
#######################################################
#                                                     #
#                        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   91 (   91),  selected   91 , name T0299TS599_2-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS599_2-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    R       3      -       -           -
LGA    Y       4      -       -           -
LGA    A       5      -       -           -
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    V       8      -       -           -
LGA    R       9      -       -           -
LGA    G      10      -       -           -
LGA    I      11      -       -           -
LGA    N      12      -       -           -
LGA    V      13      -       -           -
LGA    G      14      -       -           -
LGA    G      15      M       1           #
LGA    K      16      T       2          1.828
LGA    N      17      R       3          3.717
LGA    K      18      Y       4           -
LGA    V      19      A       5           -
LGA    V      20      L       6           -
LGA    M      21      L       7           -
LGA    A      22      V       8           -
LGA    E      23      R       9           -
LGA    L      24      G      10           -
LGA    R      25      I      11           -
LGA    Q      26      -       -           -
LGA    E      27      -       -           -
LGA    L      28      -       -           -
LGA    T      29      -       -           -
LGA    N      30      -       -           -
LGA    L      31      -       -           -
LGA    G      32      -       -           -
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    K      35      -       -           -
LGA    V      36      N      12           #
LGA    E      37      V      13           -
LGA    S      38      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    Y      39      V      19           #
LGA    I      40      V      20          5.683
LGA    N      41      M      21           #
LGA    S      42      A      22          3.840
LGA    G      43      E      23          2.082
LGA    -       -      L      24           -
LGA    -       -      R      25           -
LGA    N      44      Q      26          2.208
LGA    -       -      E      27           -
LGA    I      45      L      28           #
LGA    F      46      T      29          2.394
LGA    -       -      N      30           -
LGA    -       -      L      31           -
LGA    -       -      G      32           -
LGA    -       -      L      33           -
LGA    F      47      E      34          1.779
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    -       -      G      43           -
LGA    -       -      N      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      F      47           -
LGA    T      48      T      48          4.229
LGA    S      49      S      49          1.393
LGA    I      50      I      50          0.742
LGA    D      51      D      51          1.248
LGA    S      52      S      52          0.760
LGA    K      53      K      53          0.586
LGA    A      54      A      54          0.432
LGA    Q      55      Q      55          0.259
LGA    L      56      L      56          0.587
LGA    V      57      V      57          0.845
LGA    E      58      E      58          0.686
LGA    K      59      K      59          0.502
LGA    L      60      L      60          0.366
LGA    E      61      E      61          0.501
LGA    T      62      T      62          0.661
LGA    F      63      F      63          0.724
LGA    F      64      F      64          0.280
LGA    A      65      A      65          0.688
LGA    V      66      V      66          1.051
LGA    H      67      H      67          1.533
LGA    Y      68      Y      68          2.841
LGA    P      69      P      69          3.103
LGA    F      70      F      70          3.465
LGA    I      71      I      71           #
LGA    Q      72      Q      72          1.335
LGA    S      73      S      73          2.281
LGA    F      74      F      74          4.219
LGA    S      75      S      75           #
LGA    L      76      -       -           -
LGA    L      77      -       -           -
LGA    S      78      -       -           -
LGA    A     168      -       -           -
LGA    K     169      -       -           -
LGA    T     170      -       -           -
LGA    F     171      L      76           #
LGA    D     172      -       -           -
