
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0350AL381_2-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350AL381_2-D1.T0350_D1.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           -
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    V      56      T       8          2.603
LGA    H      57      L       9          3.422
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    L      58      Q      55           #
LGA    K      59      V      56          2.549
LGA    -       -      H      57           -
LGA    F      60      L      58          1.438
LGA    E      61      K      59          0.564
LGA    L      62      F      60          0.684
LGA    H      63      E      61          0.548
LGA    D      64      L      62          0.559
LGA    K      65      H      63          1.535
LGA    L      66      D      64          2.022
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    N      67      Y      69          2.376
LGA    E      68      Y      70          1.774
LGA    Y      69      V      71          0.743
LGA    Y      70      K      72          1.278
LGA    V      71      V      73          0.912
LGA    K      72      I      74          0.177
LGA    V      73      E      75          0.835
LGA    I      74      D      76          2.007
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    -       -      V      81           -
LGA    -       -      I      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      I      85           -
LGA    -       -      P      86           -
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    -       -      W      90           -
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    -       -      Y      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   91    5.0     18    1.69     5.56     17.293     1.005

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.294427 * X  +  -0.949225 * Y  +  -0.110839 * Z  +  43.862522
  Y_new =  -0.954773 * X  +   0.297200 * Y  +  -0.009006 * Z  +  41.501476
  Z_new =   0.041490 * X  +   0.103175 * Y  +  -0.993798 * Z  + -17.930592 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.038145   -0.103448  [ DEG:   174.0729     -5.9271 ]
  Theta =  -0.041502   -3.100091  [ DEG:    -2.3779   -177.6221 ]
  Phi   =  -1.869918    1.271675  [ DEG:  -107.1384     72.8616 ]
 
# 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: T0350AL381_2-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_2-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   91   5.0   18   1.69    5.56  17.293
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_2-D1
REMARK Aligment from pdb entry: 1nnxA
ATOM      1  N   VAL    56      10.095  -5.399  -8.800  1.00  0.00              
ATOM      2  CA  VAL    56      11.141  -4.360  -8.763  1.00  0.00              
ATOM      3  C   VAL    56      10.609  -3.002  -9.124  1.00  0.00              
ATOM      4  O   VAL    56       9.532  -2.866  -9.808  1.00  0.00              
ATOM      5  N   HIS    57      11.261  -1.993  -8.595  1.00  0.00              
ATOM      6  CA  HIS    57      10.919  -0.654  -8.954  1.00  0.00              
ATOM      7  C   HIS    57      12.081  -0.115  -9.847  1.00  0.00              
ATOM      8  O   HIS    57      13.269  -0.208  -9.461  1.00  0.00              
ATOM      9  N   LEU    58      11.783   0.455 -10.999  1.00  0.00              
ATOM     10  CA  LEU    58      12.793   1.054 -11.855  1.00  0.00              
ATOM     11  C   LEU    58      12.500   2.517 -12.044  1.00  0.00              
ATOM     12  O   LEU    58      11.334   2.935 -12.030  1.00  0.00              
ATOM     13  N   LYS    59      13.545   3.321 -12.143  1.00  0.00              
ATOM     14  CA  LYS    59      13.443   4.744 -12.401  1.00  0.00              
ATOM     15  C   LYS    59      14.380   5.049 -13.552  1.00  0.00              
ATOM     16  O   LYS    59      15.512   4.527 -13.587  1.00  0.00              
ATOM     17  N   PHE    60      13.948   5.887 -14.475  1.00  0.00              
ATOM     18  CA  PHE    60      14.783   6.258 -15.610  1.00  0.00              
ATOM     19  C   PHE    60      14.002   7.101 -16.568  1.00  0.00              
ATOM     20  O   PHE    60      12.929   7.607 -16.213  1.00  0.00              
ATOM     21  N   GLU    61      14.521   7.233 -17.765  1.00  0.00              
ATOM     22  CA  GLU    61      13.876   8.084 -18.785  1.00  0.00              
