Contacts of the strand formed by residues 25 - 31 (chain P) in PDB entry 2ZJQ


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 25 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22P  LYS*     3.5    53.8    +      -       +      +
     23P  PRO      3.2     3.6    -      -       -      +
     24P  GLY*     1.3    78.0    -      -       -      +
     26P  ALA*     1.3    66.2    +      -       -      +
     27P  VAL*     3.7    35.7    -      -       +      -
     75P  ALA*     4.1     2.9    -      -       -      -
     78P  ASN*     3.4    20.1    -      -       -      +
     96P  TYR*     4.3    14.8    -      -       -      -
    125P  THR*     4.4     7.2    -      -       +      -
    126P  ILE      3.9     1.8    -      -       -      -
    127P  ILE*     3.4    32.3    -      -       +      -
    504X    G      4.0     0.4    -      -       -      -
    505X    G      3.7    30.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 26 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25P  PHE*     1.3    82.4    -      -       -      +
     27P  VAL*     1.3    63.6    +      -       -      +
     71P  VAL*     3.8    12.3    -      -       +      +
     74P  SER*     3.9     9.0    -      -       -      +
     75P  ALA*     3.3    33.4    -      -       +      +
     78P  ASN*     4.6     1.3    -      -       -      +
    125P  THR*     3.1     4.5    -      -       -      -
    126P  ILE      2.8    30.4    +      -       -      +
    503X    G      5.9     0.9    -      -       -      +
    504X    G      3.6    12.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 27 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25P  PHE*     3.7    15.5    -      -       +      -
     26P  ALA*     1.3    77.6    -      -       -      +
     28P  ALA*     1.3    65.3    +      -       -      +
     29P  LYS*     3.9    17.9    -      -       +      -
     71P  VAL*     4.1     3.1    -      -       -      +
    123P  HIS*     4.7     3.4    -      -       +      -
    124P  ILE      3.4     5.6    -      -       -      +
    125P  THR*     3.2    30.1    -      -       +      -
    503X    G      2.7    26.3    +      -       -      +
    504X    G      3.2    45.3    +      -       -      +
    505X    G      5.0     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 28 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27P  VAL*     1.3    75.8    -      -       -      +
     29P  LYS*     1.3    61.2    +      -       -      +
     31P  VAL*     3.7    19.7    -      -       +      +
     67P  PRO*     6.2     0.7    -      -       +      -
     71P  VAL*     3.3    29.1    -      -       +      +
    123P  HIS*     3.2     4.2    -      -       -      -
    124P  ILE*     2.7    30.2    +      -       +      +
    502X    A      4.5    15.3    -      -       +      +
    503X    G      3.7     6.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 29 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27P  VAL*     3.9    21.3    -      -       +      -
     28P  ALA*     1.3    72.3    -      -       -      +
     30P  TYR*     1.3    87.5    +      -       +      +
     31P  VAL*     3.4     2.3    +      -       -      +
    123P  HIS*     3.3    35.5    +      -       +      +
     24X    G      5.0    11.1    +      -       -      -
     25X    U      4.5     9.1    +      -       -      -
    502X    A      4.7     6.4    +      -       -      +
    503X    G      3.0    39.7    +      -       -      +
    504X    G      3.5    20.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 30 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29P  LYS*     1.3    96.2    +      -       +      +
     31P  VAL*     1.3    65.9    +      -       -      +
     32P  ARG*     3.0     7.8    +      -       -      +
    101P  PRO*     3.4    26.7    -      -       +      -
    121P  THR*     4.4    13.2    -      -       +      +
    122P  SER      3.5     1.5    +      -       -      -
    123P  HIS*     3.0    25.9    +      +       -      -
     25X    U      5.4     3.7    +      -       -      -
    502X    A      5.1     4.9    -      -       -      +
    503X    G      4.2    13.0    -      -       -      -
    504X    G      5.9     0.2    -      -       -      -
    518X    A      2.8    85.3    +      +       -      +
    519X    C      5.1     2.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 31 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28P  ALA*     3.7    30.1    -      -       +      +
     29P  LYS      4.5     1.1    -      -       -      +
     30P  TYR*     1.3    68.5    -      -       -      +
     32P  ARG*     1.3    53.8    +      -       -      +
     33P  MET*     2.6    32.6    +      -       +      +
     67P  PRO*     4.1    28.9    -      -       +      -
    121P  THR*     3.3     1.0    -      -       -      -
    122P  SER*     2.7    46.2    +      -       -      +
    124P  ILE*     3.7    22.7    -      -       +      -
    502X    A      5.9     2.2    -      -       +      -
----------------------------------------------------------
 Back to top of page


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