
#######################################################
#                                                     #
#                        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   88 (   88),  selected   88 , name T0288TS168_3-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS168_3-D1.T0288_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      -       -           -
LGA    V       3      M       2           #
LGA    -       -      V       3           -
LGA    P       4      P       4          3.113
LGA    G       5      G       5          1.780
LGA    K       6      K       6          1.450
LGA    V       7      V       7          1.270
LGA    T       8      T       8          1.605
LGA    L       9      L       9          1.628
LGA    Q      10      Q      10          1.495
LGA    K      11      K      11          1.528
LGA    D      12      D      12          1.990
LGA    A      13      A      13          0.414
LGA    Q      14      Q      14          0.317
LGA    N      15      N      15          0.983
LGA    L      16      L      16          1.194
LGA    I      17      I      17          0.461
LGA    G      18      G      18          0.305
LGA    I      19      I      19          2.669
LGA    S      20      S      20          1.178
LGA    I      21      I      21          1.457
LGA    G      22      G      22          1.781
LGA    G      23      G      23          3.948
LGA    G      24      G      24          1.473
LGA    A      25      -       -           -
LGA    Q      26      -       -           -
LGA    Y      27      A      25          1.293
LGA    C      28      Q      26          6.211
LGA    P      29      P      29          2.274
LGA    C      30      C      30          1.544
LGA    L      31      L      31          2.439
LGA    Y      32      Y      32          2.537
LGA    I      33      I      33          0.867
LGA    V      34      V      34          0.725
LGA    Q      35      Q      35          0.474
LGA    V      36      V      36          0.366
LGA    F      37      F      37          1.239
LGA    D      38      D      38          0.579
LGA    N      39      N      39          1.023
LGA    T      40      T      40          1.604
LGA    P      41      P      41          1.449
LGA    A      42      A      42          0.791
LGA    A      43      A      43          1.175
LGA    L      44      L      44          2.319
LGA    D      45      D      45          2.205
LGA    G      46      G      46          0.961
LGA    T      47      T      47          0.963
LGA    V      48      V      48          0.847
LGA    A      49      A      49          0.784
LGA    A      50      A      50          1.368
LGA    G      51      G      51          1.456
LGA    D      52      D      52          1.172
LGA    E      53      E      53          1.495
LGA    I      54      I      54          0.960
LGA    T      55      T      55          1.635
LGA    G      56      G      56          2.573
LGA    V      57      V      57          1.799
LGA    N      58      N      58          0.557
LGA    G      59      G      59          1.416
LGA    R      60      R      60          0.987
LGA    S      61      S      61          1.106
LGA    I      62      I      62          1.411
LGA    K      63      K      63          2.399
LGA    G      64      G      64          2.145
LGA    K      65      K      65          1.454
LGA    T      66      T      66          1.103
LGA    K      67      K      67          1.008
LGA    V      68      V      68          1.313
LGA    E      69      E      69          1.009
LGA    V      70      V      70          0.506
LGA    A      71      A      71          0.637
LGA    K      72      K      72          0.795
LGA    M      73      M      73          0.728
LGA    I      74      I      74          0.929
LGA    Q      75      Q      75          0.610
LGA    E      76      E      76          0.957
LGA    V      77      V      77          0.851
LGA    K      78      K      78          1.199
LGA    G      79      G      79          1.416
LGA    E      80      E      80          0.782
LGA    V      81      V      81          1.897
