
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0311TS393_2-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS393_2-D1.T0311_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      -       -           -
LGA    P       9      R       8          4.627
LGA    G      10      P       9          1.446
LGA    D      11      G      10          2.056
LGA    I      12      D      11          1.500
LGA    I      13      I      12          2.113
LGA    Q      14      I      13          3.504
LGA    E      15      Q      14          3.411
LGA    S      16      E      15          2.323
LGA    L      17      S      16          5.589
LGA    D      18      L      17           #
LGA    E      19      -       -           -
LGA    L      20      D      18          3.995
LGA    N      21      E      19           #
LGA    -       -      L      20           -
LGA    V      22      N      21          2.515
LGA    S      23      V      22          1.958
LGA    -       -      S      23           -
LGA    L      24      L      24          3.325
LGA    R      25      R      25          1.843
LGA    E      26      E      26          1.303
LGA    F      27      F      27          2.291
LGA    A      28      A      28          1.324
LGA    R      29      R      29          0.363
LGA    A      30      A      30          1.506
LGA    M      31      M      31          1.495
LGA    E      32      E      32          1.411
LGA    I      33      I      33          2.032
LGA    A      34      A      34          3.356
LGA    P      35      P      35          2.612
LGA    S      36      S      36          1.672
LGA    T      37      T      37          1.250
LGA    A      38      A      38          1.667
LGA    S      39      S      39          2.232
LGA    R      40      R      40          2.090
LGA    L      41      L      41          2.365
LGA    L      42      L      42          3.164
LGA    -       -      T      43           -
LGA    T      43      G      44          0.943
LGA    G      44      K      45          1.001
LGA    K      45      A      46          2.335
LGA    A      46      A      47          1.220
LGA    A      47      L      48          4.118
LGA    L      48      T      49          1.622
LGA    T      49      P      50          3.422
LGA    P      50      E      51          1.431
LGA    E      51      M      52          4.764
LGA    M      52      A      53           #
LGA    A      53      I      54          4.926
LGA    I      54      K      55          1.863
LGA    K      55      -       -           -
LGA    L      56      -       -           -
LGA    S      57      L      56          1.093
LGA    V      58      -       -           -
LGA    V      59      -       -           -
LGA    I      60      -       -           -
LGA    G      61      -       -           -
LGA    S      62      -       -           -
LGA    S      63      S      57          3.085
LGA    P      64      V      58          2.388
LGA    Q      65      -       -           -
LGA    M      66      V      59          3.600
LGA    W      67      I      60          1.956
LGA    L      68      G      61          2.575
LGA    N      69      S      62           -
LGA    L      70      S      63           -
LGA    Q      71      P      64           -
LGA    -       -      Q      65           -
LGA    -       -      M      66           -
LGA    -       -      W      67           -
LGA    -       -      L      68           -
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      Q      71           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   64    5.0     48    2.65    45.83     51.126     1.744

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.904334 * X  +   0.365361 * Y  +  -0.220663 * Z  +  32.521187
  Y_new =  -0.158480 * X  +   0.192602 * Y  +   0.968395 * Z  +   3.655584
  Z_new =   0.396314 * X  +   0.910723 * Y  +  -0.116274 * Z  +  14.140904 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.697782   -1.443811  [ DEG:    97.2757    -82.7243 ]
  Theta =  -0.407498   -2.734094  [ DEG:   -23.3479   -156.6521 ]
  Phi   =  -2.968109    0.173484  [ DEG:  -170.0601      9.9399 ]
 
# 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: T0311TS393_2-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS393_2-D1.T0311_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   64   64   5.0   48   2.65   45.83  51.126
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS393_2-D1
PFRMAT TS
TARGET T0311
MODEL 2
PARENT N/A
ATOM      8  CA  ARG     8      41.765   6.107  10.099  1.00 25.00           C
ATOM      9  CA  PRO     9      38.727   5.310  12.337  1.00 25.00           C
ATOM     10  CA  GLY    10      36.529   2.333  11.349  1.00 25.00           C
ATOM     11  CA  ASP    11      37.525   0.501  14.560  1.00 25.00           C
