
#######################################################
#                                                     #
#                        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   96 (   96),  selected   96 , name T0321TS168_1-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS168_1-D1.T0321_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    W       2      W       2           -
LGA    E       3      -       -           -
LGA    I       4      -       -           -
LGA    Y       5      -       -           -
LGA    D       6      -       -           -
LGA    A       7      -       -           -
LGA    M       8      -       -           -
LGA    I       9      -       -           -
LGA    N      10      -       -           -
LGA    G      11      -       -           -
LGA    I      12      -       -           -
LGA    P      13      -       -           -
LGA    E      14      -       -           -
LGA    D      15      -       -           -
LGA    F      16      -       -           -
LGA    L      17      -       -           -
LGA    V      18      -       -           -
LGA    D      19      -       -           -
LGA    E      20      -       -           -
LGA    L      21      E       3          4.191
LGA    V      22      I       4          4.349
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    C      23      M       8          0.880
LGA    G      24      I       9          4.422
LGA    -       -      N      10           -
LGA    T      25      G      11          3.370
LGA    T      26      I      12          1.633
LGA    H      27      P      13          2.810
LGA    S      28      E      14          4.911
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    V      29      L      17           #
LGA    I      30      V      18          4.566
LGA    R      31      D      19           #
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      I      30           -
LGA    -       -      R      31           -
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    -       -      G      37           -
LGA    -       -      L      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      N      41           -
LGA    -       -      R      42           -
LGA    -       -      P      43           -
LGA    -       -      F      44           -
LGA    -       -      E      45           -
LGA    -       -      T      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      P      49           -
LGA    -       -      M      50           -
LGA    -       -      L      51           -
LGA    -       -      T      52           -
LGA    -       -      Q      53           -
LGA    -       -      N      54           -
LGA    S      32      L      55          4.441
LGA    G      33      L      56          3.339
LGA    N      34      G      57          1.323
LGA    G      35      L      58          5.558
LGA    V      36      P      59          5.340
LGA    G      37      L      60          1.264
LGA    L      38      R      61          3.129
LGA    -       -      V      62           -
LGA    G      39      A      63          2.762
LGA    P      40      A      64          2.091
LGA    -       -      G      65           -
LGA    N      41      C      66           #
LGA    R      42      V      67           #
LGA    P      43      -       -           -
LGA    F      44      -       -           -
LGA    E      45      -       -           -
LGA    T      46      -       -           -
LGA    R      47      -       -           -
LGA    M      48      -       -           -
LGA    P      49      -       -           -
LGA    M      50      -       -           -
LGA    L      51      -       -           -
LGA    T      52      -       -           -
LGA    Q      53      -       -           -
LGA    N      54      -       -           -
LGA    L      55      -       -           -
LGA    L      56      -       -           -
LGA    G      57      -       -           -
LGA    L      58      -       -           -
LGA    P      59      -       -           -
LGA    L      60      -       -           -
LGA    R      61      -       -           -
LGA    V      62      -       -           -
LGA    A      63      -       -           -
LGA    A      64      -       -           -
LGA    G      65      -       -           -
LGA    C      66      K      68           #
LGA    V      67      S      69           #
LGA    K      68      W      70          3.733
LGA    S      69      N      71          3.187
LGA    W      70      Y      72           #
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    N      71      S      76          1.214
LGA    Y      72      I      77          0.931
LGA    V      73      G      78          0.575
LGA    E      74      L      79          0.695
LGA    A      75      A      80          1.084
