Contacts of the strand formed by residues 321 - 325 (chain B) in PDB entry 2E4Y


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 ILE 321 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  ILE*     4.2    17.5    -      -       +      -
    208B  PHE*     5.4     1.6    -      -       +      -
    210B  TRP*     4.6     8.7    -      -       +      -
    296B  THR*     5.5     3.0    -      -       +      +
    297B  TRP      2.5    17.3    +      -       -      +
    298B  VAL*     2.9    21.9    -      -       +      +
    299B  ALA      2.8    22.3    +      -       -      +
    319B  GLY      5.3     0.4    -      -       -      +
    320B  ALA*     1.3    78.7    -      -       -      +
    322B  THR*     1.3    65.2    +      -       -      +
    323B  LEU*     5.6     1.3    -      -       +      -
    468B  VAL*     4.0    22.4    -      -       +      -
    469B  PHE      3.1    15.5    -      -       -      +
    470B  ASN*     4.7     4.3    -      -       +      +
    483B  VAL*     5.8     0.9    -      -       +      -
    492B  LEU*     5.8     1.6    -      -       +      -
    497B  ILE*     4.4    17.0    -      -       +      -
    499B  TRP*     3.6    37.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297B  TRP      4.8     2.0    -      -       -      +
    299B  ALA*     3.2    32.1    -      -       +      -
    303B  TRP*     3.5    31.4    -      -       +      +
    304B  GLY      2.7    25.4    +      -       -      -
    320B  ALA*     4.2     2.5    +      -       +      -
    321B  ILE*     1.3    79.7    -      -       -      +
    323B  LEU*     1.3    63.8    +      -       -      +
    469B  PHE*     2.8    43.5    +      -       -      +
    471B  LEU*     5.6     1.3    +      -       +      +
    480B  TYR*     3.6    13.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197B  GLN*     4.1    20.0    -      -       +      +
    200B  ALA*     3.9    24.7    -      -       +      +
    201B  MET*     3.4    36.3    -      -       +      +
    204B  ILE*     4.2     8.5    -      -       +      -
    299B  ALA      2.9    12.5    +      -       -      +
    301B  ASP*     3.0    25.8    +      -       -      -
    304B  GLY*     3.4    10.4    -      -       -      -
    321B  ILE*     5.7     1.3    -      -       +      -
    322B  THR*     1.3    74.6    -      -       -      +
    324B  GLU*     1.3    61.8    +      -       -      +
    466B  TYR*     4.8     8.5    -      -       +      -
    467B  ASN      3.4    15.9    -      -       -      +
    468B  VAL*     3.5    34.8    -      -       +      -
    486B  TRP*     5.8     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  ARG*     4.0    12.8    +      -       -      -
    301B  ASP*     3.6     9.5    -      -       -      +
    304B  GLY*     3.8    19.5    -      -       -      -
    305B  ALA*     4.0    10.6    +      -       +      +
    306B  GLN*     5.8     0.2    -      -       -      +
    323B  LEU*     1.3    75.6    -      -       -      +
    325B  LEU*     1.3    84.7    +      -       -      +
    387B  GLU*     4.9     0.9    -      -       -      +
    388B  SER*     3.1    37.3    +      -       -      +
    389B  LYS*     3.0    27.1    +      -       -      +
    466B  TYR*     3.1     9.1    -      -       -      +
    467B  ASN*     2.7    35.1    +      -       +      +
    469B  PHE*     4.6    17.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  THR*     4.5    10.3    -      -       +      -
    191B  VAL*     3.7    37.2    -      -       +      -
    192B  PRO*     4.1    12.8    -      -       +      -
    197B  GLN*     5.2     2.9    -      -       -      +
    301B  ASP*     5.1     5.4    -      -       +      +
    324B  GLU*     1.3   102.0    +      -       +      +
    326B  ALA*     1.3    62.5    +      -       -      +
    327B  SER*     3.2     9.9    +      -       -      -
    388B  SER*     3.9     0.7    +      -       -      +
    389B  LYS*     4.0    16.6    -      -       -      +
    392B  PHE*     3.7    23.1    -      -       +      -
    465B  ARG      3.7     2.7    -      -       -      +
    466B  TYR*     3.2    37.5    -      -       +      -
    467B  ASN*     3.8     7.0    +      -       -      -
----------------------------------------------------------
 Back to top of page


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