Contacts of the strand formed by residues 114 - 118 (chain N) in PDB entry 5DST


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 VAL 114 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113N  LYS*     1.3    76.0    -      -       -      +
    115N  VAL*     1.3    61.0    +      -       -      +
    135N  LYS*     4.1    21.1    -      -       -      -
    136N  LYS*     3.3    15.7    -      -       +      +
    138N  PHE*     4.0    30.5    -      -       +      -
    176N  VAL*     4.6    11.2    -      -       +      -
    178N  LYS      4.9     1.3    -      -       -      +
    179N  VAL*     3.4    20.4    -      -       +      +
    180N  ASP*     3.0    37.4    +      -       -      +
    181N  ILE      3.4     8.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 115 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110N  PHE*     3.9    19.7    -      -       +      -
    113N  LYS*     4.3     2.2    -      -       +      +
    114N  VAL*     1.3    80.3    -      -       -      +
    116N  LEU*     1.3    60.3    +      -       -      +
    129N  ALA*     4.2     6.1    -      -       +      -
    134N  ALA*     3.8    24.2    -      -       +      -
    136N  LYS      2.9    11.1    +      -       -      +
    137N  VAL*     3.2    11.6    -      -       +      +
    138N  PHE*     2.7    34.7    +      -       -      +
    179N  VAL*     4.3     2.0    -      -       -      -
    181N  ILE*     3.4    19.5    -      -       +      +
    183N  ILE*     3.8    39.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 116 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115N  VAL*     1.3    73.9    -      -       -      +
    117N  ASP*     1.3    60.3    +      -       -      +
    118N  VAL*     3.6    23.0    +      -       +      -
    138N  PHE*     3.4    19.5    -      -       +      +
    140N  ILE*     3.8    27.8    -      -       +      -
    174N  LEU*     4.2    13.0    -      -       +      -
    179N  VAL*     3.8    18.3    -      -       +      +
    181N  ILE      2.9     8.7    +      -       -      -
    182N  ILE*     3.5    18.6    -      -       +      +
    183N  ILE      2.9    28.9    +      -       -      +
    203N  ALA*     4.2     3.4    -      -       +      -
    207N  TRP*     3.7    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 117 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115N  VAL*     4.0     1.6    +      -       -      +
    116N  LEU*     1.3    72.0    -      -       -      +
    118N  VAL*     1.3    69.3    +      -       -      +
    119N  GLY      3.5     3.8    +      -       -      +
    120N  SER*     3.4    26.4    +      -       -      +
    125N  LEU*     3.4    18.2    -      -       -      +
    126N  SER*     2.7    41.7    +      -       -      +
    137N  VAL*     4.8     0.9    -      -       +      -
    138N  PHE      2.8    12.1    +      -       -      +
    139N  GLY*     3.5     2.8    -      -       -      -
    140N  ILE      3.1    25.5    +      -       -      +
    183N  ILE*     3.5    18.9    -      -       +      +
    401N  SAH      4.1     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 118 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116N  LEU*     3.8    29.6    -      -       +      -
    117N  ASP*     1.3    70.3    -      -       -      +
    119N  GLY*     1.3    66.6    +      -       -      +
    140N  ILE*     4.5     1.3    -      -       +      +
    169N  VAL*     4.1    12.1    -      -       +      -
    182N  ILE*     4.0    16.2    -      -       +      -
    183N  ILE      3.0     7.3    +      -       -      -
    184N  SER*     2.8    38.1    +      -       -      +
    185N  GLU      4.6     1.9    +      -       -      +
    196N  MET*     3.4     9.2    -      -       +      +
    199N  THR*     3.9    28.3    -      -       +      +
    200N  VAL*     4.1    15.3    -      -       +      -
    203N  ALA*     3.8    13.7    -      -       +      -
----------------------------------------------------------
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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