
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0299AL381_1-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299AL381_1-D1.T0299_D1.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    -       -      R       3           -
LGA    -       -      Y       4           -
LGA    -       -      A       5           -
LGA    -       -      L       6           -
LGA    -       -      L       7           -
LGA    -       -      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    -       -      N      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    -       -      V      20           -
LGA    V      57      M      21          2.141
LGA    E      58      A      22          1.323
LGA    K      59      E      23          0.462
LGA    L      60      L      24          1.402
LGA    E      61      R      25          1.242
LGA    T      62      Q      26          0.446
LGA    F      63      E      27          1.406
LGA    F      64      L      28          0.984
LGA    A      65      T      29          0.541
LGA    V      66      N      30          1.603
LGA    H      67      L      31          1.687
LGA    Y      68      G      32          1.090
LGA    P      69      L      33          3.625
LGA    F      70      E      34          1.893
LGA    I      71      K      35          2.541
LGA    Q      72      V      36          1.902
LGA    S      73      E      37          1.555
LGA    F      74      S      38          1.190
LGA    S      75      Y      39          1.324
LGA    L      76      I      40          0.723
LGA    L      77      N      41          5.599
LGA    S      78      S      42           #
LGA    -       -      G      43           -
LGA    -       -      N      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      F      47           -
LGA    -       -      T      48           -
LGA    -       -      S      49           -
LGA    -       -      I      50           -
LGA    -       -      D      51           -
LGA    -       -      S      52           -
LGA    -       -      K      53           -
LGA    -       -      A      54           -
LGA    -       -      Q      55           -
LGA    -       -      L      56           -
LGA    -       -      V      57           -
LGA    -       -      E      58           -
LGA    -       -      K      59           -
LGA    -       -      L      60           -
LGA    -       -      E      61           -
LGA    -       -      T      62           -
LGA    -       -      F      63           -
LGA    -       -      F      64           -
LGA    -       -      A      65           -
LGA    -       -      V      66           -
LGA    -       -      H      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      F      70           -
LGA    -       -      I      71           -
LGA    -       -      Q      72           -
LGA    -       -      S      73           -
LGA    -       -      F      74           -
LGA    -       -      S      75           -
LGA    -       -      L      76           -
LGA    -       -      L      77           -
LGA    -       -      S      78           -
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    -       -      I     174           -
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22   91    5.0     21    2.00     4.76     20.834     0.998

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.200526 * X  +  -0.970382 * Y  +   0.134713 * Z  +  25.520277
  Y_new =   0.374797 * X  +  -0.051059 * Y  +  -0.925700 * Z  +  48.820518
  Z_new =   0.905161 * X  +   0.236117 * Y  +   0.353457 * Z  + -27.707460 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.588939   -2.552654  [ DEG:    33.7437   -146.2563 ]
  Theta =  -1.131759   -2.009834  [ DEG:   -64.8450   -115.1550 ]
  Phi   =   1.079522   -2.062070  [ DEG:    61.8521   -118.1479 ]
 
# 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: T0299AL381_1-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_1-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22   91   5.0   21   2.00    4.76  20.834
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_1-D1
REMARK Aligment from pdb entry: 1atg
ATOM      1  N   VAL    57      -5.343  34.495  -5.336  1.00  0.00              
ATOM      2  CA  VAL    57      -6.078  35.748  -5.180  1.00  0.00              
ATOM      3  C   VAL    57      -7.467  35.628  -5.799  1.00  0.00              
ATOM      4  O   VAL    57      -8.412  36.224  -5.257  1.00  0.00              
ATOM      5  N   GLU    58      -7.634  34.868  -6.883  1.00  0.00              
ATOM      6  CA  GLU    58      -8.973  34.660  -7.445  1.00  0.00              
ATOM      7  C   GLU    58      -9.840  33.944  -6.425  1.00  0.00              
ATOM      8  O   GLU    58     -11.015  34.297  -6.228  1.00  0.00              
ATOM      9  N   LYS    59      -9.308  32.930  -5.753  1.00  0.00              
ATOM     10  CA  LYS    59     -10.050  32.240  -4.702  1.00  0.00              
ATOM     11  C   LYS    59     -10.379  33.202  -3.565  1.00  0.00              
ATOM     12  O   LYS    59     -11.521  33.223  -3.062  1.00  0.00              
ATOM     13  N   LEU    60      -9.409  33.987  -3.123  1.00  0.00              
ATOM     14  CA  LEU    60      -9.619  34.940  -2.039  1.00  0.00              
ATOM     15  C   LEU    60     -10.656  35.990  -2.399  1.00  0.00              
ATOM     16  O   LEU    60     -11.547  36.268  -1.582  1.00  0.00              
ATOM     17  N   GLU    61     -10.539  36.592  -3.571  1.00  0.00              
ATOM     18  CA  GLU    61     -11.501  37.588  -4.035  1.00  0.00              
ATOM     19  C   GLU    61     -12.900  36.998  -4.082  1.00  0.00              
