
#######################################################
#                                                     #
#                        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 (   84),  selected   21 , name T0300AL381_3
# Molecule2: number of CA atoms   89 (  695),  selected   89 , name T0300
# PARAMETERS: T0300AL381_3.T0300  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       7           -
LGA    -       -      K       8           -
LGA    -       -      T       9           -
LGA    -       -      Y      10           -
LGA    -       -      E      11           -
LGA    -       -      E      12           -
LGA    -       -      M      13           -
LGA    -       -      V      14           -
LGA    -       -      K      15           -
LGA    -       -      E      16           -
LGA    -       -      V      17           -
LGA    -       -      E      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      K      21           -
LGA    -       -      L      22           -
LGA    -       -      E      23           -
LGA    -       -      N      24           -
LGA    -       -      K      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      Q      29           -
LGA    -       -      K      30           -
LGA    -       -      V      31           -
LGA    -       -      S      39           -
LGA    -       -      D      40           -
LGA    -       -      D      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      L      44           -
LGA    -       -      T      45           -
LGA    -       -      A      46           -
LGA    -       -      A      47           -
LGA    -       -      K      48           -
LGA    -       -      R      49           -
LGA    -       -      E      50           -
LGA    -       -      S      51           -
LGA    -       -      I      52           -
LGA    -       -      I      53           -
LGA    -       -      V      54           -
LGA    -       -      S      55           -
LGA    S      57      S      56          0.487
LGA    R      58      S      57          0.607
LGA    A      59      R      58          0.742
LGA    L      60      A      59          0.161
LGA    G      61      L      60          0.484
LGA    A      62      G      61          0.363
LGA    V      63      A      62          0.098
LGA    A      64      V      63          0.297
LGA    M      65      A      64          0.441
LGA    R      66      M      65          0.375
LGA    K      67      R      66          0.584
LGA    I      68      K      67          0.328
LGA    E      69      I      68          0.580
LGA    A      70      E      69          0.444
LGA    K      71      A      70          0.602
LGA    V      72      K      71          0.282
LGA    R      73      V      72          0.278
LGA    S      74      R      73          0.542
LGA    R      75      S      74          0.427
LGA    A      76      R      75          0.356
LGA    A      77      A      76          1.207
LGA    -       -      A      77           -
LGA    -       -      K      78           -
LGA    -       -      A      79           -
LGA    -       -      V      80           -
LGA    -       -      T      81           -
LGA    -       -      E      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      S      87           -
LGA    -       -      L      88           -
LGA    -       -      L      89           -
LGA    -       -      Q      90           -
LGA    -       -      S      91           -
LGA    -       -      L      92           -
LGA    -       -      T      93           -
LGA    -       -      L      94           -
LGA    -       -      R      95           -
LGA    -       -      V      96           -
LGA    -       -      D      97           -
LGA    -       -      V      98           -
LGA    -       -      S      99           -
