Contacts of the strand formed by residues 154 - 158 (chain D) in PDB entry 3AP3


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 154 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  PRO*     3.5    28.7    -      -       +      +
     71D  ILE*     3.7    29.6    -      -       +      -
     93D  GLU*     2.7    18.8    +      -       +      +
     94D  VAL*     3.3    16.6    -      -       +      +
     95D  ARG      3.1    24.6    +      -       -      -
    152D  ALA*     3.5     4.7    -      -       -      +
    153D  ARG*     1.3   107.7    -      -       -      +
    155D  LEU*     1.3    58.4    +      -       -      +
    258D  ILE*     4.1    14.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 155 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64D  TYR*     4.9     5.4    -      -       +      -
     68D  MET*     4.2    21.8    -      -       +      +
     69D  PRO      3.7     4.7    +      -       -      +
     70D  LEU*     3.2    28.1    -      -       +      +
     71D  ILE*     3.0    21.1    +      -       -      +
     95D  ARG*     3.4    48.7    -      -       +      +
    142D  LEU*     5.3     2.5    -      -       +      +
    145D  ILE*     3.7    13.0    -      -       +      -
    146D  ALA*     3.6    28.0    -      -       +      +
    151D  PRO*     5.3     0.4    -      -       +      -
    152D  ALA      4.4    21.5    -      -       -      +
    153D  ARG      4.1     1.8    +      -       -      -
    154D  VAL*     1.3    74.8    -      -       -      +
    156D  CYS*     1.3    59.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 156 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70D  LEU*     5.2     0.4    -      -       -      -
     71D  ILE*     3.1    36.3    -      -       +      +
     73D  VAL*     4.0     9.6    -      -       -      -
     94D  VAL*     4.4     2.0    -      -       +      -
     95D  ARG*     2.8    12.7    +      -       -      +
     96D  CYS*     2.0    64.2    -      -       -      +
    145D  ILE*     3.9    12.8    -      -       -      +
    148D  HIS*     5.1     0.5    +      -       -      -
    155D  LEU*     1.3    74.7    -      -       -      +
    157D  ASN*     1.3    81.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  ILE      2.7     9.5    +      -       -      -
     72D  PHE*     3.5    17.2    -      -       +      -
     73D  VAL      3.0    25.3    +      -       -      +
     96D  CYS      4.2     2.7    -      -       -      -
     98D  GLU      4.4     4.4    +      -       -      -
    100D  THR*     3.2    32.3    -      -       -      +
    103D  ILE*     3.6    14.3    -      -       -      +
    145D  ILE*     4.0    22.8    -      -       +      +
    148D  HIS*     4.6     4.4    +      -       -      -
    156D  CYS*     1.3    79.4    -      -       -      +
    158D  LYS*     1.3    67.5    +      -       -      +
    159D  ASP*     3.6    21.3    +      -       -      +
    162D  THR*     4.2     9.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 158 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  A3P      5.2     0.8    +      -       -      -
     73D  VAL*     3.4    28.0    -      -       +      +
     81D  THR*     3.4    30.5    +      -       -      +
     82D  THR*     3.3    40.0    +      -       -      +
     85D  ARG*     3.8    26.2    -      -       +      +
     96D  CYS      4.6     4.4    +      -       -      -
     97D  GLY      4.6     4.5    -      -       -      +
     98D  GLU      3.7     2.2    +      -       -      +
     99D  GLU*     2.8    63.9    +      -       -      +
    156D  CYS*     4.5     0.4    -      -       -      -
    157D  ASN*     1.3    76.3    -      -       -      +
    159D  ASP*     1.3    61.8    +      -       -      +
    160D  PRO*     3.9     8.3    -      -       +      -
    283D  GLU*     4.7     2.4    +      -       -      -
----------------------------------------------------------
 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