Contacts of the strand formed by residues 141 - 145 (chain I) in PDB entry 4ZZ7


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 141 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46I  ILE*     4.2    10.1    -      -       +      +
     49I  ALA*     3.9    20.9    -      -       +      +
     50I  GLN*     3.3    52.1    +      -       +      +
     53I  PHE*     5.3     0.9    -      -       +      -
    140I  GLY*     1.3    73.5    -      -       -      -
    142I  VAL*     1.3    66.4    +      -       -      +
    168I  CYS*     3.5     4.7    -      -       +      +
    170I  VAL*     4.1    17.7    -      -       +      -
    216I  ARG      3.5    15.5    +      -       -      +
    217I  VAL*     3.7    17.3    -      -       +      -
    218I  LYS*     3.0    28.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 142 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139I  MET*     4.4     7.2    -      -       +      -
    140I  GLY      4.2     0.4    -      -       -      +
    141I  VAL*     1.3    81.4    -      -       -      +
    143I  ALA*     1.3    65.5    +      -       -      +
    167I  ASN*     3.7    34.3    -      -       +      +
    168I  CYS      2.9    11.8    +      -       -      +
    169I  PHE*     3.4    22.1    -      -       +      -
    170I  VAL*     2.8    28.0    +      -       -      +
    219I  ALA*     3.6    25.1    -      -       +      +
    471I  TYR*     3.8    32.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 143 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142I  VAL*     1.3    80.8    -      -       -      +
    144I  GLY*     1.3    58.3    +      -       -      +
    145I  ILE*     5.4     0.2    -      -       +      -
    170I  VAL*     3.4     5.8    -      -       -      +
    211I  LEU*     4.0    32.1    -      -       +      -
    217I  VAL*     3.8    22.5    -      -       +      +
    219I  ALA      2.8    11.6    +      -       -      +
    220I  VAL*     3.3    13.4    -      -       +      -
    221I  SER*     2.9    25.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 144 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143I  ALA*     1.3    72.6    -      -       -      +
    145I  ILE*     1.3    62.7    +      -       -      +
    158I  MET*     3.7     7.6    -      -       -      -
    169I  PHE*     3.6    23.1    -      -       -      -
    170I  VAL      3.0     8.6    +      -       -      +
    171I  LEU*     3.5     7.0    -      -       -      +
    172I  LYS*     2.8    31.9    +      -       -      +
    211I  LEU*     4.8     0.5    -      -       -      +
    221I  SER      3.4     5.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 145 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143I  ALA      5.3     0.2    -      -       -      -
    144I  GLY*     1.3    79.7    -      -       -      +
    146I  THR*     1.3    64.3    +      -       -      +
    158I  MET*     3.4     7.7    -      -       -      +
    172I  LYS*     3.5    12.1    -      -       +      +
    208I  VAL*     3.8    35.2    -      -       +      +
    211I  LEU*     4.5    17.7    -      -       +      -
    212I  LEU*     4.8     3.4    -      -       +      -
    220I  VAL*     3.9    25.1    -      -       +      -
    221I  SER      2.8    10.7    +      -       -      +
    222I  PHE*     3.5    27.8    -      -       +      -
    223I  VAL      3.2    25.1    +      -       -      +
    232I  ILE*     4.4     4.9    -      -       +      -
    501I  NAD      3.6    22.2    -      -       -      +
----------------------------------------------------------
 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