Contacts of the strand formed by residues 273 - 278 (chain C) in PDB entry 4ZTZ


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 PHE 273 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260C  LEU*     4.6    15.5    -      -       +      +
    263C  TRP*     3.5    57.2    -      +       +      -
    264C  ARG*     5.2     1.8    -      -       +      +
    267C  ALA*     3.5    32.5    -      -       +      -
    269C  SER      4.0     6.7    -      -       -      -
    270C  PRO*     3.0    22.2    +      -       +      +
    271C  SER*     3.3     4.6    -      -       -      +
    272C  ASN*     1.3    80.0    -      -       +      +
    274C  SER*     1.3    59.4    +      -       -      +
    289C  LEU*     6.4     0.7    -      -       +      -
    290C  TYR      3.7     8.7    -      -       -      -
    291C  TYR*     3.5    38.6    -      +       +      -
    300C  ILE*     5.0     5.8    -      -       +      -
    348C  ALA*     4.3     8.3    -      -       +      -
    349C  TYR*     3.9    16.6    -      +       -      -
    352C  ASP*     5.0     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 274 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260C  LEU*     4.3     5.8    -      -       -      +
    271C  SER      5.5     2.2    -      -       -      -
    272C  ASN      4.0     1.3    +      -       -      -
    273C  PHE*     1.3    76.0    -      -       -      +
    275C  SER*     1.3    72.8    +      -       -      +
    276C  SER*     5.5     0.9    -      -       -      -
    289C  LEU*     3.4     8.3    -      -       -      +
    290C  TYR*     2.9    45.1    +      -       -      +
    292C  ASN*     6.1     0.9    -      -       -      -
    297C  LYS*     5.7     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 275 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256C  LEU*     3.8    19.5    -      -       -      +
    260C  LEU*     3.9    20.3    -      -       -      +
    274C  SER*     1.3    82.3    +      -       -      +
    276C  SER*     1.3    60.6    +      -       -      +
    277C  ASP*     4.2     6.5    +      -       -      +
    288C  LYS      3.8     3.8    -      -       -      -
    289C  LEU*     3.7    19.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 276 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274C  SER*     4.3     1.5    -      -       -      -
    275C  SER*     1.3    72.5    -      -       -      +
    277C  ASP*     1.3    75.6    +      -       -      +
    287C  ASN*     3.3     6.9    -      -       -      +
    288C  LYS*     2.9    45.5    +      -       -      -
    290C  TYR*     3.8    24.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 277 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256C  LEU*     4.7     6.0    -      -       -      +
    275C  SER*     4.2     6.4    +      -       -      +
    276C  SER*     1.3    90.2    +      -       -      +
    278C  CYS*     1.3    65.5    +      -       -      +
    285C  LYS*     4.2    12.6    +      -       +      +
    287C  ASN*     3.3    23.6    +      -       -      +
    288C  LYS*     4.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 278 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277C  ASP*     1.3    77.6    -      -       -      +
    279C  GLN*     1.3    66.4    +      -       -      +
    285C  LYS*     3.8     4.5    -      -       -      +
    286C  GLY      2.8    48.0    +      -       -      +
    287C  ASN*     4.5     0.4    -      -       -      -
    288C  LYS*     2.9    37.9    -      -       -      +
    304C  TRP*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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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