
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0352AL381_3
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352AL381_3.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      T       2           -
LGA    W      50      T       3          1.617
LGA    L      51      H       4          0.603
LGA    Q      52      D       5          0.973
LGA    W      53      R       6          1.551
LGA    V      54      V       7          0.210
LGA    L      55      R       8          0.374
LGA    I      56      L       9          0.631
LGA    P      57      Q      10          0.689
LGA    R      58      L      11          0.709
LGA    M      59      Q      12          0.872
LGA    H      60      A      13          1.293
LGA    D      61      L      14          1.843
LGA    L      62      -       -           -
LGA    L      63      E      15          1.468
LGA    D      64      A      16          2.263
LGA    -       -      L      17           -
LGA    -       -      L      18           -
LGA    -       -      R      19           -
LGA    -       -      E      20           -
LGA    -       -      H      21           -
LGA    -       -      Q      22           -
LGA    -       -      H      23           -
LGA    -       -      W      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      E      28           -
LGA    -       -      P      29           -
LGA    -       -      Q      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      Q      33           -
LGA    -       -      F      34           -
LGA    -       -      N      35           -
LGA    -       -      S      36           -
LGA    -       -      T      37           -
LGA    -       -      Q      38           -
LGA    -       -      P      39           -
LGA    -       -      F      40           -
LGA    -       -      F      41           -
LGA    -       -      M      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      M      45           -
LGA    -       -      E      46           -
LGA    -       -      P      47           -
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    -       -      W      50           -
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    -       -      W      53           -
LGA    -       -      V      54           -
LGA    -       -      L      55           -
LGA    -       -      I      56           -
LGA    -       -      P      57           -
LGA    -       -      R      58           -
LGA    -       -      M      59           -
LGA    -       -      H      60           -
LGA    -       -      D      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    -       -      N      65           -
LGA    -       -      K      66           -
LGA    -       -      Q      67           -
LGA    -       -      P      68           -
LGA    -       -      L      69           -
LGA    -       -      P      70           -
LGA    -       -      G      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      A      74           -
LGA    -       -      V      75           -
LGA    -       -      A      76           -
LGA    -       -      P      77           -
LGA    -       -      Y      78           -
LGA    -       -      Y      79           -
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      A      82           -
LGA    -       -      L      83           -
LGA    -       -      A      84           -
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    -       -      H      87           -
LGA    -       -      P      88           -
LGA    -       -      Q      89           -
LGA    -       -      R      90           -
LGA    -       -      A      91           -
LGA    -       -      L      92           -
LGA    -       -      I      93           -
LGA    -       -      L      94           -
LGA    -       -      A      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      E      98           -
LGA    -       -      K      99           -
LGA    -       -      L     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      A     105           -
LGA    -       -      D     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      S     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  109    5.0     14    1.22     7.14     12.281     1.057

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.621589 * X  +  -0.676080 * Y  +   0.395655 * Z  +  85.252350
  Y_new =  -0.379443 * X  +  -0.182013 * Y  +  -0.907135 * Z  + 137.899384
  Z_new =   0.685310 * X  +  -0.713994 * Y  +  -0.143397 * Z  + -13.906345 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.768997    1.372596  [ DEG:  -101.3561     78.6439 ]
  Theta =  -0.755029   -2.386563  [ DEG:   -43.2600   -136.7400 ]
  Phi   =  -2.593532    0.548061  [ DEG:  -148.5984     31.4016 ]
 
# 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: T0352AL381_3                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352AL381_3.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  109   5.0   14   1.22    7.14  12.281
REMARK  ---------------------------------------------------------- 
