Contacts of the strand formed by residues 53 - 59 (chain U) in PDB entry 2FD6


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 53 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  TYR*     2.8    35.9    +      -       -      +
     25A  PHE*     3.2    12.4    -      -       +      -
     49U  GLU      4.5     2.0    +      -       -      -
     50U  LYS*     4.0    18.5    -      -       -      +
     51U  THR*     3.1    46.7    +      -       -      +
     52U  ASN*     1.3    74.8    -      -       -      +
     54U  THR*     1.3    65.9    +      -       -      +
     67U  THR*     4.5     0.2    +      -       -      -
     68U  GLU*     2.9    41.4    +      -       +      +
    149U  TYR*     3.2    16.8    -      -       -      +
    150U  LEU*     3.9    17.5    -      -       +      -
    151U  PRO*     3.8    15.0    -      -       +      +
    252U  LEU*     5.2     1.4    -      -       -      +
    254U  ASP*     2.6    36.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 54 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  PHE*     3.7     2.5    -      -       -      -
     53U  ARG*     1.3    75.8    +      -       -      +
     55U  LEU*     1.3    81.5    +      -       -      +
     56U  SER*     4.7     3.6    -      -       -      +
     65U  SER*     6.0     1.3    -      -       -      -
     66U  LEU      3.4    13.5    -      -       -      +
     67U  THR*     4.0    13.1    -      -       +      -
    120U  GLU*     3.1    31.0    +      -       -      +
    123U  LEU*     4.1     0.2    -      -       -      +
    148U  GLY*     3.1     7.6    -      -       -      -
    149U  TYR*     2.9    33.1    +      -       -      +
    150U  LEU*     3.8     4.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 55 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ASN*     3.4    26.2    -      -       -      +
     24A  TYR*     6.0     0.7    -      -       +      -
     25A  PHE*     3.8    16.2    -      -       +      -
     54U  THR*     1.3    83.2    -      -       -      +
     56U  SER*     1.3    67.1    +      -       -      +
     57U  TYR*     4.1    12.1    -      -       +      -
     64U  THR      3.9     0.7    -      -       -      +
     65U  SER*     3.6     0.3    -      -       -      -
     66U  LEU*     2.8    42.7    +      -       +      +
    123U  LEU*     3.9    21.5    -      -       +      -
    125U  VAL*     5.0     8.7    -      -       +      -
    144U  LEU*     3.8    22.0    -      -       +      -
    145U  ARG      5.5     0.7    -      -       -      -
    146U  GLY      5.1     4.7    -      -       -      +
    147U  CYS      3.1    17.0    -      -       -      +
    150U  LEU*     4.8    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 56 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54U  THR*     5.2     4.7    -      -       -      -
     55U  LEU*     1.3    77.1    -      -       -      +
     57U  TYR*     1.3    63.9    +      -       -      +
     63U  ILE*     4.0    10.0    -      -       -      +
     64U  THR      3.2     5.8    +      -       -      -
     65U  SER*     3.2    22.6    +      -       -      -
    113U  LEU*     3.7    11.2    -      -       -      +
    120U  GLU*     5.1     4.5    -      -       -      -
    146U  GLY*     3.2     5.2    -      -       -      -
    147U  CYS*     2.7    44.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 57 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  VAL*     5.0     0.5    -      -       -      +
     30A  TRP*     4.0    13.2    +      -       -      -
     55U  LEU*     4.1    18.2    -      -       +      -
     56U  SER*     1.3    78.4    +      -       -      +
     58U  ARG*     1.3    64.7    +      -       -      +
     59U  THR*     4.0    14.0    +      -       +      -
     63U  ILE*     4.5     2.0    -      -       -      -
     64U  THR*     2.9    66.3    +      -       +      +
     66U  LEU*     4.6     7.1    -      -       +      +
     97U  SER*     3.0     6.5    -      -       -      +
     98U  CYS      4.2    12.8    -      -       -      +
     99U  GLY*     4.8     1.8    -      -       -      -
    101U  SER*     5.3     5.0    -      -       -      -
    113U  LEU*     3.6     4.9    -      -       -      -
    141U  ASP*     3.8    15.7    +      -       -      -
    144U  LEU*     3.9    37.0    -      -       +      +
    145U  ARG      3.2    25.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 58 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32U  TRP*     5.8     1.0    -      -       -      -
     57U  TYR*     1.3    74.4    -      -       -      +
     59U  THR*     1.3    60.3    +      -       -      +
     60U  GLY      3.7     4.8    +      -       -      +
     61U  LEU      6.2     0.2    -      -       -      -
     62U  LYS      3.3    15.3    -      -       -      +
     63U  ILE*     3.9    28.8    -      -       +      +
     97U  SER*     2.8    23.1    +      -       -      +
     98U  CYS*     3.6    22.7    -      -       -      -
    104U  SER*     4.5     0.5    +      -       -      -
    111U  GLN*     3.4    48.3    +      -       +      +
    112U  SER      3.7    20.8    +      -       -      -
    113U  LEU*     3.9    13.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 59 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57U  TYR*     4.6    17.7    -      -       +      +
     58U  ARG*     1.3    73.5    -      -       -      +
     60U  GLY*     1.3    57.5    +      -       -      +
     61U  LEU      3.8     2.1    +      -       -      -
     62U  LYS*     3.1    40.4    +      -       +      +
     64U  THR*     4.9     2.5    -      -       -      +
     99U  GLY*     4.2     6.2    +      -       -      +
    101U  SER*     3.1    20.8    +      -       -      +
    102U  ASP*     2.5    46.4    +      -       +      +
    104U  SER*     4.1     5.0    -      -       -      -
----------------------------------------------------------
 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