Contacts of the strand formed by residues 29 - 32 (chain C) in PDB entry 3J82


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 ALA 29 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  CYS      4.0     0.2    -      -       -      +
     18C  LYS*     3.7     1.4    -      -       -      -
     19C  ALA*     3.2    27.2    +      -       +      +
     27C  PRO*     4.4     1.9    -      -       -      +
     28C  ARG*     1.3    84.7    -      -       +      +
     30C  VAL*     1.3    64.6    +      -       -      +
     31C  PHE*     4.9     1.2    -      -       -      -
     89C  THR*     6.3     1.1    -      -       +      -
     93C  GLU*     3.3    48.8    -      -       +      +
     94C  LEU*     4.8     2.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 30 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  MET*     3.1    39.6    -      -       +      +
     17C  CYS      2.9    19.7    -      -       -      +
     18C  LYS*     3.7    20.2    -      -       +      -
     27C  PRO*     5.1     6.1    -      -       +      +
     28C  ARG      5.7     0.2    -      -       -      -
     29C  ALA*     1.3    75.7    -      -       -      +
     31C  PHE*     1.3    65.8    +      -       -      +
     32C  PRO*     4.5     0.5    -      -       -      +
     56C  ASP*     5.8     0.7    -      -       -      +
     93C  GLU*     4.2     4.2    +      -       -      +
    336C  LYS*     5.5     0.9    -      -       -      +
    337C  TYR*     5.4    14.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 31 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  MET*     3.1     6.4    -      -       -      -
     17C  CYS*     2.6    66.9    +      -       +      -
     19C  ALA      6.0     0.4    -      -       -      -
     29C  ALA      5.2     1.3    -      -       -      -
     30C  VAL*     1.3    79.4    -      -       -      +
     32C  PRO*     1.3    95.4    -      -       +      +
     33C  SER*     4.8     2.7    -      -       -      -
     53C  TYR      6.1     0.9    -      -       -      -
     55C  GLY*     4.0    18.4    -      -       -      -
     56C  ASP*     4.4     4.7    -      -       +      +
     85C  ILE*     3.6    20.0    -      -       +      -
     88C  HIS*     3.9    15.7    -      +       -      -
     89C  THR*     3.2    27.4    -      -       +      -
     93C  GLU*     2.8    37.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 32 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  GLY      2.8    13.2    -      -       -      +
     16C  MET*     4.1    12.3    -      -       +      -
     30C  VAL      4.5     0.2    -      -       -      +
     31C  PHE*     1.3   108.1    -      -       +      +
     33C  SER*     1.3    59.9    +      -       -      +
     34C  ILE*     3.6    24.0    +      -       +      -
     54C  VAL*     4.1     0.3    -      -       -      +
     55C  GLY*     3.7    30.9    +      -       -      +
     56C  ASP*     4.4     2.9    -      -       -      +
     59C  GLN*     4.5    27.4    -      -       +      +
    210C  ARG*     6.2     0.7    -      -       -      +
----------------------------------------------------------
 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