
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0358AL381_3
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358AL381_3.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    -       -      L      29           -
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    S      35      S      35          2.436
LGA    H      36      H      36          2.527
LGA    F      37      F      37          1.845
LGA    R      38      R      38          0.643
LGA    L      39      L      39          0.803
LGA    V      40      V      40          0.990
LGA    V      41      V      41          1.039
LGA    R      42      R      42          0.808
LGA    D      43      D      43          0.947
LGA    T      44      T      44          2.728
LGA    E      45      E      45          2.468
LGA    G      46      G      46          3.126
LGA    R      47      R      47          1.220
LGA    M      48      M      48          1.099
LGA    V      49      V      49          0.688
LGA    W      50      W      50          0.599
LGA    R      51      R      51          1.121
LGA    A      52      A      52          1.699
LGA    W      53      W      53          1.736
LGA    N      54      N      54          2.087
LGA    F      55      F      55          2.315
LGA    E      56      E      56          4.150
LGA    P      57      P      57          3.544
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   66    5.0     23    2.02   100.00     31.187     1.085

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.728958 * X  +  -0.662133 * Y  +   0.173779 * Z  +  26.712070
  Y_new =   0.683604 * X  +  -0.717494 * Y  +   0.133746 * Z  +   9.307955
  Z_new =   0.036127 * X  +   0.216292 * Y  +   0.975660 * Z  + -65.808456 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.218159   -2.923434  [ DEG:    12.4996   -167.5004 ]
  Theta =  -0.036135   -3.105458  [ DEG:    -2.0704   -177.9296 ]
  Phi   =   2.388291   -0.753301  [ DEG:   136.8390    -43.1610 ]
 
# 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: T0358AL381_3                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL381_3.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   66   5.0   23   2.02  100.00  31.187
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL381_3
REMARK Aligment from pdb entry: 1m93C
ATOM      1  N   SER    35       6.706   9.623  -6.285  1.00  0.00              
ATOM      2  CA  SER    35       6.006  10.884  -6.003  1.00  0.00              
ATOM      3  C   SER    35       4.744  10.514  -5.195  1.00  0.00              
ATOM      4  O   SER    35       4.485   9.313  -5.082  1.00  0.00              
ATOM      5  N   HIS    36       4.053  11.447  -4.557  1.00  0.00              
ATOM      6  CA  HIS    36       3.040  11.065  -3.547  1.00  0.00              
ATOM      7  C   HIS    36       2.002  10.081  -4.057  1.00  0.00              
ATOM      8  O   HIS    36       1.494  10.163  -5.187  1.00  0.00              
ATOM      9  N   PHE    37       1.681   9.113  -3.192  1.00  0.00              
ATOM     10  CA  PHE    37       0.762   8.061  -3.581  1.00  0.00              
ATOM     11  C   PHE    37      -0.122   7.669  -2.401  1.00  0.00              
ATOM     12  O   PHE    37       0.168   8.052  -1.264  1.00  0.00              
ATOM     13  N   ARG    38      -1.189   6.936  -2.680  1.00  0.00              
ATOM     14  CA  ARG    38      -2.027   6.399  -1.616  1.00  0.00              
ATOM     15  C   ARG    38      -1.875   4.894  -1.559  1.00  0.00              
ATOM     16  O   ARG    38      -1.651   4.227  -2.585  1.00  0.00              
ATOM     17  N   LEU    39      -1.947   4.313  -0.365  1.00  0.00              
ATOM     18  CA  LEU    39      -1.801   2.874  -0.234  1.00  0.00              
ATOM     19  C   LEU    39      -2.910   2.398   0.722  1.00  0.00              
ATOM     20  O   LEU    39      -3.234   3.108   1.697  1.00  0.00              
ATOM     21  N   VAL    40      -3.472   1.238   0.391  1.00  0.00              
ATOM     22  CA  VAL    40      -4.569   0.624   1.129  1.00  0.00              
ATOM     23  C   VAL    40      -4.226  -0.814   1.499  1.00  0.00              
ATOM     24  O   VAL    40      -3.871  -1.559   0.571  1.00  0.00              
ATOM     25  N   VAL    41      -4.328  -1.170   2.782  1.00  0.00              
ATOM     26  CA  VAL    41      -4.212  -2.578   3.165  1.00  0.00              
ATOM     27  C   VAL    41      -5.621  -3.148   3.294  1.00  0.00              
ATOM     28  O   VAL    41      -6.460  -2.608   4.024  1.00  0.00              
ATOM     29  N   ARG    42      -5.922  -4.221   2.556  1.00  0.00              
ATOM     30  CA  ARG    42      -7.308  -4.681   2.623  1.00  0.00              
ATOM     31  C   ARG    42      -7.400  -6.206   2.582  1.00  0.00              
ATOM     32  O   ARG    42      -6.466  -6.901   2.176  1.00  0.00              
