Contacts of the strand formed by residues 141 - 145 (chain R) in PDB entry 1BKD


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 TYR 141 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82R  PHE*     3.9    15.8    -      +       -      -
     84R  ILE*     3.9     4.5    -      -       -      +
    113R  LEU*     3.3    26.9    -      -       +      -
    115R  GLY*     3.9    18.5    -      -       -      -
    125R  VAL*     5.6     0.3    +      -       -      +
    127R  SER*     4.1     9.6    -      -       -      -
    130R  ALA*     3.4    31.8    -      -       +      +
    131R  GLN*     3.9    38.4    +      -       -      +
    134R  ALA*     3.7    17.0    -      -       +      +
    139R  ILE      4.0     0.4    +      -       -      -
    140R  PRO*     1.3    73.7    -      -       -      +
    142R  ILE*     1.3    70.4    +      -       -      +
    143R  GLU*     2.7    47.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 142 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112R  VAL*     3.4    30.1    -      -       +      -
    113R  LEU      2.9    10.1    +      -       -      +
    114R  VAL*     3.3     9.9    -      -       +      +
    115R  GLY      3.0    21.9    +      -       -      -
    140R  PRO*     4.8     1.6    -      -       +      -
    141R  TYR*     1.3    82.3    -      -       -      +
    143R  GLU*     1.3    73.6    +      -       -      +
    144R  THR*     4.3     0.9    -      -       +      -
    151R  GLY*     3.9     7.6    -      -       -      +
    154R  ASP*     4.1    16.6    -      -       +      +
    155R  ALA*     3.4    45.1    -      -       +      +
    158R  THR*     3.5    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 143 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84R  ILE*     3.3    14.3    -      -       +      +
    115R  GLY      3.3     3.1    -      -       -      +
    117R  LYS*     5.8     0.3    -      -       -      +
    123R  ARG*     2.9    39.3    +      -       -      -
    127R  SER*     3.8    15.5    -      -       -      -
    141R  TYR*     2.7    40.1    +      -       +      +
    142R  ILE*     1.3    77.6    -      -       -      +
    144R  THR*     1.3    64.0    +      -       -      +
    150R  GLN      4.3     0.3    -      -       -      +
    151R  GLY*     3.8    12.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 144 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19R  LEU*     4.6     8.0    -      -       +      +
     22R  GLN*     5.8     0.2    +      -       -      -
    114R  VAL*     3.7    24.6    -      -       +      +
    115R  GLY      2.9     5.5    +      -       -      +
    116R  ASN*     3.5    24.1    +      -       -      +
    117R  LYS*     2.8    30.9    +      -       -      +
    142R  ILE*     4.0     2.5    -      -       +      +
    143R  GLU*     1.3    80.4    -      -       -      +
    145R  SER*     1.3    60.7    +      -       -      +
    150R  GLN      3.2    10.5    -      -       -      -
    151R  GLY      3.7    22.2    -      -       -      +
    152R  VAL*     4.1    10.8    -      -       -      +
    155R  ALA*     4.2     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 145 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22R  GLN*     3.2    10.6    -      -       -      +
    116R  ASN*     4.1     1.8    -      -       -      -
    117R  LYS*     3.9    21.2    +      -       -      +
    119R  ASP*     5.7     0.2    +      -       -      -
    144R  THR*     1.3    74.1    -      -       -      +
    146R  ALA*     1.3    62.9    +      -       -      +
    147R  LYS*     3.4     6.6    +      -       -      +
    148R  THR*     3.1    39.4    +      -       -      +
    149R  ARG*     3.4    14.7    +      -       -      -
    150R  GLN*     2.9    16.8    +      -       -      +
    152R  VAL*     4.3     2.6    -      -       -      +
----------------------------------------------------------
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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