Contacts of the strand formed by residues 1042 - 1044 (chain C) in PDB entry 5UH8


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 HIS1042 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1040C  LYS      4.1     5.2    -      -       -      +
   1041C  ILE*     1.3    83.4    -      -       -      +
   1043C  ALA*     1.3    91.2    +      -       -      +
   1044C  ARG*     4.3     1.1    -      -       +      +
   1059C  GLY      5.0     0.2    -      -       -      -
   1060C  LYS*     3.9    37.3    +      -       +      +
   1063C  PHE*     3.9    29.2    -      +       -      -
   1064C  GLY      2.8    29.6    +      -       -      -
   1066C  GLN*     3.8    20.0    -      -       -      +
    425D  SER      5.4     0.6    +      -       -      -
    426D  GLY*     3.3     0.6    -      -       -      -
    427D  ARG*     2.8    38.7    +      -       +      +
    447D  MET*     4.4     2.3    -      -       -      +
     18G    A      4.9     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA1043 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1042C  HIS*     1.3    92.4    +      -       -      +
   1044C  ARG*     1.3    64.5    +      -       -      +
   1063C  PHE*     3.6     8.5    -      -       -      -
    425D  SER      3.8     7.9    -      -       -      -
    426D  GLY*     3.8     7.2    -      -       -      -
    446D  LEU      5.4     0.2    -      -       -      +
    447D  MET*     4.0    33.7    -      -       +      +
    450D  GLU*     3.5    18.8    -      -       +      +
    451D  LEU*     4.6     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1044 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1042C  HIS*     4.3     1.8    -      -       +      -
   1043C  ALA*     1.3    80.5    -      -       -      +
   1045C  SER*     1.3    61.5    +      -       -      +
   1046C  THR*     3.4    16.0    -      -       -      +
   1047C  GLY      3.1    21.8    +      -       -      +
   1048C  PRO*     2.6    37.4    +      -       -      +
   1049C  TYR*     4.1     4.4    -      -       -      -
   1056C  PRO*     4.0    10.9    -      -       -      +
   1057C  LEU      4.6     0.8    +      -       -      +
   1063C  PHE*     2.6    48.7    +      -       +      +
   1064C  GLY*     3.3    18.8    -      -       -      +
   1065C  GLY*     3.6    18.9    -      -       -      +
    422D  VAL      4.7     0.2    -      -       -      -
    423D  ASP*     2.9    31.0    +      -       -      +
    424D  TYR*     3.1     5.7    +      -       -      -
    425D  SER      3.1    33.8    +      -       -      +
    450D  GLU*     3.6     8.7    -      -       -      +
    451D  LEU*     4.1     2.3    -      -       -      +
----------------------------------------------------------
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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