Contacts of the strand formed by residues 353 - 362 (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 GLU 353 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295N  CYS*     4.0    12.1    -      -       -      -
    296N  LEU      3.4     6.5    -      -       -      +
    297N  GLN*     3.4    31.0    -      -       -      +
    298N  ILE*     4.0     1.1    -      -       -      -
    351N  GLY      4.0     7.4    -      -       -      +
    352N  GLU*     1.3    85.5    -      -       -      +
    354N  ILE*     1.3    61.3    +      -       -      +
    355N  TYR*     2.9    42.8    +      -       +      -
    378N  PHE*     2.9    24.2    -      -       -      -
    379N  LYS      4.6     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 354 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225N  ALA*     4.1    26.0    -      -       +      -
    270N  THR*     4.7     0.7    -      -       +      -
    294N  PHE*     3.9    11.8    -      -       +      +
    295N  CYS*     3.1     6.8    -      -       -      -
    296N  LEU*     2.8    48.4    +      -       +      +
    298N  ILE*     3.8    21.5    -      -       +      -
    304N  VAL*     4.6     7.9    -      -       +      -
    307N  LEU*     5.2     2.7    -      -       +      -
    346N  LEU*     4.2    16.8    -      -       +      -
    348N  VAL*     5.2     0.4    -      -       +      -
    353N  GLU*     1.3    74.4    -      -       -      +
    355N  TYR*     1.3    65.1    +      -       -      +
    376N  LEU*     3.8    36.3    -      -       +      -
    377N  ASP      3.9     4.9    -      -       -      +
    378N  PHE*     3.8    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 355 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294N  PHE*     3.5     6.1    -      -       -      -
    295N  CYS*     3.7    20.5    -      -       +      -
    353N  GLU*     2.9    42.4    +      -       +      -
    354N  ILE*     1.3    82.4    -      -       -      +
    356N  GLY*     1.3    59.0    +      -       -      +
    376N  LEU*     3.6     2.4    -      -       -      -
    377N  ASP*     2.7    50.2    +      -       +      +
    378N  PHE*     5.8     0.4    -      -       -      -
    379N  LYS      6.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 356 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293N  ALA*     3.3     5.5    -      -       -      +
    294N  PHE*     2.8    46.9    +      -       -      +
    355N  TYR*     1.3    76.8    -      -       -      +
    357N  THR*     1.3    60.8    +      -       -      +
    375N  ASP*     3.0    16.4    -      -       -      -
    376N  LEU*     4.3     0.2    -      -       -      -
    377N  ASP*     4.6     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 357 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291N  THR*     4.0    21.2    -      -       +      +
    292N  SER      3.4     8.1    -      -       -      -
    293N  ALA*     4.3    12.3    -      -       +      +
    294N  PHE*     3.7     2.3    -      -       -      -
    356N  GLY*     1.3    80.1    -      -       -      +
    358N  ILE*     1.3    63.5    +      -       -      +
    359N  SER*     4.9     3.3    +      -       -      -
    373N  THR*     3.8     1.1    +      -       -      +
    374N  VAL*     3.4     2.8    -      -       -      -
    375N  ASP*     2.9    52.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 358 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221N  LEU*     5.9     0.9    -      -       +      -
    223N  VAL*     4.9     7.2    -      -       +      -
    275N  ILE*     3.9    38.8    -      -       +      -
    290N  PHE*     4.1     4.5    -      -       +      -
    291N  THR*     3.9     0.6    -      -       -      -
    292N  SER*     2.9    34.2    +      -       -      +
    294N  PHE*     3.5    24.9    -      -       +      -
    307N  LEU*     6.4     0.7    -      -       +      -
    309N  THR*     4.9    11.7    -      -       +      -
    340N  PHE*     5.2     3.6    -      -       +      -
    357N  THR*     1.3    74.3    -      -       -      +
    359N  SER*     1.3    69.4    +      -       -      +
    360N  MET*     5.3     4.3    -      -       +      -
    372N  PHE*     4.3    22.9    -      -       +      -
    373N  THR      3.4     7.0    -      -       -      +
    374N  VAL*     4.3    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 359 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290N  PHE      3.1     9.2    -      -       -      -
    291N  THR*     3.1    32.4    +      -       -      +
    357N  THR*     4.9     3.1    +      -       -      -
    358N  ILE*     1.3    76.2    +      -       -      +
    360N  MET*     1.3    63.1    +      -       -      +
    361N  LYS*     5.9     1.3    -      -       -      -
    372N  PHE*     3.2     6.9    -      -       -      +
    373N  THR*     2.9    48.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 360 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190N  CYS      5.1     1.6    -      -       -      +
    192N  PHE*     3.5    45.5    -      -       +      -
    221N  LEU*     5.0     6.7    -      -       -      -
    288N  LEU*     3.6    18.2    -      -       +      +
    289N  SER*     3.4     4.3    -      -       -      -
    290N  PHE*     3.1    51.0    +      -       +      -
    358N  ILE*     5.3     3.4    -      -       +      -
    359N  SER*     1.3    76.3    -      -       -      +
    361N  LYS*     1.3    67.8    +      -       -      +
    362N  PRO*     6.0     0.7    -      -       +      -
    370N  LEU*     3.8    19.1    -      -       +      -
    371N  ASP      3.1    13.5    -      -       -      +
    372N  PHE*     3.7    33.9    -      -       +      -
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Residues in contact with LYS 361 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289N  SER*     3.9    15.0    -      -       -      +
    290N  PHE      5.6     0.2    -      -       -      +
    359N  SER*     5.9     1.1    -      -       -      -
    360N  MET*     1.3    77.7    -      -       -      +
    362N  PRO*     1.3    81.1    +      -       +      +
    364N  ALA*     5.8     4.9    -      -       -      +
    370N  LEU*     3.6    10.3    -      -       -      +
    371N  ASP*     2.9    50.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 362 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195N  SER*     4.2    13.2    -      -       -      +
    198N  ASN*     5.1     6.7    -      -       -      +
    288N  LEU*     4.7    10.5    -      -       +      +
    289N  SER*     3.3    17.9    -      -       -      +
    360N  MET*     6.0     0.7    -      -       +      -
    361N  LYS*     1.3   100.3    -      -       +      +
    363N  ASN*     1.3    64.4    +      -       -      +
    364N  ALA*     3.6     1.7    +      -       -      -
    367N  VAL*     3.6    33.2    -      -       +      +
    369N  ASP      3.6     8.1    -      -       -      +
    370N  LEU*     4.7     5.4    -      -       +      -
    371N  ASP*     5.2     0.2    -      -       -      -
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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