ATOM     12  CA  ILE    12      36.671   3.609  16.629  1.00 25.00           C
ATOM     13  CA  ILE    13      33.265   3.857  14.895  1.00 25.00           C
ATOM     14  CA  GLN    14      32.596   0.157  15.624  1.00 25.00           C
ATOM     15  CA  GLU    15      33.529   0.688  19.300  1.00 25.00           C
ATOM     16  CA  SER    16      31.168   3.698  19.490  1.00 25.00           C
ATOM     17  CA  LEU    17      28.350   1.617  17.943  1.00 25.00           C
ATOM     18  CA  ASP    18      28.983  -1.176  20.487  1.00 25.00           C
ATOM     19  CA  GLU    19      28.876   1.370  23.346  1.00 25.00           C
ATOM     20  CA  LEU    20      25.235   2.043  22.354  1.00 25.00           C
ATOM     21  CA  ASN    21      21.973   3.929  22.247  1.00 25.00           C
ATOM     22  CA  VAL    22      22.489   3.891  18.467  1.00 25.00           C
ATOM     23  CA  SER    23      21.653   0.207  18.850  1.00 25.00           C
ATOM     24  CA  LEU    24      24.275  -1.138  16.409  1.00 25.00           C
ATOM     25  CA  ARG    25      22.160  -4.311  16.054  1.00 25.00           C
ATOM     26  CA  GLU    26      19.380  -2.299  14.354  1.00 25.00           C
ATOM     27  CA  PHE    27      21.930  -0.762  11.946  1.00 25.00           C
ATOM     28  CA  ALA    28      23.295  -4.246  11.130  1.00 25.00           C
ATOM     29  CA  ARG    29      19.742  -5.510  10.469  1.00 25.00           C
ATOM     30  CA  ALA    30      19.082  -2.524   8.163  1.00 25.00           C
ATOM     31  CA  MET    31      22.336  -3.234   6.273  1.00 25.00           C
ATOM     32  CA  GLU    32      22.825  -6.931   6.567  1.00 25.00           C
ATOM     33  CA  ILE    33      24.142  -9.502   8.966  1.00 25.00           C
ATOM     34  CA  ALA    34      23.483  -9.497  12.694  1.00 25.00           C
ATOM     35  CA  PRO    35      26.370  -7.928  14.606  1.00 25.00           C
ATOM     36  CA  SER    36      29.131 -10.455  13.795  1.00 25.00           C
ATOM     37  CA  THR    37      29.415  -9.043  10.246  1.00 25.00           C
ATOM     38  CA  ALA    38      29.669  -5.490  11.653  1.00 25.00           C
ATOM     39  CA  SER    39      32.411  -6.620  14.077  1.00 25.00           C
ATOM     40  CA  ARG    40      34.318  -8.265  11.192  1.00 25.00           C
ATOM     41  CA  LEU    41      34.027  -5.048   9.133  1.00 25.00           C
ATOM     42  CA  LEU    42      35.334  -3.005  12.098  1.00 25.00           C
ATOM     43  CA  THR    43      38.285  -5.414  12.490  1.00 25.00           C
ATOM     44  CA  GLY    44      39.624  -8.982  12.311  1.00 25.00           C
ATOM     45  CA  LYS    45      39.133  -9.402   8.580  1.00 25.00           C
ATOM     46  CA  ALA    46      39.722  -5.842   7.375  1.00 25.00           C
ATOM     47  CA  ALA    47      39.277  -5.151   3.697  1.00 25.00           C
ATOM     48  CA  LEU    48      35.834  -3.588   3.501  1.00 25.00           C
ATOM     49  CA  THR    49      33.875  -4.691   0.468  1.00 25.00           C
ATOM     50  CA  PRO    50      30.299  -4.280  -0.865  1.00 25.00           C
ATOM     51  CA  GLU    51      28.130  -5.990   1.787  1.00 25.00           C
ATOM     52  CA  MET    52      30.846  -5.402   4.423  1.00 25.00           C
ATOM     53  CA  ALA    53      31.054  -1.711   3.421  1.00 25.00           C
ATOM     54  CA  ILE    54      27.248  -1.396   3.700  1.00 25.00           C
ATOM     55  CA  LYS    55      27.343  -3.011   7.172  1.00 25.00           C
ATOM     56  CA  LEU    56      30.098  -0.580   8.253  1.00 25.00           C
ATOM     57  CA  SER    57      28.027   2.375   6.972  1.00 25.00           C
ATOM     58  CA  VAL    58      24.974   1.103   8.902  1.00 25.00           C
ATOM     59  CA  VAL    59      27.088   0.774  12.079  1.00 25.00           C
ATOM     60  CA  ILE    60      28.390   4.346  11.613  1.00 25.00           C
ATOM     61  CA  GLY    61      30.834   6.018   9.138  1.00 25.00           C
ATOM     62  CA  SER    62      31.148   6.740   5.376  1.00 25.00           C
ATOM     63  CA  SER    63      28.768   8.302   2.809  1.00 25.00           C
ATOM     64  CA  PRO    64      25.194   7.066   2.870  1.00 25.00           C
ATOM     65  CA  GLN    65      22.516   9.236   4.541  1.00 25.00           C
ATOM     66  CA  MET    66      22.407   6.843   7.529  1.00 25.00           C
ATOM     67  CA  TRP    67      26.223   6.990   7.816  1.00 25.00           C
ATOM     68  CA  LEU    68      26.107  10.817   7.725  1.00 25.00           C
ATOM     69  CA  ASN    69      23.433  10.826  10.465  1.00 25.00           C
ATOM     70  CA  LEU    70      25.577   8.481  12.602  1.00 25.00           C
ATOM     71  CA  GLN    71      28.609  10.771  12.116  1.00 25.00           C
TER
END
