Contacts of the strand formed by residues 214 - 218 (chain A) in PDB entry 3BUC


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 VAL 214 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ARG*     5.3     7.2    -      -       -      +
     60A  ILE*     3.9    30.3    -      -       +      -
     61A  ARG      5.8     1.3    -      -       -      +
     62A  ALA*     5.2     6.1    -      -       +      -
     65A  LEU*     4.0    17.7    -      -       +      -
    195A  PHE      4.0     0.3    -      -       -      +
    196A  VAL*     3.6     1.0    -      -       -      -
    197A  PHE*     2.7    54.8    +      -       +      +
    212A  ALA*     4.8     1.3    -      -       +      +
    213A  VAL*     1.3    78.3    -      -       -      +
    215A  ARG*     1.3    66.3    +      -       -      +
    216A  LEU*     5.3     2.7    -      -       +      -
    234A  TRP*     4.3     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ARG*     4.8     6.6    +      -       -      -
    194A  ASP*     5.7     7.6    -      -       +      +
    195A  PHE      3.3     9.9    -      -       -      +
    196A  VAL*     3.9    21.0    -      -       +      +
    213A  VAL*     3.5    31.5    +      -       +      +
    214A  VAL*     1.3    79.1    -      -       -      +
    216A  LEU*     1.3    64.4    +      -       -      +
    217A  PRO*     4.8     0.7    -      -       -      +
    241A  ARG*     5.3     7.0    -      -       -      +
      3C    G      4.6    18.6    +      -       -      -
      4C    C      5.2     7.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ARG*     3.6    27.1    -      -       -      +
     60A  ILE*     4.4    13.5    -      -       +      -
     69A  TYR*     4.0    40.2    -      -       +      -
    194A  ASP*     4.2     4.3    -      -       -      -
    195A  PHE*     2.9    49.8    +      -       +      +
    197A  PHE*     4.5    22.7    -      -       +      -
    214A  VAL*     5.3     2.9    -      -       +      -
    215A  ARG*     1.3    78.0    -      -       -      +
    217A  PRO*     1.3    77.5    -      -       +      +
    218A  LEU*     3.5     6.9    +      -       +      -
    224A  LEU*     4.5     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ARG*     5.3     1.8    -      -       -      +
     69A  TYR*     4.0    10.9    +      -       -      -
    192A  SER*     3.8    17.0    -      -       -      +
    193A  ARG      3.6     7.9    -      -       -      +
    194A  ASP*     3.9    15.0    -      -       -      +
    215A  ARG      4.8     0.4    -      -       -      +
    216A  LEU*     1.3    96.5    -      -       +      +
    218A  LEU*     1.3    61.5    +      -       -      +
    219A  ALA*     3.8     4.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  TYR*     3.8    25.8    -      -       +      -
    186A  SER*     4.4     5.8    -      -       -      +
    188A  SER*     4.0    16.3    -      -       -      +
    191A  ALA      4.4     1.9    -      -       -      +
    192A  SER*     3.4     5.5    +      -       -      -
    193A  ARG      2.8    33.3    +      -       -      +
    195A  PHE*     3.8    35.9    -      -       +      -
    216A  LEU*     4.2    10.3    -      -       +      -
    217A  PRO*     1.3    73.3    -      -       -      +
    219A  ALA*     1.3    62.9    +      -       -      +
    222A  SER*     4.0     4.5    -      -       -      +
    224A  LEU*     4.0    27.6    -      -       +      -
    238A  LEU*     5.0     0.2    -      -       +      -
    248A  ARG*     3.3    28.3    +      -       -      +
    259A  AKG      3.9     2.7    -      -       -      +
----------------------------------------------------------
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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