Contacts of the strand formed by residues 230 - 238 (chain A) in PDB entry 2Y05


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 MET 230 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  GLY*     5.2     0.4    -      -       -      -
    211A  TYR*     3.5    28.0    -      -       -      +
    212A  ASP      3.8    18.4    -      -       -      +
    213A  CYS      3.9     0.4    -      -       -      -
    214A  TYR*     3.8    25.8    -      -       +      +
    226A  VAL*     3.7    18.6    -      -       -      +
    227A  ILE*     3.3    18.6    +      -       -      +
    228A  GLY      5.1     0.5    -      -       -      +
    229A  GLN*     1.3    80.9    -      -       -      +
    231A  LYS*     1.3    59.3    +      -       -      +
    234A  GLY*     4.0     2.5    -      -       -      -
    235A  ARG      3.8    24.0    -      -       -      +
    236A  ILE*     4.3     8.1    -      -       +      -
    263A  GLN*     3.1    22.9    +      -       -      +
    265A  LEU*     3.5    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  THR*     4.5     5.7    +      -       -      -
    209A  ASP*     3.4    36.9    -      -       -      +
    210A  GLY*     3.5    16.7    +      -       -      -
    211A  TYR      2.8    20.5    +      -       -      +
    212A  ASP*     2.9    42.5    +      -       -      +
    229A  GLN      3.7     0.2    +      -       -      -
    230A  MET*     1.3    75.9    -      -       -      +
    232A  LYS*     1.3    61.4    +      -       -      +
    233A  PHE      3.4     0.3    +      -       -      -
    234A  GLY*     2.8    27.9    +      -       -      +
    263A  GLN*     3.7     2.2    -      -       -      +
    265A  LEU*     3.7     5.9    -      -       -      +
   1331A  EDO      3.4    17.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  LYS*     1.3    78.3    -      -       -      +
    233A  PHE*     1.3   102.0    +      -       +      +
    234A  GLY*     3.2     0.3    +      -       -      -
    262A  TYR*     4.5     9.6    -      -       +      +
    263A  GLN*     3.3    27.1    -      -       -      +
    264A  GLU*     3.5    21.7    +      -       -      +
   1331A  EDO      2.8    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  LYS*     1.3   103.5    -      -       +      +
    234A  GLY*     1.3    65.9    +      -       -      +
    235A  ARG*     3.6    15.1    +      -       -      +
    263A  GLN      2.7    12.9    +      -       -      -
    264A  GLU*     3.4    49.1    -      -       +      -
    266A  ARG*     5.1     2.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  TYR      4.6     0.9    -      -       -      -
    212A  ASP*     3.5    14.4    -      -       -      -
    230A  MET*     4.0     9.4    -      -       -      -
    231A  LYS      2.8    19.5    +      -       -      -
    232A  LYS      3.1     1.3    -      -       -      -
    233A  PHE*     1.3    79.2    -      -       -      +
    235A  ARG*     1.3    59.7    +      -       -      +
    236A  ILE*     5.1     0.4    -      -       -      +
    265A  LEU*     3.6    14.2    -      -       -      +
    266A  ARG      3.1    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ILE      4.6     4.5    -      -       -      +
    137A  CYS*     2.8    46.8    +      -       -      +
    138A  GLY*     3.2    17.2    +      -       -      -
    140A  LYS*     5.8     0.6    -      -       -      +
    143A  GLU*     3.7    14.8    +      -       -      +
    212A  ASP*     3.1    30.2    +      -       -      +
    213A  CYS*     3.3    28.0    -      -       -      +
    214A  TYR      3.0    23.4    +      -       -      +
    230A  MET*     3.8     1.3    -      -       -      +
    233A  PHE      3.9    12.4    +      -       -      +
    234A  GLY*     1.3    76.5    -      -       -      +
    236A  ILE*     1.3    63.0    +      -       -      +
    237A  ALA      4.1     0.2    +      -       -      -
    266A  ARG*     3.4    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ILE*     4.5     4.2    -      -       -      +
    137A  CYS*     4.9     0.2    -      -       -      -
    214A  TYR*     3.3    36.3    -      -       +      +
    216A  ASP*     4.4     6.3    -      -       +      +
    227A  ILE*     3.8    30.7    -      -       +      -
    230A  MET*     4.3    10.1    -      -       +      -
    234A  GLY      5.1     2.0    -      -       -      +
    235A  ARG*     1.3    76.9    -      -       -      +
    237A  ALA*     1.3    70.0    +      -       -      +
    238A  ILE*     3.7    14.5    +      -       +      -
    265A  LEU*     4.4     7.0    -      -       +      -
    266A  ARG*     2.8    15.2    +      -       -      +
    267A  MET*     3.4    27.8    -      -       +      -
    268A  GLU*     3.0    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  GLY      3.8     9.4    -      -       -      +
    136A  ILE*     3.5    22.4    -      -       +      -
    137A  CYS*     3.6    23.0    -      -       -      -
    214A  TYR      2.8     9.5    +      -       -      +
    215A  PHE*     4.5     6.5    -      -       +      -
    216A  ASP*     2.9    29.3    +      -       -      +
    236A  ILE*     1.3    71.7    -      -       -      +
    238A  ILE*     1.3    60.9    +      -       -      +
    239A  CYS*     3.3     3.1    +      -       -      +
    268A  GLU      3.5     4.3    -      -       -      -
    270A  PHE*     4.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  ASP*     4.2    10.3    -      -       -      +
    236A  ILE*     4.1    15.9    -      -       +      -
    237A  ALA*     1.3    68.5    -      -       -      +
    239A  CYS*     1.3    60.4    +      -       -      +
    240A  GLY*     4.6    13.5    -      -       -      +
    241A  ALA*     5.9     2.9    -      -       +      -
    267A  MET*     4.0    31.0    -      -       +      +
    268A  GLU      2.8    14.6    +      -       -      +
    269A  ALA*     3.2    37.0    -      -       +      +
    270A  PHE*     3.4    10.2    +      -       -      +
----------------------------------------------------------
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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