Contacts of the strand formed by residues 197 - 201 (chain A) in PDB entry 5IYB


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 GLU 197 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PHE*     5.4     3.4    -      -       -      -
    193A  ARG*     3.8     1.6    -      -       -      +
    194A  SER*     2.8    43.9    +      -       -      +
    196A  LEU*     1.3    83.7    +      -       -      +
    198A  LEU*     1.3    63.0    +      -       -      +
    199A  TYR*     3.5    15.7    -      -       +      -
    215A  LEU*     4.3    15.9    -      -       +      -
    308A  LYS*     2.3    29.4    +      -       -      +
    311A  GLN*     6.4     0.4    -      -       +      -
     93M  PHE*     1.8    55.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PHE*     4.2    32.8    -      -       +      -
    100A  LEU*     4.3    21.5    -      -       +      +
    104A  MET*     5.4    12.3    -      -       +      -
    107A  LEU*     4.1    16.8    -      -       +      -
    191A  ILE*     4.4     8.3    -      -       +      -
    192A  ARG      3.7    10.5    -      -       -      +
    193A  ARG*     5.3     7.2    -      -       +      -
    196A  LEU      5.1     0.2    -      -       -      -
    197A  GLU*     1.3    82.6    -      -       -      +
    199A  TYR*     1.3    64.1    +      -       -      +
    215A  LEU*     3.2    10.5    -      -       -      +
    216A  LEU*     3.0    59.7    +      -       +      +
    221A  VAL*     5.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  ARG      3.8     1.0    -      -       -      +
    191A  ILE*     3.7     5.2    -      -       -      +
    192A  ARG*     3.0    46.3    +      -       +      +
    194A  SER*     3.6    18.2    -      -       -      +
    197A  GLU*     3.3    12.8    -      -       +      -
    198A  LEU*     1.3    80.5    -      -       -      +
    200A  ALA*     1.3    61.7    +      -       -      +
    213A  LYS*     5.4     7.4    -      -       +      -
    214A  ILE*     3.3    16.4    -      -       -      -
    215A  LEU*     4.6    15.7    -      -       +      +
    216A  LEU*     4.7     2.0    -      -       -      -
     93M  PHE*     1.9    59.6    -      +       -      -
     95M  GLU*     4.7    21.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  PRO*     4.1    12.6    -      -       +      -
    190A  ARG      3.9     4.7    -      -       -      -
    191A  ILE*     5.5     0.9    -      -       -      -
    199A  TYR*     1.3    76.5    -      -       -      +
    201A  GLU*     1.3    62.0    +      -       -      +
    202A  TRP*     3.7    25.4    -      -       +      -
    213A  LYS*     3.5     8.3    +      -       -      +
    214A  ILE*     2.7    34.3    +      -       +      +
    216A  LEU*     3.7    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  PRO*     3.2     2.3    -      -       -      +
    190A  ARG*     3.1    42.8    +      -       +      +
    192A  ARG*     4.4    19.4    +      -       -      +
    200A  ALA*     1.3    76.1    -      -       -      +
    202A  TRP*     1.3    86.8    +      -       -      +
    203A  LYS*     2.7    35.7    +      -       +      +
    212A  LYS      4.3    11.7    -      -       -      +
    213A  LYS*     4.4    25.1    +      -       +      +
----------------------------------------------------------
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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