Contacts of the strand formed by residues 353 - 362 (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 GLU 353 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273D  CYS*     3.1    32.0    -      -       -      +
    274D  LEU*     4.7     3.4    -      -       -      +
    293D  ALA      4.8     1.0    -      -       -      +
    295D  CYS*     4.3     4.6    -      -       -      +
    295I  CYS*     4.1    10.9    -      -       -      -
    296I  LEU      3.3    10.5    -      -       -      +
    297I  GLN*     3.5    24.0    -      -       -      +
    298I  ILE*     4.1     1.6    -      -       -      -
    351I  GLY      3.9     8.5    -      -       -      +
    352I  GLU*     1.3    86.5    -      -       -      +
    354I  ILE*     1.3    60.5    +      -       -      +
    355I  TYR*     2.9    41.7    +      -       +      -
    377I  ASP      4.3     1.9    -      -       -      +
    378I  PHE*     3.2    21.8    -      -       -      -
    379I  LYS      4.7     3.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 354 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225I  ALA*     4.1    25.4    -      -       +      -
    270I  THR*     4.7     0.4    -      -       +      -
    294I  PHE*     3.8    12.2    -      -       +      +
    295I  CYS*     3.2     4.2    -      -       -      -
    296I  LEU*     2.8    49.1    +      -       +      +
    298I  ILE*     3.8    22.9    -      -       +      -
    304I  VAL*     4.6     8.5    -      -       +      -
    307I  LEU*     5.2     2.5    -      -       +      -
    346I  LEU*     4.1    17.3    -      -       +      -
    348I  VAL*     5.1     0.4    -      -       +      -
    353I  GLU*     1.3    73.6    -      -       -      +
    355I  TYR*     1.3    65.7    +      -       -      +
    376I  LEU*     3.7    37.5    -      -       +      -
    377I  ASP      3.9     3.4    -      -       -      +
    378I  PHE*     3.8    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 355 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293D  ALA*     3.5    22.6    -      -       +      -
    294D  PHE*     3.2    33.2    +      -       -      -
    295D  CYS*     3.5    10.4    +      -       +      -
    355D  TYR*     4.4    16.6    -      +       -      -
    294I  PHE*     3.4     8.5    -      -       -      -
    295I  CYS*     3.6    21.1    -      -       +      -
    353I  GLU*     2.9    43.5    +      -       +      -
    354I  ILE*     1.3    81.3    -      -       -      +
    356I  GLY*     1.3    59.0    +      -       -      +
    376I  LEU*     3.6     3.1    -      -       -      -
    377I  ASP*     2.8    43.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 356 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293I  ALA*     3.3     4.7    -      -       -      +
    294I  PHE*     2.7    48.9    +      -       -      +
    355I  TYR*     1.3    77.2    -      -       -      +
    357I  THR*     1.3    60.6    +      -       -      +
    375I  ASP*     3.0    16.6    -      -       -      -
    376I  LEU*     4.3     0.4    -      -       -      -
    377I  ASP*     4.6     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 357 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291I  THR*     4.0    21.8    -      -       +      +
    292I  SER      3.4     8.5    -      -       -      -
    293I  ALA*     4.2    13.7    -      -       +      -
    294I  PHE*     3.6     2.3    -      -       -      -
    356I  GLY*     1.3    79.2    -      -       -      +
    358I  ILE*     1.3    61.9    +      -       -      +
    359I  SER*     5.0     2.8    +      -       -      -
    373I  THR      3.7     0.3    +      -       -      +
    374I  VAL*     3.5     2.3    -      -       -      -
    375I  ASP*     2.9    47.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 358 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221I  LEU*     5.9     0.9    -      -       +      -
    223I  VAL*     4.9     8.1    -      -       +      -
    275I  ILE*     3.9    37.9    -      -       +      -
    290I  PHE*     4.1     4.7    -      -       +      -
    291I  THR*     3.9     0.2    -      -       -      -
    292I  SER*     2.9    31.9    +      -       -      +
    294I  PHE*     3.5    24.0    -      -       +      -
    307I  LEU*     6.4     0.9    -      -       +      -
    309I  THR*     4.9    11.4    -      -       +      -
    340I  PHE*     5.3     3.4    -      -       +      -
    357I  THR*     1.3    75.7    -      -       -      +
    359I  SER*     1.3    68.7    +      -       -      +
    360I  MET*     5.3     4.3    -      -       +      -
    372I  PHE*     4.3    21.3    -      -       +      -
    373I  THR      3.3     6.7    -      -       -      +
    374I  VAL*     4.3    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 359 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290I  PHE      3.0     9.4    -      -       -      -
    291I  THR*     3.1    31.8    +      -       -      +
    357I  THR*     5.0     2.3    +      -       -      -
    358I  ILE*     1.3    76.5    -      -       -      +
    360I  MET*     1.3    62.1    +      -       -      +
    361I  LYS*     6.0     1.6    -      -       -      -
    372I  PHE*     3.2     6.9    -      -       -      +
    373I  THR*     2.8    47.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 360 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190I  CYS      5.1     2.0    -      -       -      +
    192I  PHE*     3.6    45.8    -      -       +      -
    221I  LEU*     4.9     6.7    -      -       -      -
    288I  LEU*     3.6    19.0    -      -       +      +
    289I  SER*     3.3     4.9    -      -       -      -
    290I  PHE*     3.1    51.8    +      -       +      -
    358I  ILE*     5.3     2.7    -      -       +      -
    359I  SER*     1.3    75.2    -      -       -      +
    361I  LYS*     1.3    65.1    +      -       -      +
    362I  PRO*     6.0     0.2    -      -       +      -
    370I  LEU*     3.8    19.7    -      -       +      -
    371I  ASP      3.0    13.5    -      -       -      +
    372I  PHE*     3.6    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 361 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288I  LEU      4.9     0.2    -      -       -      -
    289I  SER*     3.8    14.4    -      -       -      +
    290I  PHE      5.7     0.4    -      -       -      +
    359I  SER*     6.0     1.6    -      -       -      -
    360I  MET*     1.3    78.1    -      -       -      +
    362I  PRO*     1.3    81.8    +      -       +      +
    364I  ALA*     5.7     5.4    -      -       -      +
    370I  LEU*     3.6    10.3    -      -       -      +
    371I  ASP*     2.9    49.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 362 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195I  SER*     4.0    14.6    -      -       -      +
    198I  ASN*     5.1     7.2    -      -       -      +
    288I  LEU*     4.7     9.9    -      -       +      +
    289I  SER*     3.5    16.6    -      -       -      +
    360I  MET*     6.0     0.4    -      -       +      -
    361I  LYS*     1.3   102.7    +      -       +      +
    363I  ASN*     1.3    66.4    +      -       -      +
    364I  ALA*     3.6     1.9    +      -       -      -
    367I  VAL*     3.7    33.9    -      -       +      +
    369I  ASP      3.6     7.6    -      -       -      +
    370I  LEU*     4.6     5.4    -      -       +      -
----------------------------------------------------------
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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