Contacts of the strand formed by residues 339 - 345 (chain A) in PDB entry 3JRQ


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 ASP 339 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254A  ILE*     5.5     1.1    -      -       -      -
    266A  LEU*     3.9    11.7    -      -       -      +
    267A  CYS      3.6     4.7    -      -       -      +
    268A  ARG*     3.1    35.0    +      -       -      +
    335A  ARG*     3.3    21.2    +      -       -      +
    336A  VAL      2.8    41.0    +      -       -      +
    337A  LYS      3.0     1.1    -      -       -      +
    338A  GLU*     1.3    70.5    -      -       -      +
    340A  ASP*     1.3    61.2    +      -       -      +
    422A  LEU*     4.0    24.2    -      -       +      +
    423A  LYS*     3.2    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  CYS*     2.7    26.9    +      -       -      +
    269A  GLY*     3.1    25.1    +      -       -      -
    338A  GLU      3.6     6.3    -      -       -      +
    339A  ASP*     1.3    73.2    -      -       -      +
    341A  CYS*     1.3    58.1    +      -       +      +
    363A  ARG*     3.4    32.5    -      -       +      -
    367A  LEU*     5.8     1.6    -      -       -      +
    421A  ASP*     3.0    13.0    -      -       -      +
    422A  LEU*     2.7    30.3    +      -       -      +
    423A  LYS*     3.1    31.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  VAL      4.1     0.3    -      -       -      +
    266A  LEU*     3.6     2.8    -      -       -      +
    267A  CYS*     2.9    45.3    +      -       -      -
    340A  ASP*     1.3    86.6    -      -       -      +
    342A  LEU*     1.3    60.3    +      -       -      +
    343A  ILE*     4.8     8.1    -      -       -      +
    359A  CYS      4.8     0.7    -      -       -      -
    362A  ALA*     4.4    13.0    -      -       -      -
    363A  ARG*     4.2    23.3    -      -       -      -
    366A  ILE*     4.1    17.7    -      -       +      -
    419A  VAL*     4.4     4.5    -      -       +      -
    420A  VAL      3.1    13.7    -      -       -      +
    422A  LEU*     3.5     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  PHE*     6.2     0.2    -      -       +      -
    247A  ALA*     3.7    30.5    -      -       +      -
    249A  VAL*     4.1    13.2    -      -       +      -
    254A  ILE*     3.8    20.0    -      -       +      -
    256A  VAL*     5.1     0.4    -      -       +      -
    264A  ALA*     4.6     2.0    -      -       +      -
    265A  VAL      3.3    24.0    -      -       -      +
    266A  LEU*     4.3     4.5    -      -       +      -
    275A  LEU*     4.1    20.6    -      -       +      -
    341A  CYS*     1.3    73.5    -      -       -      +
    343A  ILE*     1.3    61.8    +      -       -      +
    344A  LEU*     4.1    14.4    -      -       +      -
    418A  VAL      3.6     0.3    -      -       -      +
    419A  VAL*     3.4     5.5    -      -       -      +
    420A  VAL*     2.9    46.7    +      -       +      +
    422A  LEU*     3.6    14.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263A  ARG      3.8     0.7    -      -       -      +
    264A  ALA*     3.2     4.7    -      -       -      -
    265A  VAL*     2.8    53.1    +      -       +      +
    341A  CYS*     4.8     8.1    -      -       -      +
    342A  LEU*     1.3    78.2    -      -       -      +
    344A  LEU*     1.3    71.8    +      -       -      +
    345A  ALA*     4.3     1.6    -      -       +      -
    350A  TRP*     4.0    20.0    -      -       +      -
    358A  ALA*     3.8    15.5    -      -       +      +
    359A  CYS*     3.7    33.7    -      -       -      +
    362A  ALA*     4.1    15.0    -      -       +      -
    402A  LEU*     4.3     7.4    -      -       +      -
    417A  VAL*     4.2    14.6    -      -       +      -
    418A  VAL      3.4     5.8    -      -       -      +
    419A  VAL*     4.9     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  PHE*     3.7    25.8    -      -       +      +
    175A  VAL*     3.6    18.4    -      -       +      +
    245A  VAL*     3.6    33.7    -      -       +      +
    247A  ALA*     4.1    23.3    -      -       +      +
    263A  ARG      3.6     3.4    -      -       -      -
    264A  ALA*     3.6    22.4    -      -       +      -
    342A  LEU*     4.1    11.7    -      -       +      -
    343A  ILE*     1.3    80.9    -      -       -      +
    345A  ALA*     1.3    61.4    +      -       -      +
    417A  VAL*     3.1     4.3    -      -       -      +
    418A  VAL*     2.7    49.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  VAL*     4.3     3.6    -      -       -      +
    245A  VAL*     4.8     0.6    -      -       -      +
    262A  SER*     3.4     4.6    -      -       -      -
    263A  ARG      2.9    23.4    +      -       -      -
    343A  ILE*     4.1     3.8    -      -       +      -
    344A  LEU*     1.3    77.4    -      -       -      +
    346A  SER*     1.3    63.2    +      -       -      +
    349A  VAL*     3.9     6.7    -      -       +      -
    350A  TRP*     2.7    42.5    +      -       +      +
    416A  SER      3.1    11.7    -      -       -      +
    417A  VAL*     3.7    16.2    -      -       +      -
----------------------------------------------------------
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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