
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0378AL257_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL257_4-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    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    L      10      R      41          1.317
LGA    R      11      C      42          2.230
LGA    S      12      R      43          0.724
LGA    L      13      M      44          4.521
LGA    R      14      L      45          3.858
LGA    E      15      -       -           -
LGA    R      16      -       -           -
LGA    K      17      -       -           -
LGA    Y      18      -       -           -
LGA    R      19      -       -           -
LGA    L      20      V      46          3.388
LGA    V      33      G      47          3.165
LGA    G      34      T      48          3.032
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    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    E      35      V      64          4.120
LGA    M      36      E      65          4.279
LGA    L      37      L      66          3.256
LGA    P      38      P      67          3.570
LGA    F      39      -       -           -
LGA    Y      40      E      68          2.445
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)   19   89    5.0     13    3.26    15.38      8.851     0.387

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.155988 * X  +  -0.971434 * Y  +  -0.178841 * Z  +  -1.160409
  Y_new =  -0.850125 * X  +  -0.039843 * Y  +  -0.525072 * Z  +  52.669411
  Z_new =   0.502947 * X  +   0.233942 * Y  +  -0.832055 * Z  +  44.461369 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.867507   -0.274085  [ DEG:   164.2961    -15.7039 ]
  Theta =  -0.527006   -2.614587  [ DEG:   -30.1952   -149.8048 ]
  Phi   =  -1.389327    1.752266  [ DEG:   -79.6026    100.3974 ]
 
# 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_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL257_4-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   89   5.0   13   3.26   15.38   8.851
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL257_4-D1
REMARK Aligment from pdb entry: 1v2x_A
ATOM      1  N   LEU    10       7.368  16.006  56.741  1.00  0.00              
ATOM      2  CA  LEU    10       6.238  15.573  55.865  1.00  0.00              
ATOM      3  C   LEU    10       5.091  16.578  55.835  1.00  0.00              
ATOM      4  O   LEU    10       4.572  16.901  54.766  1.00  0.00              
ATOM      5  N   ARG    11       4.681  17.061  57.006  1.00  0.00              
ATOM      6  CA  ARG    11       3.589  18.021  57.050  1.00  0.00              
ATOM      7  C   ARG    11       4.141  19.420  56.783  1.00  0.00              
ATOM      8  O   ARG    11       3.406  20.338  56.429  1.00  0.00              
ATOM      9  N   SER    12       5.446  19.585  56.944  1.00  0.00              
ATOM     10  CA  SER    12       6.063  20.876  56.683  1.00  0.00              
ATOM     11  C   SER    12       6.039  21.041  55.158  1.00  0.00              
ATOM     12  O   SER    12       5.842  22.133  54.615  1.00  0.00              
ATOM     13  N   LEU    13       6.221  19.912  54.484  1.00  0.00              
ATOM     14  CA  LEU    13       6.235  19.822  53.034  1.00  0.00              
ATOM     15  C   LEU    13       4.825  19.937  52.452  1.00  0.00              
ATOM     16  O   LEU    13       4.615  20.523  51.388  1.00  0.00              
ATOM     17  N   ARG    14       3.853  19.392  53.169  1.00  0.00              
ATOM     18  CA  ARG    14       2.488  19.398  52.683  1.00  0.00              
ATOM     19  C   ARG    14       1.584  20.363  53.469  1.00  0.00              
ATOM     20  O   ARG    14       0.979  21.266  52.893  1.00  0.00              
ATOM     21  N   GLU    15       1.527  20.198  54.783  1.00  0.00              
ATOM     22  CA  GLU    15       0.683  21.046  55.619  1.00  0.00              
ATOM     23  C   GLU    15       1.002  22.522  55.447  1.00  0.00              
ATOM     24  O   GLU    15       0.137  23.366  55.644  1.00  0.00              
ATOM     25  N   ARG    16       2.229  22.840  55.063  1.00  0.00              
