Contacts of the strand formed by residues 470 - 474 (chain A) in PDB entry 1DY7


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 VAL 470 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438A  LEU*     4.0     5.6    -      -       -      -
    455A  TYR*     4.1     8.7    -      -       +      -
    456A  VAL      3.5    17.5    -      -       -      +
    457A  ASP*     4.2    10.8    -      -       +      -
    469A  SER*     1.3    82.3    -      -       -      +
    471A  ALA*     1.3    76.5    +      -       -      +
    472A  VAL*     3.9     2.2    +      -       +      -
    488A  LYS      3.6     0.2    -      -       -      +
    489A  THR*     3.5     3.8    -      -       -      -
    490A  LEU*     2.9    34.6    +      -       +      +
    492A  ILE*     4.1    13.2    -      -       +      -
    505A  VAL*     3.8    19.1    -      -       +      -
    519A  PHE*     3.7    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    437A  ALA*     4.1    10.1    -      -       +      -
    438A  LEU*     4.0    25.1    -      -       +      +
    454A  LEU      3.6     1.3    -      -       -      +
    455A  TYR*     3.3     4.3    -      -       -      -
    456A  VAL*     2.8    39.6    +      -       +      +
    470A  VAL*     1.3    74.8    -      -       -      +
    472A  VAL*     1.3    59.5    +      -       -      +
    473A  PHE*     4.2     6.3    -      -       +      -
    487A  PHE*     3.7    25.1    -      -       +      -
    488A  LYS      3.5     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453A  TYR*     3.5    40.1    -      -       +      -
    454A  LEU      3.3     5.4    -      -       -      +
    455A  TYR*     3.5    27.1    -      -       +      -
    470A  VAL*     4.3     2.9    -      -       +      +
    471A  ALA*     1.3    79.2    -      -       -      +
    473A  PHE*     1.3    62.0    +      -       -      +
    474A  ASP      4.1     0.7    +      -       -      -
    487A  PHE*     3.3     5.3    -      -       -      +
    488A  LYS*     2.8    41.7    +      -       +      +
    490A  LEU*     3.6    32.8    -      -       +      -
    539A  LEU*     4.0    13.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    414A  VAL*     4.5     0.4    -      -       +      -
    435A  PHE*     3.6    29.2    -      +       -      -
    436A  PRO      3.4    18.4    -      -       -      -
    437A  ALA*     3.9    12.1    -      -       +      -
    453A  TYR*     3.3    10.7    -      -       -      -
    454A  LEU*     2.9    46.9    +      -       +      +
    456A  VAL*     3.9    24.5    -      -       +      -
    471A  ALA*     4.3     3.1    -      -       +      -
    472A  VAL*     1.3    76.1    -      -       -      +
    474A  ASP*     1.3    60.2    +      -       -      +
    475A  ILE      3.4     1.9    +      -       -      -
    478A  MET*     3.7    19.3    -      -       +      -
    485A  PRO*     3.6    31.6    -      -       +      -
    486A  GLU      3.5    16.8    -      -       -      +
    487A  PHE*     3.7    21.8    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASP 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452A  GLN*     2.9    30.9    -      -       -      +
    453A  TYR*     3.9    17.9    +      -       +      -
    472A  VAL      4.1     1.0    +      -       -      -
    473A  PHE*     1.3    70.6    -      -       -      +
    475A  ILE*     1.3    65.1    +      -       -      +
    476A  LYS*     3.0    14.6    +      -       -      +
    477A  ALA*     3.1    30.2    +      -       +      +
    478A  MET*     3.5    12.8    +      -       -      +
    485A  PRO*     6.1     0.2    -      -       -      +
    486A  GLU      4.6     4.4    +      -       -      -
----------------------------------------------------------
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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