
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS168_3-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      E       3           -
LGA    I       4      I       4           -
LGA    Y       5      Y       5           -
LGA    D       6      D       6           -
LGA    A       7      A       7           -
LGA    M       8      M       8           -
LGA    I       9      I       9           -
LGA    N      10      N      10           -
LGA    G      11      G      11           -
LGA    I      12      I      12           -
LGA    P      13      P      13           -
LGA    E      14      E      14           -
LGA    D      15      D      15           -
LGA    F      16      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    L      17      D      19          4.917
LGA    V      18      E      20          4.190
LGA    D      19      L      21          4.072
LGA    E      20      V      22           -
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      C      23          2.227
LGA    N      34      G      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    G      35      V      29          2.796
LGA    V      36      I      30          4.759
LGA    G      37      R      31           -
LGA    L      38      S      32           -
LGA    G      39      G      33           -
LGA    P      40      N      34           -
LGA    N      41      G      35           -
LGA    R      42      V      36           -
LGA    P      43      G      37           -
LGA    F      44      L      38           -
LGA    E      45      G      39           -
LGA    T      46      P      40           -
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      N      41           #
LGA    L      56      R      42          2.726
LGA    G      57      P      43          3.958
LGA    L      58      F      44          1.116
LGA    P      59      -       -           -
LGA    L      60      E      45          1.731
LGA    R      61      T      46           #
LGA    V      62      R      47          3.992
LGA    A      63      M      48          3.538
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           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    A      64      Y      72          4.599
LGA    G      65      V      73          4.086
LGA    C      66      E      74          5.194
LGA    V      67      -       -           -
LGA    K      68      -       -           -
LGA    S      69      -       -           -
LGA    W      70      -       -           -
LGA    N      71      A      75          2.072
LGA    Y      72      S      76          1.533
LGA    V      73      I      77          1.699
LGA    E      74      G      78          1.657
LGA    A      75      L      79          0.566
LGA    S      76      A      80          0.302
LGA    I      77      A      81          1.463
LGA    G      78      I      82          2.186
LGA    L      79      N      83          2.266
LGA    A      80      A      84          2.120
LGA    A      81      Y      85          2.427
LGA    I      82      Y      86          3.368
LGA    N      83      N      87          2.664
LGA    A      84      N      88          0.936
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    Y      85      V      91          3.300
LGA    Y      86      A      92          2.473
LGA    N      87      R      93          1.662
LGA    N      88      E      94          2.450
LGA    P      89      H      95          1.450
LGA    Q      90      G      96          5.919
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     35    3.08     5.71     24.080     1.101

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.665619 * X  +   0.698420 * Y  +   0.262985 * Z  +  -2.571981
  Y_new =  -0.266749 * X  +  -0.551763 * Y  +   0.790192 * Z  +  58.974686
  Z_new =   0.696991 * X  +   0.455816 * Y  +   0.553566 * Z  +  70.121269 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.688857   -2.452735  [ DEG:    39.4686   -140.5314 ]
  Theta =  -0.771193   -2.370400  [ DEG:   -44.1861   -135.8139 ]
