
#######################################################
#                                                     #
#                        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   76 (   76),  selected   76 , name T0309TS599_2
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS599_2.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      A       2           -
LGA    A       2      S       3           -
LGA    S       3      K       4           -
LGA    K       4      K       5           -
LGA    K       5      V       6           -
LGA    V       6      -       -           -
LGA    H       7      -       -           -
LGA    Q       8      -       -           -
LGA    I       9      -       -           -
LGA    N      10      -       -           -
LGA    V      11      -       -           -
LGA    K      12      -       -           -
LGA    G      13      -       -           -
LGA    F      14      -       -           -
LGA    F      15      -       -           -
LGA    D      16      -       -           -
LGA    M      17      -       -           -
LGA    D      18      -       -           -
LGA    V      19      -       -           -
LGA    M      20      -       -           -
LGA    E      21      -       -           -
LGA    V      22      -       -           -
LGA    T      23      -       -           -
LGA    E      24      -       -           -
LGA    Q      25      -       -           -
LGA    T      26      -       -           -
LGA    K      27      -       -           -
LGA    E      28      -       -           -
LGA    A      29      -       -           -
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    T      32      H       7          4.257
LGA    Y      33      Q       8          0.768
LGA    D      34      I       9           #
LGA    F      35      -       -           -
LGA    K      36      -       -           -
LGA    E      37      -       -           -
LGA    I      38      N      10           #
LGA    L      39      V      11           -
LGA    S      40      -       -           -
LGA    E      41      -       -           -
LGA    F      42      -       -           -
LGA    N      43      -       -           -
LGA    G      44      -       -           -
LGA    K      45      -       -           -
LGA    N      46      -       -           -
LGA    V      47      -       -           -
LGA    S      48      K      12          4.479
LGA    I      49      G      13          2.206
LGA    T      50      F      14          2.513
LGA    V      51      F      15          2.636
LGA    K      52      D      16          3.039
LGA    E      53      M      17          2.994
LGA    -       -      D      18           -
LGA    E      54      V      19          2.405
LGA    N      55      M      20          5.021
LGA    E      56      E      21          5.404
LGA    L      57      V      22           #
LGA    P      58      T      23          3.310
LGA    V      59      E      24          4.749
LGA    K      60      Q      25          2.366
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    -       -      A      29           -
LGA    -       -      E      30           -
LGA    G      61      Y      31          4.520
LGA    V      62      T      32          3.531
LGA    E      63      Y      33          3.467
LGA    M      64      D      34          2.265
LGA    A      65      F      35          1.734
LGA    G      66      K      36          2.645
LGA    D      67      E      37          4.683
LGA    -       -      I      38           -
LGA    P      68      L      39          2.085
LGA    L      69      S      40          3.960
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    E      70      N      43          2.135
LGA    H      71      G      44          2.383
LGA    H      72      K      45          3.743
LGA    H      73      N      46           -
LGA    H      74      V      47           -
LGA    H      75      S      48           -