LGA    S      76      A      81          0.838
LGA    I      77      I      82          0.538
LGA    G      78      N      83          1.054
LGA    L      79      A      84          1.077
LGA    A      80      Y      85          1.392
LGA    A      81      Y      86          1.342
LGA    I      82      N      87          2.066
LGA    N      83      N      88          3.263
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    A      84      V      91          3.303
LGA    Y      85      A      92          2.630
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    Y      86      H      95          3.820
LGA    N      87      G      96          2.836
LGA    N      88      -       -           -
LGA    P      89      -       -           -
LGA    Q      90      -       -           -
LGA    V      91      -       -           -
LGA    A      92      -       -           -
LGA    R      93      -       -           -
LGA    E      94      -       -           -
LGA    H      95      -       -           -
LGA    G      96      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   96   96    5.0     37    2.99     8.11     24.925     1.199

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.659851 * X  +  -0.653151 * Y  +  -0.371471 * Z  + -13.149243
  Y_new =  -0.608189 * X  +  -0.754576 * Y  +   0.246418 * Z  +  46.833191
  Z_new =  -0.441251 * X  +   0.063325 * Y  +  -0.895147 * Z  +  60.054485 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.070968   -0.070625  [ DEG:   175.9535     -4.0465 ]
  Theta =   0.456993    2.684600  [ DEG:    26.1837    153.8163 ]
  Phi   =  -0.744679    2.396914  [ DEG:   -42.6670    137.3331 ]
 
# 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: T0321TS168_1-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS168_1-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   96   96   5.0   37   2.99    8.11  24.925
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS168_1-D1
PFRMAT TS
TARGET T0321
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1     -27.333  31.718  70.459  1.00 25.00           C
ATOM      2  CA  TRP     2     -26.965  33.826  67.260  1.00 25.00           C
ATOM      3  CA  GLU     3     -28.755  30.805  65.730  1.00 25.00           C
ATOM      4  CA  ILE     4     -27.484  31.781  62.253  1.00 25.00           C
ATOM      5  CA  TYR     5     -23.919  32.095  63.617  1.00 25.00           C
ATOM      6  CA  ASP     6     -24.213  28.644  65.249  1.00 25.00           C
ATOM      7  CA  ALA     7     -25.459  27.160  61.945  1.00 25.00           C
ATOM      8  CA  MET     8     -22.517  28.760  60.088  1.00 25.00           C
ATOM      9  CA  ILE     9     -20.076  27.320  62.665  1.00 25.00           C
ATOM     10  CA  ASN    10     -21.650  23.853  62.254  1.00 25.00           C
ATOM     11  CA  GLY    11     -24.886  22.102  61.201  1.00 25.00           C
ATOM     12  CA  ILE    12     -24.401  19.997  58.146  1.00 25.00           C
ATOM     13  CA  PRO    13     -22.955  22.310  55.568  1.00 25.00           C
ATOM     14  CA  GLU    14     -20.634  21.703  52.637  1.00 25.00           C
ATOM     15  CA  ASP    15     -20.453  25.421  51.863  1.00 25.00           C
ATOM     16  CA  PHE    16     -19.059  28.810  50.804  1.00 25.00           C
ATOM     17  CA  LEU    17     -18.451  32.407  51.820  1.00 25.00           C
ATOM     18  CA  VAL    18     -16.685  34.870  54.116  1.00 25.00           C
ATOM     19  CA  ASP    19     -15.871  35.836  57.667  1.00 25.00           C
ATOM     20  CA  GLU    20     -12.280  36.690  58.512  1.00 25.00           C
ATOM     21  CA  LEU    21      -9.122  38.495  57.502  1.00 25.00           C
ATOM     22  CA  VAL    22      -8.062  39.894  60.916  1.00 25.00           C
ATOM     23  CA  CYS    23      -8.321  40.270  64.748  1.00 25.00           C
ATOM     24  CA  GLY    24      -9.836  42.807  67.207  1.00 25.00           C
ATOM     25  CA  THR    25     -11.852  41.925  70.345  1.00 25.00           C
ATOM     26  CA  THR    26     -14.266  44.577  69.139  1.00 25.00           C
ATOM     27  CA  HIS    27     -16.982  45.872  66.802  1.00 25.00           C
ATOM     28  CA  SER    28     -16.862  47.116  63.184  1.00 25.00           C
ATOM     29  CA  VAL    29     -15.867  49.857  60.749  1.00 25.00           C
ATOM     30  CA  ILE    30     -15.618  53.555  61.754  1.00 25.00           C
ATOM     31  CA  ARG    31     -15.908  54.964  58.217  1.00 25.00           C
ATOM     32  CA  SER    32     -19.189  56.494  57.059  1.00 25.00           C
ATOM     33  CA  GLY    33     -19.361  58.152  60.425  1.00 25.00           C
ATOM     34  CA  ASN    34     -18.886  57.046  63.994  1.00 25.00           C
ATOM     35  CA  GLY    35     -18.118  54.998  67.109  1.00 25.00           C
