      52.304  -4.199  14.674  1.00  0.00              
ATOM     24  O   GLY    52      52.439  -3.289  15.487  1.00  0.00              
ATOM     25  N   TYR    53      51.567  -5.314  14.952  1.00  0.00              
ATOM     26  CA  TYR    53      50.922  -5.607  16.244  1.00  0.00              
ATOM     27  C   TYR    53      51.610  -6.851  16.809  1.00  0.00              
ATOM     28  O   TYR    53      51.934  -7.731  16.014  1.00  0.00              
ATOM     29  N   TYR    54      51.835  -7.017  18.154  1.00  0.00              
ATOM     30  CA  TYR    54      52.508  -8.208  18.697  1.00  0.00              
ATOM     31  C   TYR    54      51.409  -9.210  18.970  1.00  0.00              
ATOM     32  O   TYR    54      50.482  -8.910  19.722  1.00  0.00              
ATOM     33  N   ASP    55      51.478 -10.394  18.290  1.00  0.00              
ATOM     34  CA  ASP    55      50.508 -11.441  18.354  1.00  0.00              
ATOM     35  C   ASP    55      50.856 -12.390  19.487  1.00  0.00              
ATOM     36  O   ASP    55      51.904 -13.039  19.508  1.00  0.00              
ATOM     37  N   GLN    56      49.952 -12.447  20.479  1.00  0.00              
ATOM     38  CA  GLN    56      50.057 -13.138  21.754  1.00  0.00              
ATOM     39  C   GLN    56      50.142 -14.660  21.747  1.00  0.00              
ATOM     40  O   GLN    56      50.912 -15.240  22.510  1.00  0.00              
ATOM     41  N   GLU    57      49.378 -15.363  20.871  1.00  0.00              
ATOM     42  CA  GLU    57      49.448 -16.823  20.740  1.00  0.00              
ATOM     43  C   GLU    57      50.491 -17.244  19.697  1.00  0.00              
ATOM     44  O   GLU    57      50.742 -18.431  19.514  1.00  0.00              
ATOM     45  N   LYS    58      51.144 -16.262  19.013  1.00  0.00              
ATOM     46  CA  LYS    58      52.222 -16.481  18.049  1.00  0.00              
ATOM     47  C   LYS    58      53.631 -16.324  18.635  1.00  0.00              
ATOM     48  O   LYS    58      54.502 -17.154  18.375  1.00  0.00              
ATOM     49  N   LYS    59      53.885 -15.227  19.413  1.00  0.00              
ATOM     50  CA  LYS    59      55.166 -14.868  20.038  1.00  0.00              
ATOM     51  C   LYS    59      56.059 -13.999  19.139  1.00  0.00              
ATOM     52  O   LYS    59      57.267 -13.865  19.338  1.00  0.00              
ATOM     53  N   GLU    60      55.450 -13.349  18.121  1.00  0.00              
ATOM     54  CA  GLU    60      56.075 -12.425  17.190  1.00  0.00              
ATOM     55  C   GLU    60      55.040 -11.378  16.791  1.00  0.00              
ATOM     56  O   GLU    60      53.850 -11.537  17.070  1.00  0.00              
ATOM     57  N   TYR    61      55.449 -10.275  16.094  1.00  0.00              
ATOM     58  CA  TYR    61      54.568  -9.240  15.575  1.00  0.00              
ATOM     59  C   TYR    61      54.118  -9.545  14.167  1.00  0.00              
ATOM     60  O   TYR    61      54.888 -10.026  13.340  1.00  0.00              
ATOM     61  N   VAL    62      52.838  -9.237  13.880  1.00  0.00              
ATOM     62  CA  VAL    62      52.216  -9.428  12.582  1.00  0.00              
ATOM     63  C   VAL    62      51.954  -8.046  11.981  1.00  0.00              
ATOM     64  O   VAL    62      51.653  -7.126  12.745  1.00  0.00              
ATOM     65  N   LYS    63      52.036  -7.833  10.656  1.00  0.00              
ATOM     66  CA  LYS    63      51.803  -6.540  10.025  1.00  0.00              
ATOM     67  C   LYS    63      50.342  -6.295   9.711  1.00  0.00              
ATOM     68  O   LYS    63      49.571  -7.195   9.372  1.00  0.00              
ATOM     69  N   LYS    64      50.017  -4.996   9.761  1.00  0.00              
ATOM     70  CA  LYS    64      48.754  -4.432   9.350  1.00  0.00              
ATOM     71  C   LYS    64      49.113  -3.067   8.784  1.00  0.00              
ATOM     72  O   LYS    64      50.274  -2.787   8.490  1.00  0.00              
ATOM     73  N   GLU    65      48.132  -2.159   8.669  1.00  0.00              
ATOM     74  CA  GLU    65      48.267  -0.786   8.282  1.00  0.00              
ATOM     75  C   GLU    65      47.250  -0.126   9.197  1.00  0.00              
ATOM     76  O   GLU    65      46.248  -0.759   9.506  1.00  0.00              
ATOM     77  N   LEU    66      47.471   1.123   9.630  1.00  0.00              
ATOM     78  CA  LEU    66      46.593   1.944  10.455  1.00  0.00              
ATOM     79  C   LEU    66      46.061   3.063   9.545  1.00  0.00              
ATOM     80  O   LEU    66      46.831   3.623   8.769  1.00  0.00              
ATOM     81  N   MET    67      44.738   3.421   9.628  1.00  0.00              
ATOM     82  CA  MET    67      44.111   4.495   8.834  1.00  0.00              
ATOM     83  C   MET    67      44.425   5.879   9.399  1.00  0.00              
ATOM     84  O   MET    67      44.704   6.842   8.690  1.00  0.00              
ATOM     85  N   GLU    68      44.344   5.977  10.742  1.00  0.00              
ATOM     86  CA  GLU    68      44.501   7.190  11.516  1.00  0.00              
ATOM     87  C   GLU    68      43.298   7.394  12.388  1.00  0.00              
ATOM     88  O   GLU    68      43.424   7.565  13.599  1.00  0.00              
ATOM     89  N   PRO    69      42.063   7.353  11.829  1.00  0.00              
ATOM     90  CA  PRO    69      40.827   7.634  12.543  1.00  0.00              
ATOM     91  C   PRO    69      40.250   6.493  13.411  1.00  0.00              
ATOM     92  O   PRO    69      39.162   5.986  13.140  1.00  0.00              
END
