Contacts of the strand formed by residues 735 - 738 (chain C) in PDB entry 5UHE


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 735 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    729C  HIS      4.4     0.2    -      -       -      -
    733C  ASP      3.9     8.1    -      -       -      +
    734C  ALA*     1.3    81.0    -      -       -      +
    736C  ILE*     1.3    68.8    +      -       -      +
    737C  LEU*     4.3     1.1    -      -       +      -
    885C  LEU*     3.7    24.0    -      -       +      +
    891C  ASN      5.2     2.5    -      -       -      +
    892C  LYS      4.4     5.2    -      -       -      +
    893C  GLY*     3.5    25.6    -      -       -      +
    894C  VAL      2.8    16.8    +      -       -      +
    895C  ILE*     3.5    19.3    -      -       +      +
    896C  GLY*     2.6    30.3    +      -       -      -
    897C  LYS      3.5     1.2    +      -       -      -
    915C  ILE*     3.6    31.9    -      -       +      -
    916C  ILE      4.6     1.8    -      -       -      -
    917C  LEU*     4.3    17.0    -      -       +      -
   1030C  ILE*     6.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 736 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    726C  TRP*     3.8    29.6    -      -       +      +
    729C  HIS*     3.5    39.3    -      -       +      +
    730C  ASN*     3.7    22.7    -      -       +      +
    735C  ILE*     1.3    74.1    -      -       -      +
    737C  LEU*     1.3    67.3    +      -       -      +
    897C  LYS*     3.5    16.8    -      -       +      +
    899C  LEU*     3.7    31.0    -      -       +      -
    915C  ILE*     3.4     6.8    -      -       -      +
    916C  ILE*     3.0    45.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 737 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    719C  LEU*     4.9     0.9    -      -       +      -
    735C  ILE*     4.3     1.3    -      -       +      -
    736C  ILE*     1.3    81.9    -      -       -      +
    738C  SER*     1.3    63.5    +      -       -      +
    741C  LEU*     3.7    21.5    -      -       +      -
    747C  LEU*     4.1     6.5    -      -       +      -
    879C  ILE*     3.7    32.5    -      -       +      -
    885C  LEU*     4.1    12.6    -      -       +      -
    895C  ILE*     3.6    33.2    -      -       +      -
    897C  LYS      2.9    11.5    +      -       -      +
    898C  ILE*     3.3    14.9    -      -       +      -
    899C  LEU*     3.1    26.0    +      -       -      +
    904C  MET*     3.7     7.3    -      -       -      +
    914C  ASP      3.5     2.7    -      -       -      +
    915C  ILE*     3.8    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 738 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    737C  LEU*     1.3    75.2    -      -       -      +
    739C  ASN*     1.3    60.7    +      -       -      +
    740C  ARG*     3.0    26.6    +      -       -      +
    741C  LEU*     3.1    21.6    +      -       -      +
    742C  VAL*     4.3     1.2    +      -       -      +
    898C  ILE*     4.2     1.9    -      -       -      +
    901C  VAL*     4.1    13.0    -      -       -      +
    904C  MET*     3.5    16.6    -      -       -      +
    912C  PRO*     5.2     1.4    -      -       -      +
    913C  VAL      3.3    25.9    +      -       -      -
    914C  ASP*     2.7    20.6    +      -       -      -
----------------------------------------------------------
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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