LGA    H      76      I      49           -
LGA    -       -      T      50           -
LGA    -       -      V      51           -
LGA    -       -      K      52           -
LGA    -       -      E      53           -
LGA    -       -      E      54           -
LGA    -       -      N      55           -
LGA    -       -      E      56           -
LGA    -       -      L      57           -
LGA    -       -      P      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      G      61           -
LGA    -       -      V      62           -
LGA    -       -      E      63           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76   62    5.0     26    3.40     3.85     25.776     0.743

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.623334 * X  +   0.146696 * Y  +  -0.768072 * Z  +  -1.313239
  Y_new =   0.721899 * X  +   0.485460 * Y  +  -0.493143 * Z  + -16.338741
  Z_new =   0.300526 * X  +  -0.861864 * Y  +  -0.408503 * Z  +  -4.823305 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.013410    1.128183  [ DEG:  -115.3599     64.6401 ]
  Theta =  -0.305244   -2.836349  [ DEG:   -17.4892   -162.5108 ]
  Phi   =   2.283055   -0.858538  [ DEG:   130.8094    -49.1906 ]
 
# 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: T0309TS599_2                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS599_2.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   76   62   5.0   26   3.40    3.85  25.776
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS599_2
PFRMAT TS                                                                       
TARGET T0309                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      16.449 -13.455  -4.486  1.00  0.00              
ATOM      2  CA  ALA     2      13.507 -11.703  -6.256  1.00  0.00              
ATOM      3  CA  SER     3      13.522 -12.497  -2.487  1.00  0.00              
ATOM      4  CA  LYS     4      13.484 -13.454  -6.581  1.00  0.00              
ATOM      5  CA  LYS     5      11.411 -16.484  -5.722  1.00  0.00              
ATOM      6  CA  VAL     6       8.865 -14.630  -3.622  1.00  0.00              
ATOM      7  CA  HIS     7       8.272 -11.957  -6.279  1.00  0.00              
ATOM      8  CA  GLN     8       7.545 -14.788  -8.689  1.00  0.00              
ATOM      9  CA  ILE     9       5.262 -17.344  -7.445  1.00  0.00              
ATOM     10  CA  ASN    10       5.239 -20.715  -9.057  1.00  0.00              
ATOM     11  CA  VAL    11       2.222 -22.757  -8.886  1.00  0.00              
ATOM     12  CA  LYS    12       2.711 -26.330  -9.917  1.00  0.00              
ATOM     13  CA  GLY    13       6.040 -26.422  -8.032  1.00  0.00              
ATOM     14  CA  PHE    14       4.633 -24.937  -4.825  1.00  0.00              
ATOM     15  CA  PHE    15       1.303 -26.805  -4.683  1.00  0.00              
ATOM     16  CA  ASP    16      -0.162 -27.993  -1.370  1.00  0.00              
ATOM     17  CA  MET    17      -3.708 -26.625  -1.700  1.00  0.00              
ATOM     18  CA  ASP    18      -4.590 -25.692   1.844  1.00  0.00              
ATOM     19  CA  VAL    19      -1.145 -24.783   3.182  1.00  0.00              
ATOM     20  CA  MET    20       0.305 -22.557   0.502  1.00  0.00              
ATOM     21  CA  GLU    21      -2.913 -20.627   0.086  1.00  0.00              
ATOM     22  CA  VAL    22      -3.461 -19.885   3.796  1.00  0.00              
ATOM     23  CA  THR    23       0.008 -18.629   4.490  1.00  0.00              
ATOM     24  CA  GLU    24       0.285 -16.300   1.466  1.00  0.00              
ATOM     25  CA  GLN    25      -3.083 -14.794   2.213  1.00  0.00              
ATOM     26  CA  THR    26      -2.224 -14.213   5.917  1.00  0.00              
ATOM     27  CA  LYS    27       1.072 -12.508   5.448  1.00  0.00              
ATOM     28  CA  GLU    28      -0.076 -10.050   2.854  1.00  0.00              