ATOM     20  O   GLU    61     -13.877  37.649  -3.643  1.00  0.00              
ATOM     21  N   THR    62     -13.096  35.774  -4.531  1.00  0.00              
ATOM     22  CA  THR    62     -14.382  35.101  -4.575  1.00  0.00              
ATOM     23  C   THR    62     -14.967  34.984  -3.170  1.00  0.00              
ATOM     24  O   THR    62     -16.159  35.265  -2.947  1.00  0.00              
ATOM     25  N   PHE    63     -14.153  34.569  -2.202  1.00  0.00              
ATOM     26  CA  PHE    63     -14.635  34.455  -0.830  1.00  0.00              
ATOM     27  C   PHE    63     -14.936  35.819  -0.238  1.00  0.00              
ATOM     28  O   PHE    63     -15.964  35.971   0.465  1.00  0.00              
ATOM     29  N   PHE    64     -14.130  36.832  -0.478  1.00  0.00              
ATOM     30  CA  PHE    64     -14.349  38.166   0.064  1.00  0.00              
ATOM     31  C   PHE    64     -15.649  38.733  -0.483  1.00  0.00              
ATOM     32  O   PHE    64     -16.409  39.406   0.230  1.00  0.00              
ATOM     33  N   ALA    65     -15.927  38.469  -1.761  1.00  0.00              
ATOM     34  CA  ALA    65     -17.174  38.906  -2.391  1.00  0.00              
ATOM     35  C   ALA    65     -18.367  38.188  -1.792  1.00  0.00              
ATOM     36  O   ALA    65     -19.389  38.843  -1.485  1.00  0.00              
ATOM     37  N   VAL    66     -18.301  36.894  -1.565  1.00  0.00              
ATOM     38  CA  VAL    66     -19.391  36.157  -0.943  1.00  0.00              
ATOM     39  C   VAL    66     -19.676  36.735   0.441  1.00  0.00              
ATOM     40  O   VAL    66     -20.841  36.925   0.826  1.00  0.00              
ATOM     41  N   HIS    67     -18.634  36.985   1.229  1.00  0.00              
ATOM     42  CA  HIS    67     -18.828  37.475   2.581  1.00  0.00              
ATOM     43  C   HIS    67     -19.316  38.902   2.681  1.00  0.00              
ATOM     44  O   HIS    67     -20.151  39.178   3.564  1.00  0.00              
ATOM     45  N   TYR    68     -18.817  39.817   1.879  1.00  0.00              
ATOM     46  CA  TYR    68     -19.043  41.232   2.004  1.00  0.00              
ATOM     47  C   TYR    68     -19.826  41.899   0.892  1.00  0.00              
ATOM     48  O   TYR    68     -20.216  43.054   1.053  1.00  0.00              
ATOM     49  N   PRO    69     -19.957  41.225  -0.242  1.00  0.00              
ATOM     50  CA  PRO    69     -20.644  41.809  -1.387  1.00  0.00              
ATOM     51  C   PRO    69     -19.720  42.670  -2.233  1.00  0.00              
ATOM     52  O   PRO    69     -20.141  43.184  -3.277  1.00  0.00              
ATOM     53  N   PHE    70     -18.474  42.855  -1.809  1.00  0.00              
ATOM     54  CA  PHE    70     -17.519  43.667  -2.539  1.00  0.00              
ATOM     55  C   PHE    70     -16.814  42.840  -3.617  1.00  0.00              
ATOM     56  O   PHE    70     -16.307  41.750  -3.351  1.00  0.00              
ATOM     57  N   ILE    71     -16.747  43.414  -4.811  1.00  0.00              
ATOM     58  CA  ILE    71     -16.066  42.782  -5.933  1.00  0.00              
ATOM     59  C   ILE    71     -14.705  43.446  -6.124  1.00  0.00              
ATOM     60  O   ILE    71     -14.506  44.636  -5.895  1.00  0.00              
ATOM     61  N   GLN    72     -13.718  42.635  -6.481  1.00  0.00              
ATOM     62  CA  GLN    72     -12.359  43.127  -6.698  1.00  0.00              
ATOM     63  C   GLN    72     -12.009  42.943  -8.172  1.00  0.00              
ATOM     64  O   GLN    72     -12.454  41.963  -8.759  1.00  0.00              
ATOM     65  N   SER    73     -11.239  43.861  -8.730  1.00  0.00              
ATOM     66  CA  SER    73     -10.745  43.747 -10.096  1.00  0.00              
ATOM     67  C   SER    73      -9.268  43.369  -9.981  1.00  0.00              
ATOM     68  O   SER    73      -8.501  44.138  -9.420  1.00  0.00              
ATOM     69  N   PHE    74      -8.911  42.193 -10.474  1.00  0.00              
ATOM     70  CA  PHE    74      -7.551  41.689 -10.375  1.00  0.00              
ATOM     71  C   PHE    74      -6.742  41.930 -11.647  1.00  0.00              
ATOM     72  O   PHE    74      -7.220  41.643 -12.742  1.00  0.00              
ATOM     73  N   SER    75      -5.513  42.364 -11.462  1.00  0.00              
ATOM     74  CA  SER    75      -4.530  42.457 -12.524  1.00  0.00              
ATOM     75  C   SER    75      -3.283  41.690 -12.047  1.00  0.00              
ATOM     76  O   SER    75      -3.114  41.516 -10.828  1.00  0.00              
ATOM     77  N   LEU    76      -2.419  41.290 -12.972  1.00  0.00              
ATOM     78  CA  LEU    76      -1.232  40.546 -12.539  1.00  0.00              
ATOM     79  C   LEU    76      -0.039  40.761 -13.455  1.00  0.00              
ATOM     80  O   LEU    76      -0.232  41.126 -14.635  1.00  0.00              
ATOM     81  N   LEU    77       1.139  40.556 -12.911  1.00  0.00              
ATOM     82  CA  LEU    77       2.369  40.650 -13.699  1.00  0.00              
ATOM     83  C   LEU    77       3.518  40.254 -12.786  1.00  0.00              
ATOM     84  O   LEU    77       3.272  39.916 -11.609  1.00  0.00              
ATOM     85  N   SER    78       4.747  40.222 -13.272  1.00  0.00              
ATOM     86  CA ASER    78       5.904  39.938 -12.447  1.00  0.00              
ATOM     87  C   SER    78       6.067  41.077 -11.446  1.00  0.00              
ATOM     88  O   SER    78       5.730  42.236 -11.762  1.00  0.00              
END
