
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0353AL381_2
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353AL381_2.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      I       3           -
LGA    -       -      H       4           -
LGA    -       -      V       5           -
LGA    -       -      Y       6           -
LGA    -       -      D       7           -
LGA    -       -      T       8           -
LGA    -       -      Y       9           -
LGA    -       -      V      10           -
LGA    -       -      K      11           -
LGA    -       -      A      12           -
LGA    -       -      K      13           -
LGA    -       -      D      14           -
LGA    -       -      G      15           -
LGA    -       -      H      16           -
LGA    -       -      V      17           -
LGA    -       -      M      18           -
LGA    -       -      H      19           -
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      T      24           -
LGA    S      52      D      25          2.797
LGA    E      53      V      26          1.054
LGA    E      54      R      27          2.466
LGA    C      55      D      28          2.878
LGA    -       -      D      29           -
LGA    R      56      K      30          1.378
LGA    F      57      K      31          1.588
LGA    C      58      A      32          1.962
LGA    H      59      I      33          1.484
LGA    S      60      E      34          0.774
LGA    Q      61      F      35          1.189
LGA    K      62      A      36          0.540
LGA    A      63      K      37          1.193
LGA    P      64      Q      38          1.875
LGA    -       -      W      39           -
LGA    -       -      L      40           -
LGA    -       -      S      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    D      65      E      45           #
LGA    E      66      E      46          2.936
LGA    -       -      G      47           -
LGA    -       -      A      48           -
LGA    -       -      T      49           -
LGA    -       -      V      50           -
LGA    -       -      T      51           -
LGA    -       -      S      52           -
LGA    -       -      E      53           -
LGA    -       -      E      54           -
LGA    -       -      C      55           -
LGA    -       -      R      56           -
LGA    -       -      F      57           -
LGA    -       -      C      58           -
LGA    -       -      H      59           -
LGA    -       -      S      60           -
LGA    -       -      Q      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    -       -      I      78           -
LGA    -       -      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -
LGA    -       -      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   85    5.0     14    1.88     7.14     14.501     0.706

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.845851 * X  +  -0.381910 * Y  +  -0.372399 * Z  +  17.760853
  Y_new =   0.152392 * X  +  -0.842052 * Y  +   0.517422 * Z  +  36.642586
  Z_new =  -0.511188 * X  +   0.380911 * Y  +   0.770450 * Z  + -17.316158 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.459158   -2.682434  [ DEG:    26.3078   -153.6922 ]
  Theta =   0.536566    2.605026  [ DEG:    30.7430    149.2570 ]
  Phi   =   2.963341   -0.178252  [ DEG:   169.7869    -10.2131 ]
 
# 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: T0353AL381_2                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353AL381_2.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   85   5.0   14   1.88    7.14  14.501
REMARK  ---------------------------------------------------------- 
MOLECULE T0353AL381_2
REMARK Aligment from pdb entry: 1mdvA
ATOM      1  N   SER    52       4.740   2.091 -12.212  1.00  0.00              
ATOM      2  CA  SER    52       4.864   2.442 -10.806  1.00  0.00              
ATOM      3  C   SER    52       3.428   2.681 -10.368  1.00  0.00              
ATOM      4  O   SER    52       2.616   3.140 -11.162  1.00  0.00              
ATOM      5  N   GLU    53       3.100   2.331  -9.131  1.00  0.00              
ATOM      6  CA  GLU    53       1.737   2.510  -8.630  1.00  0.00              
ATOM      7  C   GLU    53       1.328   3.974  -8.473  1.00  0.00              
