Contacts of the strand formed by residues 49 - 51 (chain j) in PDB entry 3J7Y


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 TRP 49 (chain j).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101S  PHE*     4.0    25.4    -      +       +      -
    120S  LEU*     4.2    22.6    +      -       +      +
    121S  ASP      5.5     0.7    -      -       -      -
    122S  LEU*     3.7    36.6    -      -       +      -
    128S  ILE*     3.5    29.4    -      -       +      -
    129S  ARG      3.4     7.9    -      -       -      +
    130S  LEU*     4.4     7.2    -      -       +      -
    131S  GLU*     3.8     4.3    -      -       -      -
     47j  PRO*     3.4     9.5    +      -       -      +
     48j  ASP*     1.3    88.4    -      -       +      +
     50j  SER*     1.3    88.0    +      -       -      +
     51j  TYR*     4.0    16.2    -      +       -      -
     57j  ALA*     3.4    42.8    -      -       +      +
     58j  PRO*     3.7    22.2    +      -       +      -
     60j  MET*     4.4    17.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 50 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128S  ILE*     3.2     7.6    -      -       -      +
    129S  ARG*     2.7    41.4    +      -       -      -
    131S  GLU*     2.7    23.6    +      -       -      +
    151S  LYS*     4.4     5.5    +      -       -      -
     47j  PRO*     5.6     3.3    -      -       -      +
     49j  TRP*     1.3    89.5    +      -       -      +
     51j  TYR*     1.3    61.4    +      -       -      +
     54j  GLY      6.0     0.4    -      -       -      -
     55j  ARG      3.6    13.0    +      -       -      -
     56j  PRO*     4.4     3.5    -      -       -      +
     57j  ALA      4.3     8.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 51 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121S  ASP      4.9     3.3    +      -       -      -
    122S  LEU*     3.4    26.6    -      -       +      +
    126S  GLU*     3.3    26.7    +      -       -      -
    127S  ARG      3.9    12.3    -      -       -      +
    128S  ILE*     5.9     0.4    -      -       +      -
    129S  ARG*     4.1    10.0    -      -       -      +
     49j  TRP*     4.0    16.3    -      +       -      -
     50j  SER*     1.3    79.4    -      -       -      +
     52j  ALA*     1.3    63.9    +      -       -      +
     53j  ASP*     3.2     4.7    -      -       +      +
     54j  GLY*     3.2    14.7    +      -       -      -
     55j  ARG*     3.1    63.8    +      -       +      +
     56j  PRO      3.6    18.6    -      -       -      -
     57j  ALA*     4.4     2.7    -      -       -      -
     58j  PRO*     4.3     8.7    -      -       +      +
----------------------------------------------------------
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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