LGA    -       -      M     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21   89    5.0     21    0.51     9.52     23.507     3.422

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.260622 * X  +  -0.310065 * Y  +  -0.914295 * Z  +  70.815933
  Y_new =   0.378137 * X  +  -0.838577 * Y  +   0.392175 * Z  + -79.066811
  Z_new =  -0.888307 * X  +  -0.447938 * Y  +  -0.101305 * Z  +  52.309799 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.793213    1.348380  [ DEG:  -102.7435     77.2565 ]
  Theta =   1.093645    2.047948  [ DEG:    62.6612    117.3388 ]
  Phi   =   0.967337   -2.174255  [ DEG:    55.4243   -124.5757 ]
 
# 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: T0300AL381_3                                  
REMARK     2: T0300                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0300AL381_3.T0300 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   89   5.0   21   0.51    9.52  23.507
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL381_3
REMARK Aligment from pdb entry: 1cs4A
ATOM      1  N   SER    57      40.993 -13.214  -8.334  1.00  0.00              
ATOM      2  CA  SER    57      42.263 -12.836  -7.722  1.00  0.00              
ATOM      3  C   SER    57      42.253 -13.105  -6.214  1.00  0.00              
ATOM      4  O   SER    57      41.190 -13.153  -5.599  1.00  0.00              
ATOM      5  N   ARG    58      43.433 -13.296  -5.628  1.00  0.00              
ATOM      6  CA  ARG    58      43.544 -13.569  -4.194  1.00  0.00              
ATOM      7  C   ARG    58      43.004 -12.426  -3.333  1.00  0.00              
ATOM      8  O   ARG    58      42.566 -12.641  -2.204  1.00  0.00              
ATOM      9  N   ALA    59      43.038 -11.215  -3.883  1.00  0.00              
ATOM     10  CA  ALA    59      42.554 -10.014  -3.205  1.00  0.00              
ATOM     11  C   ALA    59      41.029 -10.061  -3.084  1.00  0.00              
ATOM     12  O   ALA    59      40.488  -9.965  -1.987  1.00  0.00              
ATOM     13  N   LEU    60      40.356 -10.247  -4.218  1.00  0.00              
ATOM     14  CA  LEU    60      38.895 -10.318  -4.293  1.00  0.00              
ATOM     15  C   LEU    60      38.302 -11.414  -3.404  1.00  0.00              
ATOM     16  O   LEU    60      37.287 -11.195  -2.742  1.00  0.00              
ATOM     17  N   GLY    61      38.945 -12.583  -3.396  1.00  0.00              
ATOM     18  CA  GLY    61      38.506 -13.732  -2.599  1.00  0.00              
ATOM     19  C   GLY    61      38.423 -13.411  -1.112  1.00  0.00              
ATOM     20  O   GLY    61      37.431 -13.728  -0.454  1.00  0.00              
ATOM     21  N   ALA    62      39.477 -12.791  -0.589  1.00  0.00              
ATOM     22  CA  ALA    62      39.535 -12.434   0.820  1.00  0.00              
ATOM     23  C   ALA    62      38.496 -11.376   1.195  1.00  0.00              
ATOM     24  O   ALA    62      38.000 -11.358   2.320  1.00  0.00              
ATOM     25  N   VAL    63      38.149 -10.510   0.247  1.00  0.00              
ATOM     26  CA  VAL    63      37.142  -9.483   0.502  1.00  0.00              
ATOM     27  C   VAL    63      35.781 -10.164   0.648  1.00  0.00              
ATOM     28  O   VAL    63      35.007  -9.834   1.548  1.00  0.00              
ATOM     29  N   ALA    64      35.519 -11.137  -0.223  1.00  0.00              
ATOM     30  CA  ALA    64      34.267 -11.895  -0.220  1.00  0.00              
ATOM     31  C   ALA    64      34.126 -12.733   1.049  1.00  0.00              
ATOM     32  O   ALA    64      33.030 -12.884   1.587  1.00  0.00              
ATOM     33  N   MET    65      35.245 -13.285   1.511  1.00  0.00              
ATOM     34  CA  MET    65      35.270 -14.106   2.718  1.00  0.00              
ATOM     35  C   MET    65      35.156 -13.265   3.987  1.00  0.00              
ATOM     36  O   MET    65      34.464 -13.654   4.926  1.00  0.00              
