Contacts of the strand formed by residues 271 - 272 (chain B) in PDB entry 6EBT


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 GLU 271 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  TYR*     2.7    40.6    +      -       -      -
    196B  HIS*     2.7    33.1    +      -       +      -
    267B  PRO      4.1    10.3    -      -       -      +
    268B  ARG*     3.6    22.5    -      -       -      +
    269B  ILE      3.1     1.3    -      -       -      +
    270B  TYR*     1.3    77.0    -      -       -      +
    272B  LEU*     1.3    60.4    +      -       -      +
    273B  ALA      4.2     0.5    +      -       -      -
    306B  VAL*     3.3    16.8    -      -       +      -
    308B  ALA*     4.0    14.0    -      -       +      +
    309B  PRO*     3.3    24.0    -      -       +      +
    313B  GLU*     4.5     5.9    -      -       -      +
    314B  ALA*     6.2     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 272 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  THR*     4.0    31.9    -      -       +      +
    196B  HIS*     3.9    20.6    -      -       +      -
    197B  ILE*     4.2     1.1    -      -       +      -
    270B  TYR      3.8     7.9    -      -       -      +
    271B  GLU*     1.3    81.0    -      -       -      +
    273B  ALA*     1.3    64.8    +      -       -      +
    274B  ALA*     3.5     6.1    +      -       +      +
    293B  VAL*     5.7     0.4    -      -       +      -
    294B  ALA*     4.2    21.5    -      -       +      -
    297B  VAL*     4.3    13.7    -      -       +      -
    305B  PHE*     3.7    41.3    -      -       +      -
    306B  VAL      2.9    13.8    +      -       -      +
    307B  THR*     3.7     4.3    +      -       -      -
    308B  ALA*     2.8    24.6    +      -       -      +
    311B  LYS*     3.7     3.8    -      -       -      -
    314B  ALA*     5.3     0.2    -      -       -      -
----------------------------------------------------------
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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