
#######################################################
#                                                     #
#                        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   14 (   56),  selected   14 , name T0378TS383_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS383_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    S      76      N       5          0.770
LGA    T      77      Q       6          1.167
LGA    Q      78      I       7          1.242
LGA    T      79      K       8          0.782
LGA    T      80      F       9          0.755
LGA    P      81      L      10          1.368
LGA    Q      82      R      11          1.583
LGA    P      83      -       -           -
LGA    L      84      S      12          1.365
LGA    M      85      L      13          1.182
LGA    A      86      R      14          1.398
LGA    V      87      E      15          0.978
LGA    F      88      R      16          2.595
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    D      89      F      25          5.177
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)   14   89    5.0     13    1.94     0.00     13.710     0.638

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.732884 * X  +  -0.307474 * Y  +   0.606911 * Z  +  29.907749
  Y_new =   0.376633 * X  +  -0.926250 * Y  +  -0.014449 * Z  +  18.491459
  Z_new =   0.566594 * X  +   0.217993 * Y  +   0.794638 * Z  +  27.219894 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.267744   -2.873849  [ DEG:    15.3406   -164.6594 ]
  Theta =  -0.602366   -2.539226  [ DEG:   -34.5130   -145.4870 ]
  Phi   =   2.666883   -0.474710  [ DEG:   152.8011    -27.1989 ]
 
# 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_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS383_4-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   14   89   5.0   13   1.94    0.00  13.710
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS383_4-D1
PFRMAT TS
TARGET T0378
MODEL 4
PARENT 1v2xA
ATOM      1  N   SER    76       7.335  36.609  54.238  1.00  0.00
ATOM      2  CA  SER    76       7.941  35.655  55.216  1.00  0.00
ATOM      3  C   SER    76       8.200  34.277  54.618  1.00  0.00
ATOM      4  O   SER    76       9.275  33.705  54.810  1.00  0.00
ATOM      5  N   THR    77       7.215  33.732  53.908  1.00  0.00
ATOM      6  CA  THR    77       7.394  32.417  53.312  1.00  0.00
ATOM      7  C   THR    77       8.132  32.566  51.982  1.00  0.00
ATOM      8  O   THR    77       8.702  31.611  51.460  1.00  0.00
ATOM      9  N   GLN    78       8.131  33.772  51.434  1.00  0.00
ATOM     10  CA  GLN    78       8.833  34.013  50.183  1.00  0.00
ATOM     11  C   GLN    78      10.326  33.968  50.536  1.00  0.00
ATOM     12  O   GLN    78      11.169  33.485  49.774  1.00  0.00
ATOM     13  N   THR    79      10.619  34.464  51.731  1.00  0.00
ATOM     14  CA  THR    79      11.963  34.524  52.281  1.00  0.00
ATOM     15  C   THR    79      12.443  33.147  52.740  1.00  0.00
ATOM     16  O   THR    79      13.618  32.799  52.610  1.00  0.00
ATOM     17  N   THR    80      11.518  32.351  53.259  1.00  0.00
ATOM     18  CA  THR    80      11.876  31.045  53.775  1.00  0.00
ATOM     19  C   THR    80      11.370  29.899  52.884  1.00  0.00
ATOM     20  O   THR    80      12.155  29.077  52.412  1.00  0.00
ATOM     21  N   PRO    81      10.071  29.869  52.621  1.00  0.00
ATOM     22  CA  PRO    81       9.485  28.812  51.803  1.00  0.00
ATOM     23  C   PRO    81      10.139  28.714  50.435  1.00  0.00
ATOM     24  O   PRO    81      10.155  27.647  49.834  1.00  0.00
ATOM     25  N   GLN    82      10.696  29.812  49.945  1.00  0.00
ATOM     26  CA  GLN    82      11.309  29.779  48.627  1.00  0.00
ATOM     27  C   GLN    82      12.831  29.709  48.636  1.00  0.00
ATOM     28  O   GLN    82      13.413  28.628  48.582  1.00  0.00
ATOM     29  N   PRO    83      13.461  30.877  48.690  1.00  0.00
ATOM     30  CA  PRO    83      14.906  30.984  48.683  1.00  0.00
ATOM     31  C   PRO    83      15.526  29.955  49.620  1.00  0.00
ATOM     32  O   PRO    83      16.318  29.116  49.198  1.00  0.00
ATOM     33  N   LEU    84      15.139  30.026  50.890  1.00  0.00
ATOM     34  CA  LEU    84      15.637  29.139  51.928  1.00  0.00
ATOM     35  C   LEU    84      15.546  27.648  51.572  1.00  0.00
ATOM     36  O   LEU    84      16.547  26.938  51.623  1.00  0.00
ATOM     37  N   MET    85      14.351  27.194  51.209  1.00  0.00
ATOM     38  CA  MET    85      14.093  25.792  50.859  1.00  0.00
ATOM     39  C   MET    85      14.793  25.319  49.582  1.00  0.00
ATOM     40  O   MET    85      15.363  24.225  49.569  1.00  0.00
ATOM     41  N   ALA    86      14.762  26.114  48.513  1.00  0.00
ATOM     42  CA  ALA    86      15.425  25.684  47.283  1.00  0.00
ATOM     43  C   ALA    86      16.949  25.611  47.443  1.00  0.00
ATOM     44  O   ALA    86      17.588  24.711  46.911  1.00  0.00
ATOM     45  N   VAL    87      17.535  26.555  48.172  1.00  0.00
ATOM     46  CA  VAL    87      18.975  26.548  48.373  1.00  0.00
ATOM     47  C   VAL    87      19.441  25.316  49.172  1.00  0.00
ATOM     48  O   VAL    87      20.501  24.732  48.901  1.00  0.00
ATOM     49  N   PHE    88      18.662  24.927  50.171  1.00  0.00
ATOM     50  CA  PHE    88      19.070  23.795  50.981  1.00  0.00
ATOM     51  C   PHE    88      18.875  22.559  50.150  1.00  0.00
ATOM     52  O   PHE    88      19.672  21.633  50.234  1.00  0.00
ATOM     53  N   ASP    89      17.814  22.537  49.361  1.00  0.00
ATOM     54  CA  ASP    89      17.557  21.374  48.517  1.00  0.00
ATOM     55  C   ASP    89      18.783  21.084  47.666  1.00  0.00
ATOM     56  O   ASP    89      19.211  19.937  47.541  1.00  0.00
TER
END