MOLECULE T0352AL381_3
REMARK Aligment from pdb entry: 1jb0I
ATOM      1  N   TRP    50       0.476  -5.356  -6.602  1.00  0.00              
ATOM      2  CA  TRP    50      -0.772  -5.168  -5.851  1.00  0.00              
ATOM      3  C   TRP    50      -1.341  -3.746  -6.089  1.00  0.00              
ATOM      4  O   TRP    50      -2.482  -3.480  -5.773  1.00  0.00              
ATOM      5  N   LEU    51      -0.544  -2.844  -6.649  1.00  0.00              
ATOM      6  CA  LEU    51      -1.001  -1.477  -6.882  1.00  0.00              
ATOM      7  C   LEU    51      -2.310  -1.326  -7.690  1.00  0.00              
ATOM      8  O   LEU    51      -3.204  -0.571  -7.290  1.00  0.00              
ATOM      9  N   GLN    52      -2.442  -2.038  -8.824  1.00  0.00              
ATOM     10  CA  GLN    52      -3.645  -1.967  -9.659  1.00  0.00              
ATOM     11  C   GLN    52      -4.913  -2.359  -8.910  1.00  0.00              
ATOM     12  O   GLN    52      -6.010  -1.853  -9.191  1.00  0.00              
ATOM     13  N   TRP    53      -4.746  -3.301  -7.984  1.00  0.00              
ATOM     14  CA  TRP    53      -5.823  -3.823  -7.152  1.00  0.00              
ATOM     15  C   TRP    53      -6.534  -2.649  -6.518  1.00  0.00              
ATOM     16  O   TRP    53      -7.762  -2.615  -6.406  1.00  0.00              
ATOM     17  N   VAL    54      -5.741  -1.684  -6.080  1.00  0.00              
ATOM     18  CA  VAL    54      -6.311  -0.539  -5.432  1.00  0.00              
ATOM     19  C   VAL    54      -6.493   0.683  -6.340  1.00  0.00              
ATOM     20  O   VAL    54      -7.526   1.343  -6.257  1.00  0.00              
ATOM     21  N   LEU    55      -5.531   0.963  -7.218  1.00  0.00              
ATOM     22  CA  LEU    55      -5.645   2.117  -8.098  1.00  0.00              
ATOM     23  C   LEU    55      -6.787   2.103  -9.114  1.00  0.00              
ATOM     24  O   LEU    55      -7.264   3.167  -9.519  1.00  0.00              
ATOM     25  N   ILE    56      -7.245   0.934  -9.542  1.00  0.00              
ATOM     26  CA  ILE    56      -8.356   0.962 -10.466  1.00  0.00              
ATOM     27  C   ILE    56      -9.619   1.401  -9.702  1.00  0.00              
ATOM     28  O   ILE    56     -10.402   2.184 -10.223  1.00  0.00              
ATOM     29  N   PRO    57      -9.852   0.885  -8.472  1.00  0.00              
ATOM     30  CA  PRO    57     -11.058   1.344  -7.766  1.00  0.00              
ATOM     31  C   PRO    57     -10.931   2.837  -7.428  1.00  0.00              
ATOM     32  O   PRO    57     -11.904   3.579  -7.487  1.00  0.00              
ATOM     33  N   ARG    58      -9.727   3.281  -7.095  1.00  0.00              
ATOM     34  CA  ARG    58      -9.539   4.680  -6.780  1.00  0.00              
ATOM     35  C   ARG    58      -9.771   5.580  -7.995  1.00  0.00              
ATOM     36  O   ARG    58     -10.463   6.573  -7.899  1.00  0.00              
ATOM     37  N   MET    59      -9.217   5.223  -9.145  1.00  0.00              
ATOM     38  CA  MET    59      -9.368   6.051 -10.333  1.00  0.00              
ATOM     39  C   MET    59     -10.742   5.948 -10.975  1.00  0.00              
ATOM     40  O   MET    59     -11.223   6.910 -11.565  1.00  0.00              
ATOM     41  N   HIS    60     -11.390   4.802 -10.834  1.00  0.00              
ATOM     42  CA  HIS    60     -12.676   4.584 -11.484  1.00  0.00              
ATOM     43  C   HIS    60     -13.910   4.767 -10.635  1.00  0.00              
ATOM     44  O   HIS    60     -14.996   5.032 -11.160  1.00  0.00              
ATOM     45  N   ASP    61     -13.766   4.607  -9.329  1.00  0.00              
ATOM     46  CA  ASP    61     -14.912   4.731  -8.463  1.00  0.00              
ATOM     47  C   ASP    61     -14.846   5.929  -7.511  1.00  0.00              
ATOM     48  O   ASP    61     -15.690   6.820  -7.561  1.00  0.00              
ATOM     49  N   LEU    62     -13.842   5.921  -6.645  1.00  0.00              
ATOM     50  CA  LEU    62     -13.655   6.939  -5.638  1.00  0.00              
ATOM     51  C   LEU    62     -13.429   8.346  -6.181  1.00  0.00              
ATOM     52  O   LEU    62     -14.170   9.258  -5.871  1.00  0.00              
ATOM     53  N   LEU    63     -12.395   8.504  -6.995  1.00  0.00              
ATOM     54  CA  LEU    63     -12.050   9.789  -7.576  1.00  0.00              
ATOM     55  C   LEU    63     -13.226  10.396  -8.365  1.00  0.00              
ATOM     56  O   LEU    63     -13.573  11.550  -8.159  1.00  0.00              
ATOM     57  N   ASP    64     -13.868   9.619  -9.255  1.00  0.00              
ATOM     58  CA  ASP    64     -14.975  10.253  -9.969  1.00  0.00              
ATOM     59  C   ASP    64     -16.194  10.574  -9.098  1.00  0.00              
ATOM     60  O   ASP    64     -16.971  11.465  -9.428  1.00  0.00              
END
