
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0378TS383_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS383_5-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    I      75      A       4          0.959
LGA    S      76      N       5          0.561
LGA    T      77      Q       6          0.301
LGA    P      81      I       7          0.603
LGA    Q      82      K       8          0.691
LGA    P      83      F       9          0.617
LGA    L      84      L      10          0.807
LGA    M      85      R      11          1.160
LGA    A      86      S      12          0.862
LGA    V      87      L      13          0.732
LGA    F      88      R      14          1.386
LGA    D      89      E      15          1.563
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    -       -      R      41           -
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
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    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
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)   12   89    5.0     12    0.92     8.33     13.222     1.175

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.438507 * X  +  -0.658106 * Y  +  -0.612052 * Z  +  96.825928
  Y_new =  -0.313891 * X  +  -0.750283 * Y  +   0.581848 * Z  +  -6.339159
  Z_new =  -0.842130 * X  +  -0.063027 * Y  +  -0.535578 * Z  + 118.789902 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.024451    0.117141  [ DEG:  -173.2883      6.7117 ]
  Theta =   1.001221    2.140371  [ DEG:    57.3658    122.6342 ]
  Phi   =  -0.621263    2.520329  [ DEG:   -35.5958    144.4042 ]
 
# 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: T0378TS383_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS383_5-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12   89   5.0   12   0.92    8.33  13.222
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS383_5-D1
PFRMAT TS
TARGET T0378
MODEL 5
PARENT 1zjrA
ATOM      1  N   ILE    75       4.810  37.383  53.295  1.00  0.00
ATOM      2  CA  ILE    75       6.167  37.558  52.701  1.00  0.00
ATOM      3  C   ILE    75       7.188  36.661  53.393  1.00  0.00
ATOM      4  O   ILE    75       8.117  36.160  52.761  1.00  0.00
ATOM      5  N   SER    76       7.009  36.467  54.696  1.00  0.00
ATOM      6  CA  SER    76       7.914  35.635  55.479  1.00  0.00
ATOM      7  C   SER    76       8.007  34.231  54.892  1.00  0.00
ATOM      8  O   SER    76       9.097  33.677  54.751  1.00  0.00
ATOM      9  N   THR    77       6.856  33.664  54.548  1.00  0.00
ATOM     10  CA  THR    77       6.807  32.323  53.982  1.00  0.00
ATOM     11  C   THR    77       7.592  32.263  52.673  1.00  0.00
ATOM     12  O   THR    77       8.102  31.207  52.295  1.00  0.00
ATOM     13  N   PRO    81       7.685  33.400  51.989  1.00  0.00
ATOM     14  CA  PRO    81       8.417  33.479  50.729  1.00  0.00
ATOM     15  C   PRO    81       9.902  33.286  51.007  1.00  0.00
ATOM     16  O   PRO    81      10.622  32.673  50.218  1.00  0.00
ATOM     17  N   GLN    82      10.350  33.819  52.140  1.00  0.00
ATOM     18  CA  GLN    82      11.747  33.725  52.543  1.00  0.00
ATOM     19  C   GLN    82      12.170  32.282  52.787  1.00  0.00
ATOM     20  O   GLN    82      13.238  31.858  52.346  1.00  0.00
ATOM     21  N   PRO    83      11.330  31.528  53.490  1.00  0.00
ATOM     22  CA  PRO    83      11.637  30.134  53.789  1.00  0.00
ATOM     23  C   PRO    83      11.705  29.326  52.494  1.00  0.00
ATOM     24  O   PRO    83      12.587  28.486  52.324  1.00  0.00
ATOM     25  N   LEU    84      10.774  29.590  51.581  1.00  0.00
ATOM     26  CA  LEU    84      10.746  28.895  50.298  1.00  0.00
ATOM     27  C   LEU    84      11.973  29.275  49.482  1.00  0.00
ATOM     28  O   LEU    84      12.535  28.448  48.760  1.00  0.00
ATOM     29  N   MET    85      12.382  30.533  49.603  1.00  0.00
ATOM     30  CA  MET    85      13.550  31.036  48.897  1.00  0.00
ATOM     31  C   MET    85      14.757  30.265  49.417  1.00  0.00
ATOM     32  O   MET    85      15.602  29.800  48.651  1.00  0.00
ATOM     33  N   ALA    86      14.818  30.128  50.735  1.00  0.00
ATOM     34  CA  ALA    86      15.911  29.423  51.383  1.00  0.00
ATOM     35  C   ALA    86      15.859  27.938  51.041  1.00  0.00
ATOM     36  O   ALA    86      16.893  27.298  50.856  1.00  0.00
ATOM     37  N   VAL    87      14.647  27.402  50.949  1.00  0.00
ATOM     38  CA  VAL    87      14.453  25.994  50.627  1.00  0.00
ATOM     39  C   VAL    87      15.018  25.741  49.231  1.00  0.00
ATOM     40  O   VAL    87      15.655  24.724  48.976  1.00  0.00
ATOM     41  N   PHE    88      14.779  26.684  48.327  1.00  0.00
ATOM     42  CA  PHE    88      15.262  26.563  46.961  1.00  0.00
ATOM     43  C   PHE    88      16.789  26.499  46.927  1.00  0.00
ATOM     44  O   PHE    88      17.369  25.662  46.241  1.00  0.00
ATOM     45  N   ASP    89      17.435  27.391  47.670  1.00  0.00
ATOM     46  CA  ASP    89      18.894  27.416  47.732  1.00  0.00
ATOM     47  C   ASP    89      19.403  26.081  48.269  1.00  0.00
ATOM     48  O   ASP    89      20.401  25.538  47.791  1.00  0.00
TER
END