ATOM     33  N   ASP    43      -8.565  -6.671   3.012  1.00  0.00              
ATOM     34  CA  ASP    43      -8.919  -8.079   2.905  1.00  0.00              
ATOM     35  C   ASP    43      -9.345  -8.321   1.463  1.00  0.00              
ATOM     36  O   ASP    43     -10.134  -7.557   0.893  1.00  0.00              
ATOM     37  N   THR    44      -8.817  -9.356   0.812  1.00  0.00              
ATOM     38  CA  THR    44      -9.188  -9.439  -0.612  1.00  0.00              
ATOM     39  C   THR    44     -10.637  -9.907  -0.661  1.00  0.00              
ATOM     40  O   THR    44     -11.103 -10.729   0.122  1.00  0.00              
ATOM     41  N   GLU    45     -11.361  -9.289  -1.589  1.00  0.00              
ATOM     42  CA  GLU    45     -12.813  -9.440  -1.620  1.00  0.00              
ATOM     43  C   GLU    45     -13.460  -8.858  -0.379  1.00  0.00              
ATOM     44  O   GLU    45     -14.616  -9.046   0.002  1.00  0.00              
ATOM     45  N   GLY    46     -12.729  -8.048   0.386  1.00  0.00              
ATOM     46  CA  GLY    46     -13.350  -7.592   1.625  1.00  0.00              
ATOM     47  C   GLY    46     -12.975  -6.169   1.995  1.00  0.00              
ATOM     48  O   GLY    46     -12.764  -5.242   1.226  1.00  0.00              
ATOM     49  N   ARG    47     -12.903  -5.996   3.307  1.00  0.00              
ATOM     50  CA  ARG    47     -12.872  -4.656   3.832  1.00  0.00              
ATOM     51  C   ARG    47     -11.468  -4.068   3.839  1.00  0.00              
ATOM     52  O   ARG    47     -10.436  -4.714   3.864  1.00  0.00              
ATOM     53  N   MET    48     -11.507  -2.750   3.828  1.00  0.00              
ATOM     54  CA  MET    48     -10.318  -1.940   4.074  1.00  0.00              
ATOM     55  C   MET    48      -9.868  -1.950   5.515  1.00  0.00              
ATOM     56  O   MET    48     -10.610  -1.665   6.462  1.00  0.00              
ATOM     57  N   VAL    49      -8.610  -2.287   5.700  1.00  0.00              
ATOM     58  CA  VAL    49      -8.046  -2.408   7.047  1.00  0.00              
ATOM     59  C   VAL    49      -7.259  -1.162   7.453  1.00  0.00              
ATOM     60  O   VAL    49      -7.359  -0.694   8.594  1.00  0.00              
ATOM     61  N   TRP    50      -6.481  -0.612   6.519  1.00  0.00              
ATOM     62  CA  TRP    50      -5.660   0.580   6.771  1.00  0.00              
ATOM     63  C   TRP    50      -5.597   1.367   5.464  1.00  0.00              
ATOM     64  O   TRP    50      -5.712   0.761   4.388  1.00  0.00              
ATOM     65  N   ARG    51      -5.419   2.669   5.553  1.00  0.00              
ATOM     66  CA  ARG    51      -5.331   3.497   4.344  1.00  0.00              
ATOM     67  C   ARG    51      -4.357   4.629   4.673  1.00  0.00              
ATOM     68  O   ARG    51      -4.425   5.204   5.783  1.00  0.00              
ATOM     69  N   ALA    52      -3.450   4.924   3.749  1.00  0.00              
ATOM     70  CA  ALA    52      -2.461   5.965   4.020  1.00  0.00              
ATOM     71  C   ALA    52      -2.106   6.767   2.785  1.00  0.00              
ATOM     72  O   ALA    52      -2.396   6.391   1.649  1.00  0.00              
ATOM     73  N   TRP    53      -1.479   7.928   3.040  1.00  0.00              
ATOM     74  CA  TRP    53      -0.873   8.756   2.024  1.00  0.00              
ATOM     75  C   TRP    53       0.616   8.804   2.328  1.00  0.00              
ATOM     76  O   TRP    53       1.020   9.132   3.468  1.00  0.00              
ATOM     77  N   ASN    54       1.412   8.479   1.319  1.00  0.00              
ATOM     78  CA  ASN    54       2.863   8.651   1.381  1.00  0.00              
ATOM     79  C   ASN    54       3.161  10.003   0.710  1.00  0.00              
ATOM     80  O   ASN    54       3.086  10.088  -0.526  1.00  0.00              
ATOM     81  N   PHE    55       3.556  10.992   1.489  1.00  0.00              
ATOM     82  CA  PHE    55       3.865  12.330   1.000  1.00  0.00              
ATOM     83  C   PHE    55       5.357  12.613   0.984  1.00  0.00              
ATOM     84  O   PHE    55       5.858  13.400   0.179  1.00  0.00              
ATOM     85  N   GLU    56       6.056  11.972   1.939  1.00  0.00              
ATOM     86  CA  GLU    56       7.472  12.277   2.091  1.00  0.00              
ATOM     87  C   GLU    56       8.187  11.198   2.904  1.00  0.00              
ATOM     88  O   GLU    56       7.645  10.578   3.821  1.00  0.00              
ATOM     89  N   PRO    57       9.437  11.018   2.512  1.00  0.00              
ATOM     90  CA  PRO    57      10.380  10.161   3.245  1.00  0.00              
ATOM     91  C   PRO    57      10.596  10.627   4.675  1.00  0.00              
ATOM     92  O   PRO    57      10.766  11.835   4.905  1.00  0.00              
END
