Contacts of the strand formed by residues 221 - 228 (chain A) in PDB entry 2DFS


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 GLY 221 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  PHE*     1.3    81.2    -      -       -      +
    222A  LYS*     1.3    60.9    +      -       -      -
    240A  ARG      4.0     0.2    -      -       -      +
    241A  THR*     3.5     2.3    -      -       -      -
    242A  TYR*     2.9    41.3    +      -       -      -
    243A  LEU*     4.5     3.4    -      -       -      +
    436A  LEU*     4.7     4.7    -      -       -      -
    437A  ASP      3.6     8.1    -      -       -      -
    438A  ILE*     4.4    18.4    -      -       -      -
    439A  TYR*     4.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  THR*     4.7     7.4    -      -       -      +
    199A  SER*     6.1     0.7    -      -       -      -
    200A  ASN*     2.8    28.8    +      -       -      +
    203A  MET*     4.3    24.3    -      -       +      +
    204A  GLU*     4.9     7.9    +      -       -      +
    220A  PHE*     3.7    30.1    +      -       +      -
    221A  GLY*     1.3    70.7    -      -       -      -
    223A  TYR*     1.3    61.5    +      -       -      +
    224A  ILE*     4.1    28.4    -      -       +      +
    239A  MET*     4.4     9.9    -      -       +      -
    240A  ARG      3.7     2.9    -      -       -      +
    435A  VAL      3.6     2.3    -      -       -      +
    436A  LEU*     3.6     2.2    -      -       -      +
    437A  ASP*     2.9    60.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  GLN      4.0     0.2    +      -       -      -
    158A  SER*     2.8    27.4    +      -       -      -
    221A  GLY      4.2     0.2    -      -       -      -
    222A  LYS*     1.3    73.7    -      -       -      +
    224A  ILE*     1.3    61.4    +      -       -      +
    225A  GLU*     3.5    35.6    +      -       +      -
    238A  ASN      3.6     1.7    -      -       -      +
    239A  MET*     3.4     3.3    -      -       -      -
    240A  ARG*     2.8    51.7    +      -       +      +
    242A  TYR*     4.1    16.8    -      +       +      -
    432A  PHE*     3.7    16.4    -      +       -      -
    434A  GLY*     3.6    29.9    -      -       -      -
    435A  VAL      3.4    15.7    -      -       -      -
    436A  LEU*     3.7    21.1    -      -       +      -
    647A  LEU*     5.6     1.1    -      -       +      -
    650A  THR*     3.8    21.8    +      -       +      +
    651A  LEU*     4.2    10.8    -      -       +      +
    654A  THR*     4.4     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  MET*     5.0     4.9    -      -       -      -
    196A  VAL*     4.2    26.0    -      -       +      -
    199A  SER*     5.3     0.7    -      -       -      +
    222A  LYS*     4.1    21.3    -      -       +      +
    223A  TYR*     1.3    72.0    -      -       -      +
    225A  GLU*     1.3    60.1    +      -       -      +
    226A  ILE*     3.8    25.0    +      -       +      +
    237A  ALA*     4.1    11.9    -      -       +      -
    238A  ASN      3.4     6.3    -      -       -      +
    239A  MET*     3.7    43.3    -      -       +      -
    423A  LEU*     4.9     2.7    -      -       +      -
    433A  ILE      3.9     0.7    -      -       -      +
    434A  GLY*     3.3     1.2    -      -       -      -
    435A  VAL*     2.8    43.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  TYR*     3.5    33.7    -      -       +      +
    224A  ILE*     1.3    69.9    -      -       -      +
    226A  ILE*     1.3    61.0    +      -       -      +
    227A  GLY*     3.7     0.6    +      -       -      -
    237A  ALA*     3.1     7.1    -      -       -      +
    238A  ASN*     2.7    61.8    +      -       +      +
    240A  ARG*     2.6    49.1    +      -       -      -
    429A  GLN*     6.1     0.9    -      -       -      +
    432A  PHE*     4.0    30.4    -      -       +      -
    433A  ILE      3.9     3.8    -      -       -      -
    434A  GLY*     3.9     2.2    -      -       -      -
    650A  THR*     4.3     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  MET*     4.3    26.2    -      -       +      -
    180A  PHE*     5.1    14.4    -      -       +      -
    192A  VAL*     6.0     4.5    -      -       +      -
    196A  VAL*     5.4     1.3    -      -       +      -
    224A  ILE*     3.8    29.8    -      -       +      +
    225A  GLU*     1.3    70.9    -      -       -      +
    227A  GLY*     1.4    58.9    +      -       -      +
    228A  PHE*     3.3    29.0    -      -       +      -
    234A  ILE*     4.2    16.8    -      -       +      -
    236A  GLY      3.9     7.0    -      -       -      +
    237A  ALA*     4.0     9.2    -      -       +      -
    432A  PHE*     3.1     5.9    -      -       -      -
    433A  ILE*     2.8    43.3    +      -       +      +
    435A  VAL*     5.1     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  GLU      3.7     3.0    +      -       -      -
    226A  ILE*     1.4    72.1    -      -       -      +
    228A  PHE*     1.3    61.3    +      -       -      -
    233A  ARG      3.8     0.5    -      -       -      +
    234A  ILE*     3.9     2.8    -      -       -      -
    235A  ILE*     3.1    34.2    +      -       -      +
    236A  GLY      2.9    19.3    +      -       -      +
    237A  ALA*     4.4     0.4    -      -       -      +
    429A  GLN*     3.3    27.4    -      -       -      -
    431A  SER      3.7     0.4    -      -       -      -
    432A  PHE*     4.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  TYR*     4.0    22.2    -      +       -      -
    150A  MET*     4.0    12.6    -      -       -      -
    180A  PHE*     4.4    14.4    -      +       +      -
    184A  SER*     4.5     3.6    -      -       -      -
    226A  ILE*     3.3    39.5    -      -       +      -
    227A  GLY*     1.3    71.9    -      -       -      -
    229A  ASP*     1.4    52.4    +      -       -      +
    232A  TYR*     3.7    26.9    -      +       +      -
    233A  ARG      3.5    22.0    -      -       -      +
    234A  ILE*     3.6    23.8    -      -       +      -
    235A  ILE*     4.3     4.5    -      -       -      -
    429A  GLN*     3.6     1.7    -      -       -      +
    430A  HIS*     2.7    29.9    +      -       -      +
    431A  SER      2.8    23.5    +      -       -      +
    432A  PHE*     4.1     1.3    -      -       -      -
    433A  ILE*     3.9    24.0    -      -       +      -
----------------------------------------------------------
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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