Contacts of the strand formed by residues 290 - 297 (chain I) 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 PHE 290 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192I  PHE*     4.2     7.9    -      +       -      -
    221I  LEU*     4.8     5.2    -      -       +      -
    275I  ILE*     3.9    10.8    -      -       +      -
    276I  LYS*     3.8    37.9    -      -       +      +
    287I  GLU      3.7    16.6    -      -       -      +
    288I  LEU*     3.5    17.3    -      -       -      -
    289I  SER*     1.3    75.3    -      -       -      +
    291I  THR*     1.3    67.2    +      -       -      +
    292I  SER*     3.6    27.8    -      -       -      -
    358I  ILE*     4.1     9.9    -      -       +      -
    359I  SER*     3.0    24.3    -      -       -      -
    360I  MET*     3.1    47.0    +      -       +      +
    361I  LYS*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 291 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379D  LYS*     5.7     3.1    +      -       -      -
    290I  PHE*     1.3    76.8    -      -       -      +
    292I  SER*     1.3    66.4    +      -       -      +
    357I  THR*     4.0    25.4    -      -       +      +
    358I  ILE      3.9     0.7    -      -       -      +
    359I  SER*     3.1    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 292 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274I  LEU      5.0     0.2    +      -       -      -
    275I  ILE*     2.5    40.0    +      -       -      +
    276I  LYS*     5.7     0.2    -      -       -      +
    290I  PHE*     3.6    15.5    -      -       -      -
    291I  THR*     1.3    83.1    -      -       -      +
    293I  ALA*     1.3    67.1    +      -       -      +
    357I  THR*     3.4     2.0    -      -       -      -
    358I  ILE*     2.9    37.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 293 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353D  GLU*     4.7     0.5    -      -       -      +
    355D  TYR*     3.4    30.7    +      -       +      +
    273I  CYS*     4.4     2.8    -      -       -      -
    274I  LEU      4.5     2.9    -      -       -      +
    275I  ILE*     4.4     4.5    -      -       -      +
    292I  SER*     1.3    79.7    +      -       -      +
    294I  PHE*     1.3    61.5    +      -       -      +
    356I  GLY      3.3     9.9    -      -       -      +
    357I  THR*     4.0    11.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 294 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355D  TYR*     3.1    11.8    -      -       -      -
    223I  VAL*     4.1     8.7    -      -       +      -
    273I  CYS*     3.6    16.4    -      -       -      -
    275I  ILE*     4.0    10.8    -      -       +      -
    293I  ALA*     1.3    76.3    -      -       -      +
    295I  CYS*     1.3    64.0    +      -       -      +
    296I  LEU*     4.2    20.4    -      -       +      -
    307I  LEU*     4.0    25.1    -      -       +      -
    354I  ILE*     4.2    15.0    -      -       +      -
    355I  TYR*     3.4     9.3    -      -       -      +
    356I  GLY*     2.7    76.6    +      -       -      +
    357I  THR      3.4    13.5    -      -       -      -
    358I  ILE*     3.5    22.9    -      -       +      -
    374I  VAL*     4.3     5.6    -      -       +      -
    375I  ASP      3.8     6.3    -      -       -      -
    376I  LEU*     4.7     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 295 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295D  CYS*     3.4    45.1    -      -       +      -
    353D  GLU*     4.2     4.2    -      -       -      +
    355D  TYR*     3.3     7.1    +      -       +      -
    271I  ASN*     4.6     3.3    +      -       -      +
    272I  ALA      5.1     0.5    -      -       -      +
    273I  CYS*     3.3    23.9    -      -       -      +
    294I  PHE*     1.3    76.9    -      -       -      +
    296I  LEU*     1.3    68.2    +      -       -      +
    297I  GLN*     4.2     1.0    +      -       -      -
    353I  GLU*     4.1    15.0    -      -       -      -
    354I  ILE      3.2     9.0    -      -       -      -
    355I  TYR*     3.6    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 296 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223I  VAL*     3.5    22.4    -      -       +      +
    224I  VAL*     3.8     6.3    -      -       -      +
    225I  ALA*     3.6    31.2    -      -       +      +
    270I  THR*     3.9    13.2    -      -       +      +
    271I  ASN*     3.4    24.2    -      -       -      +
    273I  CYS*     3.8    11.4    -      -       +      +
    294I  PHE*     4.2    17.7    -      -       +      -
    295I  CYS*     1.3    85.2    -      -       -      +
    297I  GLN*     1.3    62.3    +      -       -      +
    298I  ILE*     3.7     2.4    +      -       -      +
    307I  LEU*     4.2    13.5    -      -       +      -
    353I  GLU*     3.3     5.2    -      -       -      -
    354I  ILE*     2.8    46.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 297 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271D  ASN*     4.2    20.6    +      -       -      +
    272D  ALA      3.3    22.3    +      -       -      +
    273D  CYS*     4.6     1.0    -      -       -      +
    274D  LEU      5.5     0.3    +      -       -      -
    295D  CYS      5.7     0.2    -      -       -      +
    270I  THR*     3.3    21.4    -      -       -      -
    271I  ASN*     2.8    25.9    +      -       -      +
    295I  CYS*     4.2     1.6    -      -       -      -
    296I  LEU*     1.3    72.9    -      -       -      +
    298I  ILE*     1.3    69.1    +      -       -      +
    299I  GLN*     3.3    22.0    +      -       -      +
    351I  GLY*     4.8     9.4    -      -       -      +
    352I  GLU      3.9     7.6    -      -       -      +
    353I  GLU*     3.5    20.7    -      -       +      +
----------------------------------------------------------
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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