Contacts of the strand formed by residues 87 - 89 (chain A) in PDB entry 4BEI


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 TYR 87 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  ILE      3.5     6.5    -      -       -      +
     81A  LYS*     3.6    28.3    -      -       +      -
     85A  GLY*     3.3    36.2    +      -       -      -
     86A  ILE*     1.3    76.1    -      -       -      +
     88A  PHE*     1.3    60.4    +      -       -      +
   1272A  O4B      2.9    32.1    +      -       -      -
     87B  TYR*     4.1     1.6    +      -       -      -
    203B  TRP*     2.9    21.6    +      -       -      -
    205B  THR*     3.7    20.5    +      -       -      +
    207B  VAL*     3.6    28.5    -      -       +      -
    213B  ILE*     3.9    25.1    -      -       +      -
    250B  ASN*     4.5     7.2    +      -       -      +
    252B  GLN*     3.7     6.7    +      -       -      -
   1272B  O4B      3.6    34.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  SER*     3.8     1.7    -      -       -      -
     80A  ILE*     2.8    75.7    +      -       +      +
     86A  ILE*     4.2    15.5    -      -       +      -
     87A  TYR*     1.3    77.0    -      -       -      +
     89A  PRO*     1.4    82.8    -      -       +      +
    118A  PHE*     5.0     2.2    -      +       -      -
    119A  TRP      4.6     2.2    -      -       -      -
    120A  VAL*     4.6    18.4    -      -       +      -
    124A  MET*     4.5    15.5    -      -       +      -
    129A  TYR*     4.1    17.9    -      +       -      -
    203B  TRP*     3.5    24.0    -      +       +      +
    205B  THR*     4.1     5.8    -      -       -      +
    213B  ILE*     5.3     0.4    -      -       -      +
    219B  ARG*     3.7    32.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LEU      3.9     5.4    -      -       -      +
     79A  SER*     4.4     4.7    -      -       -      +
     88A  PHE*     1.4    90.4    -      -       +      +
     90A  ALA*     1.3    65.5    +      -       -      +
     91A  LYS*     3.5    12.5    -      -       +      +
    203B  TRP*     4.1    15.5    -      -       +      -
    204B  MET      4.1     8.7    -      -       -      +
    205B  THR*     4.0    10.2    -      -       +      -
    215B  PRO*     3.9    26.7    -      -       +      -
    217B  ASN      3.6    20.6    -      -       -      +
    218B  ALA*     4.2     7.9    -      -       -      -
    219B  ARG*     3.0    26.3    -      -       -      -
----------------------------------------------------------
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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