Contacts of the strand formed by residues 18 - 26 (chain A) in PDB entry 6DV9


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 18 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     3.1    47.5    +      -       +      +
     15A  THR*     3.2    22.4    +      -       -      +
     17A  ASN*     1.3    81.3    -      -       -      +
     19A  SER*     1.3    66.3    +      -       -      +
     20A  GLN*     5.1     1.4    -      -       -      +
    195A  ASP*     2.9    40.8    +      -       -      +
    196A  VAL      3.3     5.8    -      -       -      +
    197A  GLU*     3.9    15.2    -      -       +      +
    204A  PRO*     3.6     3.0    -      -       -      +
    996C  ARG*     3.5    37.7    -      -       -      +
    997C  ASP*     2.8    42.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLU*     3.5    18.5    +      -       -      -
     12A  ASP      3.2    12.8    -      -       -      -
     13A  VAL*     3.8    11.8    -      -       -      +
     14A  LEU*     4.4     1.3    -      -       -      +
     15A  THR      4.6     1.7    +      -       -      -
     18A  ARG*     1.3    80.5    +      -       -      +
     20A  GLN*     1.3    63.7    +      -       -      +
     21A  PHE*     3.7    17.2    -      -       -      -
    195A  ASP*     3.7     0.9    -      -       -      +
    196A  VAL      3.0    31.3    +      -       -      +
    204A  PRO*     3.6    24.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  SER      4.2     0.3    -      -       -      +
     11A  GLU*     3.6     0.3    -      -       -      +
     12A  ASP*     2.7    55.3    +      -       +      +
     14A  LEU*     3.6    32.1    -      -       +      +
     18A  ARG*     5.1     2.0    -      -       -      +
     19A  SER*     1.3    76.0    -      -       -      +
     21A  PHE*     1.3    62.3    +      -       -      +
     22A  VAL*     5.7     2.1    -      -       +      +
    177A  LYS*     5.3     7.4    -      -       -      +
    193A  ILE*     3.6    24.0    -      -       +      +
    194A  LEU      3.1     6.7    -      -       -      +
    195A  ASP*     3.7    24.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  LEU*     3.6    22.0    -      -       +      -
     10A  SER      3.8     2.9    -      -       -      -
     11A  GLU*     3.6    30.5    -      -       +      -
     19A  SER*     3.7    31.4    -      -       -      -
     20A  GLN*     1.3    74.2    -      -       -      +
     22A  VAL*     1.3    61.8    +      -       -      +
     23A  ILE*     4.9     3.5    -      -       +      +
    192A  LEU*     3.4     1.7    -      -       -      +
    193A  ILE*     3.3     2.4    -      -       -      -
    194A  LEU*     2.6    52.5    +      -       +      +
    196A  VAL*     4.1    20.6    -      -       +      -
    204A  PRO*     4.1     2.7    -      -       +      -
    205A  ARG*     3.8    25.8    -      -       +      -
    208A  LEU*     3.5    30.5    -      -       +      -
    225B  LEU*     4.1    13.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  THR      3.5     1.7    -      -       -      +
      9A  LEU*     3.3     5.0    -      -       -      +
     10A  SER*     3.1    58.6    +      -       -      +
     12A  ASP*     4.9    16.2    -      -       -      +
     20A  GLN*     5.7     2.2    -      -       +      +
     21A  PHE*     1.3    73.7    -      -       -      +
     23A  ILE*     1.3    60.8    +      -       -      +
     24A  GLU*     5.2     8.4    -      -       +      +
    191A  LYS*     4.6    16.2    -      -       +      +
    192A  LEU      3.1     3.6    -      -       -      +
    193A  ILE*     3.8    33.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PRO*     4.5     5.8    -      -       +      -
      8A  THR      3.3     6.3    -      -       -      +
      9A  LEU*     3.8    31.2    -      -       +      -
     21A  PHE*     4.9     4.7    -      -       +      +
     22A  VAL*     1.3    77.6    -      -       -      +
     24A  GLU*     1.3    67.8    +      -       -      +
     26A  LEU*     4.1    28.0    -      -       +      +
     34A  LEU*     5.6     2.9    -      -       +      -
     38A  LEU*     4.6    16.2    -      -       +      -
    191A  LYS*     3.6     1.6    -      -       -      +
    192A  LEU*     2.8    54.2    +      -       +      +
    194A  LEU*     6.0     2.2    -      -       +      -
    208A  LEU*     6.0     2.2    -      -       +      -
    218B  LEU*     4.5    16.2    -      -       +      +
    221B  LEU*     4.7     7.4    -      -       +      -
    222B  ALA*     6.3     1.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PRO*     3.6     4.5    -      -       -      -
      8A  THR*     2.5    49.8    +      -       +      +
     22A  VAL*     5.2     7.8    -      -       +      +
     23A  ILE*     1.3    82.2    -      -       -      +
     25A  PRO*     1.3    72.4    -      -       +      +
     26A  LEU      3.9     0.7    -      -       -      +
    189A  PHE*     3.9    14.3    -      -       +      -
    191A  LYS*     3.1    36.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  GLN*     3.5    44.5    -      -       +      +
      6A  ARG      3.8     4.7    -      -       -      +
      7A  PRO*     3.6    20.0    -      -       +      +
      8A  THR*     5.5     0.4    -      -       +      -
     24A  GLU*     1.3    84.3    -      -       +      +
     26A  LEU*     1.3    65.6    +      -       -      +
     27A  GLU*     5.8     0.2    -      -       -      +
    189A  PHE*     3.5    30.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PRO*     4.4     7.0    -      -       +      -
     23A  ILE*     4.1    20.6    -      -       +      +
     24A  GLU*     3.9     0.2    -      -       -      +
     25A  PRO*     1.3    77.2    -      -       -      +
     27A  GLU*     1.3    66.0    +      -       -      +
     30A  PHE*     4.3     8.1    -      -       +      +
     31A  GLY*     4.1    12.6    -      -       -      +
     34A  LEU*     3.6    35.0    -      -       +      -
    189A  PHE*     3.4     8.3    -      -       -      +
    190A  ASP*     2.8    42.0    +      -       +      +
    192A  LEU*     3.9    27.4    -      -       +      -
    218B  LEU*     3.7    22.9    -      -       +      -
----------------------------------------------------------
 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