LGA    T      82      T      82          0.523
LGA    I      83      I      83          0.496
LGA    H      84      H      84          0.379
LGA    Y      85      Y      85          1.248
LGA    N      86      N      86          0.675
LGA    K      87      K      87          1.115
LGA    L      88      L      88          1.482

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     83    1.60    97.59     89.003     4.875

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.221482 * X  +  -0.807281 * Y  +   0.547031 * Z  +  27.589209
  Y_new =   0.646625 * X  +   0.541481 * Y  +   0.537285 * Z  +  17.395077
  Z_new =  -0.729947 * X  +   0.234725 * Y  +   0.641936 * Z  +  13.140738 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.350549   -2.791044  [ DEG:    20.0850   -159.9150 ]
  Theta =   0.818244    2.323349  [ DEG:    46.8819    133.1181 ]
  Phi   =   1.240800   -1.900793  [ DEG:    71.0926   -108.9074 ]
 
# 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: T0288TS168_3-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS168_3-D1.T0288_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   88   86   5.0   83   1.60   97.59  89.003
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS168_3-D1
PFRMAT TS
TARGET T0288
MODEL 3
PARENT N/A
ATOM      1  CA  SER     1      24.050   8.683  31.926  1.00 25.00           C
ATOM      2  CA  MET     2      25.132  11.679  29.846  1.00 25.00           C
ATOM      3  CA  VAL     3      25.030   9.954  26.432  1.00 25.00           C
ATOM      4  CA  PRO     4      24.003  13.126  24.546  1.00 25.00           C
ATOM      5  CA  GLY     5      21.587  16.035  24.273  1.00 25.00           C
ATOM      6  CA  LYS     6      20.703  17.664  20.961  1.00 25.00           C
ATOM      7  CA  VAL     7      21.474  20.376  18.460  1.00 25.00           C
ATOM      8  CA  THR     8      18.550  21.835  16.537  1.00 25.00           C
ATOM      9  CA  LEU     9      20.427  24.249  14.187  1.00 25.00           C
ATOM     10  CA  GLN    10      17.776  25.918  11.977  1.00 25.00           C
ATOM     11  CA  LYS    11      18.597  26.422   8.334  1.00 25.00           C
ATOM     12  CA  ASP    12      17.996  29.363   5.981  1.00 25.00           C
ATOM     13  CA  ALA    13      19.549  30.513   2.713  1.00 25.00           C
ATOM     14  CA  GLN    14      22.593  28.777   1.175  1.00 25.00           C
ATOM     15  CA  ASN    15      21.533  25.742   3.088  1.00 25.00           C
ATOM     16  CA  LEU    16      24.573  24.458   4.877  1.00 25.00           C
ATOM     17  CA  ILE    17      24.105  24.469   8.634  1.00 25.00           C
ATOM     18  CA  GLY    18      27.496  26.179   8.813  1.00 25.00           C
ATOM     19  CA  ILE    19      29.662  23.485   7.199  1.00 25.00           C
ATOM     20  CA  SER    20      32.987  21.680   7.353  1.00 25.00           C
ATOM     21  CA  ILE    21      32.959  17.877   7.423  1.00 25.00           C
ATOM     22  CA  GLY    22      36.454  16.471   7.462  1.00 25.00           C
ATOM     23  CA  GLY    23      35.785  12.849   6.581  1.00 25.00           C
ATOM     24  CA  GLY    24      36.053  10.098   9.151  1.00 25.00           C
ATOM     25  CA  ALA    25      35.651   6.382   8.278  1.00 25.00           C
ATOM     26  CA  GLN    26      39.409   5.757   7.667  1.00 25.00           C
ATOM     27  CA  TYR    27      41.081   8.242  10.074  1.00 25.00           C
ATOM     28  CA  CYS    28      38.587   7.191  12.788  1.00 25.00           C
ATOM     29  CA  PRO    29      35.183   5.776  13.636  1.00 25.00           C
ATOM     30  CA  CYS    30      32.911   8.731  12.852  1.00 25.00           C
ATOM     31  CA  LEU    31      30.740  11.545  11.431  1.00 25.00           C
ATOM     32  CA  TYR    32      33.006  14.591  11.317  1.00 25.00           C
ATOM     33  CA  ILE    33      33.226  18.160  12.718  1.00 25.00           C
ATOM     34  CA  VAL    34      35.946  20.345  11.168  1.00 25.00           C
ATOM     35  CA  GLN    35      34.737  23.801  12.190  1.00 25.00           C
ATOM     36  CA  VAL    36      31.753  26.076  12.374  1.00 25.00           C
