
#######################################################
#                                                     #
#                        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   31 (   31),  selected   31 , name T0385TS464_4_2
# Molecule2: number of CA atoms  142 ( 1050),  selected  142 , name T0385.pdb
# PARAMETERS: T0385TS464_4_2.T0385.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S      17           -
LGA    -       -      E      18           -
LGA    -       -      G      19           -
LGA    -       -      S      20           -
LGA    -       -      A      21           -
LGA    -       -      D      22           -
LGA    -       -      N      23           -
LGA    -       -      A      24           -
LGA    -       -      A      25           -
LGA    -       -      L      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    A      25      A      31          1.974
LGA    L      26      V      32          2.056
LGA    C      27      E      33          3.253
LGA    D      28      H      34          3.296
LGA    A      29      A      35          1.303
LGA    -       -      T      36           -
LGA    -       -      I      37           -
LGA    -       -      Y      38           -
LGA    -       -      G      39           -
LGA    -       -      Y      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      V      43           -
LGA    -       -      S      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      S      47           -
LGA    -       -      P      48           -
LGA    -       -      P      49           -
LGA    -       -      G      50           -
LGA    -       -      V      51           -
LGA    -       -      N      52           -
LGA    -       -      F      53           -
LGA    -       -      L      54           -
LGA    -       -      V      55           -
LGA    -       -      A      56           -
LGA    -       -      D      57           -
LGA    -       -      A      58           -
LGA    -       -      L      59           -
LGA    -       -      K      60           -
LGA    -       -      Q      61           -
LGA    -       -      H      62           -
LGA    -       -      R      63           -
LGA    -       -      H      64           -
LGA    -       -      R      65           -
LGA    -       -      R      66           -
LGA    -       -      D      67           -
LGA    -       -      D      68           -
LGA    -       -      V      69           -
LGA    -       -      I      70           -
LGA    -       -      V      71           -
LGA    -       -      M      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      A      75           -
LGA    -       -      R      76           -
LGA    -       -      G      77           -
LGA    -       -      V      78           -
LGA    -       -      T      79           -
LGA    -       -      A      80           -
LGA    -       -      P      81           -
LGA    -       -      I      82           -
LGA    -       -      A      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      G      86           -
LGA    -       -      Y      87           -
LGA    -       -      Q      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      M      91           -
LGA    -       -      Q      92           -
LGA    -       -      V      93           -
LGA    -       -      S      94           -
LGA    -       -      S      95           -
LGA    -       -      A      96           -
LGA    -       -      A      97           -
LGA    -       -      D      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      A     103           -
LGA    L      54      V     104          2.828
LGA    V      55      R     105          2.329
LGA    -       -      M     106           -
LGA    A      56      E     107          0.572
LGA    D      57      N     108          0.701
LGA    A      58      D     109          0.683
LGA    L      59      G     110          0.435
LGA    K      60      A     111          1.022
LGA    Q      61      T     112          1.376
LGA    H      62      A     113          0.970
LGA    R      63      W     114          0.912
LGA    H      64      R     115          1.119
LGA    R      65      A     116          1.086
LGA    R      66      V     117          1.446
LGA    D      67      V     118          1.611
LGA    D      68      E     119          0.926
LGA    V      69      H     120          1.493
LGA    R     143      A     121           -
LGA    W     144      E     122           -