ATOM     26  CA  ARG    16       2.595  24.240  54.913  1.00  0.00              
ATOM     27  C   ARG    16       2.640  24.732  53.472  1.00  0.00              
ATOM     28  O   ARG    16       1.660  25.264  52.955  1.00  0.00              
ATOM     29  N   LYS    17       3.796  24.561  52.841  1.00  0.00              
ATOM     30  CA  LYS    17       4.011  24.995  51.476  1.00  0.00              
ATOM     31  C   LYS    17       2.820  24.625  50.600  1.00  0.00              
ATOM     32  O   LYS    17       2.185  25.490  50.002  1.00  0.00              
ATOM     33  N   TYR    18       2.521  23.331  50.552  1.00  0.00              
ATOM     34  CA  TYR    18       1.431  22.791  49.757  1.00  0.00              
ATOM     35  C   TYR    18       0.086  23.495  49.981  1.00  0.00              
ATOM     36  O   TYR    18      -0.534  23.962  49.029  1.00  0.00              
ATOM     37  N   ARG    19      -0.345  23.572  51.236  1.00  0.00              
ATOM     38  CA  ARG    19      -1.619  24.194  51.615  1.00  0.00              
ATOM     39  C   ARG    19      -1.681  25.706  51.376  1.00  0.00              
ATOM     40  O   ARG    19      -2.686  26.199  50.858  1.00  0.00              
ATOM     41  N   LEU    20      -0.636  26.447  51.741  1.00  0.00              
ATOM     42  CA  LEU    20      -0.673  27.891  51.521  1.00  0.00              
ATOM     43  C   LEU    20      -0.669  28.249  50.029  1.00  0.00              
ATOM     44  O   LEU    20      -1.345  29.182  49.611  1.00  0.00              
ATOM     45  N   VAL    33       0.088  27.513  49.223  1.00  0.00              
ATOM     46  CA  VAL    33       0.138  27.788  47.796  1.00  0.00              
ATOM     47  C   VAL    33      -1.223  27.550  47.114  1.00  0.00              
ATOM     48  O   VAL    33      -1.632  28.292  46.209  1.00  0.00              
ATOM     49  N   GLY    34      -1.921  26.504  47.532  1.00  0.00              
ATOM     50  CA  GLY    34      -3.194  26.210  46.901  1.00  0.00              
ATOM     51  C   GLY    34      -4.175  27.243  47.373  1.00  0.00              
ATOM     52  O   GLY    34      -5.027  27.675  46.607  1.00  0.00              
ATOM     53  N   GLU    35      -4.068  27.630  48.634  1.00  0.00              
ATOM     54  CA  GLU    35      -4.981  28.635  49.169  1.00  0.00              
ATOM     55  C   GLU    35      -4.940  29.876  48.291  1.00  0.00              
ATOM     56  O   GLU    35      -5.978  30.441  47.944  1.00  0.00              
ATOM     57  N   MET    36      -3.738  30.297  47.931  1.00  0.00              
ATOM     58  CA  MET    36      -3.556  31.451  47.076  1.00  0.00              
ATOM     59  C   MET    36      -3.979  31.194  45.629  1.00  0.00              
ATOM     60  O   MET    36      -4.558  32.065  44.964  1.00  0.00              
ATOM     61  N   LEU    37      -3.712  29.981  45.132  1.00  0.00              
ATOM     62  CA  LEU    37      -4.081  29.648  43.775  1.00  0.00              
ATOM     63  C   LEU    37      -5.600  29.718  43.637  1.00  0.00              
ATOM     64  O   LEU    37      -6.134  30.036  42.569  1.00  0.00              
ATOM     65  N   PRO    38      -6.276  29.416  44.734  1.00  0.00              
ATOM     66  CA  PRO    38      -7.743  29.418  44.757  1.00  0.00              
ATOM     67  C   PRO    38      -8.352  30.813  44.680  1.00  0.00              
ATOM     68  O   PRO    38      -9.558  30.962  44.461  1.00  0.00              
ATOM     69  N   PHE    39      -7.530  31.844  44.859  1.00  0.00              
ATOM     70  CA  PHE    39      -8.013  33.210  44.754  1.00  0.00              
ATOM     71  C   PHE    39      -7.554  33.835  43.418  1.00  0.00              
ATOM     72  O   PHE    39      -7.839  34.983  43.162  1.00  0.00              
ATOM     73  N   TYR    40      -6.849  33.095  42.570  1.00  0.00              
ATOM     74  CA  TYR    40      -6.399  33.680  41.307  1.00  0.00              
ATOM     75  C   TYR    40      -7.555  33.984  40.359  1.00  0.00              
ATOM     76  O   TYR    40      -8.462  33.164  40.214  1.00  0.00              
END
