Contacts of the strand formed by residues 206 - 213 (chain A) in PDB entry 2BGY


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 206 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  LYS*     3.6     1.6    -      -       -      -
    202A  THR*     3.0    35.1    +      -       -      +
    203A  LYS*     3.2    38.1    +      -       +      +
    204A  ASP      3.0     8.6    +      -       -      +
    205A  ASN*     1.3    84.7    -      -       +      +
    207A  TRP*     1.3    69.0    +      -       -      +
    228A  THR*     4.1    10.1    -      -       +      +
    229A  LEU      3.2     4.0    -      -       -      +
    230A  LYS*     3.6    44.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  LEU*     3.7    41.7    -      -       +      +
    158A  ASN      3.5    25.6    -      -       -      -
    161A  ASP*     3.8    15.5    -      -       +      -
    178A  ASN*     3.7    25.1    -      -       +      -
    199A  PHE*     4.3    11.4    -      -       +      -
    200A  VAL      3.5     7.4    -      -       -      +
    201A  LYS*     3.6    36.0    -      -       +      +
    206A  GLU*     1.3    83.1    +      -       -      +
    208A  ALA*     1.3    66.0    +      -       -      +
    209A  VAL*     3.8     1.9    +      -       -      +
    228A  THR*     3.4     3.5    -      -       -      +
    229A  LEU*     2.8    44.3    +      -       +      +
    231A  PHE*     3.7    24.7    -      +       -      -
    267A  GLN*     2.9    25.1    +      -       -      -
    273A  ASN*     4.0    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  TYR      3.5     0.9    -      -       -      +
    199A  PHE*     3.4     4.2    -      -       -      -
    200A  VAL*     2.8    37.6    +      -       +      +
    202A  THR*     3.7    22.9    -      -       +      +
    207A  TRP*     1.3    73.4    -      -       -      +
    209A  VAL*     1.3    60.9    +      -       -      +
    210A  TYR*     4.1    22.9    -      -       +      +
    225A  ALA*     4.1    11.2    -      -       +      -
    227A  THR      3.7     4.9    -      -       -      -
    228A  THR*     4.0     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  VAL*     3.6    29.4    -      -       +      -
    198A  TYR      3.2     4.3    -      -       -      +
    199A  PHE*     4.0    15.5    -      -       +      -
    207A  TRP      3.9     3.6    -      -       -      +
    208A  ALA*     1.3    78.2    -      -       -      +
    210A  TYR*     1.3    60.7    -      -       -      +
    211A  THR*     4.6     5.6    -      -       +      -
    225A  ALA*     3.4     1.9    -      -       -      +
    226A  SER*     2.8    33.8    +      -       -      -
    227A  THR*     2.9    29.6    +      -       +      +
    229A  LEU*     3.8    29.8    -      -       +      -
    260A  LEU*     5.7     0.2    -      -       +      -
    262A  PHE*     3.8    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  PHE*     3.4    55.2    -      +       +      +
    196A  ASN      3.8     0.3    -      -       -      +
    197A  VAL*     3.4     4.9    -      -       -      +
    198A  TYR*     2.8    36.3    +      -       +      +
    200A  VAL*     3.9    28.1    -      -       +      +
    208A  ALA*     4.1    18.9    -      -       +      +
    209A  VAL*     1.3    76.8    -      -       -      +
    211A  THR*     1.3    63.5    +      -       -      +
    222A  PRO*     4.1    13.2    -      -       +      -
    223A  THR*     3.9    15.2    +      -       -      -
    224A  THR      3.6    17.7    -      -       -      -
    225A  ALA*     3.5    23.9    +      -       +      +
    226A  SER      4.5     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  MET*     4.6    11.7    -      -       +      -
    196A  ASN      3.2    10.5    -      -       -      +
    197A  VAL*     4.4    11.9    -      -       +      -
    198A  TYR*     5.4     0.4    -      -       -      -
    209A  VAL*     4.6     3.4    -      -       +      -
    210A  TYR*     1.3    78.6    -      -       -      +
    212A  HIS*     1.3    64.8    +      -       -      +
    222A  PRO*     3.5    18.0    -      -       -      +
    224A  THR      5.7     0.2    +      -       -      -
    226A  SER*     2.7    30.0    +      -       -      +
    245A  ILE*     3.6    27.3    -      -       +      +
    260A  LEU*     4.4    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  VAL*     4.5    20.5    -      -       +      +
    195A  MET*     3.5     7.6    -      -       -      +
    196A  ASN*     2.9    37.2    +      -       +      +
    198A  TYR*     4.7     4.5    -      -       +      -
    211A  THR*     1.3    78.8    +      -       -      +
    213A  ASP*     1.3    74.3    +      -       -      +
    214A  SER*     3.3    13.1    +      -       -      -
    216A  ASP      5.0     1.8    +      -       -      -
    219A  ALA*     3.6    29.6    +      -       +      +
    220A  THR      3.4    28.1    +      -       -      -
    221A  ALA*     4.3     2.2    -      -       -      -
    222A  PRO*     3.7    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  HIS*     2.5    41.0    +      -       -      +
    194A  ASP      4.1     1.3    +      -       -      -
    195A  MET*     3.7    17.4    -      -       +      +
    212A  HIS*     1.3    84.3    +      -       -      +
    214A  SER*     1.3    58.8    +      -       -      +
    215A  SER*     3.1    27.7    +      -       -      -
    216A  ASP*     3.3    23.9    +      -       +      +
    219A  ALA*     4.2     4.9    -      -       +      +
    247A  THR*     3.4     1.1    -      -       -      -
    248A  GLY*     2.9    30.3    +      -       -      +
----------------------------------------------------------
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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