Contacts of the strand formed by residues 263 - 268 (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 ALA 263 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99D  PHE*     4.5     0.2    -      -       +      -
    101D  ILE*     4.0    15.9    -      -       +      -
    116D  ILE*     3.8    21.1    -      -       +      +
    117D  GLU      3.5    24.2    -      -       -      +
    118D  SER*     3.7     9.8    -      -       -      +
    218D  LYS      2.9    13.9    +      -       -      +
    219D  LEU*     3.3     5.2    -      -       +      +
    220D  LEU*     2.8    26.2    +      -       -      +
    262D  VAL*     1.3    70.7    -      -       -      +
    264D  VAL*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 264 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116D  ILE*     4.5     2.3    -      -       -      +
    120D  ALA      3.3     9.5    +      -       -      +
    121D  ILE*     3.9    25.4    -      -       +      -
    122D  THR*     2.9    32.6    +      -       -      +
    220D  LEU*     3.1    20.6    -      -       +      +
    222D  ILE*     5.0     1.3    -      -       +      -
    253D  LEU*     4.1    21.8    -      -       +      +
    257D  SER*     3.3    37.9    -      -       -      +
    262D  VAL*     4.2     6.5    -      -       +      +
    263D  ALA*     1.3    76.5    -      -       -      +
    265D  PHE*     1.3    56.1    +      -       -      +
    266D  VAL*     4.0    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 265 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116D  ILE*     4.3    13.9    -      -       +      -
    122D  THR*     3.3    26.0    -      -       +      -
    124D  ALA*     3.8    25.1    -      -       +      -
    132D  LYS      4.5     0.7    -      -       -      -
    135D  LEU*     3.4    34.3    -      -       +      -
    136D  SER*     3.7    23.3    -      -       -      -
    139D  LEU*     3.6    31.9    -      -       +      -
    219D  LEU*     4.1    12.1    -      -       +      -
    220D  LEU      2.8     8.5    +      -       -      +
    221D  ILE*     3.3    17.4    -      -       +      -
    222D  ILE      3.0    24.3    +      -       -      +
    263D  ALA      4.0     1.2    +      -       -      -
    264D  VAL*     1.3    71.5    -      -       -      +
    266D  VAL*     1.3    68.0    +      -       -      +
    267D  THR*     3.9    14.1    -      -       +      -
    301D  ILE*     5.9     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 266 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121D  ILE*     4.2    13.0    -      -       +      -
    122D  THR      2.8     8.8    +      -       -      +
    123D  GLU*     3.8    27.4    -      -       +      -
    124D  ALA*     2.8    32.1    +      -       -      -
    222D  ILE*     3.3    24.9    -      -       +      +
    225D  ILE*     3.9    31.2    -      -       +      -
    253D  LEU*     4.6     1.1    -      -       +      -
    264D  VAL*     4.0    19.5    -      -       +      -
    265D  PHE*     1.3    86.4    -      -       -      +
    267D  THR*     1.3    59.9    +      -       -      +
    293D  LEU*     5.6     1.8    -      -       +      -
    297D  SER*     5.0     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 267 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  ALA      3.1     6.7    -      -       -      +
    132D  LYS*     3.9    31.2    -      -       +      +
    136D  SER*     3.8    20.0    -      -       -      +
    222D  ILE      3.3     3.4    +      -       -      +
    223D  ASP*     2.4    36.6    +      -       +      +
    224D  SER*     3.0    14.7    -      -       -      -
    225D  ILE*     3.0    30.9    +      -       -      +
    265D  PHE*     3.9    12.1    -      -       +      -
    266D  VAL*     1.3    77.1    -      -       -      +
    268D  ASN*     1.3    62.2    +      -       -      +
    269D  GLN*     5.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 268 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123D  GLU*     3.8    13.8    -      -       +      +
    124D  ALA      2.9     7.4    +      -       -      +
    125D  PHE*     3.5    22.8    -      -       +      +
    126D  GLY      3.6     1.6    -      -       -      +
    132D  LYS*     3.4    22.0    +      -       -      +
    225D  ILE*     3.5    19.9    -      -       +      +
    226D  MET*     3.6     5.9    -      -       -      +
    267D  THR*     1.3    73.7    +      -       -      +
    269D  GLN*     1.3    83.3    +      -       -      +
    287D  PRO*     4.4     1.4    -      -       -      +
    288D  ILE*     3.0    49.9    +      -       -      +
    293D  LEU*     3.5    13.3    -      -       -      +
----------------------------------------------------------
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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