Contacts of the strand formed by residues 109 - 113 (chain A) in PDB entry 2J6U


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 109 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     3.5    26.8    -      -       +      -
      9A  VAL      3.0    12.6    -      -       -      +
     10A  ASP*     4.0     3.6    -      -       -      +
     11A  PHE*     5.1     0.7    -      -       -      -
     92A  MET*     3.3    13.4    -      -       -      +
    105A  ALA*     3.3    33.9    +      -       +      +
    106A  SER*     3.3    23.3    +      -       -      +
    108A  ASP*     1.3    81.7    -      -       -      +
    110A  ALA*     1.3    64.9    +      -       -      +
    111A  TYR*     4.4     3.5    +      -       -      -
    155A  LYS*     3.3    24.8    +      -       -      -
   1001A   CA      2.6    25.5    -      -       -      -
     13P    C      5.4     4.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  LEU      3.7     1.0    -      -       -      +
      8A  PHE*     3.4     4.2    -      -       -      -
      9A  VAL*     3.0    31.7    +      -       -      +
     92A  MET*     3.9    20.9    -      -       -      -
     95A  LEU*     4.2    14.1    -      -       +      -
    102A  ILE*     4.5     9.6    -      -       +      -
    103A  GLU      3.1    15.3    -      -       -      +
    104A  ILE*     4.0     4.7    -      -       -      -
    105A  ALA      4.2     1.1    -      -       -      +
    109A  GLU*     1.3    80.0    -      -       -      +
    111A  TYR*     1.3    67.7    +      -       -      +
    112A  LEU*     5.0     1.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     3.9    10.3    -      -       +      -
      7A  LEU      3.5     2.7    -      -       -      -
      8A  PHE*     3.4    30.6    -      +       +      -
    102A  ILE*     3.3     1.2    -      -       -      -
    103A  GLU*     2.8    47.9    +      -       +      +
    105A  ALA*     3.7    23.8    -      -       +      -
    109A  GLU*     4.4     2.3    +      -       -      -
    110A  ALA*     1.3    76.9    -      -       -      +
    112A  LEU*     1.3    67.5    +      -       -      +
    113A  ASP      4.2     0.2    -      -       -      -
    151A  LYS*     3.1    61.3    +      -       +      +
    152A  VAL*     5.4     0.5    -      -       -      -
    155A  LYS*     3.6    26.6    -      -       +      +
    240A  ILE*     3.8    19.7    -      -       +      +
    243A  ARG*     5.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     3.6     5.8    -      -       -      -
      7A  LEU*     2.7    47.8    +      -       +      +
      9A  VAL*     5.5     0.4    -      -       +      -
     95A  LEU*     3.9    37.0    -      -       +      +
     98A  TYR*     4.1    15.7    -      -       +      -
     99A  SER*     4.4     9.6    -      -       -      +
    101A  LYS      3.5     3.4    -      -       -      +
    102A  ILE*     3.2    34.3    -      -       +      -
    110A  ALA*     5.0     2.0    -      -       +      +
    111A  TYR*     1.3    87.3    -      -       -      +
    113A  ASP*     1.3    59.8    +      -       -      +
    114A  ILE*     3.2    18.4    +      -       +      -
    131A  ILE*     4.2    16.4    -      -       +      -
    240A  ILE*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  MET*     3.8    24.8    -      -       -      +
      5A  ILE      4.0     4.5    +      -       -      +
      6A  VAL*     5.0     0.4    -      -       -      +
     99A  SER*     2.7    23.4    +      -       -      -
    101A  LYS*     2.9    44.4    +      -       +      +
    112A  LEU*     1.3    71.6    -      -       -      +
    114A  ILE*     1.3    56.7    +      -       -      +
    115A  SER*     2.9    32.7    +      -       -      -
    116A  ASP*     5.6     0.2    -      -       -      +
    117A  LYS*     3.2     9.5    +      -       -      -
    240A  ILE*     4.2    19.2    +      -       +      +
----------------------------------------------------------
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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