Contacts of the strand formed by residues 20 - 28 (chain A) in PDB entry 5D4C


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 TYR 20 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ARG      6.0     0.2    -      -       -      -
     15A  THR*     4.0     3.3    -      -       -      -
     16A  GLN*     3.4    63.1    +      -       +      +
     17A  GLY      4.1     3.1    -      -       -      +
     18A  ARG      3.6     0.6    -      -       -      -
     19A  GLU*     1.3    83.1    -      -       +      +
     21A  GLY*     1.3    70.5    +      -       -      +
     22A  GLU*     2.5    41.9    +      -       +      +
    198A  ARG*     3.1    27.5    +      -       +      -
    199A  ILE      3.4     7.9    -      -       -      -
    200A  TRP*     3.4    50.0    -      +       +      -
    207A  PRO*     3.5    10.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ARG      3.5     9.4    -      -       -      -
     15A  THR*     4.6     1.3    -      -       -      -
     20A  TYR*     1.3    82.4    -      -       -      +
     22A  GLU*     1.3    66.3    +      -       -      +
     23A  PHE*     3.8     9.0    -      -       -      -
    198A  ARG*     3.4     3.6    -      -       -      -
    199A  ILE      2.9    34.4    +      -       -      -
    207A  PRO*     3.7    13.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  THR      4.0     0.2    -      -       -      +
     13A  VAL*     3.7     0.7    -      -       -      -
     14A  ARG*     2.9    79.9    +      -       +      +
     16A  GLN*     5.9     0.4    +      -       -      -
     20A  TYR*     2.5    37.9    +      -       +      +
     21A  GLY*     1.3    75.3    -      -       -      +
     23A  PHE*     1.3    68.5    +      -       -      +
     24A  VAL*     4.2     1.5    -      -       -      +
    196A  THR*     4.7     4.5    -      -       +      -
    197A  LEU      3.3     4.9    -      -       -      +
    198A  ARG*     4.3     7.0    +      -       +      -
    932C  GLU*     4.3     6.9    -      -       -      +
    934C  PHE*     3.3    27.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.9    10.5    -      +       +      -
     12A  THR      3.5     2.7    -      -       -      -
     13A  VAL*     3.8    30.3    -      -       +      -
     15A  THR*     5.0     3.4    -      -       +      -
     21A  GLY*     3.8    20.6    -      -       -      -
     22A  GLU*     1.3    77.8    -      -       -      +
     24A  VAL*     1.3    62.8    +      -       -      +
    195A  LEU*     3.5     2.6    -      -       -      +
    196A  THR*     3.4     2.1    -      -       -      +
    197A  LEU*     2.9    53.8    +      -       +      +
    199A  ILE*     4.1    12.8    -      -       +      -
    207A  PRO*     3.7    19.3    -      -       +      -
    208A  LEU*     3.5    48.5    -      -       +      -
    211A  LEU*     3.5    27.4    -      -       +      -
    225B  PHE*     5.4     2.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  VAL      4.3     0.4    -      -       -      -
     11A  PHE*     3.2    12.0    -      -       -      -
     12A  THR*     2.9    45.3    +      -       -      +
     14A  ARG*     3.3    37.2    -      -       +      +
     22A  GLU      5.2     0.9    -      -       -      -
     23A  PHE*     1.3    75.4    -      -       -      +
     25A  LEU*     1.3    67.6    +      -       -      +
     26A  GLU*     4.2     9.6    -      -       +      +
    194A  LYS*     3.8    33.0    -      -       +      -
    195A  LEU      3.2     9.6    -      -       -      +
    196A  THR*     3.6    15.9    -      -       +      +
    225B  PHE*     6.2     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  PRO*     4.1    11.4    -      -       +      -
     10A  VAL      3.5     2.9    -      -       -      +
     11A  PHE*     3.5    29.2    -      -       +      +
     23A  PHE      4.1     0.9    +      -       -      +
     24A  VAL*     1.3    71.8    -      -       -      +
     26A  GLU*     1.3    60.6    +      -       -      +
     28A  LEU*     3.9    22.8    -      -       +      +
     36A  LEU*     3.8    28.5    -      -       +      -
    193A  ASP      3.9     2.8    -      -       -      +
    194A  LYS*     3.7     1.0    -      -       -      -
    195A  LEU*     2.9    41.8    +      -       +      +
    224B  TYR*     3.4    40.6    -      -       +      +
    225B  PHE*     4.2    18.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  PRO*     3.5     3.3    -      -       -      +
     10A  VAL*     2.9    53.4    +      -       +      +
     12A  THR*     5.6     2.7    +      -       -      +
     24A  VAL*     4.4     9.0    -      -       +      +
     25A  LEU*     1.3    76.3    -      -       -      +
     27A  PRO*     1.3    75.9    -      -       +      +
    184A  THR*     3.7    17.0    +      -       +      -
    194A  LYS*     3.5    44.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     3.9    21.3    -      -       +      +
      9A  PRO*     3.2    24.1    -      -       +      +
     10A  VAL*     4.9     1.3    -      -       +      +
     26A  GLU*     1.3    88.4    -      -       +      +
     28A  LEU*     1.3    60.9    +      -       -      +
    184A  THR*     4.0    15.3    -      -       +      +
    185A  ARG      5.3     0.7    -      -       -      +
    186A  LEU*     4.1    34.5    -      -       +      -
    192A  LEU*     3.9    20.9    -      -       +      -
    193A  ASP      3.5     3.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     5.3     4.5    -      -       -      -
      9A  PRO*     3.8    24.7    -      -       +      -
     25A  LEU*     3.9    31.2    -      -       +      +
     27A  PRO*     1.3    75.1    -      -       -      +
     29A  GLU*     1.3    63.7    +      -       -      +
     32A  PHE*     4.2    16.6    -      -       +      +
     33A  GLY*     4.7     0.7    -      -       -      +
     36A  LEU*     4.0    11.7    -      -       +      -
    192A  LEU*     3.5     8.9    -      -       -      +
    193A  ASP*     2.7    46.4    +      -       +      +
    195A  LEU*     4.0    24.9    -      -       +      -
    221B  HIS*     4.0    26.7    -      -       +      +
    224B  TYR*     4.5     0.4    -      -       +      -
----------------------------------------------------------
 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