Contacts of the strand formed by residues 122 - 125 (chain D) in PDB entry 2ZOT


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 122 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93D  PHE*     3.6    27.1    -      -       +      -
    116D  ILE*     3.7    22.1    -      -       -      +
    117D  ILE      4.6     0.5    +      -       -      -
    118D  ASP*     2.9    33.5    +      -       +      +
    119D  GLU*     3.8    14.4    -      -       -      +
    121D  GLU*     1.3    79.7    -      -       -      +
    123D  GLN*     1.3    64.8    +      -       -      +
    132D  VAL*     4.4     9.4    -      -       +      +
    133D  THR      3.3     7.6    -      -       -      -
    135D  SER*     3.3     5.2    +      -       -      -
    140D  ARG*     4.7     0.9    -      -       -      +
    143D  ILE*     4.5    15.9    -      -       +      -
    144D  GLN      5.0     8.2    +      -       -      +
    145D  VAL*     4.9     3.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 123 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116D  ILE*     4.4    11.8    -      -       -      +
    122D  THR*     1.3    78.3    -      -       -      +
    124D  PHE*     1.3    78.2    +      -       -      +
    125D  MET*     4.8     3.4    -      -       -      +
    126D  SER*     5.0     4.9    -      -       -      +
    132D  VAL*     3.5     3.9    -      -       -      +
    133D  THR*     2.8    51.9    +      -       -      +
    134D  GLU      4.1     8.9    +      -       -      -
    135D  SER*     3.4    22.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 124 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  PHE*     3.3    45.5    -      -       +      -
    115D  GLN*     4.7     0.9    -      -       -      -
    116D  ILE*     4.2    28.0    -      -       +      +
    123D  GLN*     1.3    89.1    +      -       -      +
    125D  MET*     1.3    63.9    +      -       -      +
    126D  SER*     3.4     4.3    +      -       -      -
    129D  PRO*     2.9    32.8    -      -       +      +
    130D  VAL*     4.6     6.1    -      -       -      -
    131D  ALA      3.2    13.0    -      -       -      -
    132D  VAL*     3.9     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 125 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  ARG*     5.3     8.1    -      -       -      -
     47D  ILE*     4.1     6.7    -      -       +      -
     94D  THR*     3.2    34.5    -      -       +      -
    123D  GLN*     3.6     4.6    +      -       -      +
    124D  PHE*     1.3    69.4    -      -       -      +
    126D  SER*     1.3    62.1    +      -       -      +
    127D  ASN*     3.3     6.5    -      -       +      +
    128D  CYS*     2.9    51.9    -      -       -      +
    129D  PRO*     3.2     7.3    -      -       -      +
    131D  ALA*     3.0    24.9    +      -       +      +
    133D  THR*     3.4    26.2    +      -       +      +
    169D  ILE*     4.0    19.1    -      -       +      -
----------------------------------------------------------
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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