Contacts of the strand formed by residues 27 - 30 (chain F) in PDB entry 5U0A


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 THR 27 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25F  PRO*     3.3    17.9    +      -       +      +
     26F  LYS*     1.3    75.9    -      -       -      +
     28F  VAL*     1.3    63.5    +      -       -      +
     29F  VAL*     5.6     2.6    -      -       -      +
     34F  GLU*     3.2    39.3    +      -       +      +
     35F  ARG      3.5     4.5    -      -       -      -
     36F  THR*     4.0    13.7    -      -       -      +
     37F  ARG*     3.9    11.6    +      -       -      +
    197F  THR      5.7     1.3    -      -       -      +
    199F  VAL*     4.6     9.6    -      -       +      -
     14G  TYR*     4.8     0.7    -      -       -      -
    200G  GLU*     3.5    15.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 28 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27F  THR*     1.3    71.5    -      -       -      +
     29F  VAL*     1.3    67.3    +      -       -      +
     30F  TYR*     3.2    27.8    +      -       +      +
     34F  GLU*     4.3     0.7    -      -       -      -
     35F  ARG*     2.7    37.1    +      -       +      +
     37F  ARG*     3.3    37.7    -      -       +      +
    190F  HIS*     5.8     0.7    -      -       +      -
    192F  PHE*     4.7    11.9    -      -       +      -
     14G  TYR*     3.5    33.2    -      -       +      -
    200G  GLU*     4.5     5.4    -      -       +      +
    228G  ALA*     4.5     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 29 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27F  THR*     5.6     2.9    -      -       -      +
     28F  VAL*     1.3    76.9    -      -       -      +
     30F  TYR*     1.3    56.5    +      -       -      +
     31F  GLY      4.1     0.7    +      -       -      -
     32F  GLY*     4.2    26.2    +      -       -      +
     33F  LYS      3.8     7.0    -      -       -      +
     34F  GLU*     4.1    14.8    -      -       +      +
    195G  HIS*     5.8     2.3    +      -       -      -
    198G  THR*     5.4     8.7    -      -       +      -
    200G  GLU*     3.1    27.1    +      -       -      +
    228G  ALA*     5.2     6.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 30 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28F  VAL*     3.2    21.6    +      -       +      -
     29F  VAL*     1.3    72.5    -      -       -      +
     31F  GLY*     1.3    69.1    +      -       -      +
     32F  GLY      3.1     0.2    -      -       -      -
     33F  LYS      2.9    20.9    +      -       -      +
     35F  ARG*     3.1    44.9    +      -       -      -
    192F  PHE*     3.7    29.4    -      +       +      -
    297F  ALA*     2.9    27.1    +      -       -      +
    298F  PRO*     3.5     3.8    -      -       -      +
    300F  PHE      3.8     0.7    -      -       -      -
    301F  GLU*     3.3    37.5    -      -       +      +
     11G  THR*     4.2     8.9    +      -       -      -
     12G  LEU      4.5     5.6    -      -       -      -
     13G  PRO*     4.3    22.3    -      -       +      +
    228G  ALA*     4.0    19.3    -      -       +      -
    229G  GLY*     5.0     6.3    -      -       -      -
    230G  THR*     6.3     0.2    -      -       +      -
----------------------------------------------------------
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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