
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0352AL381_4
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352AL381_4.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    -       -      T       3           -
LGA    -       -      H       4           -
LGA    -       -      D       5           -
LGA    -       -      R       6           -
LGA    -       -      V       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      L      11           -
LGA    -       -      Q      12           -
LGA    -       -      A      13           -
LGA    -       -      L      14           -
LGA    -       -      E      15           -
LGA    -       -      A      16           -
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    Q      33      D      43          1.920
LGA    F      34      T      44          3.633
LGA    N      35      M      45          1.192
LGA    S      36      E      46          1.861
LGA    T      37      P      47          1.224
LGA    Q      38      L      48          0.715
LGA    P      39      E      49          1.250
LGA    F      40      W      50          4.547
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    -       -      W      53           -
LGA    F      41      V      54          1.011
LGA    M      42      L      55          2.184
LGA    D      43      I      56          2.040
LGA    -       -      P      57           -
LGA    T      44      R      58          1.425
LGA    M      45      M      59          3.083
LGA    -       -      H      60           -
LGA    E      46      D      61          2.873
LGA    P      47      L      62          2.438
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    L      48      N      65          1.155
LGA    E      49      K      66          2.039
LGA    W      50      Q      67          4.388
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)   18  109    5.0     18    2.43     5.56     13.144     0.711

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.224004 * X  +   0.936104 * Y  +  -0.271167 * Z  +   8.931165
  Y_new =   0.638750 * X  +   0.069131 * Y  +   0.766302 * Z  + -118.386345
  Z_new =   0.736085 * X  +  -0.344863 * Y  +  -0.582451 * Z  +  65.361465 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.607010    0.534582  [ DEG:  -149.3707     30.6293 ]
  Theta =  -0.827268   -2.314325  [ DEG:   -47.3990   -132.6010 ]
  Phi   =   1.233506   -1.908086  [ DEG:    70.6747   -109.3253 ]
 
# 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_4                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352AL381_4.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  109   5.0   18   2.43    5.56  13.144
REMARK  ---------------------------------------------------------- 
MOLECULE T0352AL381_4
REMARK Aligment from pdb entry: 2mev2
ATOM      1  N   GLN    33      -8.928  19.770  -0.912  1.00  0.00              
ATOM      2  CA  GLN    33      -8.462  20.939  -1.656  1.00  0.00              
ATOM      3  C   GLN    33      -7.777  22.069  -0.871  1.00  0.00              
ATOM      4  O   GLN    33      -6.644  22.550  -1.116  1.00  0.00              
ATOM      5  N   PHE    34      -8.539  22.509   0.110  1.00  0.00              
ATOM      6  CA  PHE    34      -8.296  23.530   1.099  1.00  0.00              
ATOM      7  C   PHE    34      -7.351  23.099   2.221  1.00  0.00              
ATOM      8  O   PHE    34      -6.646  23.982   2.759  1.00  0.00              
ATOM      9  N   ASN    35      -7.442  21.802   2.523  1.00  0.00              
ATOM     10  CA  ASN    35      -6.534  21.259   3.542  1.00  0.00              
ATOM     11  C   ASN    35      -5.115  21.395   2.934  1.00  0.00              
ATOM     12  O   ASN    35      -4.471  20.499   2.375  1.00  0.00              
ATOM     13  N   SER    36      -4.680  22.638   3.032  1.00  0.00              
ATOM     14  CA  SER    36      -3.416  23.185   2.558  1.00  0.00              
ATOM     15  C   SER    36      -2.220  22.670   3.364  1.00  0.00              
ATOM     16  O   SER    36      -1.164  22.324   2.788  1.00  0.00              
ATOM     17  N   THR    37      -2.447  22.663   4.683  1.00  0.00              
ATOM     18  CA  THR    37      -1.346  22.243   5.567  1.00  0.00              
ATOM     19  C   THR    37      -1.573  20.865   6.140  1.00  0.00              
