Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 5ZCJ


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 TYR 96 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ILE      4.4     0.9    +      -       -      -
     13A  SER*     5.2     0.2    -      -       -      -
     14A  ARG*     3.6    56.8    +      -       +      +
     74A  LEU*     5.1     1.3    -      -       +      -
     93A  GLU      3.1    17.2    +      -       -      +
     94A  ALA      4.4     5.0    -      -       -      +
     95A  ASP*     1.3    77.6    -      -       -      +
     97A  LEU*     1.3    67.2    +      -       -      +
     98A  SER*     3.5    21.4    -      -       -      -
     99A  SER*     2.4    38.4    +      -       -      -
    111A  HIS*     4.3    10.3    -      -       +      -
    112A  LEU      4.2     1.8    -      -       -      -
    113A  TYR*     3.4    33.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  ASP      3.4     4.4    +      -       -      +
     96A  TYR*     1.3    84.9    -      -       -      +
     98A  SER*     1.3    63.6    +      -       -      +
    112A  LEU*     2.9    43.3    +      -       +      +
    113A  TYR*     4.6     1.3    -      -       -      -
    114A  ALA*     4.0    20.6    -      -       +      +
    175A  PHE*     4.3    14.9    -      -       +      -
    176A  ALA*     4.1    15.0    -      -       +      -
    179A  VAL*     4.4    12.8    -      -       +      -
    180A  LEU*     4.2    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLN*     4.0    11.9    -      -       -      -
     96A  TYR*     3.4    13.7    -      -       -      -
     97A  LEU*     1.3    81.1    -      -       -      +
     99A  SER*     1.3    62.4    +      -       -      +
    100A  HIS*     3.1    25.5    +      -       -      -
    110A  ALA      4.6     0.2    -      -       -      -
    111A  HIS*     3.5     0.7    -      -       -      -
    112A  LEU*     2.8    36.8    +      -       -      +
    175A  PHE*     3.2    27.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLN*     3.4     8.2    +      -       -      +
     12A  ILE*     3.0    48.9    +      -       -      +
     13A  SER      4.9     0.2    -      -       -      -
     14A  ARG*     4.6     1.7    -      -       -      -
     17A  ALA*     4.7     2.0    -      -       -      -
     96A  TYR*     2.4    27.8    +      -       -      -
     98A  SER*     1.3    72.2    +      -       -      +
    100A  HIS*     1.3    63.7    +      -       -      +
    109A  VAL*     4.2     0.7    -      -       -      -
    110A  ALA      3.3     5.2    -      -       -      -
    111A  HIS*     2.6    33.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLU*     5.3     2.4    -      -       -      +
      9A  LEU*     3.5    50.1    +      -       +      -
     10A  LYS      3.4     3.6    -      -       -      -
     11A  GLN*     3.3    31.8    -      -       +      +
     98A  SER*     3.1    32.4    +      -       -      -
     99A  SER*     1.3    73.9    -      -       -      +
    101A  LEU*     1.3    64.3    +      -       -      +
    102A  THR      3.7     0.3    +      -       -      -
    109A  VAL*     3.4     2.5    -      -       -      -
    110A  ALA*     2.7    46.2    +      -       +      +
    112A  LEU*     5.3     0.8    -      -       +      +
    171A  CYS      6.4     0.2    -      -       -      -
    172A  GLN*     4.9    15.3    +      -       +      +
    175A  PHE*     4.0    28.8    -      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  LEU*     3.6    20.3    -      -       -      +
     10A  LYS*     2.9    23.7    +      -       +      +
     12A  ILE*     4.0    31.9    -      -       +      -
     20A  LEU*     4.7     2.2    -      -       +      -
     24A  TRP*     3.8    22.4    -      -       +      -
    100A  HIS*     1.3    73.1    -      -       -      +
    102A  THR*     1.3    64.8    +      -       -      +
    108A  VAL      3.7     3.1    -      -       -      +
    109A  VAL*     4.1    11.7    -      -       +      -
   1495C  TRP*     3.7    35.7    -      -       +      -
   1523C  TYR*     3.6    42.0    -      -       +      +
----------------------------------------------------------
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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