Contacts of the strand formed by residues 721 - 727 (chain D) in PDB entry 2JDQ


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 LYS 721 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438B  LYS*     4.8    20.3    -      -       -      +
    509B  GLU*     4.2    12.1    +      -       -      -
    697D  LEU*     3.6    31.0    -      -       +      +
    704D  TYR*     3.5    56.9    +      -       +      +
    716D  LEU*     4.4     2.5    -      -       -      +
    719D  GLY      5.2     3.1    -      -       -      +
    720D  GLU*     1.3    87.1    -      -       -      +
    722D  ALA*     1.3    63.4    +      -       -      +
    733D  LEU*     4.0    13.7    -      -       +      -
    734D  VAL      3.3     7.2    -      -       -      +
    735D  MET*     4.3    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 722 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    704D  TYR*     4.5     7.6    -      -       -      +
    708D  LEU*     3.6    23.8    -      -       +      -
    713D  LEU*     5.1     0.2    -      -       +      -
    716D  LEU*     3.6    28.0    -      -       +      +
    721D  LYS*     1.3    78.1    -      -       -      +
    723D  ASN*     1.3    62.0    +      -       -      +
    733D  LEU*     3.5     8.2    -      -       -      +
    734D  VAL*     2.9    37.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 723 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    700D  GLU*     3.4    19.5    -      -       +      +
    701D  ASP      3.0    43.1    +      -       -      -
    702D  ARG      4.3     0.2    -      -       -      +
    704D  TYR*     3.9     8.5    +      -       -      +
    705D  GLY      2.8    25.0    +      -       -      +
    706D  PRO      4.1     1.4    +      -       -      +
    707D  ALA*     3.9    11.4    -      -       -      +
    708D  LEU*     2.7    37.0    +      -       -      +
    722D  ALA*     1.3    74.3    -      -       -      +
    724D  VAL*     1.3    56.7    +      -       -      +
    731D  VAL*     3.9    13.7    -      -       +      -
    732D  VAL      3.4     3.1    -      -       -      -
    733D  LEU*     3.5    14.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 724 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707D  ALA*     4.3     0.2    -      -       -      -
    708D  LEU      3.5    11.4    -      -       -      +
    709D  SER      3.9    10.3    -      -       -      +
    710D  ILE*     4.3     5.8    -      -       +      +
    713D  LEU*     3.6    36.3    -      -       +      -
    722D  ALA      3.9     0.4    -      -       -      +
    723D  ASN*     1.3    76.5    -      -       -      +
    725D  LEU*     1.3    63.2    +      -       -      +
    726D  ILE*     3.2    22.9    +      -       +      +
    731D  VAL*     3.2     6.4    -      -       -      +
    732D  VAL      2.8    33.5    +      -       -      +
    734D  VAL*     3.3    39.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 725 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707D  ALA*     3.9    10.7    -      -       +      +
    708D  LEU      3.0    17.8    +      -       -      +
    709D  SER*     5.3     2.4    -      -       -      -
    710D  ILE*     4.7    12.1    +      -       -      +
    724D  VAL*     1.3    74.0    -      -       -      +
    726D  ILE*     1.3    62.8    +      -       -      +
    727D  GLY*     3.2    30.7    -      -       -      +
    728D  GLN      3.6    12.8    -      -       -      +
    729D  GLY*     4.5     1.6    -      -       -      -
    730D  ASP      3.9     2.7    -      -       -      +
    731D  VAL*     3.5    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 726 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    691D  LEU*     3.8    43.3    -      -       +      -
    696D  ILE*     5.7     2.0    -      -       +      -
    710D  ILE*     4.8    11.9    -      -       +      +
    724D  VAL*     3.9    18.4    -      -       +      -
    725D  LEU*     1.3    71.9    -      -       -      +
    727D  GLY*     1.3    57.0    +      -       -      +
    730D  ASP*     2.9    25.2    +      -       -      +
    732D  VAL*     3.4    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 727 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    725D  LEU*     3.2    16.3    -      -       -      +
    726D  ILE*     1.3    80.0    -      -       -      +
    728D  GLN*     1.3    79.2    +      -       -      +
    730D  ASP*     2.7    17.5    +      -       -      +
----------------------------------------------------------
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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