Contacts of the strand formed by residues 368 - 370 (chain A) in PDB entry 4X4R


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 PHE 368 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  ARG*     4.1    14.1    -      -       +      -
    366A  ARG*     4.6     3.6    -      -       -      +
    367A  PRO*     1.3    78.0    -      -       +      +
    369A  ILE*     1.3    71.3    +      -       -      +
    370A  GLU*     3.5    25.6    -      -       +      -
    374A  TRP*     3.4     9.9    -      -       -      -
    375A  TRP*     2.8    71.8    +      +       +      +
    376A  ALA      4.6     1.6    -      -       -      -
    377A  PHE*     3.4    44.2    -      +       -      -
    237C  ARG*     5.8     0.9    -      -       -      +
    317C  ARG*     3.6    47.3    -      -       +      +
    431C  GLU*     6.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 369 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349A  PHE*     5.5     0.7    -      -       +      -
    368A  PHE*     1.3    79.6    -      -       -      +
    370A  GLU*     1.3    66.6    +      -       -      +
    372A  GLY      4.4     1.1    -      -       -      +
    373A  ARG*     3.5    20.2    -      -       -      +
    374A  TRP*     3.6    44.2    -      -       +      +
    233C  ASP*     4.0    19.3    -      -       -      +
    236C  ALA*     4.0    22.4    -      -       +      +
    237C  ARG*     3.8    65.3    +      -       +      +
    240C  HIS*     5.1     1.3    -      -       +      -
    317C  ARG*     4.5     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 370 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  ARG*     3.0    41.0    +      -       -      +
    368A  PHE*     3.5    11.9    -      -       +      -
    369A  ILE*     1.3    77.0    -      -       -      +
    371A  ASN*     1.3    90.2    +      -       +      +
    372A  GLY      2.9     2.9    +      -       -      -
    373A  ARG*     2.9    22.1    +      -       -      +
    375A  TRP*     3.6    21.7    +      -       +      +
    233C  ASP*     3.8     3.6    -      -       -      -
    305C  PHE*     5.7     3.1    -      -       -      -
    316C  LEU      4.6     0.2    -      -       -      +
    317C  ARG*     4.4     8.4    +      -       -      +
----------------------------------------------------------
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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