Contacts of the strand formed by residues 324 - 328 (chain B) in PDB entry 4HXG


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 324 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ALA      6.1     0.2    -      -       -      -
     17B  LEU*     4.2     3.1    -      -       -      +
    315B  LEU*     3.3     7.2    -      -       -      -
    316B  LYS      2.9    29.7    +      -       -      +
    321B  ARG*     3.4    18.6    +      -       +      +
    322B  PRO      3.6     7.4    -      -       -      +
    323B  ALA*     1.3    79.7    -      -       -      +
    325B  LEU*     1.3    59.4    +      -       -      +
    326B  TYR*     3.2    23.1    -      -       +      +
    334B  GLN*     4.5     4.3    -      -       -      +
    336B  THR*     2.8    34.8    +      -       -      +
    337B  ASP*     3.9     2.2    -      -       -      -
    338B  TYR*     2.9    37.0    +      -       -      +
    339B  ASN*     3.2    20.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU*     4.3     4.2    -      -       +      +
     20B  PRO*     4.4     3.8    -      -       +      -
     27B  VAL*     3.5    29.8    -      -       +      -
     29B  TYR*     3.9    23.8    -      -       +      -
     48B  GLU*     5.5     1.6    -      -       -      +
    313B  ILE*     3.9    14.6    -      -       +      -
    314B  TYR      3.5    28.0    -      -       -      +
    315B  LEU*     3.7    20.7    -      -       +      +
    324B  GLU*     1.3    74.7    -      -       -      +
    326B  TYR*     1.3    66.3    +      -       -      +
    334B  GLN*     3.9     1.7    -      -       -      +
    335B  LEU*     2.9    40.1    +      -       +      +
    336B  THR*     3.2    25.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313B  ILE*     3.2     8.5    -      -       -      +
    314B  TYR*     2.8    58.1    +      +       +      +
    316B  LYS*     3.3    45.4    +      -       +      +
    318B  THR*     5.8     1.9    -      -       -      +
    324B  GLU*     3.2    33.9    -      -       +      +
    325B  LEU*     1.3    73.6    -      -       -      +
    327B  LEU*     1.3    60.8    +      -       -      +
    332B  GLU*     3.5    26.5    -      -       +      -
    333B  ARG      3.6     3.4    -      -       -      +
    334B  GLN*     3.3    52.5    +      -       +      -
    335B  LEU*     3.9     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  LEU*     4.5    11.2    -      -       +      -
    311B  ARG*     3.6    37.2    -      -       +      +
    312B  LEU      3.3    28.3    -      -       -      +
    313B  ILE*     3.6    13.0    -      -       +      -
    314B  TYR*     4.7     2.0    -      -       -      -
    326B  TYR*     1.3    75.6    -      -       -      +
    328B  TRP*     1.3    69.5    +      -       -      +
    329B  ASP*     4.0    10.0    +      -       +      +
    331B  GLU      3.9     0.7    -      -       -      +
    332B  GLU*     3.7     1.6    -      -       -      +
    333B  ARG*     2.8    44.6    +      -       +      +
    335B  LEU*     3.6    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275B  TYR*     6.3     0.7    -      +       -      -
    288B  LEU*     5.4     6.3    -      -       +      -
    295B  GLU      5.1     2.9    -      -       -      -
    296B  ILE*     3.7    59.3    +      -       +      -
    311B  ARG*     5.6     0.2    -      -       -      -
    312B  LEU*     3.0    35.8    +      -       +      +
    314B  TYR*     3.9    19.5    -      -       +      +
    327B  LEU*     1.3    76.9    -      -       -      +
    329B  ASP*     1.3    58.8    +      -       -      +
    330B  GLY*     3.3    40.0    +      -       -      -
    331B  GLU*     4.0     1.3    -      -       -      +
    332B  GLU*     3.7    28.4    -      -       +      +
----------------------------------------------------------
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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