Contacts of the strand formed by residues 50 - 54 (chain D) in PDB entry 4JZJ


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 ILE 50 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  ILE*     3.6    24.7    -      -       +      -
     41D  TRP*     3.6    19.3    -      -       +      +
     43D  LEU*     4.4     1.6    -      -       +      -
     47D  VAL*     4.1    14.6    -      -       +      -
     49D  ASP*     1.3    90.2    +      -       -      +
     51D  GLU*     1.3    66.1    +      -       -      +
     52D  CYS*     4.7     0.2    -      -       -      -
     61D  PRO*     3.8     2.1    -      -       -      +
     62D  ALA*     3.0    29.3    +      -       +      +
     65D  ASN*     3.4    40.4    +      -       +      +
     83D  VAL*     3.5    27.6    -      -       +      -
     84D  ARG      3.4     3.1    -      -       -      +
     85D  VAL*     3.7    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 51 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ARG*     3.9    26.3    +      -       -      +
    104A  ALA*     4.4     1.7    -      -       +      +
     98B  TYR      4.6     4.0    -      -       -      +
    102B  TYR*     2.5    30.7    +      -       -      -
     50D  ILE*     1.3    76.3    -      -       -      +
     52D  CYS*     1.3    63.0    +      -       -      +
     53D  VAL*     4.1    10.7    +      -       +      +
     59D  SER*     2.7    18.6    +      -       -      +
     60D  MET      3.5    14.3    +      -       -      +
     61D  PRO*     4.5     2.0    -      -       +      -
     82D  THR      3.8     0.7    -      -       -      +
     83D  VAL*     3.5     2.3    -      -       -      -
     84D  ARG*     2.9    69.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 52 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39D  LEU*     4.0    19.1    -      -       +      -
     41D  TRP*     3.9    23.1    -      -       -      -
     50D  ILE*     4.7     0.2    -      -       -      -
     51D  GLU*     1.3    74.7    -      -       -      +
     53D  VAL*     1.3    60.7    +      -       -      +
     54D  LYS      4.1     0.8    +      -       -      -
     59D  SER*     3.3     2.3    -      -       -      -
     60D  MET*     2.9    34.4    +      -       -      +
     62D  ALA*     4.6     1.1    -      -       -      -
     68D  CYS*     2.0    53.6    -      -       +      -
     70D  PHE*     4.1     9.8    -      -       +      -
     82D  THR      3.5     3.8    -      -       -      -
     83D  VAL*     4.5     4.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 53 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  PHE*     5.7     6.3    -      -       +      -
    100B  TYR*     4.7    10.8    -      -       +      -
    102B  TYR*     4.7     3.8    -      -       -      +
     51D  GLU*     4.1    17.9    -      -       +      +
     52D  CYS*     1.3    74.7    -      -       -      +
     54D  LYS*     1.3    59.5    +      -       -      +
     55D  ASP      3.1     6.9    +      -       -      +
     56D  ALA*     3.9    21.5    -      -       -      +
     58D  TYR      3.7    10.1    -      -       -      +
     59D  SER*     3.5    16.8    -      -       -      +
     70D  PHE*     5.2     0.7    -      -       -      -
     80D  ASN      3.8     0.2    -      -       -      +
     81D  TYR*     3.7     3.1    -      -       -      -
     82D  THR*     2.7    52.3    +      -       +      +
     84D  ARG*     5.0     9.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 54 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  CYS      4.1     2.4    +      -       -      -
     53D  VAL*     1.3    68.9    -      -       -      +
     55D  ASP*     1.3    78.7    +      -       -      +
     56D  ALA      3.4     1.6    -      -       -      -
     57D  ASP*     2.6    46.7    +      -       -      +
     58D  TYR*     3.1    50.7    +      -       +      +
     59D  SER*     4.3     0.2    -      -       -      +
     70D  PHE*     4.0    13.7    -      -       +      -
     73D  ILE*     5.6     1.8    -      -       +      -
     77D  GLU*     5.9     1.0    +      -       -      -
     79D  THR*     3.7    23.9    +      -       +      -
     81D  TYR*     3.9    28.3    -      -       +      -
----------------------------------------------------------
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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