Contacts of the strand formed by residues 4 - 9 (chain D) in PDB entry 5FLZ


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 GLU 4 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  MET      3.1    32.5    +      -       -      +
      3D  GLY*     1.4    71.5    -      -       -      -
      5D  ILE*     1.3    59.1    -      -       -      +
     51D  LYS*     3.7    21.0    -      -       -      +
     52D  PRO*     3.6    10.0    -      -       -      +
     55D  ARG*     3.8    13.5    -      -       -      +
     65D  ARG*     3.4    27.1    -      -       -      +
    130D  THR*     3.5    11.4    -      -       +      -
    131D  ASP*     3.2    37.3    +      -       -      +
    132D  ASN      3.1    14.0    +      -       -      +
    133D  PHE*     3.2     7.1    -      -       -      -
    134D  GLU*     2.7    25.3    +      -       -      +
    135D  GLY      3.2     1.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 5 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3D  GLY      4.2     7.2    -      -       -      +
      4D  GLU*     1.3    79.9    -      -       -      +
      6D  ILE*     1.3    77.4    +      -       -      +
      7D  THR*     4.3     1.5    +      -       +      -
     52D  PRO*     2.7    25.2    +      -       +      +
     53D  PHE*     3.9    22.9    -      -       +      -
     65D  ARG*     3.8    13.1    +      -       -      +
    134D  GLU*     4.4    12.3    -      -       +      -
    135D  GLY      3.2    13.9    -      -       -      +
    136D  PHE      4.3     0.4    -      -       -      -
    137D  GLN*     3.6    41.1    -      -       +      +
    242D  ILE*     4.0    22.7    -      -       +      -
    252D  MET*     5.7    10.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 6 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  ILE*     1.3    73.4    -      -       -      +
      7D  THR*     1.4    72.0    +      -       -      +
      8D  LEU*     4.0    15.5    +      -       +      +
     65D  ARG*     3.8    25.6    -      -       -      +
     66D  ALA*     4.9     0.9    -      -       -      -
     67D  ILE*     4.7     9.9    -      -       +      +
    123D  ILE*     4.4     5.4    -      -       +      +
    126D  GLU*     3.6    37.5    -      -       +      +
    127D  ILE*     3.8    26.0    -      -       +      -
    133D  PHE*     3.5    24.7    -      -       +      -
    135D  GLY      3.3     5.1    +      -       -      -
    136D  PHE*     3.4    11.7    -      -       +      +
    137D  GLN      2.9    24.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 7 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  ILE*     4.5     0.2    -      -       +      -
      6D  ILE*     1.4    79.8    -      -       -      +
      8D  LEU*     1.3    60.4    +      -       -      +
      9D  GLN*     3.3    14.3    +      -       -      +
     21D  LEU*     6.5     0.7    -      -       +      -
     22D  TRP*     3.5    14.7    -      -       +      -
     53D  PHE*     4.4    27.8    -      -       +      -
     65D  ARG      3.7     5.2    +      -       -      +
     66D  ALA*     3.1    24.4    -      -       -      +
     67D  ILE*     3.0    22.9    +      -       -      +
    137D  GLN*     3.2    17.7    -      -       +      +
    139D  LEU*     4.0    11.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 8 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  ILE*     4.0     8.3    -      -       +      +
      7D  THR*     1.3    78.1    -      -       -      +
      9D  GLN*     1.3    57.8    +      -       -      +
     67D  ILE*     3.6    24.7    -      -       +      -
     69D  MET*     4.3     7.2    -      -       +      -
    123D  ILE*     4.9     7.9    -      -       +      -
    136D  PHE*     3.8    29.4    -      -       +      -
    137D  GLN      2.8     9.6    +      -       -      +
    138D  LEU*     3.4    29.0    -      -       +      +
    139D  LEU*     2.8    33.8    +      -       -      +
    154D  LEU*     4.5    18.4    -      -       +      -
    155D  LEU*     5.3     3.4    -      -       +      -
    158D  LEU*     3.7    25.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 9 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  THR*     3.3    22.0    +      -       -      +
      8D  LEU*     1.3    75.6    -      -       -      +
     10D  ALA*     1.3    57.5    +      -       -      +
     14D  GLY*     3.0    25.6    -      -       -      +
     15D  ASN*     3.4    19.3    -      -       -      +
     18D  GLY*     3.7    12.3    -      -       -      -
     21D  LEU*     5.3     2.2    -      -       -      +
     22D  TRP*     3.3    36.7    -      -       -      -
     66D  ALA*     3.9     4.8    -      -       -      +
     67D  ILE      3.0    18.7    +      -       -      +
     68D  MET*     4.1    11.0    -      -       +      -
     69D  MET*     2.9    35.8    +      -       -      +
    139D  LEU*     3.8    16.8    -      -       +      +
----------------------------------------------------------
 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