Contacts of the strand formed by residues 343 - 347 (chain D) in PDB entry 6NYY


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 GLY 343 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323D  PHE*     4.0     7.9    -      -       -      -
    341D  PRO      3.2     5.6    +      -       -      -
    342D  LYS*     1.3    78.7    -      -       -      +
    344D  ALA*     1.3    63.4    +      -       -      +
    448D  VAL*     4.6     5.4    -      -       -      -
    449D  ILE      3.2    20.6    -      -       -      -
    468D  ARG      4.4     4.6    +      -       -      -
    469D  PHE*     4.3     2.2    -      -       -      -
    470D  ASP*     3.2    23.4    +      -       -      +
    471D  ARG      3.4     5.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 344 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323D  PHE*     3.6    21.5    -      -       +      -
    343D  GLY*     1.3    75.9    -      -       -      +
    345D  ILE*     1.3    61.5    +      -       -      +
    346D  LEU*     5.3     1.3    -      -       +      +
    449D  ILE      3.2     7.0    +      -       -      +
    450D  LEU*     3.4    14.5    -      -       +      +
    451D  ALA      3.0    24.3    +      -       -      +
    469D  PHE*     3.9     9.2    -      -       -      -
    471D  ARG*     3.3    23.3    -      -       +      +
    473D  ILE*     4.1    13.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 345 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344D  ALA*     1.3    73.6    -      -       -      +
    346D  LEU*     1.3    63.0    +      -       -      +
    347D  THR*     4.1     7.9    -      -       +      -
    409D  ILE*     4.1    18.2    -      -       +      -
    451D  ALA*     3.3    33.4    -      -       +      +
    452D  GLY      4.2     0.2    -      -       -      +
    453D  THR*     4.1    19.1    -      -       +      -
    459D  LEU*     4.8     2.2    -      -       +      -
    464D  LEU*     4.3    18.8    -      -       +      -
    469D  PHE*     3.8    25.5    -      -       +      -
    471D  ARG      3.1     5.2    +      -       -      +
    472D  GLN*     3.7    33.7    -      -       +      -
    473D  ILE*     3.0    32.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 346 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320D  ILE*     3.7    31.4    -      -       +      -
    344D  ALA      5.3     1.8    -      -       -      +
    345D  ILE*     1.3    74.6    -      -       -      +
    347D  THR*     1.3    62.4    +      -       -      +
    354D  LYS*     3.5    39.2    -      -       +      +
    357D  LEU*     5.0     1.6    -      -       +      -
    358D  ALA*     5.0     7.4    -      -       +      +
    405D  PHE*     4.7    11.4    -      -       +      -
    450D  LEU*     5.5     9.6    -      -       +      -
    451D  ALA      2.8    16.6    +      -       -      +
    452D  GLY*     3.3     4.8    -      -       -      -
    453D  THR      2.8    30.7    +      -       -      +
    473D  ILE*     3.4    22.9    -      -       +      -
    475D  ILE*     3.8    18.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 347 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601C  LYS*     5.8     0.5    +      -       -      -
    345D  ILE*     4.1    18.8    -      -       +      -
    346D  LEU*     1.3    75.5    -      -       -      +
    348D  GLY*     1.3    58.9    +      -       -      +
    354D  LYS*     3.7     7.7    -      -       -      +
    453D  THR*     3.5    22.4    -      -       +      -
    456D  PRO*     3.7    29.1    -      -       +      +
    459D  LEU*     5.8     0.7    -      -       +      -
    464D  LEU*     6.2     0.9    -      -       +      -
    472D  GLN*     4.7    11.9    +      -       +      +
    473D  ILE      2.7    16.9    +      -       -      +
    474D  PHE*     3.3    18.7    -      -       -      +
    475D  ILE      2.8    26.0    +      -       -      -
----------------------------------------------------------
 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