Contacts of the strand formed by residues 230 - 238 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  GLY*     5.3     0.2    -      -       -      -
    211B  TYR*     3.5    30.1    -      -       -      +
    212B  ASP      3.6    21.1    -      -       -      +
    213B  CYS      3.9     0.2    -      -       -      -
    214B  TYR*     3.7    33.7    -      -       +      +
    226B  VAL*     3.5    18.4    -      -       +      +
    227B  ILE*     3.3    18.7    +      -       -      +
    228B  GLY      5.1     1.2    -      -       -      +
    229B  GLN*     1.3    79.0    -      -       -      +
    231B  LYS*     1.3    59.8    +      -       -      +
    234B  GLY*     3.9     3.6    -      -       -      -
    235B  ARG      3.8    16.6    -      -       -      +
    236B  ILE*     4.3     8.3    -      -       +      -
    263B  GLN*     2.9    24.3    +      -       -      +
    265B  LEU*     3.7    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 231 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  THR*     5.8     0.7    -      -       -      -
    209B  ASP*     3.5    46.3    +      -       -      +
    210B  GLY*     4.2     8.1    -      -       -      -
    211B  TYR      2.9    26.4    +      -       -      +
    212B  ASP*     3.1    38.1    +      -       -      +
    229B  GLN      3.5     1.0    +      -       -      -
    230B  MET*     1.3    76.4    -      -       -      +
    232B  LYS*     1.3    65.0    +      -       -      +
    234B  GLY*     2.9    18.9    +      -       -      +
    263B  GLN*     3.5     4.7    -      -       -      +
    265B  LEU*     3.3     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 232 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231B  LYS*     1.3    77.7    -      -       -      +
    233B  PHE*     1.3    99.9    +      -       +      +
    234B  GLY      3.2     0.9    +      -       -      -
    262B  TYR*     3.0    27.4    +      -       +      +
    263B  GLN*     3.3    25.7    -      -       -      +
    264B  GLU*     2.7    30.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 233 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232B  LYS*     1.3   101.5    -      -       +      +
    234B  GLY*     1.3    64.6    +      -       -      +
    235B  ARG*     3.7    15.9    +      -       -      +
    263B  GLN      2.8    13.7    +      -       -      -
    264B  GLU*     3.3    49.8    -      -       +      -
    266B  ARG*     4.9     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 234 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211B  TYR      4.7     0.4    -      -       -      -
    212B  ASP*     3.4    15.3    -      -       -      -
    230B  MET*     3.9    12.1    -      -       -      -
    231B  LYS*     2.9    20.9    +      -       -      -
    232B  LYS      3.1     1.7    -      -       -      -
    233B  PHE*     1.3    78.8    -      -       -      +
    235B  ARG*     1.3    60.1    +      -       -      -
    236B  ILE*     4.0     0.6    +      -       -      +
    265B  LEU*     3.6    10.3    -      -       -      +
    266B  ARG*     3.0    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 235 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136B  ILE      4.7     4.5    -      -       -      +
    137B  CYS*     3.0    38.6    +      -       -      +
    138B  GLY*     3.4    17.4    +      -       -      -
    140B  LYS*     5.5     1.8    -      -       -      +
    143B  GLU*     4.1    14.3    +      -       -      +
    212B  ASP*     3.1    34.5    +      -       -      +
    213B  CYS*     3.3    17.7    -      -       -      +
    214B  TYR      2.9    23.6    +      -       -      +
    230B  MET*     3.8     0.8    -      -       -      +
    233B  PHE      3.8    11.7    +      -       -      +
    234B  GLY*     1.3    76.0    -      -       -      +
    236B  ILE*     1.3    62.9    -      -       -      +
    237B  ALA      4.1     0.2    +      -       -      -
    266B  ARG*     3.4    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 236 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136B  ILE*     4.6     2.6    -      -       -      +
    137B  CYS*     5.0     0.7    -      -       -      -
    214B  TYR*     3.3    39.7    -      -       +      +
    216B  ASP*     4.3     5.2    -      -       +      +
    227B  ILE*     3.6    21.1    -      -       +      -
    230B  MET*     4.3    14.8    -      -       +      -
    234B  GLY      5.1     1.6    -      -       -      +
    235B  ARG*     1.3    75.5    -      -       -      +
    237B  ALA*     1.3    70.3    +      -       -      +
    238B  ILE*     3.7    14.1    +      -       +      -
    265B  LEU*     4.6     4.7    -      -       +      -
    266B  ARG*     2.8    14.2    +      -       -      +
    267B  MET*     3.3    39.5    -      -       +      -
    268B  GLU*     3.0    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 237 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  GLY      3.8     8.3    -      -       -      +
    136B  ILE*     3.6    19.1    -      -       +      -
    137B  CYS*     3.6    25.0    -      -       -      -
    214B  TYR      2.8     9.6    +      -       -      +
    215B  PHE*     4.3     8.5    -      -       +      -
    216B  ASP*     2.9    29.8    +      -       -      +
    235B  ARG      4.1     0.8    +      -       -      -
    236B  ILE*     1.3    72.5    -      -       -      +
    238B  ILE*     1.3    60.8    +      -       -      +
    239B  CYS*     3.3     3.0    +      -       -      +
    268B  GLU      3.4     5.2    -      -       -      -
    270B  PHE*     4.0    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216B  ASP*     4.2     9.6    -      -       -      +
    236B  ILE*     4.1    16.8    -      -       +      +
    237B  ALA*     1.3    69.4    -      -       -      +
    239B  CYS*     1.3    60.6    +      -       -      +
    240B  GLY      4.8    11.7    -      -       -      +
    241B  ALA*     6.2     1.3    -      -       +      -
    267B  MET*     4.1    24.7    -      -       +      +
    268B  GLU      2.8    12.1    +      -       -      +
    269B  ALA*     3.2    41.3    -      -       +      +
    270B  PHE*     3.5     8.6    +      -       -      +
----------------------------------------------------------
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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