Contacts of the strand formed by residues 116 - 121 (chain D) in PDB entry 4PEI


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 CYS 116 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101D  TYR      4.8     3.6    -      -       -      +
    102D  ASN*     6.0     0.9    -      -       -      -
    113D  LEU      3.7     5.6    -      -       -      +
    114D  GLY      4.0     2.5    -      -       -      -
    115D  VAL*     1.3    85.3    +      -       -      +
    117D  SER*     1.3    68.8    +      -       -      +
    128D  GLY      3.2    16.6    -      -       -      +
    129D  VAL*     4.5     2.0    -      -       -      -
    160D  TYR*     5.4     1.3    -      -       -      -
    161D  VAL*     3.8    29.2    -      -       +      -
    164D  MET*     4.1    14.8    -      -       -      -
    165D  LEU*     3.9    18.8    -      -       +      -
    275D  TRP*     3.1    32.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 117 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102D  ASN      6.3     1.3    -      -       -      -
    111D  TYR*     5.1     2.4    +      -       -      -
    113D  LEU*     2.8    34.9    +      -       -      +
    116D  CYS*     1.3    80.9    -      -       -      +
    118D  CYS*     1.3    64.6    +      -       -      +
    119D  ILE*     4.4     4.2    -      -       -      +
    126D  ILE      4.0     0.2    -      -       -      +
    127D  VAL*     3.2     6.4    -      -       -      +
    128D  GLY*     2.9    27.6    +      -       -      +
    165D  LEU*     4.3     6.3    -      -       -      -
    275D  TRP*     3.3    34.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 118 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  SER*     1.3    78.1    +      -       -      +
    119D  ILE*     1.3    73.5    +      -       -      +
    125D  ARG*     4.1    11.0    -      -       -      -
    126D  ILE      3.1    17.3    -      -       -      -
    127D  VAL*     3.9    18.6    -      -       +      -
    168D  LEU*     4.1     8.7    -      -       +      -
    174D  ILE*     4.2     7.9    -      -       -      -
    271D  TYR*     4.7     0.9    -      -       -      -
    272D  ASP*     3.3    44.7    +      -       +      +
    275D  TRP*     3.7    23.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 119 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85D  LEU*     4.0    14.1    -      -       +      -
    111D  TYR*     4.0    18.4    -      -       +      +
    113D  LEU*     4.1    17.5    -      -       +      -
    117D  SER*     4.4     4.0    -      -       -      +
    118D  CYS*     1.3    77.9    -      -       -      +
    120D  ASN*     1.3    85.9    +      -       -      +
    121D  ILE*     3.8    16.8    -      -       +      +
    125D  ARG*     3.6     1.0    -      -       -      -
    126D  ILE*     2.7    59.3    +      -       +      +
    269D  LEU*     3.9    13.7    -      -       +      -
    270D  GLU      3.6     7.6    -      -       -      +
    271D  TYR*     5.3     1.1    -      -       +      -
    272D  ASP*     4.1     0.7    -      -       -      +
    326D  ILE*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 120 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119D  ILE*     1.3    83.2    -      -       -      +
    121D  ILE*     1.3    63.0    +      -       -      +
    123D  GLY*     6.1     1.6    -      -       -      +
    124D  LEU      3.4     6.7    -      -       -      +
    125D  ARG*     3.8    11.9    -      -       -      +
    267D  THR*     5.9     2.2    -      -       +      -
    268D  ASP      3.7     2.4    -      -       -      +
    269D  LEU*     3.4     2.6    -      -       -      +
    270D  GLU*     2.7    56.0    +      -       +      +
    271D  TYR      3.9     4.8    +      -       -      -
    272D  ASP*     2.9    40.1    +      -       -      +
    273D  LYS*     4.3    16.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 121 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  SER      5.6     0.7    -      -       -      +
     39D  PHE*     3.5    48.2    -      -       +      -
     83D  LEU*     3.8    29.2    -      -       +      -
     85D  LEU*     4.5     2.9    -      -       +      -
    119D  ILE*     3.8    18.4    -      -       +      +
    120D  ASN*     1.3    75.8    -      -       -      +
    122D  ASN*     1.3    71.4    +      -       -      +
    123D  GLY      3.1     2.5    -      -       -      -
    124D  LEU*     2.8    34.2    +      -       +      +
    126D  ILE*     4.0     7.2    -      -       +      -
    267D  THR*     3.6    16.4    -      -       -      +
    268D  ASP*     4.4     1.3    -      -       -      -
    269D  LEU*     4.4    11.9    -      -       +      +
----------------------------------------------------------
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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