Contacts of the strand formed by residues 69 - 73 (chain A) 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 THR 69 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     3.4     7.7    +      -       -      -
     68A  VAL*     1.3    77.1    -      -       -      +
     70A  ILE*     1.3    68.8    +      -       -      +
     71A  SER*     4.5     3.6    +      -       -      +
     80A  TYR      3.8     0.5    -      -       -      +
     81A  LEU*     3.7     2.3    -      -       -      -
     82A  GLN*     2.9    64.4    +      -       +      +
     83A  TRP*     5.4     0.4    -      -       -      -
     84A  SER      5.8     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  TRP*     3.9    20.0    -      -       +      +
     48A  MET*     4.8     3.1    -      -       +      -
     49A  GLY*     3.8    36.6    -      -       -      +
     50A  ASP      4.4     2.9    -      -       -      +
     51A  ILE*     3.7    32.9    -      -       +      +
     58A  THR*     3.7    18.1    -      -       +      +
     60A  TYR*     2.8    35.0    +      -       +      +
     68A  VAL*     4.9     2.9    -      -       +      -
     69A  THR*     1.3    77.6    +      -       -      +
     71A  SER*     1.3    67.1    +      -       -      +
     80A  TYR      3.5     7.6    -      -       -      +
     81A  LEU*     3.7    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LYS*     5.4     2.4    -      -       -      +
     51A  ILE*     3.4     8.5    -      -       -      -
     69A  THR*     4.5     5.8    +      -       -      +
     70A  ILE*     1.3    76.2    -      -       -      +
     72A  ALA*     1.3    64.1    +      -       -      +
     79A  THR*     3.2     8.8    -      -       -      +
     80A  TYR*     3.0    48.1    +      -       -      +
     82A  GLN*     5.3     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PHE*     4.6     6.1    -      -       +      -
     51A  ILE*     3.4    19.6    -      -       +      +
     52A  ILE      4.9     0.4    -      -       -      +
     53A  PRO*     4.2    28.5    -      -       +      +
     56A  GLY*     5.2     4.4    -      -       -      -
     71A  SER*     1.3    79.2    -      -       -      +
     73A  ASP*     1.3    62.9    +      -       -      +
     74A  LYS      4.0     0.7    -      -       -      -
     78A  THR      3.4     7.9    -      -       -      +
     79A  THR*     4.5     5.8    -      -       +      -
     80A  TYR*     5.1     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PHE*     4.6     0.7    -      -       -      -
     72A  ALA*     1.3    75.7    -      -       -      +
     74A  LYS*     1.3    62.3    +      -       -      +
     75A  SER*     2.6    26.7    +      -       -      -
     76A  ILE*     3.0    35.5    +      -       +      +
     77A  SER      3.1    16.6    +      -       -      -
     78A  THR      2.8    18.1    +      -       -      +
     80A  TYR*     4.1    14.1    +      -       +      -
----------------------------------------------------------
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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