ATOM     37  N   ARG    66      35.844 -12.124   4.016  1.00  0.00              
ATOM     38  CA  ARG    66      35.817 -11.235   5.177  1.00  0.00              
ATOM     39  C   ARG    66      34.441 -10.611   5.339  1.00  0.00              
ATOM     40  O   ARG    66      33.982 -10.385   6.455  1.00  0.00              
ATOM     41  N   LYS    67      33.792 -10.327   4.216  1.00  0.00              
ATOM     42  CA  LYS    67      32.459  -9.749   4.226  1.00  0.00              
ATOM     43  C   LYS    67      31.502 -10.779   4.821  1.00  0.00              
ATOM     44  O   LYS    67      30.660 -10.461   5.658  1.00  0.00              
ATOM     45  N   ILE    68      31.707 -12.032   4.433  1.00  0.00              
ATOM     46  CA  ILE    68      30.885 -13.142   4.886  1.00  0.00              
ATOM     47  C   ILE    68      31.118 -13.553   6.344  1.00  0.00              
ATOM     48  O   ILE    68      30.168 -13.627   7.125  1.00  0.00              
ATOM     49  N   GLU    69      32.374 -13.801   6.715  1.00  0.00              
ATOM     50  CA  GLU    69      32.694 -14.236   8.077  1.00  0.00              
ATOM     51  C   GLU    69      32.543 -13.186   9.179  1.00  0.00              
ATOM     52  O   GLU    69      32.430 -13.532  10.356  1.00  0.00              
ATOM     53  N   ALA    70      32.570 -11.908   8.807  1.00  0.00              
ATOM     54  CA  ALA    70      32.401 -10.836   9.787  1.00  0.00              
ATOM     55  C   ALA    70      30.948 -10.881  10.267  1.00  0.00              
ATOM     56  O   ALA    70      30.675 -10.827  11.474  1.00  0.00              
ATOM     57  N   LYS    71      30.030 -11.019   9.310  1.00  0.00              
ATOM     58  CA  LYS    71      28.608 -11.116   9.601  1.00  0.00              
ATOM     59  C   LYS    71      28.334 -12.356  10.452  1.00  0.00              
ATOM     60  O   LYS    71      27.605 -12.283  11.443  1.00  0.00              
ATOM     61  N   VAL    72      28.920 -13.490  10.070  1.00  0.00              
ATOM     62  CA  VAL    72      28.736 -14.730  10.818  1.00  0.00              
ATOM     63  C   VAL    72      29.173 -14.550  12.274  1.00  0.00              
ATOM     64  O   VAL    72      28.488 -14.997  13.203  1.00  0.00              
ATOM     65  N   ARG    73      30.313 -13.891  12.468  1.00  0.00              
ATOM     66  CA  ARG    73      30.837 -13.667  13.812  1.00  0.00              
ATOM     67  C   ARG    73      29.903 -12.821  14.685  1.00  0.00              
ATOM     68  O   ARG    73      29.845 -13.017  15.901  1.00  0.00              
ATOM     69  N   SER    74      29.160 -11.905  14.059  1.00  0.00              
ATOM     70  CA  SER    74      28.209 -11.043  14.771  1.00  0.00              
ATOM     71  C   SER    74      26.929 -11.835  15.072  1.00  0.00              
ATOM     72  O   SER    74      26.371 -11.741  16.169  1.00  0.00              
ATOM     73  N   ARG    75      26.492 -12.631  14.097  1.00  0.00              
ATOM     74  CA  ARG    75      25.302 -13.472  14.238  1.00  0.00              
ATOM     75  C   ARG    75      25.535 -14.525  15.313  1.00  0.00              
ATOM     76  O   ARG    75      24.589 -15.025  15.913  1.00  0.00              
ATOM     77  N   ALA    76      26.800 -14.878  15.530  1.00  0.00              
ATOM     78  CA  ALA    76      27.164 -15.874  16.532  1.00  0.00              
ATOM     79  C   ALA    76      26.936 -15.339  17.933  1.00  0.00              
ATOM     80  O   ALA    76      26.527 -16.080  18.824  1.00  0.00              
ATOM     81  N   ALA    77      27.210 -14.050  18.121  1.00  0.00              
ATOM     82  CA  ALA    77      27.030 -13.392  19.415  1.00  0.00              
ATOM     83  C   ALA    77      25.544 -13.249  19.746  1.00  0.00              
ATOM     84  O   ALA    77      25.141 -13.405  20.902  1.00  0.00              
END
