Contacts of the strand formed by residues 536 - 542 (chain A) in PDB entry 1EJ9


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 536 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    528A  ASP*     3.0    35.8    +      -       -      +
    529A  PHE      3.3     9.4    -      -       -      +
    530A  LEU*     3.5    15.7    -      -       +      -
    534A  SER      3.4     4.2    +      -       -      -
    535A  ILE*     1.3    74.6    -      -       -      +
    537A  TYR*     1.3    70.6    +      -       -      +
    538A  TYR*     3.9    20.2    +      -       +      +
    631A  ASN*     3.3    14.5    +      -       -      +
    633A  GLN*     3.9    15.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 537 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    485A  LEU*     4.1    24.0    +      -       -      +
    487A  LEU*     4.3    16.2    -      -       +      -
    527A  PHE*     3.7    25.1    -      +       +      -
    528A  ASP*     2.9     5.7    -      -       -      -
    529A  PHE*     2.4    80.8    +      +       +      +
    531A  GLY*     5.9     0.2    -      -       -      -
    535A  ILE      4.7     2.5    -      -       -      +
    536A  ARG*     1.3    74.8    -      -       -      +
    538A  TYR*     1.3    61.3    +      -       -      +
    539A  ASN*     3.2    36.1    +      -       +      -
    629A  LEU      5.8     1.8    -      -       -      -
    631A  ASN*     4.0    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 538 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    526A  GLU*     2.8    38.1    +      -       +      -
    527A  PHE      3.0    24.5    -      -       -      -
    528A  ASP*     3.6    21.5    -      -       +      +
    536A  ARG*     3.9    30.2    +      -       -      +
    537A  TYR*     1.3    79.8    -      -       -      +
    539A  ASN*     1.3    70.0    +      -       -      +
    540A  LYS*     3.2    34.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 539 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    485A  LEU*     4.2     7.1    -      -       -      +
    525A  VAL      3.1     4.5    -      -       -      +
    526A  GLU*     4.9     0.4    -      -       -      -
    527A  PHE*     2.8    44.7    +      -       -      +
    537A  TYR*     3.2    31.3    +      -       +      +
    538A  TYR*     1.3    81.5    -      -       -      +
    540A  LYS*     1.3    71.8    +      -       -      +
    541A  VAL*     3.1    24.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 540 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    518A  LEU*     3.8    23.8    -      -       +      -
    519A  ASP*     5.0     9.2    -      -       -      +
    521A  GLN*     5.3     5.6    +      -       -      +
    524A  VAL*     3.7    13.4    -      -       +      +
    525A  VAL      3.2     4.5    -      -       -      -
    526A  GLU*     3.5    27.1    -      -       +      +
    538A  TYR*     3.2    33.2    +      -       -      +
    539A  ASN*     1.3    79.1    +      -       -      +
    541A  VAL*     1.3    62.6    +      -       -      +
    542A  PRO*     3.7     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 541 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484A  LYS*     3.7    21.5    -      -       +      +
    485A  LEU*     4.1    14.8    -      -       +      -
    524A  VAL*     3.6     3.0    -      -       -      +
    525A  VAL      2.5    40.9    +      -       -      +
    527A  PHE*     3.9    18.4    -      -       +      -
    539A  ASN*     3.1    40.8    -      -       -      +
    540A  LYS*     1.3    75.7    -      -       -      +
    542A  PRO*     1.3    77.5    -      -       +      +
    543A  VAL*     3.3    16.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 542 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484A  LYS*     2.8    24.0    +      -       -      +
    521A  GLN*     3.8    38.4    -      -       +      +
    522A  GLU      4.1    11.4    -      -       -      +
    523A  TYR      3.2     8.5    -      -       -      +
    524A  VAL*     4.0     4.3    -      -       +      -
    540A  LYS      3.7     8.1    -      -       -      +
    541A  VAL*     1.3    85.1    -      -       +      +
    543A  VAL*     1.3    62.3    +      -       -      +
----------------------------------------------------------
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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