Contacts of the strand formed by residues 86 - 89 (chain D) in PDB entry 3B94


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 LYS 86 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  TRP*     3.6     7.7    +      -       -      -
     82D  VAL*     2.8    49.8    +      -       +      -
     83D  SER*     3.0    27.9    +      -       -      +
     84D  ASP      4.0     1.6    -      -       -      +
     85D  TRP*     1.3    80.5    -      -       -      +
     87D  LEU*     1.3    65.5    +      -       -      +
    147D  THR*     4.4    22.9    +      -       -      +
    148D  ILE      3.3     6.1    -      -       -      +
    149D  ASP*     2.8    33.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  ALA*     5.3     0.7    -      -       +      -
     69D  TRP*     3.9    21.5    -      -       +      -
     71D  MET*     5.5     1.1    -      -       -      -
     79D  VAL*     3.6    19.1    -      -       +      -
     80D  ASN      2.9    36.1    -      -       -      +
     81D  LYS*     3.7     6.1    -      -       -      +
     82D  VAL*     3.3     6.7    -      -       -      -
     86D  LYS*     1.3    76.2    -      -       -      +
     88D  GLU*     1.4    66.6    -      -       -      +
     89D  ILE*     4.8     3.1    -      -       +      -
    147D  THR*     3.1     8.0    -      -       -      -
    148D  ILE*     2.8    32.2    +      -       +      +
    165D  TRP*     3.7    28.3    -      -       +      -
    167D  ILE*     3.5    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  GLU*     2.5    26.7    -      -       -      +
    145B  GLY*     2.7    25.9    -      -       -      +
    147B  THR*     4.6     5.0    -      -       -      +
     79D  VAL*     3.2     6.4    -      -       -      +
     80D  ASN*     2.8    41.3    +      -       +      +
     82D  VAL*     3.6    15.7    -      -       +      +
     87D  LEU*     1.4    74.1    -      -       -      +
     89D  ILE*     1.3    74.9    +      -       -      +
     90D  LEU*     4.1     5.3    -      -       +      +
    145D  GLY*     3.8    10.3    -      -       -      +
    146D  ASP      3.5     9.0    -      -       -      +
    147D  THR*     3.7    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  GLU*     4.6     0.5    -      -       -      +
     78D  CYS      3.9     1.8    -      -       -      -
     79D  VAL*     3.9    18.4    -      -       +      -
     87D  LEU*     4.8     2.5    -      -       +      -
     88D  GLU*     1.3    79.3    -      -       -      +
     90D  LEU*     1.3    60.6    +      -       -      +
     91D  GLN      3.2    25.6    -      -       -      +
     95D  TYR*     4.1    12.1    -      -       +      +
    142D  LEU*     3.8    32.1    -      -       +      -
    143D  HIS      3.5    20.9    -      -       -      +
    145D  GLY      2.9    24.1    +      -       -      -
    146D  ASP*     2.8    27.7    +      -       +      +
    148D  ILE*     4.3     9.9    -      -       +      -
    167D  ILE*     4.0    12.3    -      -       +      -
----------------------------------------------------------
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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