ATOM     23  C   GLU    61      13.252   7.336 -19.896  1.00  0.00              
ATOM     24  O   GLU    61      13.807   6.357 -20.389  1.00  0.00              
ATOM     25  N   LEU    62      12.074   7.808 -20.297  1.00  0.00              
ATOM     26  CA  LEU    62      11.418   7.243 -21.483  1.00  0.00              
ATOM     27  C   LEU    62      12.305   7.697 -22.664  1.00  0.00              
ATOM     28  O   LEU    62      12.641   8.874 -22.772  1.00  0.00              
ATOM     29  N   HIS    63      12.752   6.754 -23.495  1.00  0.00              
ATOM     30  CA  HIS    63      13.595   7.023 -24.682  1.00  0.00              
ATOM     31  C   HIS    63      12.714   6.581 -25.833  1.00  0.00              
ATOM     32  O   HIS    63      12.551   5.388 -26.090  1.00  0.00              
ATOM     33  N   ASP    64      12.195   7.551 -26.568  1.00  0.00              
ATOM     34  CA  ASP    64      11.259   7.247 -27.635  1.00  0.00              
ATOM     35  C   ASP    64      11.767   7.806 -28.900  1.00  0.00              
ATOM     36  O   ASP    64      12.112   8.975 -28.980  1.00  0.00              
ATOM     37  N   LYS    65      11.802   6.932 -29.899  1.00  0.00              
ATOM     38  CA  LYS    65      12.246   7.278 -31.255  1.00  0.00              
ATOM     39  C   LYS    65      11.155   6.890 -32.222  1.00  0.00              
ATOM     40  O   LYS    65      10.180   6.343 -31.841  1.00  0.00              
ATOM     41  N   LEU    66      11.381   7.121 -33.519  1.00  0.00              
ATOM     42  CA  LEU    66      10.371   6.765 -34.507  1.00  0.00              
ATOM     43  C   LEU    66      10.023   5.284 -34.509  1.00  0.00              
ATOM     44  O   LEU    66       8.882   4.907 -34.764  1.00  0.00              
ATOM     45  N   ASN    67      10.974   4.439 -34.115  1.00  0.00              
ATOM     46  CA  ASN    67      10.736   3.039 -34.162  1.00  0.00              
ATOM     47  C   ASN    67      10.743   2.329 -32.838  1.00  0.00              
ATOM     48  O   ASN    67      10.652   1.118 -32.822  1.00  0.00              
ATOM     49  N   GLU    68      10.825   3.059 -31.752  1.00  0.00              
ATOM     50  CA  GLU    68      10.900   2.262 -30.530  1.00  0.00              
ATOM     51  C   GLU    68      10.627   3.100 -29.298  1.00  0.00              
ATOM     52  O   GLU    68      10.709   4.323 -29.325  1.00  0.00              
ATOM     53  N   TYR    69      10.274   2.418 -28.203  1.00  0.00              
ATOM     54  CA  TYR    69      10.160   3.144 -26.946  1.00  0.00              
ATOM     55  C   TYR    69      10.846   2.199 -25.969  1.00  0.00              
ATOM     56  O   TYR    69      10.795   0.932 -26.106  1.00  0.00              
ATOM     57  N   TYR    70      11.630   2.751 -25.055  1.00  0.00              
ATOM     58  CA  TYR    70      12.308   1.900 -24.085  1.00  0.00              
ATOM     59  C   TYR    70      12.494   2.824 -22.866  1.00  0.00              
ATOM     60  O   TYR    70      12.285   4.036 -22.902  1.00  0.00              
ATOM     61  N   VAL    71      12.818   2.229 -21.757  1.00  0.00              
ATOM     62  CA  VAL    71      13.178   3.007 -20.575  1.00  0.00              
ATOM     63  C   VAL    71      14.692   2.881 -20.359  1.00  0.00              
ATOM     64  O   VAL    71      15.208   1.743 -20.331  1.00  0.00              
ATOM     65  N   LYS    72      15.400   4.001 -20.218  1.00  0.00              
ATOM     66  CA  LYS    72      16.875   3.922 -19.921  1.00  0.00              
ATOM     67  C   LYS    72      16.907   3.950 -18.419  1.00  0.00              
ATOM     68  O   LYS    72      16.644   4.991 -17.827  1.00  0.00              
ATOM     69  N   VAL    73      17.248   2.824 -17.810  1.00  0.00              
ATOM     70  CA  VAL    73      17.155   2.715 -16.362  1.00  0.00              
ATOM     71  C   VAL    73      18.314   3.297 -15.576  1.00  0.00              
ATOM     72  O   VAL    73      19.494   2.910 -15.804  1.00  0.00              
ATOM     73  N   ILE    74      18.004   4.189 -14.637  1.00  0.00              
ATOM     74  CA  ILE    74      19.075   4.741 -13.762  1.00  0.00              
ATOM     75  C   ILE    74      19.186   3.983 -12.458  1.00  0.00              
ATOM     76  O   ILE    74      20.237   3.972 -11.825  1.00  0.00              
END
