Contacts of the strand formed by residues 141 - 150 (chain E) in PDB entry 5MWF


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with SER 141 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78E  TYR*     3.3    31.2    +      -       -      +
     90E  TYR*     4.1     8.8    +      -       -      -
    139E  PRO*     2.6    30.5    +      -       -      +
    140E  ARG*     1.3    76.7    -      -       -      +
    142E  PHE*     1.3    62.8    +      -       -      +
    170E  GLY      3.6     6.5    -      -       -      -
    171E  MET*     4.2    17.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 142 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  PHE*     4.2     6.7    -      +       -      -
     75E  LEU*     3.8    17.3    -      -       +      -
     76E  LYS      3.6    12.3    -      -       -      +
     78E  TYR*     3.3    21.2    -      -       -      +
     90E  TYR*     4.3     6.3    -      -       +      -
    138E  TRP*     4.3    16.2    -      +       +      -
    140E  ARG      3.4    11.2    -      -       -      -
    141E  SER*     1.3    75.7    -      -       -      +
    143E  THR*     1.3    81.1    +      -       -      +
    144E  LEU*     4.0    20.9    -      -       +      -
    168E  HIS*     4.6    11.2    -      +       -      -
    169E  ALA*     3.5     0.2    -      -       -      -
    170E  GLY*     3.1    51.4    +      -       -      -
    171E  MET      3.6     6.5    -      -       -      -
    172E  ILE*     3.6    24.0    -      -       +      -
    194E  ILE*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 143 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74E  CYS      3.9     0.5    -      -       -      +
     75E  LEU*     3.7     4.7    -      -       -      +
     76E  LYS*     3.0    48.7    +      -       -      +
     77E  GLU      3.1    12.9    +      -       -      -
     79E  GLN*     3.1    26.7    +      -       -      +
     82E  VAL*     4.0    26.7    -      -       +      -
    142E  PHE*     1.3    85.8    +      -       -      +
    144E  LEU*     1.3    65.5    +      -       -      +
    145E  ILE*     4.2     3.3    +      -       +      +
    168E  HIS      3.5    10.1    -      -       -      +
    169E  ALA*     3.4     5.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  PHE*     4.4     6.1    -      -       +      -
     32E  LEU*     3.8    23.8    -      -       +      -
     73E  VAL*     3.7    24.0    -      -       +      -
     74E  CYS      3.6    11.4    -      -       -      +
     75E  LEU*     4.2     9.9    -      -       +      -
    142E  PHE*     4.0    15.4    -      -       +      -
    143E  THR*     1.3    74.1    -      -       -      +
    145E  ILE*     1.3    67.2    +      -       -      +
    146E  VAL*     3.9    15.4    -      -       +      +
    167E  SER*     3.2     3.3    -      -       -      -
    168E  HIS*     2.6    44.9    +      -       +      +
    181E  LEU*     4.3    16.6    -      -       +      -
    183E  PHE*     4.9     5.4    -      -       +      -
    192E  LEU*     4.6     2.9    -      -       +      -
    194E  ILE*     3.9    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 145 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72E  ARG      3.9     0.7    -      -       -      +
     73E  VAL*     3.7     2.4    -      -       -      -
     74E  CYS*     2.9    54.7    +      -       +      +
     76E  LYS*     4.0    19.7    -      -       +      +
     82E  VAL*     4.3     5.6    -      -       +      -
     83E  THR      3.5    24.7    -      -       -      +
     84E  PRO*     4.3    12.1    -      -       +      +
     85E  THR      6.0     0.2    -      -       -      -
    143E  THR*     4.5     7.0    -      -       +      +
    144E  LEU*     1.3    80.0    -      -       -      +
    146E  VAL*     1.3    64.9    +      -       -      +
    147E  GLU*     4.3     8.0    +      -       +      +
    165E  ARG*     3.8    27.6    -      -       +      +
    166E  VAL      3.3     8.3    -      -       -      +
    167E  SER*     4.0    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32E  LEU*     4.1     9.9    -      -       +      -
     34E  LEU*     6.4     0.2    -      -       +      -
     71E  VAL*     3.7    25.6    -      -       +      -
     72E  ARG      3.6     3.1    -      -       -      +
     73E  VAL*     4.9     3.4    -      -       +      -
    144E  LEU*     3.9    26.0    -      -       +      -
    145E  ILE*     1.3    77.0    -      -       -      +
    147E  GLU*     1.3    64.2    +      -       -      +
    164E  GLU      4.1     0.3    -      -       -      +
    165E  ARG*     3.4     1.7    -      -       -      +
    166E  VAL*     2.8    50.5    +      -       +      +
    183E  PHE*     5.1     3.6    -      -       +      -
    190E  LEU*     3.9    22.2    -      -       +      +
    192E  LEU*     4.1    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 147 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71E  VAL*     3.2    13.4    -      -       -      +
     72E  ARG*     2.9    50.7    +      -       -      +
     74E  CYS*     6.2     3.1    -      -       +      -
     84E  PRO      5.0     0.5    -      -       -      +
    145E  ILE*     4.5     6.6    -      -       +      +
    146E  VAL*     1.3    79.4    -      -       -      +
    148E  ALA*     1.3    60.7    +      -       -      +
    149E  TRP*     2.6    40.8    +      -       +      +
    162E  LEU*     4.0     3.1    -      -       +      -
    164E  GLU      3.3     5.2    -      -       -      +
    165E  ARG*     2.6    52.6    +      -       +      +
    190E  LEU*     5.7     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 148 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  LEU*     4.3    20.2    -      -       +      -
     69E  THR*     4.1    16.6    -      -       +      -
     70E  TYR      3.7     4.0    -      -       -      -
     71E  VAL*     4.7     3.1    -      -       +      +
    147E  GLU*     1.3    74.0    -      -       -      +
    149E  TRP*     1.3    57.8    +      -       -      +
    162E  LEU*     3.3     3.8    -      -       -      +
    163E  ILE*     2.8    47.0    +      -       +      +
    164E  GLU*     2.8    21.9    +      -       +      +
    190E  LEU*     5.4     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 149 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69E  THR*     3.5     4.2    -      -       -      +
     70E  TYR*     2.7    69.1    +      -       +      +
     72E  ARG*     3.3    36.0    -      -       +      +
    147E  GLU*     2.6    47.3    +      -       +      -
    148E  ALA*     1.3    69.9    -      -       -      +
    150E  ASP*     1.3    59.7    +      -       -      +
    158E  ASN      3.1    28.3    -      -       -      -
    159E  GLU*     4.8     5.4    -      -       -      -
    161E  LEU*     3.0    35.2    -      -       +      -
    162E  LEU*     3.4    23.4    -      -       +      +
    163E  ILE*     3.4     4.9    -      -       -      -
    165E  ARG*     5.1     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 150 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  LEU*     4.3     6.9    -      -       +      +
     50E  CYS*     3.6    12.1    -      -       -      +
     67E  CYS*     3.2    23.6    -      -       +      -
     68E  ASP      3.4     2.6    +      -       -      -
     70E  TYR*     3.8     8.9    +      -       -      -
    149E  TRP*     1.3    74.4    -      -       -      +
    151E  TRP*     1.3    70.6    +      -       -      +
    152E  ASP*     3.4     5.4    +      -       -      +
    161E  LEU*     3.0    41.7    +      -       +      +
    163E  ILE*     3.1    20.3    -      -       +      +
    405E   CA      2.4    25.7    -      -       -      -
    406E   CA      2.8    24.8    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il