
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0386AL381_5-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386AL381_5-D1.T0386_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    -       -      I      13           -
LGA    -       -      I      14           -
LGA    -       -      S      15           -
LGA    -       -      P      16           -
LGA    -       -      H      17           -
LGA    -       -      H      18           -
LGA    -       -      Y      19           -
LGA    -       -      V      20           -
LGA    -       -      Y      21           -
LGA    -       -      P      22           -
LGA    -       -      N      23           -
LGA    -       -      T      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      N      29           -
LGA    -       -      K      30           -
LGA    -       -      Y      31           -
LGA    -       -      G      32           -
LGA    -       -      I      33           -
LGA    -       -      K      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      N      37           -
LGA    -       -      A      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      C      43           -
LGA    -       -      S      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      T      47           -
LGA    -       -      A      48           -
LGA    -       -      K      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      I      52           -
LGA    -       -      N      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      S      58           -
LGA    -       -      L      59           -
LGA    -       -      P      60           -
LGA    -       -      E      61           -
LGA    -       -      Y      62           -
LGA    I      13      F      63          2.172
LGA    I      14      D      64          2.735
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    S      15      Y      67          2.113
LGA    P      16      L      68          2.865
LGA    -       -      C      69           -
LGA    -       -      H      70           -
LGA    -       -      I      71           -
LGA    H      17      H      72          1.430
LGA    H      18      Q      73          1.652
LGA    Y      19      Q      74          2.906
LGA    V      20      L      75          2.063
LGA    Y      21      F      76          1.845
LGA    P      22      K      77          0.894
LGA    -       -      N      78           -
LGA    -       -      T      79           -
LGA    N      23      F      80          2.795
LGA    -       -      E      81           -
LGA    -       -      W      82           -
LGA    -       -      A      83           -
LGA    -       -      G      84           -
LGA    -       -      Y      85           -
LGA    -       -      L      86           -
LGA    -       -      R      87           -
LGA    -       -      H      88           -
LGA    -       -      I      89           -
LGA    -       -      P      90           -
LGA    -       -      F      91           -
LGA    -       -      T      92           -
LGA    -       -      F      93           -
LGA    -       -      A      94           -
LGA    -       -      D      95           -
LGA    -       -      G      96           -
LGA    -       -      T      97           -
LGA    -       -      T      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      M     101           -
LGA    -       -      P     102           -
LGA    -       -      E     103           -
LGA    -       -      M     104           -
LGA    -       -      K     105           -
LGA    -       -      R     106           -
LGA    -       -      T     107           -
LGA    -       -      G     108           -
LGA    -       -      W     109           -
LGA    -       -      K     110           -
LGA    -       -      N     111           -
LGA    -       -      A     112           -
LGA    -       -      F     113           -
LGA    -       -      A     114           -
LGA    -       -      I     115           -
LGA    -       -      G     116           -
LGA    -       -      D     117           -
LGA    -       -      E     118           -
LGA    -       -      I     119           -
LGA    -       -      Q     120           -
LGA    -       -      E     121           -
LGA    -       -      G     122           -
LGA    -       -      L     123           -
LGA    -       -      Q     124           -
LGA    -       -      R     125           -
LGA    -       -      L     126           -
LGA    -       -      D     127           -
LGA    -       -      Q     128           -
LGA    -       -      T     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      E     132           -
LGA    -       -      K     133           -
LGA    -       -      N     134           -
LGA    -       -      N     135           -
LGA    -       -      L     136           -
LGA    -       -      Q     137           -
LGA    -       -      G     138           -
LGA    -       -      L     139           -
LGA    -       -      T     140           -
LGA    -       -      R     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    -       -      F     144           -
LGA    -       -      N     145           -
LGA    -       -      S     146           -
LGA    -       -      E     147           -
LGA    -       -      A     148           -
LGA    -       -      I     149           -
LGA    -       -      E     150           -
LGA    -       -      L     151           -
LGA    -       -      F     152           -
LGA    -       -      N     153           -
LGA    -       -      S     154           -
LGA    -       -      L     155           -
LGA    -       -      N     156           -
LGA    -       -      Q     157           -
LGA    -       -      L     158           -
LGA    -       -      H     159           -
LGA    -       -      P     160           -
LGA    -       -      F     161           -
LGA    -       -      R     162           -
LGA    -       -      E     163           -
LGA    -       -      G     164           -
LGA    -       -      N     165           -
LGA    -       -      G     166           -
LGA    -       -      R     167           -
LGA    -       -      T     168           -
LGA    -       -      Q     169           -
LGA    -       -      R     170           -
LGA    -       -      L     171           -
LGA    -       -      F     172           -
LGA    -       -      F     173           -
