
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0309AL380_1
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309AL380_1.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      40      A       2           -
LGA    -       -      S       3           -
LGA    -       -      K       4           -
LGA    -       -      K       5           -
LGA    -       -      V       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      V      11           -
LGA    E      41      K      12          3.482
LGA    F      42      G      13          2.677
LGA    N      43      F      14          1.292
LGA    G      44      F      15          1.968
LGA    K      45      D      16          4.932
LGA    -       -      M      17           -
LGA    -       -      D      18           -
LGA    N      46      V      19           #
LGA    V      47      M      20          2.848
LGA    S      48      E      21          3.224
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           -
LGA    I      49      Y      33          3.429
LGA    -       -      D      34           -
LGA    T      50      F      35          0.764
LGA    V      51      K      36          1.361
LGA    K      52      E      37          1.493
LGA    E      53      I      38          0.758
LGA    E      54      L      39          0.673
LGA    N      55      S      40          1.490
LGA    E      56      E      41          2.301
LGA    L      57      F      42          3.158
LGA    P      58      -       -           -
LGA    V      59      -       -           -
LGA    K      60      N      43          4.558
LGA    G      61      G      44          2.392
LGA    V      62      K      45          2.205
LGA    E      63      N      46          3.818
LGA    -       -      V      47           -
LGA    -       -      S      48           -
LGA    -       -      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)   24   62    5.0     20    2.73    10.00     22.228     0.708

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.969454 * X  +   0.013871 * Y  +  -0.244881 * Z  +  47.539818
  Y_new =  -0.232304 * X  +   0.268434 * Y  +   0.934868 * Z  + -84.776711
  Z_new =   0.078702 * X  +   0.963198 * Y  +  -0.257012 * Z  +  19.953468 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.831553   -1.310040  [ DEG:   104.9403    -75.0597 ]
  Theta =  -0.078783   -3.062809  [ DEG:    -4.5139   -175.4861 ]
  Phi   =  -2.906404    0.235189  [ DEG:  -166.5247     13.4753 ]
 
# 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: T0309AL380_1                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309AL380_1.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   62   5.0   20   2.73   10.00  22.228
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL380_1
REMARK Aligment from pdb entry: 2bdtA
ATOM      1  N   SER    40       4.982 -16.048  -4.348  1.00  0.00              
ATOM      2  CA  SER    40       6.174 -16.596  -4.980  1.00  0.00              
ATOM      3  C   SER    40       5.903 -16.953  -6.442  1.00  0.00              
ATOM      4  O   SER    40       6.825 -17.019  -7.257  1.00  0.00              
ATOM      5  N   GLU    41       4.636 -17.180  -6.773  1.00  0.00              
ATOM      6  CA  GLU    41       4.271 -17.511  -8.144  1.00  0.00              
ATOM      7  C   GLU    41       3.702 -16.317  -8.913  1.00  0.00              
ATOM      8  O   GLU    41       3.395 -16.433 -10.097  1.00  0.00              
ATOM      9  N   PHE    42       3.553 -15.173  -8.249  1.00  0.00              
ATOM     10  CA  PHE    42       3.033 -13.992  -8.929  1.00  0.00              
ATOM     11  C   PHE    42       4.152 -13.167  -9.567  1.00  0.00              
ATOM     12  O   PHE    42       5.338 -13.388  -9.310  1.00  0.00              
ATOM     13  N   ASN    43       3.753 -12.226 -10.415  1.00  0.00              
ATOM     14  CA  ASN    43       4.682 -11.346 -11.115  1.00  0.00              
ATOM     15  C   ASN    43       4.537  -9.933 -10.564  1.00  0.00              
ATOM     16  O   ASN    43       3.433  -9.499 -10.250  1.00  0.00              
ATOM     17  N   GLY    44       5.654  -9.203 -10.425  1.00  0.00              
ATOM     18  CA  GLY    44       5.622  -7.829  -9.907  1.00  0.00              
ATOM     19  C   GLY    44       4.816  -6.907 -10.827  1.00  0.00              
ATOM     20  O   GLY    44       4.325  -5.854 -10.413  1.00  0.00              
ATOM     21  N   LYS    45       4.676  -7.326 -12.077  1.00  0.00              
ATOM     22  CA  LYS    45       3.934  -6.563 -13.061  1.00  0.00              
ATOM     23  C   LYS    45       2.425  -6.706 -12.810  1.00  0.00              
ATOM     24  O   LYS    45       1.606  -6.176 -13.556  1.00  0.00              
ATOM     25  N   ASN    46       2.071  -7.428 -11.749  1.00  0.00              
ATOM     26  CA  ASN    46       0.677  -7.642 -11.379  1.00  0.00              
ATOM     27  C   ASN    46       0.426  -7.045  -9.996  1.00  0.00              
ATOM     28  O   ASN    46      -0.585  -7.336  -9.344  1.00  0.00              
ATOM     29  N   VAL    47       1.356  -6.197  -9.565  1.00  0.00              
ATOM     30  CA  VAL    47       1.270  -5.541  -8.268  1.00  0.00              
ATOM     31  C   VAL    47      -0.099  -4.922  -7.982  1.00  0.00              
