Contacts of the strand formed by residues 46 - 51 (chain B) in PDB entry 6DBU


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 PHE 46 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  CYS*     4.8     3.8    -      -       +      -
     14B  LEU*     3.5    27.6    -      -       +      -
     29B  TYR*     3.0    11.8    -      -       -      +
     30B  LEU*     2.9    48.8    +      -       +      +
     33B  GLN*     3.4    27.1    -      -       +      -
     40B  SER*     6.5     0.2    -      -       -      -
     41B  CYS*     3.4    27.8    -      -       +      -
     44B  GLY*     3.0    24.9    +      -       -      -
     45B  ILE*     1.3    78.3    -      -       -      +
     47B  GLY*     1.3    63.6    +      -       -      +
     57B  LEU*     3.7    33.7    -      -       +      -
     58B  ARG      3.6    10.8    -      -       -      +
     59B  ALA*     5.3     2.5    -      -       +      -
     60B  ILE*     3.4     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  ASP*     6.1     0.9    -      -       -      -
     28B  VAL      3.7     6.7    -      -       -      -
     29B  TYR*     3.8     4.3    -      -       -      -
     46B  PHE*     1.3    73.5    -      -       -      +
     48B  VAL*     1.3    61.6    +      -       -      -
     56B  LYS      3.9     0.2    -      -       -      +
     57B  LEU*     3.3     7.2    -      -       -      +
     58B  ARG*     2.9    44.2    +      -       -      +
     60B  ILE*     3.3    20.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  LEU*     4.8     8.7    -      -       +      -
     27B  ASP*     4.5     6.5    -      -       -      +
     28B  VAL*     3.0    57.1    +      -       +      +
     29B  TYR      4.3     0.9    -      -       -      +
     30B  LEU*     4.4    11.9    -      -       +      +
     47B  GLY*     1.3    73.2    -      -       -      -
     49B  ARG*     1.3    69.9    +      -       -      +
     50B  ILE*     4.7     3.6    -      -       +      -
     55B  LEU*     3.6    31.2    -      -       +      -
     56B  LYS      3.5     3.6    -      -       -      +
     57B  LEU*     3.5    20.0    -      -       +      -
    322B  LEU*     5.1     4.7    -      -       +      -
    328B  LEU*     5.9     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  ASP*     4.0    23.8    -      -       -      +
     47B  GLY      4.3     0.6    -      -       -      -
     48B  VAL*     1.3    79.4    -      -       -      +
     50B  ILE*     1.3    65.3    +      -       -      +
     51B  LYS*     4.2    21.5    +      -       +      +
     54B  GLU      3.5     1.6    -      -       -      +
     55B  LEU*     3.6     3.3    -      -       -      -
     56B  LYS*     2.9    77.1    +      -       +      +
     58B  ARG*     3.0    53.7    -      -       +      +
    118B  ARG*     6.1     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     3.6    26.7    -      -       +      -
     48B  VAL*     4.7     3.6    -      -       +      -
     49B  ARG*     1.3    72.8    -      -       -      +
     51B  LYS*     1.3    64.1    +      -       -      +
     52B  LYS      5.1     0.7    -      -       -      +
     53B  GLY      4.7     9.2    -      -       -      +
     54B  GLU      3.2     6.5    -      -       -      +
     55B  LEU*     3.6    25.4    -      -       +      -
    322B  LEU*     3.6    35.2    -      -       +      -
    328B  LEU*     5.5     3.4    -      -       +      -
    347B  GLN*     3.6    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ARG*     5.0    21.7    -      -       +      +
     50B  ILE*     1.3    73.8    -      -       -      +
     52B  LYS*     1.3    85.6    +      -       +      +
     54B  GLU*     2.9    29.8    +      -       +      +
     56B  LYS*     6.3     1.9    -      -       +      +
----------------------------------------------------------
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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