Contacts of the strand formed by residues 198 - 204 (chain B) in PDB entry 5ODS


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 ALA 198 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168B  THR*     5.4     1.1    -      -       -      -
    181B  MET*     4.9     2.0    -      -       -      -
    196B  GLY      3.8     0.4    -      -       -      -
    197B  HIS*     1.3    79.0    -      -       -      +
    199B  ALA*     1.3    58.9    +      -       -      +
    218B  PHE*     3.3     2.1    -      -       -      +
    219B  ALA      2.7    36.5    +      -       -      +
    261B  PRO*     4.1    16.2    -      -       +      -
    262B  VAL      4.1     3.4    -      -       -      +
    263B  ALA*     4.0    36.1    -      -       -      +
    264B  MET*     3.6     7.6    -      -       +      +
    275B  LEU*     4.5     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157B  ARG*     3.1    25.4    +      -       -      -
    166B  LEU*     3.5    28.7    -      -       +      +
    168B  THR*     5.4     2.0    +      -       -      -
    181B  MET*     4.0     6.4    -      -       -      -
    198B  ALA*     1.3    77.1    -      -       -      +
    200B  SER*     1.3    63.9    +      -       -      +
    216B  PHE*     3.7     5.6    -      -       +      -
    217B  CYS      3.2    12.3    -      -       -      +
    218B  PHE*     3.5    14.4    -      -       +      -
    264B  MET*     3.9    10.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157B  ARG*     2.9    30.1    +      -       -      +
    199B  ALA*     1.3    78.7    -      -       -      +
    201B  PHE*     1.3    73.9    +      -       -      +
    216B  PHE*     3.9     3.0    -      -       -      -
    217B  CYS*     2.8    34.3    +      -       -      +
    264B  MET*     3.8    16.2    -      -       -      -
    265B  GLN*     5.1     0.2    +      -       -      -
    266B  ILE*     3.5    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157B  ARG*     3.9    18.1    +      -       +      +
    158B  THR      3.7    24.9    -      -       -      +
    159B  ASP*     3.8    28.3    -      -       +      -
    160B  ALA      5.3     0.2    -      -       -      +
    164B  TRP*     3.7    29.2    -      +       +      -
    166B  LEU*     3.9    22.4    -      -       +      -
    183B  LEU*     3.8    24.7    -      -       +      -
    200B  SER*     1.3    87.4    +      -       -      +
    202B  ALA*     1.3    63.2    +      -       -      +
    203B  GLN*     6.0     0.4    -      -       -      +
    214B  THR*     4.7     4.7    -      -       +      -
    215B  LEU      3.3    13.5    -      -       -      +
    216B  PHE*     3.8    26.2    -      +       +      -
    233B  VAL*     4.8     2.5    -      -       +      -
    266B  ILE*     4.0     2.9    -      -       -      +
    268B  GLU*     4.3     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201B  PHE*     1.3    77.3    -      -       -      +
    203B  GLN*     1.3    65.4    +      -       -      +
    204B  PHE      4.0     0.4    -      -       -      -
    213B  SER      3.5     0.9    -      -       -      +
    214B  THR*     3.5     2.6    -      -       -      +
    215B  LEU*     2.6    46.2    +      -       +      +
    266B  ILE*     3.7    29.6    -      -       +      -
    268B  GLU*     3.3    13.5    -      -       -      +
    287B  LEU*     3.9    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159B  ASP*     4.2     3.8    +      -       -      +
    160B  ALA*     3.8    34.8    -      -       +      +
    161B  LYS*     4.3    15.7    -      -       -      +
    201B  PHE*     6.0     0.2    -      -       -      +
    202B  ALA*     1.3    71.9    -      -       -      +
    204B  PHE*     1.3    61.8    +      -       -      +
    212B  GLU*     4.1    35.7    -      -       -      +
    213B  SER      3.4     7.8    -      -       -      +
    214B  THR*     3.0    40.7    +      -       -      +
    268B  GLU*     3.1    30.4    +      -       -      +
    271B  ASP*     4.8     6.1    -      -       -      +
    287B  LEU*     5.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203B  GLN*     1.3    75.0    -      -       -      +
    205B  LYS*     1.3    70.8    +      -       -      +
    206B  MET*     3.6    30.3    +      -       +      -
    212B  GLU*     4.3     2.2    -      -       -      +
    213B  SER*     2.8    40.5    +      -       -      +
    215B  LEU*     3.7    31.0    -      -       +      -
    243B  PHE*     4.3     7.4    -      +       -      -
    271B  ASP*     3.4    39.9    -      -       +      -
    287B  LEU*     4.0    12.8    -      -       +      -
    288B  GLU*     3.7    43.3    -      -       +      -
    350B  ARG*     4.8     1.1    -      -       -      -
    354B  ARG*     3.9    14.6    -      -       -      -
----------------------------------------------------------
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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