LGA    K     173      -       -           -
LGA    I     174      -       -           -
LGA    G     175      L      77          5.550
LGA    Q     176      -       -           -
LGA    M     177      -       -           -
LGA    L     178      -       -           -
LGA    K     179      S      78          5.386
LGA    K     180      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    -       -      I     174           -
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     36    2.51    72.22     31.830     1.379

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.934643 * X  +  -0.106384 * Y  +   0.339301 * Z  +  -0.268572
  Y_new =   0.331845 * X  +   0.081869 * Y  +   0.939774 * Z  +  45.894268
  Z_new =  -0.127755 * X  +   0.990949 * Y  +  -0.041215 * Z  +   0.094059 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.612364   -1.529229  [ DEG:    92.3816    -87.6184 ]
  Theta =   0.128105    3.013487  [ DEG:     7.3399    172.6601 ]
  Phi   =   2.800426   -0.341167  [ DEG:   160.4526    -19.5474 ]
 
# 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: T0299TS599_2-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS599_2-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   91   91   5.0   36   2.51   72.22  31.830
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS599_2-D1
PFRMAT TS                                                                       
TARGET T0299                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -3.445  29.112  -0.624  1.00  0.00              
ATOM      2  CA  THR     2      -3.109  32.691  -0.487  1.00  0.00              
ATOM      3  CA  ARG     3      -3.933  35.273   1.851  1.00  0.00              
ATOM      4  CA  TYR     4      -4.889  35.326  -1.607  1.00  0.00              
ATOM      5  CA  ALA     5      -8.265  33.676  -1.063  1.00  0.00              
ATOM      6  CA  LEU     6      -9.484  35.893   1.765  1.00  0.00              
ATOM      7  CA  LEU     7      -8.523  39.118  -0.014  1.00  0.00              
ATOM      8  CA  VAL     8     -10.189  38.036  -3.304  1.00  0.00              
ATOM      9  CA  ARG     9     -13.549  36.753  -2.069  1.00  0.00              
ATOM     10  CA  GLY    10     -14.250  39.937  -0.182  1.00  0.00              
ATOM     11  CA  ILE    11     -12.944  43.080  -1.485  1.00  0.00              
ATOM     12  CA  ASN    12     -13.799  46.328   0.170  1.00  0.00              
ATOM     13  CA  VAL    13     -13.798  49.456  -2.004  1.00  0.00              
ATOM     14  CA  GLY    14     -13.138  52.725  -0.278  1.00  0.00              
ATOM     15  CA  GLY    15     -14.736  55.171  -2.719  1.00  0.00              
ATOM     16  CA  LYS    16     -17.999  53.326  -3.320  1.00  0.00              
ATOM     17  CA  ASN    17     -17.192  51.411  -6.403  1.00  0.00              
ATOM     18  CA  LYS    18     -18.280  47.778  -6.541  1.00  0.00              
ATOM     19  CA  VAL    19     -15.796  46.362  -9.090  1.00  0.00              
ATOM     20  CA  VAL    20     -16.686  43.572 -11.444  1.00  0.00              
ATOM     21  CA  MET    21     -14.549  40.540 -12.024  1.00  0.00              
ATOM     22  CA  ALA    22     -14.381  41.383 -15.674  1.00  0.00              
ATOM     23  CA  GLU    23     -12.840  44.805 -14.977  1.00  0.00              
ATOM     24  CA  LEU    24     -10.284  43.372 -12.656  1.00  0.00              
ATOM     25  CA  ARG    25      -9.357  40.730 -15.220  1.00  0.00              
ATOM     26  CA  GLN    26      -9.008  43.392 -17.964  1.00  0.00              
ATOM     27  CA  GLU    27      -6.828  45.509 -15.747  1.00  0.00              
ATOM     28  CA  LEU    28      -4.586  42.515 -14.882  1.00  0.00              
ATOM     29  CA  THR    29      -4.265  41.573 -18.503  1.00  0.00              
ATOM     30  CA  ASN    30      -3.267  45.080 -19.504  1.00  0.00              
ATOM     31  CA  LEU    31      -0.703  45.191 -16.736  1.00  0.00              
ATOM     32  CA  GLY    32       0.827  41.856 -17.683  1.00  0.00              
ATOM     33  CA  LEU    33      -0.602  39.804 -14.776  1.00  0.00              
ATOM     34  CA  GLU    34      -1.456  36.255 -15.671  1.00  0.00              
ATOM     35  CA  LYS    35      -0.729  34.256 -12.532  1.00  0.00              
ATOM     36  CA  VAL    36      -2.621  36.424 -10.050  1.00  0.00              
ATOM     37  CA  GLU    37      -5.515  36.613 -12.544  1.00  0.00              