ATOM     29  CA  ALA    29      -3.426  -9.263   4.324  1.00  0.00              
ATOM     30  CA  GLU    30      -6.334 -10.959   2.938  1.00  0.00              
ATOM     31  CA  TYR    31      -7.109 -13.085  -0.090  1.00  0.00              
ATOM     32  CA  THR    32      -9.241 -16.252   0.201  1.00  0.00              
ATOM     33  CA  TYR    33      -8.648 -19.409  -1.818  1.00  0.00              
ATOM     34  CA  ASP    34     -10.770 -22.506  -1.981  1.00  0.00              
ATOM     35  CA  PHE    35      -8.937 -25.796  -2.225  1.00  0.00              
ATOM     36  CA  LYS    36     -11.010 -27.079  -5.141  1.00  0.00              
ATOM     37  CA  GLU    37     -10.326 -23.812  -7.053  1.00  0.00              
ATOM     38  CA  ILE    38      -6.571 -24.017  -6.456  1.00  0.00              
ATOM     39  CA  LEU    39      -6.623 -27.664  -7.620  1.00  0.00              
ATOM     40  CA  SER    40      -8.635 -26.721 -10.703  1.00  0.00              
ATOM     41  CA  GLU    41      -6.246 -23.966 -11.637  1.00  0.00              
ATOM     42  CA  PHE    42      -3.321 -26.380 -11.226  1.00  0.00              
ATOM     43  CA  ASN    43      -4.769 -29.336 -13.143  1.00  0.00              
ATOM     44  CA  GLY    44      -1.348 -30.457 -14.448  1.00  0.00              
ATOM     45  CA  LYS    45      -0.213 -27.148 -15.740  1.00  0.00              
ATOM     46  CA  ASN    46       2.554 -25.080 -14.283  1.00  0.00              
ATOM     47  CA  VAL    47       1.182 -21.666 -13.443  1.00  0.00              
ATOM     48  CA  SER    48       3.380 -18.623 -13.041  1.00  0.00              
ATOM     49  CA  ILE    49       2.116 -15.840 -10.857  1.00  0.00              
ATOM     50  CA  THR    50       3.799 -12.466 -10.786  1.00  0.00              
ATOM     51  CA  VAL    51       2.924 -10.108  -7.906  1.00  0.00              
ATOM     52  CA  LYS    52       2.681  -6.472  -8.540  1.00  0.00              
ATOM     53  CA  GLU    53       1.779  -4.023  -5.795  1.00  0.00              
ATOM     54  CA  GLU    54      -0.160  -1.589  -8.026  1.00  0.00              
ATOM     55  CA  ASN    55       2.571  -1.632 -10.617  1.00  0.00              
ATOM     56  CA  GLU    56       0.905  -2.930 -13.719  1.00  0.00              
ATOM     57  CA  LEU    57       2.979  -6.035 -14.525  1.00  0.00              
ATOM     58  CA  PRO    58       0.917  -8.610 -16.476  1.00  0.00              
ATOM     59  CA  VAL    59       2.881 -10.893 -18.729  1.00  0.00              
ATOM     60  CA  LYS    60       0.797 -14.123 -18.456  1.00  0.00              
ATOM     61  CA  GLY    61      -0.259 -14.093 -14.858  1.00  0.00              
ATOM     62  CA  VAL    62      -0.201 -10.834 -13.075  1.00  0.00              
ATOM     63  CA  GLU    63      -1.682 -10.559  -9.646  1.00  0.00              
ATOM     64  CA  MET    64      -2.227  -7.254  -8.203  1.00  0.00              
ATOM     65  CA  ALA    65      -1.938  -6.944  -4.518  1.00  0.00              
ATOM     66  CA  GLY    66      -2.305  -3.586  -2.908  1.00  0.00              
ATOM     67  CA  ASP    67      -5.608  -4.200  -1.202  1.00  0.00              
ATOM     68  CA  PRO    68      -5.877  -7.354   0.842  1.00  0.00              
ATOM     69  CA  LEU    69      -7.774  -6.148   3.940  1.00  0.00              
ATOM     70  CA  GLU    70     -10.516  -8.644   4.528  1.00  0.00              
ATOM     71  CA  HIS    71     -12.703  -7.957   7.513  1.00  0.00              
ATOM     72  CA  HIS    72     -13.927 -11.550   7.988  1.00  0.00              
ATOM     73  CA  HIS    73     -16.396 -14.100   8.473  1.00  0.00              
ATOM     74  CA  HIS    74     -14.934 -16.607   5.400  1.00  0.00              
ATOM     75  CA  HIS    75     -12.650 -18.343   2.273  1.00  0.00              
ATOM     76  CA  HIS    76      -9.361 -20.693   2.135  1.00  0.00              
TER                                                                             
END
