Contacts of the strand formed by residues 32 - 39 (chain A) in PDB entry 2EBJ


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 32 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET      4.1    19.2    -      -       -      +
      2A  ILE*     4.0    13.6    -      -       +      +
     28A  GLU*     3.3     2.9    -      -       -      -
     29A  VAL      2.8    32.4    +      -       -      +
     30A  ASP*     4.2    13.0    -      -       +      +
     31A  GLY*     1.3    86.1    -      -       -      +
     33A  PRO*     1.3    80.8    -      -       +      +
     34A  LEU      3.6     0.2    +      -       -      -
     59A  LYS*     4.9     9.1    -      -       -      +
    192A  LEU*     6.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     3.4    17.9    -      -       +      +
      2A  ILE*     2.8    29.6    +      -       -      +
     27A  SER      3.7     8.7    -      -       -      +
     28A  GLU*     4.1     5.1    -      -       +      +
     31A  GLY      3.8     6.7    -      -       -      +
     32A  LYS*     1.3    95.9    -      -       +      +
     34A  LEU*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     5.0     0.2    -      -       -      -
      2A  ILE*     3.6    11.0    -      -       +      -
      4A  VAL*     3.5    31.0    -      -       +      -
     25A  LEU*     3.9    12.8    -      -       +      -
     26A  PRO*     3.4    18.4    -      -       +      +
     27A  SER*     3.1    19.0    +      -       -      +
     28A  GLU*     4.4     2.7    -      -       -      +
     29A  VAL*     4.3    12.6    -      -       +      +
     32A  LYS      3.6     0.2    +      -       -      -
     33A  PRO*     1.3    72.3    -      -       -      +
     35A  ARG*     1.3    60.5    +      -       -      +
     36A  LYS*     3.2    43.1    +      -       +      +
    189A  LEU*     3.8    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     3.5    26.0    -      -       +      -
      2A  ILE      2.7    16.2    +      -       -      +
      3A  LEU*     3.3    16.0    -      -       +      +
      4A  VAL      2.9    25.5    +      -       -      -
     33A  PRO      3.9     1.0    +      -       -      -
     34A  LEU*     1.3    71.6    -      -       -      +
     36A  LYS*     1.3    81.2    +      -       -      +
     37A  ALA*     3.6     9.7    -      -       -      +
     53A  LEU*     3.7    15.6    -      -       -      +
     56A  GLU*     2.7    43.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  VAL      3.3     6.5    -      -       -      +
     22A  LEU*     3.0    49.1    -      -       +      +
     23A  ASP*     5.4     0.7    -      -       -      +
     25A  LEU*     3.5    23.8    +      -       -      -
     26A  PRO      2.7    27.1    +      -       -      -
     27A  SER*     4.3     3.8    -      -       -      +
     34A  LEU*     3.2    30.8    +      -       +      +
     35A  ARG*     1.3    90.1    +      -       -      +
     37A  ALA*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  LEU*     4.3     8.1    -      -       +      -
      4A  VAL      3.0     6.7    +      -       -      -
      5A  THR*     3.0     8.4    -      -       +      -
      6A  GLY      2.9    24.3    +      -       -      -
     22A  LEU*     3.6     3.6    -      -       -      +
     35A  ARG*     3.6    14.8    -      -       -      +
     36A  LYS*     1.3    77.1    -      -       -      +
     38A  VAL*     1.3    65.3    +      -       -      +
     39A  LEU      4.1     0.2    -      -       -      -
     53A  LEU*     3.8    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  GLY      3.5     2.9    -      -       -      +
      7A  PHE      3.8     5.2    -      -       -      -
      8A  GLU*     3.5    29.8    -      -       +      +
     19A  GLN*     3.7    39.3    -      -       +      +
     22A  LEU*     3.9    15.0    -      -       +      -
     37A  ALA*     1.3    76.1    -      -       -      +
     39A  LEU*     1.3    67.4    +      -       -      +
     40A  PRO*     4.1     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  THR*     4.0    24.0    -      -       -      +
      6A  GLY      2.8    12.9    +      -       -      +
      7A  PHE*     3.5    31.5    -      -       +      -
      8A  GLU*     3.2    25.2    +      -       -      +
     38A  VAL*     1.3    77.6    -      -       -      +
     40A  PRO*     1.3    68.0    -      -       +      +
     46A  LEU*     4.0    17.3    -      -       +      -
     49A  ALA*     4.2    20.4    -      -       +      -
     50A  LEU*     4.2    16.4    -      -       +      -
     53A  LEU*     3.7    28.5    -      -       +      -
     63A  HIS*     4.3     1.6    -      -       -      +
    142A  ALA*     4.1    11.7    -      -       +      -
----------------------------------------------------------
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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