  Phi   =  -2.760437    0.381155  [ DEG:  -158.1614     21.8386 ]
 
# 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_3-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS168_3-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   35   3.08    5.71  24.080
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS168_3-D1
PFRMAT TS
TARGET T0321
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1     -17.128  76.818  68.803  1.00 25.00           C
ATOM      2  CA  TRP     2     -14.699  74.872  66.639  1.00 25.00           C
ATOM      3  CA  GLU     3     -16.636  76.493  63.760  1.00 25.00           C
ATOM      4  CA  ILE     4     -14.447  74.649  61.216  1.00 25.00           C
ATOM      5  CA  TYR     5     -15.069  71.341  63.042  1.00 25.00           C
ATOM      6  CA  ASP     6     -18.839  72.006  63.017  1.00 25.00           C
ATOM      7  CA  ALA     7     -18.706  72.756  59.263  1.00 25.00           C
ATOM      8  CA  MET     8     -16.779  69.502  58.657  1.00 25.00           C
ATOM      9  CA  ILE     9     -19.379  67.555  60.684  1.00 25.00           C
ATOM     10  CA  ASN    10     -22.201  69.157  58.651  1.00 25.00           C
ATOM     11  CA  GLY    11     -24.565  71.311  56.538  1.00 25.00           C
ATOM     12  CA  ILE    12     -27.340  69.095  57.842  1.00 25.00           C
ATOM     13  CA  PRO    13     -28.402  65.441  58.027  1.00 25.00           C
ATOM     14  CA  GLU    14     -26.747  62.038  58.605  1.00 25.00           C
ATOM     15  CA  ASP    15     -23.101  61.012  58.894  1.00 25.00           C
ATOM     16  CA  PHE    16     -19.997  60.614  61.120  1.00 25.00           C
ATOM     17  CA  LEU    17     -16.926  60.416  63.380  1.00 25.00           C
ATOM     18  CA  VAL    18     -13.769  58.361  63.887  1.00 25.00           C
ATOM     19  CA  ASP    19     -10.465  56.573  63.804  1.00 25.00           C
ATOM     20  CA  GLU    20      -8.987  56.149  67.242  1.00 25.00           C
ATOM     21  CA  LEU    21      -8.889  57.489  70.803  1.00 25.00           C
ATOM     22  CA  VAL    22      -5.300  56.299  70.383  1.00 25.00           C
ATOM     23  CA  CYS    23      -4.881  55.164  73.939  1.00 25.00           C
ATOM     24  CA  GLY    24      -4.873  54.153  77.650  1.00 25.00           C
ATOM     25  CA  THR    25      -1.585  54.097  79.613  1.00 25.00           C
ATOM     26  CA  THR    26       0.793  52.336  77.152  1.00 25.00           C
ATOM     27  CA  HIS    27      -0.723  52.119  73.701  1.00 25.00           C
ATOM     28  CA  SER    28       0.716  54.139  70.743  1.00 25.00           C
ATOM     29  CA  VAL    29      -1.577  55.690  68.089  1.00 25.00           C
ATOM     30  CA  ILE    30      -2.497  58.688  66.038  1.00 25.00           C
ATOM     31  CA  ARG    31      -2.664  61.454  63.369  1.00 25.00           C
ATOM     32  CA  SER    32      -3.924  58.866  60.884  1.00 25.00           C
ATOM     33  CA  GLY    33      -6.354  61.502  59.609  1.00 25.00           C
ATOM     34  CA  ASN    34      -9.271  61.062  61.919  1.00 25.00           C
ATOM     35  CA  GLY    35      -6.918  60.115  64.730  1.00 25.00           C
ATOM     36  CA  VAL    36      -5.690  60.217  68.358  1.00 25.00           C
ATOM     37  CA  GLY    37      -3.093  60.090  71.157  1.00 25.00           C
ATOM     38  CA  LEU    38       0.548  58.825  70.919  1.00 25.00           C
ATOM     39  CA  GLY    39       3.771  60.845  71.173  1.00 25.00           C
ATOM     40  CA  PRO    40       6.715  62.110  69.118  1.00 25.00           C
ATOM     41  CA  ASN    41       7.667  62.557  72.752  1.00 25.00           C
ATOM     42  CA  ARG    42      10.294  60.660  74.773  1.00 25.00           C
ATOM     43  CA  PRO    43      12.516  63.540  73.712  1.00 25.00           C
ATOM     44  CA  PHE    44      11.856  63.183  69.966  1.00 25.00           C
ATOM     45  CA  GLU    45      14.546  65.928  69.716  1.00 25.00           C
