Contacts of the strand formed by residues 801 - 803 (chain C) in PDB entry 5UHF


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 801 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    773C  ILE*     4.1    12.3    -      -       +      -
    776C  ILE*     4.4     9.4    -      -       +      -
    780C  VAL*     3.9    32.3    +      -       +      +
    781C  LEU*     4.1    22.9    -      -       +      -
    783C  ASP*     6.2     0.2    -      -       -      +
    784C  LEU*     4.2    23.7    -      -       +      +
    790C  VAL*     4.9     2.4    -      -       -      +
    796C  VAL*     4.7     4.5    -      -       -      +
    799C  GLY      5.1     0.9    -      -       -      +
    800C  ASP*     1.3    82.3    -      -       -      +
    802C  LEU*     1.3    69.5    +      -       -      +
    803C  VAL      4.1     5.6    -      -       -      +
    804C  GLY*     4.1    10.5    -      -       -      +
    836C  SER*     3.2    27.1    -      -       -      +
    837C  LEU      4.0     2.0    -      -       -      -
    838C  LYS*     4.4    17.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 802 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    755C  HIS*     4.1    39.0    -      -       +      -
    784C  LEU*     4.5     1.0    -      -       -      +
    788C  GLY      4.0     1.3    -      -       -      +
    789C  ILE*     3.9     1.2    -      -       -      -
    790C  VAL*     3.2    34.3    +      -       +      +
    796C  VAL*     3.6    31.6    -      -       +      -
    801C  ILE*     1.3    74.7    -      -       -      +
    803C  VAL*     1.3    68.8    +      -       +      +
    804C  GLY      4.1     0.7    -      -       -      -
    837C  LEU*     2.8    29.3    +      -       +      +
    838C  LYS      4.6     0.4    -      -       -      +
    839C  VAL*     3.7    30.3    -      -       +      -
    871C  VAL*     4.1    23.6    -      -       +      -
    873C  VAL*     4.7     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 803 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    757C  ILE*     3.7    28.4    -      -       +      +
    769C  ILE*     3.6    27.6    -      -       +      -
    788C  GLY      4.0     2.2    -      -       -      -
    789C  ILE*     3.7    11.7    -      -       +      -
    801C  ILE*     4.2     0.2    -      -       -      -
    802C  LEU*     1.3    86.4    -      -       +      +
    804C  GLY*     1.3    55.2    +      -       -      +
    805C  LYS*     2.9     9.2    +      -       +      +
    836C  SER*     2.6    19.5    +      -       -      -
    837C  LEU*     3.2    17.4    +      -       +      -
    869C  VAL*     3.6    33.4    -      -       +      +
    871C  VAL*     3.8    13.2    -      -       +      -
----------------------------------------------------------
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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