Contacts of the strand formed by residues 87 - 93 (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 GLY 87 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  LEU*     5.6     1.1    -      -       -      -
     86A  ASP*     1.3    81.6    -      -       -      +
     88A  ILE*     1.3    60.8    +      -       -      -
    108A  LEU*     3.8    12.4    -      -       -      +
    129A  PHE      3.1    15.0    -      -       -      -
    130A  ASP*     4.5     0.2    -      -       -      -
    131A  THR*     4.5     2.9    -      -       -      -
    217A  ALA*     3.4    17.8    -      -       -      -
    218A  ALA      3.5     3.8    +      -       -      -
    224A  GLN*     3.5     4.8    +      -       -      -
    226A  HIS*     3.1    20.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LEU*     3.5    28.0    -      -       +      -
     73A  PHE*     5.9     0.9    -      -       +      -
     75A  PHE*     3.7    59.2    -      -       +      -
     77A  LEU*     4.5     5.2    -      -       +      -
     87A  GLY*     1.3    74.8    -      -       -      -
     89A  ALA*     1.3    70.7    +      -       -      +
    108A  LEU*     5.2     1.9    -      -       -      +
    128A  GLU*     3.6     0.5    -      -       -      +
    129A  PHE*     2.9    36.8    +      -       +      +
    215A  PHE*     4.5    13.0    -      -       +      -
    216A  SER      3.3    10.8    -      -       -      +
    217A  ALA*     4.1     0.7    -      -       +      -
    226A  HIS*     4.1    15.7    -      -       +      -
    228A  LEU*     4.7     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  ILE*     1.3    78.2    -      -       -      +
     90A  PHE*     1.3    63.2    +      -       -      +
     91A  PHE*     3.9     0.7    +      -       -      -
    108A  LEU*     4.6     5.8    -      -       +      -
    110A  LEU*     3.9    28.7    -      -       +      -
    126A  ALA*     4.5     1.1    -      -       +      -
    127A  VAL      3.2    13.7    -      -       -      +
    128A  GLU*     4.0    12.6    -      -       +      -
    129A  PHE*     4.8     0.9    -      -       -      -
    215A  PHE*     3.1    11.0    -      -       -      +
    216A  SER      2.8    37.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  PHE*     4.6     2.9    -      +       -      -
     71A  SER*     3.4    31.4    -      -       -      -
     73A  PHE*     3.9    16.5    -      +       +      -
     89A  ALA*     1.3    73.0    -      -       -      +
     91A  PHE*     1.3    60.2    +      -       -      +
     92A  ILE*     4.1    30.5    -      -       +      -
    125A  ILE      5.9     0.2    -      -       -      -
    126A  ALA*     3.1     3.5    -      -       -      +
    127A  VAL*     2.8    42.1    +      -       +      +
    129A  PHE*     5.1     1.4    -      -       -      -
    174A  VAL*     4.5    24.9    -      -       +      -
    213A  VAL*     4.2    13.2    -      -       +      -
    214A  GLY      3.3    18.6    -      -       -      -
    215A  PHE*     3.8    26.9    -      +       +      -
    231A  TRP*     4.2    17.0    -      +       -      -
    233A  PHE*     4.4     8.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ARG*     3.8    33.9    -      -       +      -
     50A  ILE      4.4     0.2    -      -       -      -
     51A  LEU*     3.5    28.5    -      -       +      -
     89A  ALA      4.2     0.7    -      -       -      +
     90A  PHE*     1.3    78.0    -      -       -      +
     92A  ILE*     1.3    67.3    +      -       -      +
     93A  ALA*     3.9    24.9    -      -       +      -
     97A  THR*     4.2     3.6    -      -       +      -
    110A  LEU*     3.6    21.1    -      -       +      -
    124A  VAL*     4.2     4.9    -      -       +      -
    125A  ILE      3.3    10.1    -      -       -      +
    126A  ALA*     3.8    11.4    -      -       +      -
    213A  VAL*     3.4     4.3    -      -       -      +
    214A  GLY      2.9    44.8    +      -       -      +
    215A  PHE*     3.5    36.1    -      -       -      -
    216A  SER*     3.9     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  LEU*     4.7     4.5    -      -       +      -
     69A  PHE*     3.5    39.3    -      -       +      -
     90A  PHE*     4.1    15.5    -      -       +      -
     91A  PHE*     1.3    79.2    -      -       -      +
     93A  ALA*     1.3    66.6    +      -       -      +
    124A  VAL*     3.5     4.3    -      -       -      +
    125A  ILE*     2.9    46.3    +      -       +      +
    183A  LEU*     5.9     0.2    -      -       +      -
    207A  LEU*     3.7    24.6    -      -       +      +
    211A  VAL*     3.5    29.6    -      -       +      -
    212A  ARG      3.5     6.1    -      -       -      +
    213A  VAL*     4.1    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  PHE*     3.9    19.2    -      -       +      -
     92A  ILE*     1.3    76.9    -      -       -      +
     94A  PRO*     1.4    79.6    -      -       +      +
     97A  THR*     4.0    22.7    -      -       +      +
    123A  GLN      4.0     7.0    -      -       -      +
    124A  VAL*     4.6     3.6    -      -       +      -
    207A  LEU*     4.1     2.9    -      -       -      -
    211A  VAL*     3.2     9.1    -      -       -      +
    212A  ARG      2.8    28.5    +      -       -      +
----------------------------------------------------------
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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