LGA    N     145      T     123           -
LGA    R     146      A     124           -
LGA    V     147      D     125           -
LGA    L     148      D     126           -
LGA    -       -      R     127           -
LGA    -       -      V     128           -
LGA    -       -      F     129           -
LGA    -       -      A     130           -
LGA    -       -      S     131           -
LGA    G     149      T     132          1.382
LGA    A     150      A     133          1.969
LGA    W     151      L     134           -
LGA    P     152      T     135           -
LGA    -       -      E     136           -
LGA    -       -      S     137           -
LGA    -       -      A     138           -
LGA    -       -      V     139           -
LGA    -       -      M     140           -
LGA    -       -      A     141           -
LGA    -       -      T     142           -
LGA    -       -      R     143           -
LGA    -       -      W     144           -
LGA    -       -      N     145           -
LGA    -       -      R     146           -
LGA    -       -      V     147           -
LGA    -       -      L     148           -
LGA    -       -      G     149           -
LGA    -       -      A     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      I     153           -
LGA    -       -      T     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      F     157           -
LGA    -       -      P     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   31  142    5.0     23    1.71    13.04     15.088     1.274

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.632104 * X  +   0.601956 * Y  +  -0.487948 * Z  +  51.230011
  Y_new =   0.499806 * X  +  -0.164481 * Y  +  -0.850376 * Z  +  -5.551966
  Z_new =  -0.592147 * X  +  -0.781406 * Y  +  -0.196892 * Z  +  97.044365 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.817630    1.323963  [ DEG:  -104.1425     75.8575 ]
  Theta =   0.633721    2.507872  [ DEG:    36.3095    143.6905 ]
  Phi   =   2.472547   -0.669045  [ DEG:   141.6665    -38.3335 ]
 
# 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: T0385TS464_4_2                                
REMARK     2: T0385.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS464_4_2.T0385.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31  142   5.0   23   1.71   13.04  15.088
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0385
PARENT N/A
ATOM      1  CA  ALA    25      26.982   8.887  29.597  1.00  0.00
ATOM      2  CA  LEU    26      23.498   9.630  28.297  1.00  0.00
ATOM      3  CA  CYS    27      24.816  12.937  26.930  1.00  0.00
ATOM      4  CA  ASP    28      27.590  11.018  25.129  1.00  0.00
ATOM      5  CA  ALA    29      24.972   8.716  23.605  1.00  0.00
ATOM      6  CA  LEU    54      17.405  17.687  17.415  1.00  0.00
ATOM      7  CA  VAL    55      19.703  15.218  19.099  1.00  0.00
ATOM      8  CA  ALA    56      22.223  18.010  19.744  1.00  0.00
ATOM      9  CA  ASP    57      19.360  19.829  21.424  1.00  0.00
ATOM     10  CA  ALA    58      19.126  16.768  23.721  1.00  0.00
ATOM     11  CA  LEU    59      22.774  16.625  24.790  1.00  0.00
ATOM     12  CA  LYS    60      22.857  20.402  25.283  1.00  0.00
ATOM     13  CA  GLN    61      19.640  20.358  27.249  1.00  0.00
ATOM     14  CA  HIS    62      21.156  17.782  29.577  1.00  0.00
ATOM     15  CA  ARG    63      24.452  19.713  29.461  1.00  0.00
ATOM     16  CA  HIS    64      22.768  22.670  31.118  1.00  0.00
ATOM     17  CA  ARG    65      20.865  20.216  33.276  1.00  0.00
ATOM     18  CA  ARG    66      24.032  18.590  34.648  1.00  0.00
ATOM     19  CA  ASP    67      25.580  22.008  35.300  1.00  0.00
ATOM     20  CA  ASP    68      22.396  22.881  37.143  1.00  0.00
ATOM     21  CA  VAL    69      22.790  19.724  39.274  1.00  0.00
ATOM     22  CA  ARG   143      31.880  18.510  18.969  1.00  0.00
ATOM     23  CA  TRP   144      28.514  20.259  19.165  1.00  0.00
ATOM     24  CA  ASN   145      27.895  18.968  22.671  1.00  0.00
ATOM     25  CA  ARG   146      31.329  20.045  23.925  1.00  0.00
ATOM     26  CA  VAL   147      30.954  23.400  22.184  1.00  0.00
ATOM     27  CA  LEU   148      27.985  24.169  24.453  1.00  0.00
ATOM     28  CA  GLY   149      30.248  23.860  27.504  1.00  0.00
ATOM     29  CA  ALA   150      28.821  20.454  28.334  1.00  0.00
ATOM     30  CA  TRP   151      31.027  17.808  30.007  1.00  0.00
ATOM     31  CA  PRO   152      28.355  15.157  29.722  1.00  0.00
TER
END
