
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS599_3.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      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      -       -           -
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      V       6          4.073
LGA    A      29      H       7          3.213
LGA    E      30      Q       8          1.289
LGA    Y      31      I       9          3.384
LGA    T      32      N      10          4.788
LGA    Y      33      V      11           #
LGA    D      34      -       -           -
LGA    F      35      -       -           -
LGA    K      36      -       -           -
LGA    E      37      K      12          3.963
LGA    I      38      G      13          2.553
LGA    L      39      F      14          4.418
LGA    S      40      F      15           -
LGA    -       -      D      16           -
LGA    -       -      M      17           -
LGA    -       -      D      18           -
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    -       -      V      22           -
LGA    E      41      T      23           #
LGA    F      42      E      24          1.469
LGA    N      43      Q      25          1.688
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    -       -      A      29           -
LGA    G      44      E      30          1.933
LGA    K      45      Y      31          1.020
LGA    N      46      T      32          1.407
LGA    V      47      Y      33          1.039
LGA    S      48      D      34          2.642
LGA    I      49      F      35          2.140
LGA    -       -      K      36           -
LGA    -       -      E      37           -
LGA    T      50      I      38          1.873
LGA    V      51      L      39          1.477
LGA    K      52      S      40          3.536
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    E      53      N      43          2.750
LGA    E      54      G      44          3.507
LGA    -       -      K      45           -
LGA    -       -      N      46           -
LGA    N      55      V      47          4.941
LGA    E      56      S      48          5.092
LGA    L      57      I      49           #
LGA    P      58      -       -           -
LGA    V      59      T      50           #
LGA    K      60      V      51          4.586
LGA    G      61      K      52           -
LGA    V      62      E      53           -
LGA    E      63      E      54           -
LGA    M      64      N      55           -
LGA    A      65      E      56           -
LGA    G      66      L      57           -
LGA    D      67      P      58           -
LGA    P      68      V      59           -
LGA    L      69      K      60           -
LGA    E      70      G      61           -
LGA    H      71      V      62           -
LGA    H      72      E      63           -
LGA    H      73      -       -           -
LGA    H      74      -       -           -
LGA    H      75      -       -           -
LGA    H      76      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76   62    5.0     24    3.15     0.00     26.121     0.738

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.433650 * X  +  -0.890886 * Y  +  -0.135169 * Z  +  -7.806548
  Y_new =   0.150671 * X  +  -0.076205 * Y  +   0.985642 * Z  +  -9.374972
  Z_new =  -0.888395 * X  +  -0.447789 * Y  +   0.101184 * Z  +  -6.265035 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.348565    1.793027  [ DEG:   -77.2671    102.7329 ]
  Theta =   1.093838    2.047755  [ DEG:    62.6723    117.3277 ]
  Phi   =   0.334399   -2.807193  [ DEG:    19.1597   -160.8403 ]
 
# 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_3                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS599_3.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   24   3.15    0.00  26.121
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS599_3
PFRMAT TS                                                                       
TARGET T0309                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -1.462   5.932   4.643  1.00  0.00              
ATOM      2  CA  ALA     2      -4.429   5.507   1.736  1.00  0.00              
ATOM      3  CA  SER     3      -7.582   6.151   4.454  1.00  0.00              
ATOM      4  CA  LYS     4      -4.438   4.700   3.499  1.00  0.00              
ATOM      5  CA  LYS     5      -5.273   1.215   4.619  1.00  0.00              
ATOM      6  CA  VAL     6      -8.646   1.168   2.805  1.00  0.00              
ATOM      7  CA  HIS     7      -7.294   2.376  -0.515  1.00  0.00              
ATOM      8  CA  GLN     8      -4.192   0.098  -0.402  1.00  0.00              
ATOM      9  CA  ILE     9      -6.190  -2.992   0.293  1.00  0.00              
ATOM     10  CA  ASN    10      -9.077  -3.354  -1.879  1.00  0.00              
ATOM     11  CA  VAL    11     -12.048  -5.313  -0.698  1.00  0.00              
ATOM     12  CA  LYS    12     -14.508  -6.284  -3.316  1.00  0.00              
ATOM     13  CA  GLY    13     -17.628  -4.577  -1.960  1.00  0.00              
ATOM     14  CA  PHE    14     -15.802  -1.242  -1.715  1.00  0.00              
