Contacts of the strand formed by residues 838 - 841 (chain M) in PDB entry 5D4C


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 838 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564M  MET*     4.5     1.2    -      -       -      -
    567M  GLN*     4.4     3.8    +      -       -      -
    836M  GLY      3.8     0.6    +      -       -      +
    837M  ASP*     1.3    73.2    -      -       -      +
    839M  LEU*     1.3    70.1    +      -       -      +
    846M  LYS*     3.9    15.7    -      -       -      +
    847M  GLY      3.8     9.4    -      -       -      +
    848M  VAL*     4.1    12.8    -      -       +      -
    996M  LYS*     3.7     2.4    -      -       -      +
    997M  LEU*     2.9    56.1    +      -       +      +
    999M  HIS*     3.4    49.2    +      -       +      +
    741N  ASP      3.4    21.8    -      -       -      +
    742N  GLY*     4.8     5.8    -      -       -      -
   1605N    C      3.0    25.3    +      -       -      -
   1608N  ATP      3.6     9.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 839 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    688M  ILE*     4.1    20.2    -      -       +      +
    690M  ILE*     4.1    15.9    -      -       +      -
    700M  TYR*     4.6    10.5    -      -       +      -
    833M  LEU*     4.1    28.5    -      -       +      -
    837M  ASP      4.4     0.2    -      -       -      +
    838M  LYS*     1.3    82.0    -      -       -      +
    840M  ALA*     1.3    64.0    +      -       -      +
    846M  LYS*     3.4     1.6    -      -       -      +
    847M  GLY      2.9    37.4    +      -       -      +
    849M  VAL*     3.6    29.4    -      -       +      -
    869M  VAL*     5.3     3.1    -      -       +      -
    994M  ILE*     3.9    17.0    -      -       +      -
    995M  MET      3.3     6.3    -      -       -      +
    996M  LYS*     3.9    20.2    -      -       +      -
    997M  LEU*     4.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 840 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564M  MET*     3.8    19.3    -      -       +      -
    688M  ILE*     5.9     0.4    -      -       -      -
    839M  LEU*     1.3    77.3    -      -       -      +
    841M  ASN*     1.3    62.7    +      -       -      +
    845M  ASN      3.3    11.4    -      -       -      +
    846M  LYS*     3.8     2.9    -      -       +      -
    994M  ILE*     4.1     4.7    -      -       -      -
    995M  MET*     2.9    44.4    +      -       +      +
    997M  LEU*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 841 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    561M  GLY*     4.2     5.7    -      -       -      -
    564M  MET*     4.3     0.7    -      -       -      +
    840M  ALA*     1.3    81.5    -      -       -      +
    842M  ARG*     1.3    64.6    +      -       -      +
    843M  HIS*     3.0    15.9    +      -       +      -
    844M  GLY      3.3     5.0    +      -       -      -
    845M  ASN*     2.9    42.3    +      -       -      +
    871M  LEU*     4.8     0.8    -      -       -      +
    884M  GLN*     2.8    33.9    +      -       -      +
    992M  MET*     3.5    27.8    -      -       +      -
    993M  PHE      3.5    19.5    -      -       -      +
    994M  ILE*     4.3     4.0    -      -       +      +
    995M  MET*     4.0     6.7    -      -       -      +
----------------------------------------------------------
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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