Contacts of the strand formed by residues 52 - 55 (chain B) in PDB entry 1EKF


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 ARG 52 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LEU*     4.6     0.2    -      -       -      -
     11B  GLN*     3.5    21.2    -      -       +      +
     13B  GLU*     5.5     9.6    -      -       -      +
     38B  MET      3.5     0.5    -      -       -      +
     39B  LEU*     3.2    11.8    -      -       -      +
     40B  MET*     2.8    65.4    +      -       -      +
     42B  GLU*     4.3    17.4    +      -       -      +
     50B  GLN      4.4     6.0    +      -       -      +
     51B  PRO*     1.3    77.2    -      -       -      +
     53B  ILE*     1.3    73.0    +      -       -      +
     54B  GLN*     2.4    52.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LEU*     4.5    11.2    -      -       +      -
     11B  GLN      3.3     9.2    +      -       -      +
     12B  LEU*     3.8    18.3    -      -       +      -
     13B  GLU      3.2    24.5    +      -       -      +
     37B  HIS*     3.9    19.5    -      -       +      -
     38B  MET      3.3     3.4    -      -       -      -
     39B  LEU*     4.2    12.3    -      -       +      -
     52B  ARG*     1.3    78.5    -      -       -      +
     54B  GLN*     1.3    63.0    +      -       -      +
    120B  CYS      4.4     1.1    -      -       -      +
    123B  ARG*     3.7    21.3    -      -       +      +
    124B  LEU*     3.5    53.6    -      -       +      +
    127B  VAL*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  GLU*     3.8     6.9    +      -       +      -
     37B  HIS*     3.2     7.0    -      -       -      -
     38B  MET*     2.8    45.6    +      -       +      +
     40B  MET*     3.7    24.4    -      -       +      +
     52B  ARG*     2.4    47.2    +      -       +      +
     53B  ILE*     1.3    75.4    -      -       -      +
     55B  PRO*     1.3    80.6    -      -       +      +
     57B  GLN*     3.5    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  GLU*     3.3    38.6    -      -       -      +
     14B  MET      4.1     2.2    -      -       -      +
     15B  THR*     4.0    24.0    -      -       -      +
     16B  GLN      5.7     0.2    -      -       -      +
     36B  ASP      3.5     9.4    -      -       -      +
     37B  HIS*     4.3     2.7    -      -       +      -
     38B  MET*     3.8     0.7    -      -       -      +
     54B  GLN*     1.3    93.3    -      -       +      +
     56B  PHE*     1.3    71.1    +      -       -      +
     57B  GLN*     3.0    27.3    +      -       +      +
----------------------------------------------------------
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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