ATOM     15  CA  PHE    15     -14.415  -1.348  -5.285  1.00  0.00              
ATOM     16  CA  ASP    16     -17.231  -2.745  -7.369  1.00  0.00              
ATOM     17  CA  MET    17     -15.150  -4.554  -9.974  1.00  0.00              
ATOM     18  CA  ASP    18     -17.026  -7.678 -11.041  1.00  0.00              
ATOM     19  CA  VAL    19     -18.779  -8.259  -7.775  1.00  0.00              
ATOM     20  CA  MET    20     -19.094 -12.024  -8.086  1.00  0.00              
ATOM     21  CA  GLU    21     -15.390 -12.643  -8.916  1.00  0.00              
ATOM     22  CA  VAL    22     -14.125 -10.501  -6.034  1.00  0.00              
ATOM     23  CA  THR    23     -16.534 -12.161  -3.528  1.00  0.00              
ATOM     24  CA  GLU    24     -16.147 -15.835  -4.316  1.00  0.00              
ATOM     25  CA  GLN    25     -12.390 -15.962  -4.204  1.00  0.00              
ATOM     26  CA  THR    26     -12.325 -13.855  -1.092  1.00  0.00              
ATOM     27  CA  LYS    27     -14.927 -15.906   0.858  1.00  0.00              
ATOM     28  CA  GLU    28     -13.008 -19.097   0.329  1.00  0.00              
ATOM     29  CA  ALA    29      -9.621 -17.534   1.302  1.00  0.00              
ATOM     30  CA  GLU    30      -7.564 -19.451  -1.311  1.00  0.00              
ATOM     31  CA  TYR    31      -4.352 -17.551  -1.678  1.00  0.00              
ATOM     32  CA  THR    32      -0.879 -19.147  -2.022  1.00  0.00              
ATOM     33  CA  TYR    33       1.781 -18.141  -4.471  1.00  0.00              
ATOM     34  CA  ASP    34       4.517 -20.318  -6.045  1.00  0.00              
ATOM     35  CA  PHE    35       6.899 -18.011  -7.878  1.00  0.00              
ATOM     36  CA  LYS    36       6.831 -19.900 -11.182  1.00  0.00              
ATOM     37  CA  GLU    37       3.012 -19.919 -11.011  1.00  0.00              
ATOM     38  CA  ILE    38       2.824 -16.247 -10.248  1.00  0.00              
ATOM     39  CA  LEU    39       5.225 -15.449 -13.081  1.00  0.00              
ATOM     40  CA  SER    40       3.218 -17.629 -15.513  1.00  0.00              
ATOM     41  CA  GLU    41      -0.014 -15.930 -14.494  1.00  0.00              
ATOM     42  CA  PHE    42       1.600 -12.495 -15.025  1.00  0.00              
ATOM     43  CA  ASN    43       3.011 -13.086 -18.488  1.00  0.00              
ATOM     44  CA  GLY    44       1.160 -10.171 -20.086  1.00  0.00              
ATOM     45  CA  LYS    45      -2.095 -10.684 -18.270  1.00  0.00              
ATOM     46  CA  ASN    46      -3.344  -8.210 -15.742  1.00  0.00              
ATOM     47  CA  VAL    47      -3.630  -9.684 -12.210  1.00  0.00              
ATOM     48  CA  SER    48      -5.797  -8.056  -9.648  1.00  0.00              
ATOM     49  CA  ILE    49      -4.903  -8.424  -6.024  1.00  0.00              
ATOM     50  CA  THR    50      -7.318  -7.665  -3.193  1.00  0.00              
ATOM     51  CA  VAL    51      -6.137  -7.804   0.367  1.00  0.00              
ATOM     52  CA  LYS    52      -8.708  -8.060   3.104  1.00  0.00              
ATOM     53  CA  GLU    53      -7.307  -8.572   6.548  1.00  0.00              
ATOM     54  CA  GLU    54      -9.672 -11.072   8.014  1.00  0.00              
ATOM     55  CA  ASN    55     -10.075 -13.232   4.956  1.00  0.00              
ATOM     56  CA  GLU    56      -6.405 -13.891   4.498  1.00  0.00              
ATOM     57  CA  LEU    57      -5.040 -12.193   1.457  1.00  0.00              
ATOM     58  CA  PRO    58      -1.991 -14.060   0.016  1.00  0.00              
ATOM     59  CA  VAL    59      -1.350 -13.608  -3.639  1.00  0.00              
ATOM     60  CA  LYS    60       2.385 -13.586  -3.918  1.00  0.00              
ATOM     61  CA  GLY    61       3.371 -11.014  -6.595  1.00  0.00              
ATOM     62  CA  VAL    62       0.141  -9.199  -7.048  1.00  0.00              
ATOM     63  CA  GLU    63      -0.328  -6.991 -10.097  1.00  0.00              
ATOM     64  CA  MET    64      -2.987  -4.425  -9.969  1.00  0.00              
ATOM     65  CA  ALA    65      -4.483  -3.158 -13.045  1.00  0.00              
ATOM     66  CA  GLY    66      -7.371  -0.985 -12.062  1.00  0.00              
ATOM     67  CA  ASP    67      -9.712  -1.778 -14.878  1.00  0.00              
ATOM     68  CA  PRO    68     -12.333  -3.998 -13.156  1.00  0.00              
ATOM     69  CA  LEU    69     -13.535  -6.199 -15.946  1.00  0.00              
ATOM     70  CA  GLU    70     -17.339  -5.935 -15.937  1.00  0.00              
ATOM     71  CA  HIS    71     -18.816  -8.971 -17.700  1.00  0.00              
ATOM     72  CA  HIS    72     -22.177  -7.646 -18.722  1.00  0.00              
ATOM     73  CA  HIS    73     -24.808 -10.406 -18.738  1.00  0.00              
ATOM     74  CA  HIS    74     -22.253 -12.024 -16.436  1.00  0.00              
ATOM     75  CA  HIS    75     -22.633 -14.559 -13.712  1.00  0.00              
ATOM     76  CA  HIS    76     -19.186 -16.241 -12.317  1.00  0.00              
TER                                                                             
END
