Contacts of the strand formed by residues 143 - 148 (chain B) in PDB entry 5FDK


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 GLN 143 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  SER*     3.4     1.6    +      -       -      -
    140B  ALA      2.6    39.8    +      -       -      +
    141B  PHE      2.9     4.9    -      -       -      +
    142B  ASP*     1.3    81.4    -      -       +      +
    144B  VAL*     1.3    71.8    +      -       -      +
    145B  TYR*     3.4    38.5    +      -       +      +
    178B  PRO*     3.5    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  LEU*     4.5    11.2    -      -       +      -
     38B  ASP*     5.9     1.1    -      -       -      +
    137B  ILE*     5.3     4.5    -      -       +      -
    138B  ILE      3.3     5.6    -      -       -      +
    139B  SER*     3.7    23.1    -      -       -      +
    143B  GLN*     1.3    85.2    -      -       -      +
    145B  TYR*     1.3    53.8    +      -       -      +
    178B  PRO*     3.6     2.8    -      -       -      +
    179B  ILE*     2.7    54.0    +      -       +      +
    181B  LEU*     4.6     9.4    -      -       +      -
    187B  ILE*     4.4    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  ILE*     3.6     6.9    -      -       -      +
    138B  ILE*     2.8    45.3    +      -       +      +
    140B  ALA      3.4    23.8    -      -       -      -
    141B  PHE*     3.9    21.5    +      +       -      +
    143B  GLN*     3.4    32.1    +      -       +      +
    144B  VAL*     1.3    74.3    -      -       -      +
    146B  PHE*     1.3    61.1    +      -       -      +
    147B  LEU*     3.7     1.4    +      -       +      +
    169B  LYS*     5.2     1.7    -      -       -      -
    172B  LEU*     3.6    33.7    -      -       +      -
    173B  GLU*     4.1    30.5    +      -       +      +
    176B  ALA*     4.1    20.0    -      -       +      -
    177B  TYR      4.6     1.6    -      -       -      -
    178B  PRO*     3.8    24.2    -      -       +      -
    179B  ILE*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  ILE*     5.7     1.1    -      -       +      -
    135B  PHE*     3.3    58.1    -      +       +      -
    136B  VAL      4.2     2.0    -      -       -      -
    137B  ILE*     4.8     4.3    -      -       +      +
    144B  VAL      4.1     0.8    +      -       -      -
    145B  TYR*     1.3    73.0    -      -       -      +
    147B  LEU*     1.3    57.0    +      -       -      +
    148B  GLU*     3.7    25.6    +      -       +      -
    176B  ALA*     3.4    13.9    -      -       -      +
    177B  TYR*     3.1    22.5    +      -       +      +
    179B  ILE*     4.6    11.2    -      -       +      +
    189B  TYR*     4.6    10.5    -      -       +      -
    192B  ILE*     3.8    34.5    -      -       +      -
    193B  ILE*     4.3    12.6    -      -       +      -
    196B  LEU*     4.8    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  PHE*     3.3     4.5    -      -       -      +
    136B  VAL*     2.9    51.4    +      -       +      +
    138B  ILE*     3.7    27.6    -      -       +      -
    145B  TYR*     3.7     1.9    +      -       +      +
    146B  PHE*     1.3    72.4    -      -       -      +
    148B  GLU*     1.3    73.1    +      -       -      +
    151B  LYS*     3.9    20.9    -      -       +      -
    152B  LEU*     4.1    21.1    -      -       +      -
    155B  PHE*     4.9     2.0    -      -       +      -
    167B  ILE*     4.6    10.1    -      -       +      -
    172B  LEU*     4.4    10.3    -      -       +      -
    175B  THR*     4.3    12.6    -      -       -      +
    176B  ALA*     3.7    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  LYS*     3.9    21.1    -      -       -      -
    134B  CYS      4.3     6.6    -      -       -      +
    135B  PHE*     4.4     2.7    -      -       -      -
    146B  PHE*     3.7    27.1    +      -       +      -
    147B  LEU*     1.3    82.4    -      -       -      +
    149B  ALA*     1.3    67.7    +      -       -      +
    150B  ASP*     3.2    21.5    -      -       -      +
    151B  LYS*     3.5    22.0    +      -       +      +
    152B  LEU*     3.2    18.5    +      -       -      +
    175B  THR      5.1     2.3    +      -       -      +
    176B  ALA*     5.3     0.2    -      -       -      +
    196B  LEU*     5.1     7.3    -      -       -      +
----------------------------------------------------------
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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