Contacts of the strand formed by residues 121 - 127 (chain D) in PDB entry 2BG9


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 PRO 121 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  ASN*     2.5    28.9    +      -       -      +
     55D  ARG*     4.0    28.7    -      -       +      +
    101D  ALA      3.7     6.0    -      -       -      +
    102D  ILE*     3.6    31.5    -      -       +      +
    106D  THR*     5.5     6.7    -      -       +      -
    119D  THR      3.7     6.5    -      -       -      +
    120D  PRO*     1.3    80.1    -      -       +      +
    122D  ALA*     1.3    54.5    +      -       -      +
    123D  ILE*     3.5     3.6    +      -       -      +
    148E  GLN*     4.7    20.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 122 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  THR      3.9     0.2    -      -       -      +
     53D  ASN*     2.8     6.7    +      -       -      -
     54D  VAL*     2.7    45.2    +      -       -      +
     56D  LEU*     3.8    12.1    -      -       +      -
    100D  PHE*     3.9    18.2    -      -       +      -
    101D  ALA      3.5     7.0    -      -       -      -
    103D  VAL*     3.6    27.8    -      -       +      -
    120D  PRO      2.5    12.5    +      -       -      +
    121D  PRO*     1.3    66.7    -      -       -      +
    123D  ILE*     1.3    58.7    +      -       -      +
    124D  PHE*     4.4     2.5    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 123 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39D  GLN*     5.8     4.3    -      -       +      +
     41D  ILE*     4.5     9.6    -      -       +      -
     51D  GLU*     4.4    13.0    -      -       -      +
     52D  THR      3.1     9.6    -      -       -      +
     53D  ASN*     3.1    37.5    -      -       +      +
     99D  ASP      3.7     0.2    -      -       -      +
    101D  ALA*     2.7    46.4    +      -       +      +
    102D  ILE*     4.5    10.8    -      -       +      -
    121D  PRO      4.1     2.0    -      -       -      +
    122D  ALA*     1.3    72.7    -      -       -      +
    124D  PHE*     1.3    64.6    +      -       -      +
     95E  VAL      5.2     2.7    -      -       -      +
     96E  ASP*     3.6    41.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 124 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50D  VAL      3.2     2.6    -      -       -      +
     51D  GLU*     3.0    26.5    -      -       -      -
     52D  THR*     3.0    19.7    +      -       +      +
     54D  VAL*     4.9    15.9    -      -       +      -
     92D  LEU*     3.0    49.6    -      -       +      -
     96D  ALA*     4.3     3.6    -      -       -      -
     98D  GLY      3.5     9.6    -      -       -      -
     99D  ASP      2.8    27.1    -      -       -      +
    100D  PHE*     3.3    38.1    -      +       -      -
    122D  ALA*     5.2     4.3    -      -       +      -
    123D  ILE*     1.3    75.9    -      -       -      +
    125D  LYS*     1.3    85.1    +      -       -      +
    126D  SER*     4.2     9.9    -      -       -      -
    146D  LEU*     5.7     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 125 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  ILE*     2.7    53.5    -      -       +      +
     50D  VAL      3.4     0.4    -      -       -      -
     51D  GLU*     3.4    32.3    +      -       +      +
     97D  ASP*     3.2    24.1    +      -       -      +
     98D  GLY*     2.6    40.7    +      -       -      -
     99D  ASP      4.4     0.2    +      -       -      -
    124D  PHE*     1.3    83.7    -      -       -      +
    126D  SER*     1.3    60.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 126 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  ILE*     3.2    12.1    -      -       -      +
     50D  VAL*     2.6    55.2    +      -       -      +
     52D  THR*     5.9     2.2    -      -       -      -
     95D  ASN*     3.3    20.9    +      -       -      -
     96D  ALA      4.3     0.7    -      -       -      +
     97D  ASP*     3.7     8.1    -      -       -      +
    124D  PHE*     4.2    13.9    -      -       -      -
    125D  LYS*     1.3    73.7    -      -       -      +
    127D  TYR*     1.3    64.4    +      -       -      +
    128D  CYS*     4.1     1.0    +      -       -      -
    144D  MET*     4.5     9.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 127 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  ASN*     4.5    17.8    +      -       -      -
     43C  ILE*     4.3    25.3    -      -       +      +
    185C  THR*     5.5     6.2    +      -       -      +
    187C  ASN*     4.8     9.7    +      -       -      +
     47D  ASN      4.1     4.3    -      -       -      -
     48D  GLN*     2.8    38.8    +      -       +      -
     49D  ILE*     3.9    15.5    -      -       +      -
     94D  ASN      2.3    43.6    -      -       -      +
     95D  ASN*     2.6    24.1    +      -       -      +
     97D  ASP*     3.7    19.1    -      -       +      -
    126D  SER*     1.3    80.5    +      -       -      +
    128D  CYS*     1.3    54.1    +      -       -      +
----------------------------------------------------------
 Back to top of page


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