ATOM      8  O   GLU    53       2.098   4.787  -7.955  1.00  0.00              
ATOM      9  N   GLU    54       0.119   4.299  -8.936  1.00  0.00              
ATOM     10  CA  GLU    54      -0.422   5.659  -8.860  1.00  0.00              
ATOM     11  C   GLU    54      -1.201   5.837  -7.558  1.00  0.00              
ATOM     12  O   GLU    54      -1.359   4.876  -6.811  1.00  0.00              
ATOM     13  N   CYS    55      -1.709   7.046  -7.303  1.00  0.00              
ATOM     14  CA  CYS    55      -2.455   7.299  -6.070  1.00  0.00              
ATOM     15  C   CYS    55      -3.664   6.367  -5.978  1.00  0.00              
ATOM     16  O   CYS    55      -3.878   5.707  -4.958  1.00  0.00              
ATOM     17  N   ARG    56      -4.430   6.296  -7.065  1.00  0.00              
ATOM     18  CA  ARG    56      -5.618   5.449  -7.135  1.00  0.00              
ATOM     19  C   ARG    56      -5.235   3.973  -7.217  1.00  0.00              
ATOM     20  O   ARG    56      -5.869   3.123  -6.582  1.00  0.00              
ATOM     21  N   PHE    57      -4.197   3.677  -7.994  1.00  0.00              
ATOM     22  CA  PHE    57      -3.732   2.307  -8.149  1.00  0.00              
ATOM     23  C   PHE    57      -3.434   1.556  -6.856  1.00  0.00              
ATOM     24  O   PHE    57      -3.905   0.436  -6.675  1.00  0.00              
ATOM     25  N   CYS    58      -2.670   2.170  -5.956  1.00  0.00              
ATOM     26  CA  CYS    58      -2.316   1.539  -4.684  1.00  0.00              
ATOM     27  C   CYS    58      -3.467   1.538  -3.667  1.00  0.00              
ATOM     28  O   CYS    58      -3.600   0.597  -2.883  1.00  0.00              
ATOM     29  N   HIS    59      -4.304   2.575  -3.693  1.00  0.00              
ATOM     30  CA  HIS    59      -5.432   2.670  -2.758  1.00  0.00              
ATOM     31  C   HIS    59      -6.477   1.552  -2.918  1.00  0.00              
ATOM     32  O   HIS    59      -7.189   1.216  -1.971  1.00  0.00              
ATOM     33  N   SER    60      -6.562   0.975  -4.114  1.00  0.00              
ATOM     34  CA  SER    60      -7.512  -0.108  -4.389  1.00  0.00              
ATOM     35  C   SER    60      -7.114  -1.404  -3.662  1.00  0.00              
ATOM     36  O   SER    60      -7.960  -2.074  -3.057  1.00  0.00              
ATOM     37  N   GLN    61      -5.826  -1.739  -3.715  1.00  0.00              
ATOM     38  CA  GLN    61      -5.294  -2.941  -3.065  1.00  0.00              
ATOM     39  C   GLN    61      -5.365  -2.823  -1.549  1.00  0.00              
ATOM     40  O   GLN    61      -5.634  -3.799  -0.857  1.00  0.00              
ATOM     41  N   LYS    62      -5.122  -1.613  -1.048  1.00  0.00              
ATOM     42  CA  LYS    62      -5.148  -1.311   0.380  1.00  0.00              
ATOM     43  C   LYS    62      -6.548  -1.436   0.993  1.00  0.00              
ATOM     44  O   LYS    62      -6.679  -1.817   2.153  1.00  0.00              
ATOM     45  N   ALA    63      -7.587  -1.103   0.227  1.00  0.00              
ATOM     46  CA  ALA    63      -8.956  -1.182   0.735  1.00  0.00              
ATOM     47  C   ALA    63      -9.530  -2.598   0.684  1.00  0.00              
ATOM     48  O   ALA    63     -10.402  -2.956   1.482  1.00  0.00              
ATOM     49  N   PRO    64      -9.052  -3.385  -0.275  1.00  0.00              
ATOM     50  CA  PRO    64      -9.500  -4.761  -0.428  1.00  0.00              
ATOM     51  C   PRO    64     -10.995  -5.030  -0.505  1.00  0.00              
ATOM     52  O   PRO    64     -11.672  -4.595  -1.440  1.00  0.00              
ATOM     53  N   ASP    65     -11.507  -5.740   0.496  1.00  0.00              
ATOM     54  CA  ASP    65     -12.915  -6.111   0.550  1.00  0.00              
ATOM     55  C   ASP    65     -13.777  -5.216   1.419  1.00  0.00              
ATOM     56  O   ASP    65     -14.954  -5.511   1.624  1.00  0.00              
ATOM     57  N   GLU    66     -13.195  -4.151   1.964  1.00  0.00              
ATOM     58  CA  GLU    66     -13.969  -3.231   2.791  1.00  0.00              
ATOM     59  C   GLU    66     -14.594  -2.205   1.851  1.00  0.00              
ATOM     60  O   GLU    66     -13.909  -1.311   1.354  1.00  0.00              
END
