Contacts of the strand formed by residues 325 - 331 (chain D) in PDB entry 4HYY


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 GLU 325 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  GLU*     4.7     2.3    -      -       -      +
    110D  LYS*     4.7     5.2    +      -       -      -
    111D  LEU*     4.7     1.6    -      -       -      -
    304D  ARG*     3.6    15.6    +      -       -      -
    312D  ILE*     3.1    28.0    -      -       +      +
    313D  ALA      3.2     5.4    -      -       -      +
    314D  LYS*     3.5    38.2    +      -       +      +
    320D  GLU      5.2     2.3    -      -       -      +
    322D  PRO*     3.1    28.8    +      -       +      +
    323D  GLU      3.3     2.6    -      -       -      +
    324D  ASN*     1.3    77.6    -      -       -      +
    326D  ALA*     1.3    61.7    +      -       -      +
    327D  THR*     5.3     1.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 326 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  GLU*     3.4    42.8    -      -       +      +
    108D  PHE*     4.0     8.3    -      -       -      +
    110D  LYS*     4.7     2.0    -      -       +      -
    111D  LEU*     4.2    14.7    -      -       +      +
    311D  ARG      3.5     4.9    -      -       -      +
    312D  ILE*     3.6     4.3    -      -       -      +
    313D  ALA*     3.1    32.5    +      -       +      +
    325D  GLU*     1.3    75.3    -      -       -      +
    327D  THR*     1.3    64.4    +      -       -      +
    328D  PHE*     3.9     2.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 327 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105D  SER*     4.4     0.9    +      -       -      -
    107D  GLU*     3.6    27.7    +      -       -      +
    310D  LEU*     4.6    16.6    -      -       +      -
    311D  ARG      3.6     9.2    -      -       -      +
    312D  ILE*     3.6    16.5    -      -       +      +
    325D  GLU      5.3     0.9    +      -       -      -
    326D  ALA*     1.3    74.3    -      -       -      +
    328D  PHE*     1.3    64.6    +      -       -      +
    337D  ASP*     4.7     1.6    -      -       -      +
    338D  ALA*     3.8    32.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 328 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105D  SER*     3.7    18.8    -      -       -      +
    108D  PHE*     4.1    23.8    -      +       +      -
    131D  GLY*     4.7     7.2    -      -       -      -
    135D  LEU*     6.1     0.9    -      -       +      -
    303D  LEU*     4.0    28.0    -      -       +      -
    310D  LEU*     3.8     2.4    -      -       -      -
    311D  ARG*     3.0    64.0    +      -       +      +
    312D  ILE      4.1     3.4    -      -       -      -
    313D  ALA*     4.2     2.2    -      -       +      -
    326D  ALA*     4.4     6.3    -      -       +      -
    327D  THR*     1.3    78.5    -      -       -      +
    329D  ALA*     1.3    65.6    +      -       -      +
    330D  ILE*     3.7    17.3    -      -       +      -
    335D  ILE*     3.5    34.1    -      -       +      -
    336D  GLY      3.2    15.3    -      -       -      +
    338D  ALA*     4.3     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 329 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309D  GLU*     3.4    32.8    -      -       -      +
    310D  LEU*     4.7     4.0    -      -       -      -
    311D  ARG      4.7     0.2    -      -       -      +
    328D  PHE*     1.3    80.8    -      -       -      +
    330D  ILE*     1.3    65.4    +      -       -      +
    331D  THR*     4.2     4.8    +      -       +      -
    335D  ILE*     3.7     0.7    -      -       -      -
    336D  GLY*     3.0    32.4    +      -       -      +
    337D  ASP      4.1    14.1    -      -       -      +
    338D  ALA*     4.1     9.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 330 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131D  GLY*     4.4     7.6    -      -       -      -
    134D  GLN*     3.3    36.6    -      -       +      +
    309D  GLU*     3.3    31.8    +      -       +      +
    311D  ARG*     4.2    26.9    -      -       +      +
    328D  PHE*     3.7    23.3    -      -       +      -
    329D  ALA*     1.3    77.4    -      -       -      +
    331D  THR*     1.3    65.6    +      -       -      +
    334D  GLY      4.4     2.7    -      -       -      -
    335D  ILE*     4.2    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 331 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134D  GLN*     4.2     3.4    +      -       -      -
    169D  ARG*     3.4     5.8    +      -       -      -
    176D  ARG*     5.1     1.2    +      -       -      -
    309D  GLU*     4.1    12.6    -      -       -      +
    329D  ALA*     4.8     6.1    +      -       +      -
    330D  ILE*     1.3    83.7    -      -       -      +
    332D  ALA*     1.3    58.7    +      -       -      +
    333D  GLY*     3.8     7.4    +      -       -      -
    334D  GLY*     2.7    43.5    +      -       -      -
    336D  GLY*     4.9     3.3    +      -       -      -
----------------------------------------------------------
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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