ATOM     32  O   VAL    47      -0.618  -5.069  -6.877  1.00  0.00              
ATOM     33  N   SER    48      -0.690  -4.238  -8.962  1.00  0.00              
ATOM     34  CA  SER    48      -2.006  -3.629  -8.746  1.00  0.00              
ATOM     35  C   SER    48      -3.123  -4.647  -8.517  1.00  0.00              
ATOM     36  O   SER    48      -4.098  -4.354  -7.828  1.00  0.00              
ATOM     37  N   ILE    49      -2.988  -5.844  -9.081  1.00  0.00              
ATOM     38  CA  ILE    49      -4.007  -6.867  -8.878  1.00  0.00              
ATOM     39  C   ILE    49      -3.896  -7.407  -7.460  1.00  0.00              
ATOM     40  O   ILE    49      -4.904  -7.602  -6.780  1.00  0.00              
ATOM     41  N   THR    50      -2.662  -7.651  -7.025  1.00  0.00              
ATOM     42  CA  THR    50      -2.385  -8.151  -5.682  1.00  0.00              
ATOM     43  C   THR    50      -2.988  -7.232  -4.620  1.00  0.00              
ATOM     44  O   THR    50      -3.717  -7.684  -3.740  1.00  0.00              
ATOM     45  N   VAL    51      -2.680  -5.941  -4.705  1.00  0.00              
ATOM     46  CA  VAL    51      -3.198  -4.985  -3.736  1.00  0.00              
ATOM     47  C   VAL    51      -4.714  -4.841  -3.875  1.00  0.00              
ATOM     48  O   VAL    51      -5.399  -4.444  -2.936  1.00  0.00              
ATOM     49  N   LYS    52      -5.228  -5.164  -5.056  1.00  0.00              
ATOM     50  CA  LYS    52      -6.655  -5.083  -5.326  1.00  0.00              
ATOM     51  C   LYS    52      -7.329  -6.248  -4.613  1.00  0.00              
ATOM     52  O   LYS    52      -8.440  -6.127  -4.105  1.00  0.00              
ATOM     53  N   GLU    53      -6.640  -7.381  -4.575  1.00  0.00              
ATOM     54  CA  GLU    53      -7.181  -8.561  -3.934  1.00  0.00              
ATOM     55  C   GLU    53      -7.236  -8.440  -2.422  1.00  0.00              
ATOM     56  O   GLU    53      -8.309  -8.520  -1.822  1.00  0.00              
ATOM     57  N   GLU    54      -6.073  -8.245  -1.806  1.00  0.00              
ATOM     58  CA  GLU    54      -5.986  -8.128  -0.356  1.00  0.00              
ATOM     59  C   GLU    54      -6.772  -6.941   0.184  1.00  0.00              
ATOM     60  O   GLU    54      -6.951  -6.808   1.393  1.00  0.00              
ATOM     61  N   ASN    55      -7.261  -6.089  -0.708  1.00  0.00              
ATOM     62  CA  ASN    55      -8.033  -4.932  -0.275  1.00  0.00              
ATOM     63  C   ASN    55      -9.488  -5.310  -0.035  1.00  0.00              
ATOM     64  O   ASN    55     -10.159  -4.724   0.810  1.00  0.00              
ATOM     65  N   GLU    56      -9.967  -6.303  -0.774  1.00  0.00              
ATOM     66  CA  GLU    56     -11.353  -6.728  -0.657  1.00  0.00              
ATOM     67  C   GLU    56     -11.520  -8.185  -0.244  1.00  0.00              
ATOM     68  O   GLU    56     -12.569  -8.572   0.278  1.00  0.00              
ATOM     69  N   LEU    57     -10.490  -8.992  -0.476  1.00  0.00              
ATOM     70  CA  LEU    57     -10.559 -10.403  -0.122  1.00  0.00              
ATOM     71  C   LEU    57     -10.928 -10.526   1.358  1.00  0.00              
ATOM     72  O   LEU    57     -10.261  -9.965   2.222  1.00  0.00              
ATOM     73  N   PRO    58     -12.004 -11.263   1.665  1.00  0.00              
ATOM     74  CA  PRO    58     -12.461 -11.447   3.045  1.00  0.00              
ATOM     75  C   PRO    58     -11.629 -12.388   3.907  1.00  0.00              
ATOM     76  O   PRO    58     -11.723 -12.351   5.132  1.00  0.00              
ATOM     77  N   VAL    59     -10.812 -13.222   3.275  1.00  0.00              
ATOM     78  CA  VAL    59      -9.983 -14.170   4.014  1.00  0.00              
ATOM     79  C   VAL    59      -9.059 -13.471   5.016  1.00  0.00              
ATOM     80  O   VAL    59      -8.722 -14.037   6.053  1.00  0.00              
ATOM     81  N   LYS    60      -8.653 -12.244   4.706  1.00  0.00              
ATOM     82  CA  LYS    60      -7.763 -11.503   5.593  1.00  0.00              
ATOM     83  C   LYS    60      -8.539 -10.647   6.589  1.00  0.00              
ATOM     84  O   LYS    60      -7.947 -10.027   7.472  1.00  0.00              
ATOM     85  N   GLY    61      -9.861 -10.630   6.451  1.00  0.00              
ATOM     86  CA  GLY    61     -10.717  -9.821   7.312  1.00  0.00              
ATOM     87  C   GLY    61     -10.498 -10.056   8.805  1.00  0.00              
ATOM     88  O   GLY    61     -11.259  -9.557   9.636  1.00  0.00              
ATOM     89  N   VAL    62      -9.459 -10.815   9.138  1.00  0.00              
ATOM     90  CA  VAL    62      -9.117 -11.109  10.528  1.00  0.00              
ATOM     91  C   VAL    62     -10.278 -11.791  11.237  1.00  0.00              
ATOM     92  O   VAL    62     -10.845 -11.252  12.200  1.00  0.00              
ATOM     93  N   GLU    63     -10.626 -12.978  10.745  1.00  0.00              
ATOM     94  CA  GLU    63     -11.715 -13.775  11.300  1.00  0.00              
ATOM     95  C   GLU    63     -11.651 -13.813  12.828  1.00  0.00              
ATOM     96  O   GLU    63     -12.491 -13.221  13.506  1.00  0.00              
END