LGA    -       -      E     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      A     177           -
LGA    -       -      K     178           -
LGA    -       -      A     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      H     182           -
LGA    -       -      Q     183           -
LGA    -       -      L     184           -
LGA    -       -      N     185           -
LGA    -       -      F     186           -
LGA    -       -      S     187           -
LGA    -       -      L     188           -
LGA    -       -      I     189           -
LGA    -       -      T     190           -
LGA    -       -      K     191           -
LGA    -       -      E     192           -
LGA    -       -      R     193           -
LGA    -       -      M     194           -
LGA    -       -      M     195           -
LGA    -       -      V     196           -
LGA    -       -      A     197           -
LGA    -       -      S     198           -
LGA    -       -      V     199           -
LGA    -       -      A     200           -
LGA    -       -      V     201           -
LGA    -       -      A     202           -
LGA    -       -      E     203           -
LGA    -       -      N     204           -
LGA    -       -      G     205           -
LGA    -       -      D     206           -
LGA    -       -      L     207           -
LGA    -       -      E     208           -
LGA    -       -      P     209           -
LGA    -       -      M     210           -
LGA    -       -      Q     211           -
LGA    -       -      H     212           -
LGA    -       -      L     213           -
LGA    -       -      F     214           -
LGA    -       -      E     215           -
LGA    -       -      D     216           -
LGA    -       -      I     217           -
LGA    -       -      S     218           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   11  206    5.0     11    2.22     9.09      4.354     0.473

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.149197 * X  +   0.649816 * Y  +   0.745305 * Z  + -15.406816
  Y_new =   0.988638 * X  +   0.111994 * Y  +   0.100263 * Z  +  11.758921
  Z_new =  -0.018318 * X  +   0.751796 * Y  +  -0.659141 * Z  +  67.645142 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.290620   -0.850973  [ DEG:   131.2429    -48.7571 ]
  Theta =   0.018319    3.123274  [ DEG:     1.0496    178.9504 ]
  Phi   =   1.720578   -1.421015  [ DEG:    98.5818    -81.4182 ]
 
# 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: T0386AL381_5-D1                               
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL381_5-D1.T0386_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11  206   5.0   11   2.22    9.09   4.354
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL381_5-D1
REMARK Aligment from pdb entry: 1fdw
ATOM      5  N   ILE    13      -3.008  57.437  52.580  1.00  0.00              
ATOM      6  CA  ILE    13      -2.710  58.209  51.395  1.00  0.00              
ATOM      7  C   ILE    13      -1.218  58.116  51.104  1.00  0.00              
ATOM      8  O   ILE    13      -0.319  58.242  51.945  1.00  0.00              
ATOM      9  N   ILE    14      -0.924  57.815  49.843  1.00  0.00              
ATOM     10  CA  ILE    14       0.455  57.695  49.396  1.00  0.00              
ATOM     11  C   ILE    14       1.054  59.082  49.220  1.00  0.00              
ATOM     12  O   ILE    14       0.755  59.768  48.241  1.00  0.00              
ATOM     13  N   SER    15       1.944  59.476  50.139  1.00  0.00              
ATOM     14  CA  SER    15       2.552  60.803  49.969  1.00  0.00              
ATOM     15  C   SER    15       3.851  60.676  49.207  1.00  0.00              
ATOM     16  O   SER    15       4.129  59.608  48.684  1.00  0.00              
ATOM     17  N   PRO    16       4.645  61.751  49.160  1.00  0.00              
ATOM     18  CA  PRO    16       5.937  61.726  48.492  1.00  0.00              
ATOM     19  C   PRO    16       6.833  62.844  48.995  1.00  0.00              
ATOM     20  O   PRO    16       6.405  63.870  49.494  1.00  0.00              
ATOM     21  N   HIS    17       8.142  62.698  48.787  1.00  0.00              
ATOM     22  CA  HIS    17       9.047  63.779  49.164  1.00  0.00              
ATOM     23  C   HIS    17       8.745  64.959  48.250  1.00  0.00              
ATOM     24  O   HIS    17       8.894  66.128  48.635  1.00  0.00              
ATOM     25  N   HIS    18       8.245  64.724  47.038  1.00  0.00              
ATOM     26  CA  HIS    18       7.911  65.848  46.164  1.00  0.00              
ATOM     27  C   HIS    18       6.700  66.630  46.649  1.00  0.00              
ATOM     28  O   HIS    18       6.378  67.692  46.090  1.00  0.00              
ATOM     29  N   TYR    19       5.983  66.159  47.648  1.00  0.00              
ATOM     30  CA  TYR    19       4.827  66.817  48.200  1.00  0.00              
ATOM     31  C   TYR    19       5.198  67.636  49.432  1.00  0.00              
ATOM     32  O   TYR    19       4.304  68.209  50.056  1.00  0.00              
ATOM     33  N   VAL    20       6.471  67.664  49.793  1.00  0.00              
ATOM     34  CA  VAL    20       7.035  68.421  50.870  1.00  0.00              
ATOM     35  C   VAL    20       8.154  69.378  50.413  1.00  0.00              
ATOM     36  O   VAL    20       8.595  70.149  51.279  1.00  0.00              
ATOM     37  N   TYR    21       8.616  69.319  49.172  1.00  0.00              
ATOM     38  CA  TYR    21       9.648  70.288  48.750  1.00  0.00              
ATOM     39  C   TYR    21       9.675  70.274  47.224  1.00  0.00              
ATOM     40  O   TYR    21       9.535  69.160  46.691  1.00  0.00              
ATOM     41  N   PRO    22       9.825  71.403  46.550  1.00  0.00              
ATOM     42  CA  PRO    22       9.773  71.399  45.093  1.00  0.00              
ATOM     43  C   PRO    22      11.008  70.907  44.387  1.00  0.00              
ATOM     44  O   PRO    22      12.145  71.237  44.729  1.00  0.00              
ATOM     45  N   ASN    23      10.865  70.104  43.351  1.00  0.00              
ATOM     46  CA  ASN    23      11.892  69.528  42.502  1.00  0.00              
ATOM     47  C   ASN    23      11.766  70.100  41.091  1.00  0.00              
ATOM     48  O   ASN    23      10.731  70.021  40.417  1.00  0.00              
END
