
#######################################################
#                                                     #
#                        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 T0318AL170_1-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318AL170_1-D1.T0318_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       2           -
LGA    -       -      Q       3           -
LGA    -       -      V       4           -
LGA    -       -      L       5           -
LGA    -       -      V       6           -
LGA    -       -      R       7           -
LGA    -       -      N       8           -
LGA    -       -      G       9           -
LGA    -       -      I      10           -
LGA    -       -      Q      11           -
LGA    -       -      A      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      D      15           -
LGA    -       -      G      16           -
LGA    -       -      L      17           -
LGA    R     142      T      18          0.931
LGA    E     143      S      19          1.992
LGA    L     144      L      20          1.890
LGA    N     145      I      21          0.930
LGA    -       -      I      22           -
LGA    -       -      V      23           -
LGA    -       -      G      24           -
LGA    -       -      K      25           -
LGA    -       -      K      26           -
LGA    -       -      S      27           -
LGA    -       -      V      28           -
LGA    -       -      L      29           -
LGA    -       -      K      30           -
LGA    -       -      N      31           -
LGA    -       -      V      32           -
LGA    -       -      T      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      G      36           -
LGA    -       -      K      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      Q      43           -
LGA    -       -      K      44           -
LGA    -       -      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    -       -      D      48           -
LGA    -       -      G      49           -
LGA    -       -      D      50           -
LGA    -       -      S      51           -
LGA    -       -      W      52           -
LGA    -       -      N      53           -
LGA    -       -      S      54           -
LGA    -       -      M      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      P      60           -
LGA    -       -      A      61           -
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    -       -      H      65           -
LGA    -       -      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      A      72           -
LGA    V     146      H      73          2.021
LGA    N     147      L      74          1.659
LGA    I     148      I      75          1.847
LGA    D     149      T      76          2.150
LGA    V     150      V      77          1.121
LGA    V     151      P      78          5.354
LGA    -       -      D      79           -
LGA    -       -      A      80           -
LGA    -       -      S      81           -
LGA    -       -      S      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      N      85           -
LGA    -       -      T      86           -
LGA    -       -      P      87           -
LGA    -       -      T      88           -
LGA    C     152      N      89          3.301
LGA    -       -      A      90           -
LGA    -       -      H      91           -
LGA    D     153      S      92          1.714
LGA    K     154      I      93          0.728
LGA    L     155      Y      94          1.754
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      K      98           -
LGA    -       -      P      99           -
LGA    -       -      I     100           -
LGA    -       -      N     101           -
LGA    -       -      Y     102           -
LGA    -       -      P     103           -
LGA    -       -      E     104           -
LGA    -       -      D     105           -
LGA    -       -      T     106           -
LGA    -       -      K     107           -
LGA    -       -      N     108           -
LGA    -       -      V     109           -
LGA    -       -      H     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      L     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      E     116           -
LGA    -       -      Y     117           -
LGA    -       -      P     118           -
LGA    -       -      D     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      S     122           -
LGA    -       -      H     123           -
LGA    -       -      V     124           -
LGA    -       -      A     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      A     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      F     131           -
LGA    -       -      C     132           -
LGA    -       -      K     133           -
LGA    -       -      F     134           -
LGA    -       -      S     135           -
LGA    -       -      M     136           -
LGA    -       -      K     137           -
LGA    -       -      T     138           -
LGA    -       -      S     139           -
LGA    -       -      G     140           -
LGA    -       -      I     141           -
LGA    -       -      R     142           -
LGA    -       -      E     143           -
LGA    -       -      L     144           -
LGA    -       -      N     145           -
LGA    -       -      V     146           -
LGA    -       -      N     147           -
LGA    -       -      I     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      D     153           -
