Contacts of the strand formed by residues 47 - 51 (chain A) in PDB entry 3K72


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 LEU 47 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  VAL*     4.7    11.0    -      -       +      -
     32A  VAL      3.8    15.5    -      -       -      +
     33A  GLY*     4.3     0.9    -      -       -      -
     34A  ALA      5.3     0.2    -      -       -      +
     46A  GLY*     1.3    75.2    -      -       -      +
     48A  TYR*     1.3    73.6    +      -       -      +
     59A  PRO*     4.1     0.7    -      -       -      +
     60A  ILE*     3.3    43.3    +      -       +      +
     62A  LEU*     4.2    18.4    -      -       +      +
     73A  LEU*     3.4    16.1    -      -       +      +
     74A  GLY*     3.4    32.8    -      -       -      +
     77A  LEU*     4.4     5.4    -      -       +      -
     86A  LEU*     5.2     3.4    -      -       +      -
     88A  ALA*     3.1    31.2    -      -       +      -
    108A  PHE*     6.0     0.7    -      -       +      -
    110A  LEU*     5.6     4.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  VAL*     4.2    11.0    -      -       +      +
     15A  SER*     3.7    22.9    +      -       -      -
     18A  PHE*     3.7    22.7    -      +       +      -
     30A  VAL      3.7     1.0    -      -       -      +
     31A  VAL*     3.6     5.5    -      -       -      -
     32A  VAL*     3.2    44.1    +      -       +      +
     34A  ALA*     5.2     3.6    -      -       +      -
     37A  LYS*     3.0    36.4    +      -       +      -
     47A  LEU*     1.3    82.6    -      -       -      +
     49A  GLN*     1.3    59.7    +      -       -      +
     50A  CYS      4.0     0.2    +      -       -      -
     57A  CYS*     4.3    18.8    -      -       +      -
     58A  GLU      3.6     4.9    -      -       -      +
     59A  PRO*     3.4    48.1    -      -       +      +
     60A  ILE*     4.8     1.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  TYR*     5.4     5.8    -      -       +      -
     29A  TRP*     3.4    45.5    -      -       +      +
     30A  VAL      3.8     5.2    -      -       -      +
     31A  VAL*     4.8    11.9    -      -       +      -
     48A  TYR*     1.3    73.4    -      -       -      +
     50A  CYS*     1.3    61.4    +      -       -      +
     56A  ALA      4.5     0.2    -      -       -      +
     58A  GLU*     3.1    44.0    +      -       +      +
     59A  PRO      4.9     5.2    +      -       -      +
     60A  ILE*     4.9    22.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.6    27.1    -      -       +      -
     18A  PHE*     5.2     0.4    -      -       -      -
     29A  TRP*     3.4    10.3    -      -       -      -
     30A  VAL*     3.1    41.3    +      -       +      +
     32A  VAL*     4.9     7.4    -      -       -      -
     48A  TYR*     4.5     8.5    -      -       -      -
     49A  GLN*     1.3    76.6    -      -       -      +
     51A  GLY*     1.3    59.7    +      -       -      +
     56A  ALA      3.9     3.8    -      -       -      -
     57A  CYS*     2.0    53.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.3    15.1    -      -       -      -
     28A  SER      4.4     7.9    -      -       -      -
     29A  TRP*     3.7    19.3    -      -       -      -
     50A  CYS*     1.3    74.1    -      -       -      +
     52A  TYR*     1.3    61.3    +      -       -      -
     53A  SER*     3.5     2.9    -      -       -      -
     54A  THR*     2.8    23.7    -      -       -      +
     56A  ALA      4.0     4.9    +      -       -      -
----------------------------------------------------------
 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