ATOM     37  CA  PHE    37      32.363  29.396  10.703  1.00 25.00           C
ATOM     38  CA  ASP    38      30.322  32.604  10.866  1.00 25.00           C
ATOM     39  CA  ASN    39      26.662  33.489  11.421  1.00 25.00           C
ATOM     40  CA  THR    40      24.849  31.297   8.971  1.00 25.00           C
ATOM     41  CA  PRO    41      24.106  28.672  11.682  1.00 25.00           C
ATOM     42  CA  ALA    42      25.616  25.772  13.677  1.00 25.00           C
ATOM     43  CA  ALA    43      26.683  28.792  15.809  1.00 25.00           C
ATOM     44  CA  LEU    44      23.128  29.531  16.842  1.00 25.00           C
ATOM     45  CA  ASP    45      22.272  27.763  20.164  1.00 25.00           C
ATOM     46  CA  GLY    46      25.981  28.464  20.843  1.00 25.00           C
ATOM     47  CA  THR    47      26.476  24.797  20.248  1.00 25.00           C
ATOM     48  CA  VAL    48      28.735  22.026  18.825  1.00 25.00           C
ATOM     49  CA  ALA    49      32.394  22.602  17.964  1.00 25.00           C
ATOM     50  CA  ALA    50      35.915  21.354  17.243  1.00 25.00           C
ATOM     51  CA  GLY    51      36.670  17.713  16.787  1.00 25.00           C
ATOM     52  CA  ASP    52      33.358  16.602  18.248  1.00 25.00           C
ATOM     53  CA  GLU    53      31.565  14.094  15.974  1.00 25.00           C
ATOM     54  CA  ILE    54      27.897  13.877  14.921  1.00 25.00           C
ATOM     55  CA  THR    55      25.665  10.730  15.064  1.00 25.00           C
ATOM     56  CA  GLY    56      23.599  11.288  11.908  1.00 25.00           C
ATOM     57  CA  VAL    57      20.876  13.536  10.488  1.00 25.00           C
ATOM     58  CA  ASN    58      17.614  12.665  12.193  1.00 25.00           C
ATOM     59  CA  GLY    59      17.093   9.377  14.065  1.00 25.00           C
ATOM     60  CA  ARG    60      20.039   7.574  12.508  1.00 25.00           C
ATOM     61  CA  SER    61      23.581   6.382  13.304  1.00 25.00           C
ATOM     62  CA  ILE    62      26.803   7.415  11.463  1.00 25.00           C
ATOM     63  CA  LYS    63      29.199   5.242  13.532  1.00 25.00           C
ATOM     64  CA  GLY    64      30.203   2.676  10.896  1.00 25.00           C
ATOM     65  CA  LYS    65      29.363   4.898   7.875  1.00 25.00           C
ATOM     66  CA  THR    66      31.604   6.114   5.052  1.00 25.00           C
ATOM     67  CA  LYS    67      31.562   9.768   6.135  1.00 25.00           C
ATOM     68  CA  VAL    68      30.323  10.323   2.554  1.00 25.00           C
ATOM     69  CA  GLU    69      26.861   8.998   3.521  1.00 25.00           C
ATOM     70  CA  VAL    70      26.780  11.349   6.544  1.00 25.00           C
ATOM     71  CA  ALA    71      27.746  14.302   4.305  1.00 25.00           C
ATOM     72  CA  LYS    72      24.968  13.371   1.838  1.00 25.00           C
ATOM     73  CA  MET    73      22.443  13.187   4.712  1.00 25.00           C
ATOM     74  CA  ILE    74      23.573  16.627   5.959  1.00 25.00           C
ATOM     75  CA  GLN    75      23.182  18.062   2.430  1.00 25.00           C
ATOM     76  CA  GLU    76      19.664  16.569   2.187  1.00 25.00           C
ATOM     77  CA  VAL    77      17.475  17.815   4.998  1.00 25.00           C
ATOM     78  CA  LYS    78      16.182  21.171   3.891  1.00 25.00           C
ATOM     79  CA  GLY    79      13.515  22.051   6.437  1.00 25.00           C
ATOM     80  CA  GLU    80      15.818  21.173   9.292  1.00 25.00           C
ATOM     81  CA  VAL    81      19.335  20.474  10.675  1.00 25.00           C
ATOM     82  CA  THR    82      18.910  17.845  13.439  1.00 25.00           C
ATOM     83  CA  ILE    83      22.450  16.651  14.152  1.00 25.00           C
ATOM     84  CA  HIS    84      23.359  14.761  17.361  1.00 25.00           C
ATOM     85  CA  TYR    85      26.020  15.296  20.036  1.00 25.00           C
ATOM     86  CA  ASN    86      29.282  13.754  21.146  1.00 25.00           C
ATOM     87  CA  LYS    87      30.406  16.772  23.263  1.00 25.00           C
ATOM     88  CA  LEU    88      34.038  15.670  23.144  1.00 25.00           C
TER
END
