Contacts of the strand formed by residues 18 - 22 (chain A) in PDB entry 2ARE


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 LEU 18 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     4.0    18.2    -      -       +      -
     11A  PHE*     4.1    21.5    -      -       +      -
     15A  GLN*     3.6    35.1    -      -       +      +
     16A  LYS      3.5     5.1    -      -       -      +
     17A  ASN*     1.3    83.9    -      -       -      +
     19A  ILE*     1.3    64.5    +      -       -      +
     20A  PHE*     3.7    36.5    -      -       +      -
     31A  VAL*     4.9     1.8    -      -       +      -
     50A  ILE*     4.3    22.7    -      -       +      -
     51A  LEU      3.5    15.3    -      -       -      +
     52A  PHE*     4.2     8.5    -      -       +      -
    231A  TRP*     4.4     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LEU*     1.3    75.0    -      -       -      +
     20A  PHE*     1.3    65.0    +      -       -      +
     21A  GLN*     4.1    26.4    -      -       +      +
     50A  ILE*     3.1     7.8    -      -       -      +
     51A  LEU*     2.9    42.0    +      -       +      +
     52A  PHE      4.5     1.8    -      -       -      +
     53A  SER*     4.1    18.4    -      -       -      -
    212A  ARG*     3.8    40.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  GLN*     4.4    13.2    -      -       +      -
     18A  LEU*     3.7    37.2    -      -       +      -
     19A  ILE*     1.3    77.1    -      -       -      +
     21A  GLN*     1.3    63.3    +      -       -      +
     22A  GLY      5.9     0.4    -      -       -      +
     24A  ALA      3.6    26.9    -      -       -      +
     25A  GLN*     4.3     9.6    -      -       -      -
     26A  ILE*     3.9    34.5    -      -       +      -
     31A  VAL*     4.8     1.3    -      -       +      -
     49A  ARG      3.7     2.0    -      -       -      -
     50A  ILE*     3.6    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ILE*     4.1    17.2    -      -       +      +
     20A  PHE*     1.3    80.6    -      -       -      +
     22A  GLY*     1.3    69.4    +      -       -      +
     23A  ASP      3.4     0.7    +      -       -      -
     24A  ALA      3.5     4.2    +      -       -      -
     48A  GLY*     3.4     0.5    -      -       -      -
     49A  ARG*     2.9    71.3    +      -       +      +
     51A  LEU*     3.9    16.0    -      -       -      +
     97A  THR      3.1    22.0    +      -       -      -
     98A  THR*     3.9    15.8    -      -       -      +
     99A  ILE*     3.8    13.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     5.4     0.9    -      -       -      +
     21A  GLN*     1.3    74.8    -      -       -      +
     23A  ASP*     1.3    64.0    +      -       -      +
     24A  ALA      3.6     1.9    +      -       -      +
     47A  VAL      3.6     3.8    -      -       -      -
     99A  ILE*     3.5    20.6    -      -       -      +
----------------------------------------------------------
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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