Contacts of the strand formed by residues 218 - 226 (chain E) 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 ARG 218 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216E  PRO*     3.9     1.8    -      -       -      +
    217E  ASP*     1.3    84.9    +      -       -      +
    219E  ALA*     1.3    63.8    +      -       -      +
    220E  ALA*     3.8    26.0    -      -       -      +
    222E  TYR*     5.2     3.2    +      -       -      -
    274E  LEU*     5.9     0.2    -      -       -      +
    277E  GLU*     3.2    33.1    +      -       -      +
    278E  VAL      3.4     9.6    +      -       -      +
    279E  ASP*     5.0     6.7    -      -       +      +
    280E  ILE*     4.1     3.4    -      -       -      +
    312E  ASN*     5.7     4.0    +      -       -      +
    313E  ILE*     3.7     6.3    -      -       -      +
    314E  GLU*     2.9    68.8    +      -       +      +
    316E  THR*     4.1    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 219 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186E  TRP*     4.2    18.2    -      -       +      -
    191E  LEU*     4.1    18.2    -      -       +      -
    218E  ARG*     1.3    79.0    +      -       -      +
    220E  ALA*     1.3    63.6    +      -       -      +
    276E  LYS      4.1     0.2    -      -       -      +
    277E  GLU*     3.6     2.4    -      -       -      +
    278E  VAL*     2.8    40.9    +      -       +      +
    312E  ASN      3.3     7.6    -      -       -      -
    313E  ILE*     3.7    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 220 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191E  LEU*     4.6     2.6    -      -       -      +
    218E  ARG*     3.8    20.6    -      -       -      +
    219E  ALA*     1.3    76.7    -      -       -      +
    221E  LEU*     1.3    61.3    +      -       -      +
    222E  TYR*     3.7    24.3    -      -       +      +
    274E  LEU*     3.9    13.0    -      -       +      -
    276E  LYS      3.2     5.6    -      -       -      +
    277E  GLU*     4.7     1.8    -      -       -      -
    311E  PHE*     3.0     7.0    -      -       -      -
    312E  ASN*     2.9    37.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 221 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190E  CYS*     4.0    29.8    -      -       -      +
    191E  LEU*     4.2    10.1    -      -       +      -
    192E  PHE*     4.1    20.9    -      -       +      -
    220E  ALA*     1.3    73.5    -      -       -      +
    222E  TYR*     1.3    61.7    +      -       -      +
    274E  LEU*     3.6     4.5    -      -       -      +
    275E  ILE*     2.9    50.0    +      -       +      +
    276E  LYS*     2.8    24.7    +      -       +      +
    290E  PHE*     4.8     5.4    -      -       +      -
    309E  THR*     4.1    15.3    -      -       -      -
    310E  TYR      3.5    20.0    -      -       -      +
    311E  PHE*     4.1     8.3    -      -       +      -
    358E  ILE*     5.8     0.9    -      -       +      -
    360E  MET*     4.9     4.5    -      -       -      -
    372E  PHE*     6.1     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 222 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218E  ARG*     5.2     2.9    +      -       -      -
    220E  ALA*     3.7    30.0    -      -       +      +
    221E  LEU*     1.3    75.9    -      -       -      +
    223E  VAL*     1.3    62.3    +      -       -      +
    272E  ALA*     4.3     8.7    -      -       +      -
    273E  CYS*     3.3    17.7    -      -       -      +
    274E  LEU*     3.7    32.4    -      -       +      +
    275E  ILE*     4.3     3.4    -      -       -      -
    308E  VAL      4.5     0.2    -      -       -      -
    309E  THR*     3.1    30.8    -      -       -      +
    310E  TYR*     2.8    52.5    +      +       +      +
    312E  ASN*     3.3    23.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 223 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222E  TYR*     1.3    70.7    -      -       -      +
    224E  VAL*     1.3    71.0    +      -       -      +
    272E  ALA*     3.4     2.1    -      -       -      +
    273E  CYS*     3.0    36.1    +      -       +      +
    275E  ILE*     3.6    31.6    -      -       +      -
    294E  PHE*     3.9    24.7    -      -       +      -
    296E  LEU*     3.5     7.7    -      -       +      +
    307E  LEU*     4.7    19.5    -      -       +      -
    308E  VAL      3.4     6.7    -      -       -      +
    309E  THR*     3.6    24.9    -      -       +      -
    310E  TYR*     5.3     0.4    -      -       -      -
    358E  ILE*     5.0     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 224 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223E  VAL*     1.3    83.1    -      -       -      +
    225E  ALA*     1.3    64.5    +      -       -      +
    226E  ILE*     4.0     8.3    -      -       +      -
    268E  VAL*     3.5    37.2    -      -       +      -
    270E  THR*     3.7     6.1    -      -       -      +
    271E  ASN      3.4    18.4    -      -       -      +
    272E  ALA*     3.7    14.6    -      -       +      -
    296E  LEU*     3.8     7.4    -      -       -      -
    307E  LEU*     3.4     5.0    -      -       -      +
    308E  VAL*     2.8    41.6    +      -       +      +
    310E  TYR*     4.2    14.6    -      -       +      -
    328E  PRO*     5.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 225 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224E  VAL*     1.3    73.5    -      -       -      +
    226E  ILE*     1.3    67.0    +      -       -      +
    268E  VAL*     3.7     1.0    -      -       -      -
    269E  VAL*     2.9    26.2    +      -       -      +
    270E  THR*     3.1    28.0    +      -       +      -
    296E  LEU*     3.7    11.6    -      -       +      +
    304E  VAL*     3.8    24.5    -      -       +      -
    306E  ALA      3.5     5.8    -      -       -      +
    307E  LEU*     4.0     6.3    -      -       +      -
    354E  ILE*     4.0     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 226 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224E  VAL*     4.0     4.0    -      -       +      -
    225E  ALA*     1.3    79.7    -      -       -      +
    227E  GLU*     1.3    60.1    +      -       -      +
    228E  ASP*     3.9    26.5    -      -       +      +
    263E  VAL*     3.9    22.9    -      -       +      -
    267E  GLN*     3.3    13.9    -      -       +      +
    268E  VAL*     3.9    25.1    -      -       +      -
    269E  VAL*     4.2     6.1    -      -       -      -
    304E  VAL*     3.4     4.2    -      -       -      -
    305E  HIS      2.9    23.0    +      -       -      -
    306E  ALA*     3.0    24.6    +      -       +      +
    308E  VAL*     3.5    34.3    -      -       +      -
    328E  PRO*     6.1     0.2    -      -       +      -
    339E  VAL*     4.6     4.3    -      -       +      -
----------------------------------------------------------
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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