
#######################################################
#                                                     #
#                        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 T0378AL257_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL257_3-D1.T0378_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    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    R      14      P      30          2.546
LGA    E      15      K      31          2.886
LGA    -       -      L      32           -
LGA    R      16      V      33          2.015
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    K      17      M      36          1.049
LGA    Y      18      L      37          3.112
LGA    -       -      P      38           -
LGA    R      19      F      39          3.214
LGA    L      20      Y      40          3.876
LGA    V      33      R      41          4.370
LGA    G      34      C      42          2.430
LGA    E      35      R      43          1.878
LGA    M      36      M      44          3.763
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    L      37      D      60          3.959
LGA    P      38      A      61          2.299
LGA    F      39      E      62          1.712
LGA    Y      40      V      63          2.888
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   89    5.0     15    2.94     6.67     10.732     0.493

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.295498 * X  +   0.842861 * Y  +  -0.449740 * Z  + -68.655594
  Y_new =  -0.091663 * X  +   0.493605 * Y  +   0.864842 * Z  + -56.209812
  Z_new =   0.950936 * X  +  -0.214334 * Y  +   0.223118 * Z  +  42.948158 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.765321    2.376271  [ DEG:   -43.8497    136.1503 ]
  Theta =  -1.256247   -1.885346  [ DEG:   -71.9776   -108.0224 ]
  Phi   =  -0.300787    2.840806  [ DEG:   -17.2338    162.7662 ]
 
# 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: T0378AL257_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL257_3-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   89   5.0   15   2.94    6.67  10.732
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL257_3-D1
REMARK Aligment from pdb entry: 1gz0_A
ATOM      1  N   ARG    14       2.157  19.096  40.994  1.00  0.00              
ATOM      2  CA  ARG    14       2.942  18.670  42.156  1.00  0.00              
ATOM      3  C   ARG    14       2.348  17.409  42.774  1.00  0.00              
ATOM      4  O   ARG    14       1.242  17.440  43.311  1.00  0.00              
ATOM      5  N   GLU    15       3.068  16.298  42.694  1.00  0.00              
ATOM      6  CA  GLU    15       2.566  15.065  43.279  1.00  0.00              
ATOM      7  C   GLU    15       3.210  14.893  44.651  1.00  0.00              
ATOM      8  O   GLU    15       4.435  14.840  44.768  1.00  0.00              
ATOM      9  N   ARG    16       2.384  14.829  45.690  1.00  0.00              
ATOM     10  CA  ARG    16       2.895  14.682  47.045  1.00  0.00              
ATOM     11  C   ARG    16       3.168  13.236  47.391  1.00  0.00              
ATOM     12  O   ARG    16       2.346  12.366  47.116  1.00  0.00              
ATOM     13  N   LYS    17       4.326  12.982  47.991  1.00  0.00              
ATOM     14  CA  LYS    17       4.680  11.633  48.410  1.00  0.00              
ATOM     15  C   LYS    17       4.567  11.618  49.930  1.00  0.00              
ATOM     16  O   LYS    17       4.594  12.670  50.571  1.00  0.00              
ATOM     17  N   TYR    18       4.439  10.425  50.495  1.00  0.00              
ATOM     18  CA  TYR    18       4.310  10.242  51.933  1.00  0.00              
ATOM     19  C   TYR    18       5.285  11.098  52.709  1.00  0.00              
ATOM     20  O   TYR    18       4.955  11.645  53.759  1.00  0.00              
ATOM     21  N   ARG    19       6.491  11.215  52.168  1.00  0.00              
ATOM     22  CA  ARG    19       7.556  11.980  52.800  1.00  0.00              
ATOM     23  C   ARG    19       7.231  13.454  52.990  1.00  0.00              
ATOM     24  O   ARG    19       7.532  14.015  54.041  1.00  0.00              
ATOM     25  N   LEU    20       6.625  14.088  51.992  1.00  0.00              
ATOM     26  CA  LEU    20       6.327  15.510  52.131  1.00  0.00              
ATOM     27  C   LEU    20       4.979  15.840  52.770  1.00  0.00              
ATOM     28  O   LEU    20       4.496  16.969  52.672  1.00  0.00              
ATOM     29  N   VAL    33       4.391  14.866  53.456  1.00  0.00              
ATOM     30  CA  VAL    33       3.112  15.075  54.108  1.00  0.00              
ATOM     31  C   VAL    33       3.269  15.996  55.335  1.00  0.00              
ATOM     32  O   VAL    33       2.502  16.947  55.510  1.00  0.00              
ATOM     33  N   GLY    34       4.271  15.735  56.190  1.00  0.00              
ATOM     34  CA  GLY    34       4.492  16.566  57.377  1.00  0.00              
ATOM     35  C   GLY    34       4.675  18.053  57.094  1.00  0.00              
ATOM     36  O   GLY    34       4.298  18.894  57.912  1.00  0.00              
ATOM     37  N   GLU    35       5.245  18.378  55.940  1.00  0.00              
ATOM     38  CA  GLU    35       5.435  19.777  55.555  1.00  0.00              
ATOM     39  C   GLU    35       4.091  20.343  55.095  1.00  0.00              
ATOM     40  O   GLU    35       3.727  21.469  55.448  1.00  0.00              
ATOM     41  N   MET    36       3.364  19.561  54.293  1.00  0.00              
ATOM     42  CA  MET    36       2.059  19.977  53.786  1.00  0.00              
ATOM     43  C   MET    36       1.175  20.337  54.969  1.00  0.00              
ATOM     44  O   MET    36       0.507  21.373  54.984  1.00  0.00              
ATOM     45  N   LEU    37       1.178  19.461  55.961  1.00  0.00              
ATOM     46  CA  LEU    37       0.387  19.685  57.157  1.00  0.00              
ATOM     47  C   LEU    37       0.849  20.960  57.857  1.00  0.00              
ATOM     48  O   LEU    37       0.030  21.801  58.207  1.00  0.00              
ATOM     49  N   PRO    38       2.157  21.111  58.044  1.00  0.00              
ATOM     50  CA  PRO    38       2.693  22.303  58.696  1.00  0.00              
ATOM     51  C   PRO    38       2.254  23.602  58.005  1.00  0.00              
ATOM     52  O   PRO    38       2.132  24.640  58.657  1.00  0.00              
ATOM     53  N   PHE    39       2.010  23.551  56.698  1.00  0.00              
ATOM     54  CA  PHE    39       1.583  24.751  55.971  1.00  0.00              
ATOM     55  C   PHE    39       0.074  24.944  56.088  1.00  0.00              
ATOM     56  O   PHE    39      -0.491  25.864  55.495  1.00  0.00              
ATOM     57  N   TYR    40      -0.575  24.080  56.859  1.00  0.00              
ATOM     58  CA  TYR    40      -2.021  24.153  57.018  1.00  0.00              
ATOM     59  C   TYR    40      -2.458  24.806  58.317  1.00  0.00              
ATOM     60  O   TYR    40      -2.062  24.387  59.432  1.00  0.00              
END