ATOM     46  CA  THR    46      11.468  68.091  68.951  1.00 25.00           C
ATOM     47  CA  ARG    47       9.786  69.850  66.014  1.00 25.00           C
ATOM     48  CA  MET    48       8.519  67.730  63.070  1.00 25.00           C
ATOM     49  CA  PRO    49      12.199  66.802  63.337  1.00 25.00           C
ATOM     50  CA  MET    50      14.198  64.291  61.249  1.00 25.00           C
ATOM     51  CA  LEU    51      12.995  61.429  63.491  1.00 25.00           C
ATOM     52  CA  THR    52       9.374  62.618  63.106  1.00 25.00           C
ATOM     53  CA  GLN    53       9.797  62.750  59.302  1.00 25.00           C
ATOM     54  CA  ASN    54      11.232  59.200  59.313  1.00 25.00           C
ATOM     55  CA  LEU    55       8.273  57.983  61.417  1.00 25.00           C
ATOM     56  CA  LEU    56       5.827  59.640  58.980  1.00 25.00           C
ATOM     57  CA  GLY    57       7.605  57.852  56.123  1.00 25.00           C
ATOM     58  CA  LEU    58       5.847  59.746  53.370  1.00 25.00           C
ATOM     59  CA  PRO    59       2.764  61.168  54.995  1.00 25.00           C
ATOM     60  CA  LEU    60       0.922  58.997  52.495  1.00 25.00           C
ATOM     61  CA  ARG    61      -0.260  57.110  55.611  1.00 25.00           C
ATOM     62  CA  VAL    62      -2.893  59.810  56.278  1.00 25.00           C
ATOM     63  CA  ALA    63      -4.098  59.567  52.650  1.00 25.00           C
ATOM     64  CA  ALA    64      -4.348  55.758  52.964  1.00 25.00           C
ATOM     65  CA  GLY    65      -6.358  56.132  56.202  1.00 25.00           C
ATOM     66  CA  CYS    66      -8.710  58.618  54.484  1.00 25.00           C
ATOM     67  CA  VAL    67      -9.185  56.188  51.563  1.00 25.00           C
ATOM     68  CA  LYS    68      -9.968  53.354  54.016  1.00 25.00           C
ATOM     69  CA  SER    69      -9.423  50.545  56.472  1.00 25.00           C
ATOM     70  CA  TRP    70      -5.857  49.881  55.200  1.00 25.00           C
ATOM     71  CA  ASN    71      -2.596  51.860  55.624  1.00 25.00           C
ATOM     72  CA  TYR    72      -4.216  52.875  58.912  1.00 25.00           C
ATOM     73  CA  VAL    73      -7.709  53.444  60.377  1.00 25.00           C
ATOM     74  CA  GLU    74      -7.939  49.742  61.331  1.00 25.00           C
ATOM     75  CA  ALA    75      -4.504  49.937  63.015  1.00 25.00           C
ATOM     76  CA  SER    76      -5.606  53.049  64.955  1.00 25.00           C
ATOM     77  CA  ILE    77      -8.796  51.252  66.077  1.00 25.00           C
ATOM     78  CA  GLY    78      -6.726  48.242  67.226  1.00 25.00           C
ATOM     79  CA  LEU    79      -4.393  50.563  69.184  1.00 25.00           C
ATOM     80  CA  ALA    80      -7.412  52.246  70.835  1.00 25.00           C
ATOM     81  CA  ALA    81      -8.834  48.818  71.782  1.00 25.00           C
ATOM     82  CA  ILE    82      -5.460  47.805  73.282  1.00 25.00           C
ATOM     83  CA  ASN    83      -5.348  51.063  75.293  1.00 25.00           C
ATOM     84  CA  ALA    84      -8.900  50.423  76.574  1.00 25.00           C
ATOM     85  CA  TYR    85      -7.917  46.866  77.598  1.00 25.00           C
ATOM     86  CA  TYR    86      -5.780  44.254  79.414  1.00 25.00           C
ATOM     87  CA  ASN    87      -9.079  43.345  81.089  1.00 25.00           C
ATOM     88  CA  ASN    88     -11.584  42.635  78.354  1.00 25.00           C
ATOM     89  CA  PRO    89      -8.762  40.525  76.794  1.00 25.00           C
ATOM     90  CA  GLN    90     -10.331  37.410  78.374  1.00 25.00           C
ATOM     91  CA  VAL    91     -12.270  36.718  75.144  1.00 25.00           C
ATOM     92  CA  ALA    92      -9.049  37.084  73.105  1.00 25.00           C
ATOM     93  CA  ARG    93      -7.251  34.658  75.461  1.00 25.00           C
ATOM     94  CA  GLU    94     -10.118  32.145  75.102  1.00 25.00           C
ATOM     95  CA  HIS    95      -9.943  32.452  71.289  1.00 25.00           C
ATOM     96  CA  GLY    96     -12.953  30.809  69.657  1.00 25.00           C
TER
END