ATOM     20  O   THR    37      -0.643  20.471   6.877  1.00  0.00              
ATOM     21  N   GLN    38      -2.643  20.171   5.806  1.00  0.00              
ATOM     22  CA  GLN    38      -2.828  18.826   6.414  1.00  0.00              
ATOM     23  C   GLN    38      -1.666  17.892   6.147  1.00  0.00              
ATOM     24  O   GLN    38      -1.302  17.867   4.966  1.00  0.00              
ATOM     25  N   PRO    39      -1.176  17.205   7.166  1.00  0.00              
ATOM     26  CA  PRO    39      -0.056  16.295   6.990  1.00  0.00              
ATOM     27  C   PRO    39      -0.343  15.154   6.044  1.00  0.00              
ATOM     28  O   PRO    39       0.596  14.826   5.311  1.00  0.00              
ATOM     29  N   PHE    40      -1.510  14.542   6.087  1.00  0.00              
ATOM     30  CA  PHE    40      -1.811  13.406   5.198  1.00  0.00              
ATOM     31  C   PHE    40      -3.266  12.968   5.359  1.00  0.00              
ATOM     32  O   PHE    40      -3.889  13.549   6.244  1.00  0.00              
ATOM     33  N   PHE    41      -3.709  12.049   4.518  1.00  0.00              
ATOM     34  CA  PHE    41      -5.088  11.552   4.604  1.00  0.00              
ATOM     35  C   PHE    41      -5.000  10.043   4.919  1.00  0.00              
ATOM     36  O   PHE    41      -3.931   9.419   4.749  1.00  0.00              
ATOM     37  N   MET    42      -6.097   9.457   5.395  1.00  0.00              
ATOM     38  CA  MET    42      -6.150   8.040   5.795  1.00  0.00              
ATOM     39  C   MET    42      -6.041   7.048   4.656  1.00  0.00              
ATOM     40  O   MET    42      -5.877   5.799   4.842  1.00  0.00              
ATOM     41  N   ASP    43      -5.987   7.554   3.430  1.00  0.00              
ATOM     42  CA  ASP    43      -5.837   6.610   2.273  1.00  0.00              
ATOM     43  C   ASP    43      -4.381   6.657   1.828  1.00  0.00              
ATOM     44  O   ASP    43      -4.118   6.382   0.630  1.00  0.00              
ATOM     45  N   THR    44      -3.554   6.996   2.825  1.00  0.00              
ATOM     46  CA  THR    44      -2.113   7.049   2.520  1.00  0.00              
ATOM     47  C   THR    44      -1.652   5.615   2.226  1.00  0.00              
ATOM     48  O   THR    44      -2.250   4.624   2.675  1.00  0.00              
ATOM     49  N   MET    45      -0.627   5.546   1.412  1.00  0.00              
ATOM     50  CA  MET    45       0.069   4.378   0.924  1.00  0.00              
ATOM     51  C   MET    45       1.565   4.593   0.646  1.00  0.00              
ATOM     52  O   MET    45       1.871   4.961  -0.493  1.00  0.00              
ATOM     53  N   GLU    46       2.408   4.368   1.637  1.00  0.00              
ATOM     54  CA  GLU    46       3.863   4.515   1.460  1.00  0.00              
ATOM     55  C   GLU    46       4.383   3.357   0.633  1.00  0.00              
ATOM     56  O   GLU    46       4.803   2.355   1.234  1.00  0.00              
ATOM     57  N   PRO    47       4.357   3.485  -0.659  1.00  0.00              
ATOM     58  CA  PRO    47       4.789   2.368  -1.538  1.00  0.00              
ATOM     59  C   PRO    47       6.191   1.851  -1.261  1.00  0.00              
ATOM     60  O   PRO    47       6.441   0.718  -1.729  1.00  0.00              
ATOM     61  N   LEU    48       7.079   2.528  -0.581  1.00  0.00              
ATOM     62  CA  LEU    48       8.429   1.995  -0.284  1.00  0.00              
ATOM     63  C   LEU    48       8.288   0.694   0.520  1.00  0.00              
ATOM     64  O   LEU    48       9.206  -0.149   0.531  1.00  0.00              
ATOM     65  N   GLU    49       7.157   0.516   1.178  1.00  0.00              
ATOM     66  CA  GLU    49       6.877  -0.632   2.007  1.00  0.00              
ATOM     67  C   GLU    49       5.819  -1.582   1.465  1.00  0.00              
ATOM     68  O   GLU    49       5.348  -2.446   2.266  1.00  0.00              
ATOM     69  N   TRP    50       5.497  -1.383   0.180  1.00  0.00              
ATOM     70  CA  TRP    50       4.471  -2.290  -0.386  1.00  0.00              
ATOM     71  C   TRP    50       4.853  -3.748  -0.195  1.00  0.00              
ATOM     72  O   TRP    50       3.886  -4.518  -0.256  1.00  0.00              
END