LGA    -       -      K     154           -
LGA    -       -      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14  154    5.0     14    2.26    21.43      6.876     0.593

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.080420 * X  +   0.936488 * Y  +  -0.341354 * Z  + -10.704576
  Y_new =  -0.440020 * X  +   0.340642 * Y  +   0.830870 * Z  +  78.858894
  Z_new =   0.894380 * X  +   0.083384 * Y  +   0.439468 * Z  +  16.939304 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.187509   -2.954083  [ DEG:    10.7435   -169.2565 ]
  Theta =  -1.107043   -2.034550  [ DEG:   -63.4289   -116.5711 ]
  Phi   =  -1.390026    1.751566  [ DEG:   -79.6426    100.3574 ]
 
# 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: T0318AL170_1-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318AL170_1-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   14  154   5.0   14   2.26   21.43   6.876
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL170_1-D1
REMARK Aligment from pdb entry: 1GYT_A
ATOM      1  N   ARG   142      44.035  47.914  17.895  1.00  0.00              
ATOM      2  CA  ARG   142      43.016  48.283  16.929  1.00  0.00              
ATOM      3  C   ARG   142      41.594  48.133  17.416  1.00  0.00              
ATOM      4  O   ARG   142      40.671  48.720  16.854  1.00  0.00              
ATOM      5  N   GLU   143      41.421  47.341  18.463  1.00  0.00              
ATOM      6  CA  GLU   143      40.106  47.107  19.034  1.00  0.00              
ATOM      7  C   GLU   143      40.329  46.969  20.519  1.00  0.00              
ATOM      8  O   GLU   143      41.361  46.466  20.956  1.00  0.00              
ATOM      9  N   LEU   144      39.355  47.417  21.289  1.00  0.00              
ATOM     10  CA  LEU   144      39.427  47.346  22.729  1.00  0.00              
ATOM     11  C   LEU   144      38.046  46.962  23.262  1.00  0.00              
ATOM     12  O   LEU   144      37.050  47.618  22.959  1.00  0.00              
ATOM     13  N   ASN   145      37.995  45.888  24.047  1.00  0.00              
ATOM     14  CA  ASN   145      36.750  45.411  24.636  1.00  0.00              
ATOM     15  C   ASN   145      36.681  45.751  26.121  1.00  0.00              
ATOM     16  O   ASN   145      37.560  45.365  26.894  1.00  0.00              
ATOM     17  N   VAL   146      35.639  46.482  26.513  1.00  0.00              
ATOM     18  CA  VAL   146      35.454  46.848  27.915  1.00  0.00              
ATOM     19  C   VAL   146      34.529  45.807  28.483  1.00  0.00              
ATOM     20  O   VAL   146      33.477  45.522  27.912  1.00  0.00              
ATOM     21  N   ASN   147      34.929  45.232  29.605  1.00  0.00              
ATOM     22  CA  ASN   147      34.127  44.220  30.233  1.00  0.00              
ATOM     23  C   ASN   147      33.165  44.810  31.255  1.00  0.00              
ATOM     24  O   ASN   147      33.554  45.585  32.135  1.00  0.00              
ATOM     25  N   ILE   148      31.903  44.432  31.140  1.00  0.00              
ATOM     26  CA  ILE   148      30.883  44.893  32.078  1.00  0.00              
ATOM     27  C   ILE   148      30.516  43.724  33.000  1.00  0.00              
ATOM     28  O   ILE   148      30.539  42.566  32.586  1.00  0.00              
ATOM     29  N   ASP   149      30.174  44.016  34.262  1.00  0.00              
ATOM     30  CA  ASP   149      29.805  43.020  35.282  1.00  0.00              
ATOM     31  C   ASP   149      28.964  41.836  34.814  1.00  0.00              
ATOM     32  O   ASP   149      29.388  40.679  34.924  1.00  0.00              
ATOM     33  N   VAL   150      27.766  42.125  34.315  1.00  0.00              
ATOM     34  CA  VAL   150      26.878  41.081  33.830  1.00  0.00              
ATOM     35  C   VAL   150      26.196  41.506  32.555  1.00  0.00              
ATOM     36  O   VAL   150      26.271  42.660  32.160  1.00  0.00              
ATOM     37  N   VAL   151      25.528  40.565  31.908  1.00  0.00              
ATOM     38  CA  VAL   151      24.856  40.866  30.659  1.00  0.00              
ATOM     39  C   VAL   151      23.832  41.980  30.826  1.00  0.00              
ATOM     40  O   VAL   151      23.373  42.555  29.838  1.00  0.00              
ATOM     41  N   CYS   152      23.479  42.287  32.072  1.00  0.00              
ATOM     42  CA  CYS   152      22.499  43.336  32.321  1.00  0.00              
ATOM     43  C   CYS   152      22.961  44.646  31.726  1.00  0.00              
ATOM     44  O   CYS   152      22.244  45.235  30.910  1.00  0.00              
ATOM     45  N   ASP   153      24.157  45.094  32.115  1.00  0.00              
ATOM     46  CA  ASP   153      24.689  46.345  31.593  1.00  0.00              
ATOM     47  C   ASP   153      25.410  46.214  30.255  1.00  0.00              
ATOM     48  O   ASP   153      26.285  47.013  29.931  1.00  0.00              
ATOM     49  N   LYS   154      25.041  45.206  29.476  1.00  0.00              
ATOM     50  CA  LYS   154      25.614  45.052  28.157  1.00  0.00              
ATOM     51  C   LYS   154      24.932  46.060  27.222  1.00  0.00              
ATOM     52  O   LYS   154      25.540  46.542  26.263  1.00  0.00              
ATOM     53  N   LEU   155      23.670  46.380  27.511  1.00  0.00              
ATOM     54  CA  LEU   155      22.898  47.324  26.702  1.00  0.00              
ATOM     55  C   LEU   155      23.305  48.781  26.977  1.00  0.00              
ATOM     56  O   LEU   155      23.495  49.576  26.044  1.00  0.00              
END
