Contacts of the strand formed by residues 242 - 246 (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 ARG 242 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139I  MET*     3.3    25.4    -      -       +      +
    218I  LYS      3.5     5.9    +      -       -      +
    219I  ALA*     3.5    18.5    -      -       +      -
    220I  VAL*     3.2    20.3    +      -       -      -
    240I  GLY      3.9     1.4    +      -       -      -
    241I  LYS*     1.3    80.0    -      -       -      +
    243I  CYS*     1.3    62.1    +      -       -      +
    469I  ARG*     3.2     9.7    +      -       -      +
    470I  PHE*     3.0    38.0    +      -       +      +
    472I  THR      2.8    28.9    +      -       -      -
    473I  LYS*     3.8    13.3    -      -       -      +
    233L  TYR*     4.4     9.9    -      -       -      +
    458L  GLY*     4.2    15.6    +      -       -      +
    459L  ASP*     3.5    39.7    +      -       +      +
    461L  HIS*     5.0     6.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 243 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220I  VAL*     3.3    16.2    -      -       -      +
    232I  ILE*     4.3    14.6    -      -       -      -
    233I  TYR*     3.5    51.0    -      -       +      -
    236I  ALA*     4.0    16.8    -      -       +      -
    237I  SER*     4.8     2.9    -      -       -      +
    241I  LYS      4.4     1.3    -      -       -      +
    242I  ARG*     1.3    79.9    -      -       -      +
    244I  GLN*     1.3    74.0    +      -       -      +
    245I  ALA*     4.2     4.7    -      -       -      -
    457I  PHE      4.2     0.5    -      -       -      +
    458I  GLY*     4.3     5.0    -      -       -      -
    470I  PHE*     3.4    13.2    -      -       -      -
    233L  TYR*     5.0     3.0    +      -       -      -
    459L  ASP*     4.4     5.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 244 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158I  MET*     5.5     0.5    -      -       -      +
    220I  VAL      3.1     3.2    +      -       -      +
    221I  SER*     2.5    33.3    +      -       -      +
    222I  PHE      2.8    33.2    +      -       -      +
    243I  CYS*     1.3    76.3    -      -       -      +
    245I  ALA*     1.3    54.6    +      -       -      +
    246I  LEU*     4.1    11.0    -      -       +      -
    456I  LEU*     5.9     1.1    -      -       +      -
    457I  PHE      3.6     7.4    -      -       -      +
    458I  GLY*     5.5     1.6    -      -       -      -
    460I  LEU      2.9    36.8    +      -       -      +
    461I  HIS      3.2    20.9    +      -       -      -
    462I  ALA*     4.7     8.7    -      -       -      +
    463I  TYR      5.3     1.6    +      -       -      -
    467I  ALA*     5.5     2.2    -      -       -      +
    470I  PHE*     3.7    29.0    -      -       +      +
    471I  TYR*     3.7     8.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 245 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222I  PHE*     3.4    16.6    -      -       +      -
    229I  ALA*     3.5    31.6    -      -       +      +
    233I  TYR*     4.1    15.9    -      -       +      +
    243I  CYS*     4.2     4.7    -      -       -      -
    244I  GLN*     1.3    74.5    -      -       -      +
    246I  LEU*     1.3    63.6    +      -       -      +
    456I  LEU*     3.5     0.9    -      -       -      -
    457I  PHE*     2.8    43.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 246 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157I  TRP*     4.2     4.0    -      -       +      -
    222I  PHE*     2.9    25.4    +      -       -      +
    223I  VAL*     3.6     7.9    -      -       +      -
    224I  GLY      3.0    26.3    +      -       -      +
    229I  ALA*     4.1     0.9    -      -       -      -
    244I  GLN*     4.4    14.4    -      -       +      -
    245I  ALA*     1.3    83.3    -      -       -      +
    247I  GLY*     1.3    60.1    +      -       -      +
    449I  PHE*     3.7    18.6    -      -       +      +
    450I  GLY*     4.3     5.4    -      -       -      -
    451I  GLY      5.3     0.7    -      -       -      +
    455I  SER      3.7     4.9    -      -       -      +
    456I  LEU*     3.9    19.7    -      -       +      +
    461I  HIS*     5.7     0.2    -      -       -      -
    462I  ALA*     3.6    33.7    -      -       +      +
    501I  NAD      3.1    31.0    -      -       -      +
----------------------------------------------------------
 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