ATOM     36  CA  VAL    36     -17.615  51.644  68.835  1.00 25.00           C
ATOM     37  CA  GLY    37     -15.278  51.045  65.956  1.00 25.00           C
ATOM     38  CA  LEU    38     -12.871  48.218  64.953  1.00 25.00           C
ATOM     39  CA  GLY    39     -11.764  50.140  61.831  1.00 25.00           C
ATOM     40  CA  PRO    40     -10.427  46.557  61.413  1.00 25.00           C
ATOM     41  CA  ASN    41      -7.297  44.607  62.223  1.00 25.00           C
ATOM     42  CA  ARG    42      -4.529  44.636  64.912  1.00 25.00           C
ATOM     43  CA  PRO    43      -3.946  41.944  67.581  1.00 25.00           C
ATOM     44  CA  PHE    44      -6.407  40.258  69.852  1.00 25.00           C
ATOM     45  CA  GLU    45      -4.999  36.700  69.452  1.00 25.00           C
ATOM     46  CA  THR    46      -8.198  35.430  67.837  1.00 25.00           C
ATOM     47  CA  ARG    47      -7.544  32.368  65.675  1.00 25.00           C
ATOM     48  CA  MET    48      -6.980  33.979  62.341  1.00 25.00           C
ATOM     49  CA  PRO    49      -3.261  33.278  62.229  1.00 25.00           C
ATOM     50  CA  MET    50      -3.909  31.112  59.138  1.00 25.00           C
ATOM     51  CA  LEU    51      -5.718  34.031  57.441  1.00 25.00           C
ATOM     52  CA  THR    52      -2.780  36.351  58.246  1.00 25.00           C
ATOM     53  CA  GLN    53      -0.329  33.795  56.788  1.00 25.00           C
ATOM     54  CA  ASN    54      -2.456  33.531  53.614  1.00 25.00           C
ATOM     55  CA  LEU    55      -2.506  37.348  53.299  1.00 25.00           C
ATOM     56  CA  LEU    56       1.300  37.455  53.707  1.00 25.00           C
ATOM     57  CA  GLY    57       3.604  36.925  56.721  1.00 25.00           C
ATOM     58  CA  LEU    58       1.871  37.720  60.033  1.00 25.00           C
ATOM     59  CA  PRO    59       0.747  40.434  62.540  1.00 25.00           C
ATOM     60  CA  LEU    60       3.739  42.789  62.362  1.00 25.00           C
ATOM     61  CA  ARG    61       5.837  44.399  59.591  1.00 25.00           C
ATOM     62  CA  VAL    62       4.381  41.948  57.033  1.00 25.00           C
ATOM     63  CA  ALA    63       0.836  42.771  58.226  1.00 25.00           C
ATOM     64  CA  ALA    64       1.569  46.516  57.902  1.00 25.00           C
ATOM     65  CA  GLY    65       2.907  45.973  54.354  1.00 25.00           C
ATOM     66  CA  CYS    66      -0.244  43.996  53.443  1.00 25.00           C
ATOM     67  CA  VAL    67      -2.440  46.806  54.840  1.00 25.00           C
ATOM     68  CA  LYS    68      -0.480  49.387  52.800  1.00 25.00           C
ATOM     69  CA  SER    69      -4.115  50.510  52.725  1.00 25.00           C
ATOM     70  CA  TRP    70      -5.229  50.578  56.339  1.00 25.00           C
ATOM     71  CA  ASN    71      -2.882  52.846  58.321  1.00 25.00           C
ATOM     72  CA  TYR    72      -5.479  54.710  60.356  1.00 25.00           C
ATOM     73  CA  VAL    73      -7.346  51.377  60.073  1.00 25.00           C
ATOM     74  CA  GLU    74      -4.653  49.662  62.191  1.00 25.00           C
ATOM     75  CA  ALA    75      -4.935  52.424  64.829  1.00 25.00           C
ATOM     76  CA  SER    76      -8.743  52.012  64.888  1.00 25.00           C
ATOM     77  CA  ILE    77      -8.352  48.227  65.321  1.00 25.00           C
ATOM     78  CA  GLY    78      -5.895  48.786  68.204  1.00 25.00           C
ATOM     79  CA  LEU    79      -8.352  51.210  69.862  1.00 25.00           C
ATOM     80  CA  ALA    80     -11.170  48.642  69.496  1.00 25.00           C
ATOM     81  CA  ALA    81      -8.947  45.943  71.058  1.00 25.00           C
ATOM     82  CA  ILE    82      -8.115  48.281  73.974  1.00 25.00           C
ATOM     83  CA  ASN    83     -11.841  49.001  74.492  1.00 25.00           C
ATOM     84  CA  ALA    84     -12.592  45.246  74.488  1.00 25.00           C
ATOM     85  CA  TYR    85      -9.819  44.663  77.064  1.00 25.00           C
ATOM     86  CA  TYR    86      -7.131  42.584  75.317  1.00 25.00           C
ATOM     87  CA  ASN    87      -5.364  41.448  78.545  1.00 25.00           C
ATOM     88  CA  ASN    88      -4.376  44.680  80.367  1.00 25.00           C
ATOM     89  CA  PRO    89      -2.501  46.175  77.402  1.00 25.00           C
ATOM     90  CA  GLN    90       0.527  46.251  79.747  1.00 25.00           C
ATOM     91  CA  VAL    91       0.671  50.068  79.476  1.00 25.00           C
ATOM     92  CA  ALA    92      -3.068  50.292  80.278  1.00 25.00           C
ATOM     93  CA  ARG    93      -2.574  48.021  83.323  1.00 25.00           C
ATOM     94  CA  GLU    94       0.332  50.212  84.516  1.00 25.00           C
ATOM     95  CA  HIS    95      -1.831  53.346  84.110  1.00 25.00           C
ATOM     96  CA  GLY    96      -0.636  56.914  83.328  1.00 25.00           C
TER
END
