Contacts of the strand formed by residues 49 - 55 (chain B) 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 GLU 49 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ASN*     4.5    13.2    +      -       -      -
     42B  ILE*     3.9     1.1    -      -       -      +
     43B  LEU*     3.7     7.0    -      -       -      +
     44B  ASN*     2.6    70.1    +      -       +      +
     47B  ASN*     2.7    37.5    +      -       +      +
     48B  GLU*     1.3    78.8    -      -       -      +
     50B  MET*     1.3    59.9    +      -       -      +
     51B  THR      4.3     0.7    -      -       -      -
     97B  ASP*     4.4    13.2    -      -       -      +
    125B  ARG*     4.4    24.7    +      -       -      +
    126B  SER      3.5     6.7    -      -       -      +
    127B  SER*     4.0     0.7    -      -       -      +
    130B  ILE*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  LEU*     4.3     7.4    -      -       +      -
     42B  ILE      3.9     2.9    -      -       -      -
     43B  LEU*     4.2    18.6    -      -       +      -
     49B  GLU*     1.3    70.3    -      -       -      +
     51B  THR*     1.3    56.7    +      -       -      +
     52B  THR*     3.4    21.2    +      -       +      +
     95B  ASN*     4.5     0.2    -      -       -      -
    124B  TYR*     3.3     7.1    -      -       -      +
    125B  ARG*     4.7     0.8    -      -       -      +
    126B  SER*     2.3    79.9    +      -       -      +
    127B  SER      4.4     1.1    -      -       -      +
    128B  CYS*     4.4    13.5    -      -       +      +
    130B  ILE*     5.9     2.0    -      -       +      -
    134B  TYR*     5.5     1.8    -      -       -      +
    144B  MET*     3.6    22.7    -      -       +      +
    176B  ASN*     5.4     7.6    -      -       -      +
    211B  LEU*     3.2    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  LEU*     2.9    15.5    -      -       -      +
     41B  LEU*     3.2    18.1    +      -       +      +
     42B  ILE*     3.2    23.5    +      -       +      +
     50B  MET*     1.3    67.9    -      -       -      +
     52B  THR*     1.3    58.7    +      -       -      +
    123B  ILE*     4.2    28.3    -      -       +      -
    124B  TYR      3.5    10.1    -      -       -      +
    125B  ARG*     2.4    41.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  LEU*     4.1    23.1    -      -       +      -
     39B  SER      3.1    17.9    -      -       -      +
     40B  LEU*     2.7    33.5    -      -       +      +
     41B  LEU      4.6     0.7    -      -       -      +
     50B  MET*     3.4    20.5    +      -       +      +
     51B  THR*     1.3    73.1    -      -       -      +
     53B  SER*     1.3    69.5    +      -       -      +
    123B  ILE*     3.3     9.6    -      -       -      +
    124B  TYR*     3.0    48.7    +      -       -      -
    176B  ASN*     5.7     0.2    -      -       -      +
     99C  ASP*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  LEU*     4.0     0.7    -      -       -      +
     38B  THR*     2.3    60.4    +      -       -      -
     39B  SER*     2.8    11.4    +      -       -      +
     52B  THR*     1.3    80.9    -      -       -      +
     54B  VAL*     1.3    62.1    +      -       -      +
    121B  SER*     4.8     1.6    -      -       -      -
    122B  ALA      2.9    14.8    -      -       -      -
     99C  ASP*     2.7    36.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  LEU*     3.6    25.1    -      -       +      -
     36B  THR      3.6     6.1    -      -       -      +
     37B  LEU*     2.8    46.9    -      -       +      +
     38B  THR*     3.6     4.7    -      -       -      +
     52B  THR*     4.8     0.2    -      -       +      -
     53B  SER*     1.3    87.6    -      -       -      +
     55B  PHE*     1.3    63.6    +      -       -      +
     56B  LEU*     4.1     3.7    -      -       +      +
    120B  PRO      3.7     0.5    -      -       -      +
    121B  SER*     2.8     3.6    +      -       -      -
    122B  ALA      2.6    36.3    +      -       -      +
    124B  TYR*     3.2    35.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  LEU*     2.7    36.7    -      -       -      +
     36B  THR*     2.6    44.0    +      -       +      +
     37B  LEU      3.9     8.7    -      -       -      -
     38B  THR*     3.2    28.0    -      -       +      -
     54B  VAL*     1.3    81.4    -      -       -      +
     56B  LEU*     1.3    55.2    +      -       -      +
     57B  ASN*     3.3     7.7    +      -       +      +
    119B  HIS*     4.9     8.7    -      -       +      -
    120B  PRO      3.2    12.3    -      -       -      +
    121B  SER*     3.8     9.6    -      -       -      +
----------------------------------------------------------
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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