ATOM     38  CA  SER    38      -5.787  32.808 -12.623  1.00  0.00              
ATOM     39  CA  TYR    39      -5.917  32.669  -8.810  1.00  0.00              
ATOM     40  CA  ILE    40      -8.657  35.347  -8.799  1.00  0.00              
ATOM     41  CA  ASN    41     -10.794  33.467 -11.331  1.00  0.00              
ATOM     42  CA  SER    42     -10.907  30.425  -9.102  1.00  0.00              
ATOM     43  CA  GLY    43     -11.574  32.040  -5.781  1.00  0.00              
ATOM     44  CA  ASN    44     -14.130  34.651  -6.682  1.00  0.00              
ATOM     45  CA  ILE    45     -14.085  38.299  -5.962  1.00  0.00              
ATOM     46  CA  PHE    46     -16.995  39.982  -4.318  1.00  0.00              
ATOM     47  CA  PHE    47     -16.933  43.811  -3.990  1.00  0.00              
ATOM     48  CA  THR    48     -18.568  45.457  -1.099  1.00  0.00              
ATOM     49  CA  SER    49     -19.125  49.166  -1.002  1.00  0.00              
ATOM     50  CA  ILE    50     -20.807  50.216   2.179  1.00  0.00              
ATOM     51  CA  ASP    51     -18.225  48.888   4.567  1.00  0.00              
ATOM     52  CA  SER    52     -17.001  51.849   6.706  1.00  0.00              
ATOM     53  CA  LYS    53     -13.264  52.047   6.154  1.00  0.00              
ATOM     54  CA  ALA    54     -12.311  51.031   9.714  1.00  0.00              
ATOM     55  CA  GLN    55     -14.608  48.030   9.758  1.00  0.00              
ATOM     56  CA  LEU    56     -13.432  46.801   6.428  1.00  0.00              
ATOM     57  CA  VAL    57      -9.755  47.005   7.279  1.00  0.00              
ATOM     58  CA  GLU    58     -10.225  45.232  10.550  1.00  0.00              
ATOM     59  CA  LYS    59     -12.251  42.381   8.947  1.00  0.00              
ATOM     60  CA  LEU    60      -9.611  41.938   6.241  1.00  0.00              
ATOM     61  CA  GLU    61      -6.896  41.870   8.830  1.00  0.00              
ATOM     62  CA  THR    62      -8.631  39.238  10.890  1.00  0.00              
ATOM     63  CA  PHE    63      -9.242  37.049   7.899  1.00  0.00              
ATOM     64  CA  PHE    64      -5.688  37.227   6.663  1.00  0.00              
ATOM     65  CA  ALA    65      -4.153  36.453   9.983  1.00  0.00              
ATOM     66  CA  VAL    66      -6.446  33.535  10.508  1.00  0.00              
ATOM     67  CA  HIS    67      -5.971  31.868   7.198  1.00  0.00              
ATOM     68  CA  TYR    68      -2.315  32.202   6.600  1.00  0.00              
ATOM     69  CA  PRO    69      -1.019  32.682  10.183  1.00  0.00              
ATOM     70  CA  PHE    70       1.037  35.558   9.272  1.00  0.00              
ATOM     71  CA  ILE    71       1.538  39.023  10.151  1.00  0.00              
ATOM     72  CA  GLN    72       2.010  41.098   6.943  1.00  0.00              
ATOM     73  CA  SER    73       2.712  44.693   7.183  1.00  0.00              
ATOM     74  CA  PHE    74       2.519  46.886   4.135  1.00  0.00              
ATOM     75  CA  SER    75       3.987  50.335   4.239  1.00  0.00              
ATOM     76  CA  LEU    76       3.173  52.805   1.532  1.00  0.00              
ATOM     77  CA  LEU    77       5.364  55.820   1.023  1.00  0.00              
ATOM     78  CA  SER    78       4.162  58.838  -0.997  1.00  0.00              
ATOM    168  CA  ALA   168      -3.413  52.267  11.369  1.00  0.00              
ATOM    169  CA  LYS   169      -5.280  55.379  12.606  1.00  0.00              
ATOM    170  CA  THR   170      -2.641  57.777  11.174  1.00  0.00              
ATOM    171  CA  PHE   171      -2.528  55.959   7.884  1.00  0.00              
ATOM    172  CA  ASP   172      -6.285  56.019   7.491  1.00  0.00              
ATOM    173  CA  LYS   173      -6.113  59.785   7.846  1.00  0.00              
ATOM    174  CA  ILE   174      -3.376  60.051   5.198  1.00  0.00              
ATOM    175  CA  GLY   175      -5.303  57.831   2.783  1.00  0.00              
ATOM    176  CA  GLN   176      -8.430  59.944   3.260  1.00  0.00              
ATOM    177  CA  MET   177      -6.544  63.199   2.647  1.00  0.00              
ATOM    178  CA  LEU   178      -5.043  61.287  -0.781  1.00  0.00              
ATOM    179  CA  LYS   179      -8.836  60.094  -1.629  1.00  0.00              
ATOM    180  CA  LYS   180      -8.467  63.836  -1.749  1.00  0.00              
TER                                                                             
END
