Contacts of the strand formed by residues 220 - 224 (chain A) in PDB entry 5C51


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 TRP 220 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  LEU*     3.4    21.8    -      -       +      +
    163A  PRO*     2.7    40.9    +      -       +      -
    164A  PRO      4.2     5.6    +      -       -      -
    165A  LYS*     3.5    31.6    -      -       +      -
    166A  PRO*     4.5     7.6    -      -       +      -
    169A  TRP*     3.9    17.9    -      +       -      -
    177A  ARG*     3.5     2.8    -      -       -      -
    178A  TYR*     2.9    45.5    +      -       +      +
    213A  VAL*     3.8    13.5    -      -       +      -
    214A  ALA      4.0     2.5    -      -       -      -
    215A  ILE*     3.5    35.0    -      -       +      +
    219A  ALA*     1.3    77.0    -      -       -      +
    221A  TYR*     1.3    75.5    -      -       -      +
    397A  ALA*     3.7    33.4    -      -       +      -
    400A  VAL*     4.5     0.2    -      -       +      -
    401A  TRP*     4.8     9.2    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  TRP*     5.4     0.4    -      -       -      -
    175A  TRP*     3.6    23.6    -      +       +      -
    176A  THR      3.2     8.1    -      -       -      -
    177A  ARG*     2.7    55.1    +      -       +      -
    178A  TYR*     4.3     2.5    -      -       -      -
    187A  VAL*     5.0     5.8    -      -       +      -
    190A  PRO*     3.7    33.1    -      -       +      +
    191A  GLU      4.5     4.2    +      -       -      -
    192A  GLU*     3.1    27.2    +      -       +      +
    195A  LEU*     5.1     4.0    -      -       +      -
    213A  VAL*     3.5     7.8    -      -       -      +
    214A  ALA*     2.9    43.3    +      -       +      +
    216A  SER*     3.5    26.0    -      -       -      -
    219A  ALA      4.2     0.7    -      -       -      -
    220A  TRP*     1.3    88.4    -      -       -      +
    222A  SER*     1.3    59.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  TRP*     3.8    17.7    -      -       -      -
    170A  ALA      4.6     4.3    +      -       -      -
    172A  ALA      5.5     0.3    -      -       -      +
    174A  GLY      3.6     2.4    -      -       -      +
    175A  TRP*     3.9     1.3    -      -       -      -
    176A  THR*     2.3    62.6    +      -       -      +
    178A  TYR*     2.7    22.9    +      -       -      -
    212A  ALA      3.5     8.7    -      -       -      -
    213A  VAL*     4.6     0.4    -      -       -      -
    221A  TYR*     1.3    75.0    -      -       -      +
    223A  TRP*     1.3    61.1    +      -       -      +
    224A  CYS*     4.0     0.9    +      -       -      -
    393A  MET*     4.1    13.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  GLY*     3.2    36.0    -      -       -      -
    175A  TRP*     3.4    44.2    -      +       +      -
    199A  VAL*     5.5     1.8    -      -       +      -
    209A  PRO*     3.7    22.0    -      -       +      -
    211A  LEU*     3.6     7.6    -      -       -      -
    212A  ALA*     2.9    61.2    +      -       +      +
    222A  SER*     1.3    71.9    -      -       -      +
    224A  CYS*     1.3    70.4    +      -       -      +
    225A  SER*     3.1    33.9    -      -       -      -
    240A  SER      4.0    13.7    -      -       -      -
    242A  ALA*     3.6    42.8    -      -       +      -
    243A  ASP*     3.9     9.9    +      -       -      -
    279A  ARG*     5.6     3.0    -      -       -      +
    393A  MET*     3.9     3.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  ALA      4.3     5.8    -      -       -      -
    171A  TRP*     4.9     0.9    -      -       -      -
    172A  ALA      3.2    23.8    -      -       -      +
    173A  GLU*     4.1     0.7    -      -       -      +
    174A  GLY      2.9    28.5    +      -       -      -
    210A  THR      3.9     1.8    -      -       -      -
    211A  LEU*     3.6    13.2    -      -       -      -
    222A  SER*     4.0     1.5    +      -       -      -
    223A  TRP*     1.3    84.0    +      -       -      +
    225A  SER*     1.3    63.1    +      -       -      +
    228A  LEU*     4.0    21.3    -      -       +      -
    389A  PHE*     3.6    34.5    -      -       -      -
    393A  MET*     3.8     8.7    -      -       -      -
----------------------------------------------------------
 Back to top of page


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