Contacts of the strand formed by residues 194 - 200 (chain A) in PDB entry 5EXU


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 ARG 194 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  THR*     5.9     0.8    -      -       -      +
    138A  LYS*     4.5    14.4    -      -       -      +
    141A  SER*     4.5    11.9    -      -       -      +
    192A  ASP*     4.2     0.8    +      -       -      +
    193A  HIS*     1.3    71.7    -      -       -      +
    195A  ILE*     1.3    59.4    +      -       -      +
    196A  GLU*     4.2     1.6    -      -       +      -
    210A  TYR*     3.8    29.7    +      -       +      +
    211A  GLU*     3.3     7.0    -      -       -      +
    212A  HIS*     3.0    72.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  THR*     3.8    39.0    -      -       -      +
     59A  PRO*     3.9    12.1    -      -       +      -
     62A  CRQ      3.8    31.6    -      -       +      +
    138A  LYS*     3.1    24.9    -      -       -      +
    139A  TRP*     3.7    34.0    +      -       +      -
    140A  LYS      5.2     2.6    +      -       -      +
    193A  HIS*     3.9     5.8    +      -       +      +
    194A  ARG*     1.3    73.6    -      -       -      +
    196A  GLU*     1.3    62.9    +      -       -      +
    209A  LEU*     4.1     9.0    -      -       +      -
    210A  TYR      3.5     2.5    -      -       -      +
    211A  GLU*     4.4     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  LEU      4.5     4.6    -      -       -      +
    138A  LYS*     3.1    47.9    -      -       -      +
    194A  ARG*     4.2     1.5    -      -       +      -
    195A  ILE*     1.3    74.8    -      -       -      +
    197A  ILE*     1.3   100.8    +      -       -      +
    198A  LEU*     3.5     9.3    +      -       +      +
    209A  LEU*     3.6     4.4    -      -       -      +
    210A  TYR*     3.1    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  TYR*     4.1    22.2    -      -       +      -
     55A  ASP*     3.6    23.3    -      -       -      +
     58A  THR*     4.3     4.5    -      -       +      +
    138A  LYS*     5.6     0.2    -      -       -      +
    196A  GLU*     1.3    99.0    +      -       -      +
    198A  LEU*     1.3    62.9    +      -       -      +
    199A  SER*     3.2    29.4    -      -       -      +
    200A  HIS*     4.4    13.4    -      -       +      -
    204A  TYR*     4.0    20.0    -      -       +      -
    207A  VAL*     3.8     9.4    -      -       +      -
    208A  ARG      3.6     6.5    -      -       -      +
    209A  LEU*     3.8    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  THR*     4.8    14.4    -      -       +      +
    196A  GLU*     3.5     7.4    +      -       +      -
    197A  ILE*     1.3    74.8    -      -       -      +
    199A  SER*     1.3    62.9    +      -       -      +
    208A  ARG*     2.8    22.3    +      -       +      +
    210A  TYR*     3.2    54.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  ILE*     3.2    13.7    -      -       -      +
    198A  LEU*     1.3    79.0    -      -       -      +
    200A  HIS*     1.3    68.5    +      -       -      +
    207A  VAL*     3.5     0.2    -      -       -      -
    208A  ARG*     2.9    50.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  ILE*     4.4     7.9    -      -       +      -
    199A  SER*     1.3    83.2    -      -       -      +
    201A  ASP*     1.3    80.7    +      -       -      +
    202A  LYS*     4.8     3.8    -      -       -      -
    204A  TYR*     3.1    58.3    +      +       +      -
    206A  LYS      3.2    14.1    -      -       -      +
    207A  VAL*     4.1     2.5    -      -       +      -
----------------------------------------------------------
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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