Contacts of the strand formed by residues 934 - 942 (chain A) in PDB entry 5KZX


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 VAL 934 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777A  THR*     3.8    24.2    -      -       -      +
    779A  PRO*     4.7     4.0    -      -       +      -
    905A  THR*     3.6    29.6    -      -       +      -
    906A  VAL      3.4     3.8    -      -       -      +
    907A  LEU*     3.7    20.9    -      -       +      -
    927A  THR*     3.8     1.4    +      -       -      +
    928A  TYR*     3.4     6.1    -      -       -      -
    929A  SER*     3.0    29.9    +      -       -      -
    932A  THR*     3.3    33.0    -      -       -      +
    933A  LYS*     1.3    77.6    -      -       -      +
    935A  LEU*     1.3    64.1    +      -       -      +
    936A  ASP*     4.6     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 935 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    904A  VAL      3.7     1.7    -      -       -      +
    905A  THR*     3.5     1.7    -      -       -      +
    906A  VAL*     2.7    40.5    +      -       +      +
    909A  VAL*     4.0    17.9    -      -       +      -
    913A  PRO*     3.6    29.8    -      -       +      -
    916A  VAL*     4.2     4.0    -      -       +      -
    926A  PHE*     3.6    24.0    -      -       +      -
    927A  THR      3.5     8.7    -      -       -      +
    928A  TYR*     4.2     7.2    -      -       +      -
    933A  LYS      4.0     1.0    +      -       -      -
    934A  VAL*     1.3    72.5    -      -       -      +
    936A  ASP*     1.3    59.5    +      -       -      +
    937A  ILE*     3.9    21.8    -      -       +      -
    951A  TRP*     3.8    42.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 936 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    779A  PRO*     3.2    27.2    -      -       +      +
    903A  LYS*     3.6    24.8    +      -       -      +
    904A  VAL      3.7     0.2    -      -       -      -
    905A  THR*     2.7    29.8    +      -       +      -
    926A  PHE*     3.1     6.1    -      -       -      +
    927A  THR*     2.8    49.9    +      -       -      +
    934A  VAL*     4.0     5.4    -      -       +      +
    935A  LEU*     1.3    73.9    -      -       -      +
    937A  ILE*     1.3    62.1    +      -       -      +
    938A  CYS*     4.3     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 937 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    903A  LYS*     3.4     7.7    -      -       -      +
    904A  VAL*     2.8    52.6    +      -       +      +
    906A  VAL*     4.2    11.7    -      -       +      -
    916A  VAL*     3.7    33.2    -      -       +      -
    923A  VAL*     3.9    10.8    -      -       +      -
    925A  ASN      4.0     2.2    -      -       -      -
    926A  PHE*     4.2     1.6    -      -       +      -
    935A  LEU*     3.9    28.9    -      -       +      +
    936A  ASP*     1.3    78.8    +      -       -      +
    938A  CYS*     1.3    74.3    +      -       -      +
    939A  VAL*     3.8    14.4    +      -       +      +
    949A  VAL*     4.0    18.6    -      -       +      -
    951A  TRP*     4.9     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 938 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    902A  GLN      3.5     8.7    -      -       -      +
    903A  LYS*     4.8    10.1    -      -       -      +
    923A  VAL*     3.7    20.3    -      -       -      +
    924A  SER*     4.0    19.1    +      -       -      +
    925A  ASN*     2.9    37.7    +      -       +      +
    926A  PHE*     5.8     0.2    -      -       -      -
    936A  ASP*     4.3     2.2    -      -       -      -
    937A  ILE*     1.3    72.5    -      -       -      +
    939A  VAL*     1.3    65.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 939 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    901A  LEU*     3.4    25.1    -      -       +      +
    902A  GLN*     3.0    39.3    +      -       -      +
    903A  LYS*     4.0     3.8    -      -       -      +
    904A  VAL*     4.1    10.3    -      -       +      -
    918A  SER*     4.1    22.2    -      -       -      +
    923A  VAL*     5.6     0.2    -      -       -      -
    924A  SER*     5.6     0.7    -      -       -      -
    937A  ILE*     3.8    20.2    -      -       +      +
    938A  CYS*     1.3    79.5    -      -       -      +
    940A  SER*     1.3    64.8    +      -       -      +
    941A  LEU*     3.9    22.4    -      -       +      -
    949A  VAL*     4.5     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 940 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    901A  LEU      3.8     1.3    -      -       -      -
    902A  GLN*     4.8     6.3    -      -       -      -
    918A  SER*     5.2     1.0    +      -       -      -
    924A  SER*     5.6     1.7    +      -       -      -
    939A  VAL*     1.3    76.8    +      -       -      +
    941A  LEU*     1.3    67.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 941 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    900A  GLN*     3.5     7.4    -      -       -      +
    901A  LEU*     2.8    44.6    +      -       +      +
    918A  SER*     3.5    26.5    -      -       -      +
    919A  ASN*     3.6    25.6    -      -       +      +
    939A  VAL*     3.9    16.6    -      -       +      -
    940A  SER*     1.3    82.9    -      -       -      +
    942A  LEU*     1.3    69.0    +      -       -      +
    947A  PHE*     3.9    26.2    -      -       +      -
    949A  VAL*     3.8    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 942 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    897A  ALA      4.5    16.6    -      -       -      +
    898A  GLY*     4.6     2.7    -      -       -      +
    899A  LEU      3.4    17.9    -      -       -      +
    900A  GLN*     4.4    11.9    -      -       +      -
    901A  LEU*     4.8     1.3    -      -       -      -
    941A  LEU*     1.3    84.8    -      -       -      +
    943A  MET*     1.3    65.4    +      -       -      +
    944A  GLY      3.2     2.4    +      -       -      +
    945A  GLU*     3.0    60.8    +      -       +      +
    947A  PHE*     3.9     6.7    -      -       -      -
----------------------------------------------------------
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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