Contacts of the strand formed by residues 302 - 314 (chain H) 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 ASP 302 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319F  HIS*     3.1    22.5    +      -       -      -
    320F  LYS*     3.3    30.2    +      -       -      +
    227H  GLU*     3.7    12.1    -      -       -      +
    269H  VAL*     3.9    22.0    -      -       +      -
    300H  ARG*     2.9    43.4    +      -       +      +
    301H  ASN*     1.3    75.6    -      -       -      +
    303H  TYR*     1.3    81.6    +      -       -      +
    347H  THR*     4.1     0.2    -      -       -      -
    348H  VAL*     3.0    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 303 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105F  HIS*     2.5    44.5    +      +       +      +
    106F  ASN*     3.0    14.4    +      -       -      -
    319F  HIS*     3.6    15.7    -      -       -      +
    320F  LYS*     4.2    26.4    +      -       +      +
    227H  GLU*     3.2    27.6    +      -       +      +
    269H  VAL*     4.1     0.3    -      -       -      +
    302H  ASP*     1.3    90.1    +      -       -      +
    304H  VAL*     1.3    66.1    +      -       -      +
    305H  HIS*     3.8    22.0    -      +       +      -
    345H  TYR*     3.6    27.1    -      +       +      -
    346H  LEU      3.2     6.7    -      -       -      +
    347H  THR*     3.9    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 304 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225H  ALA*     3.9    27.6    -      -       +      -
    226H  ILE      3.3     9.4    -      -       -      +
    269H  VAL*     4.0    26.2    -      -       +      -
    298H  ILE*     5.2     0.2    -      -       +      -
    303H  TYR*     1.3    78.0    -      -       -      +
    305H  HIS*     1.3    63.6    +      -       -      +
    306H  ALA      4.0     9.9    -      -       -      +
    307H  LEU*     5.1     1.6    -      -       +      -
    342H  LEU*     4.1    16.2    -      -       +      +
    345H  TYR*     3.3     4.8    -      -       -      -
    346H  LEU*     2.9    51.1    +      -       +      -
    348H  VAL*     4.2    12.6    -      -       +      -
    354H  ILE*     4.6     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 305 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226H  ILE      2.9     5.1    +      -       -      -
    227H  GLU*     3.9     8.1    -      -       +      +
    228H  ASP*     3.3    33.8    +      -       +      +
    229H  ARG*     3.1    42.4    -      -       +      +
    232H  LYS*     4.1    25.5    -      -       +      +
    303H  TYR*     3.8    26.2    +      +       +      -
    304H  VAL*     1.3    75.3    -      -       -      +
    306H  ALA*     1.3    61.2    +      -       +      +
    341H  TYR*     4.0     4.1    -      -       +      -
    342H  LEU*     3.0    33.0    +      -       -      +
    345H  TYR*     3.7    31.6    -      +       +      +
----------------------------------------------------------
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Residues in contact with ALA 306 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225H  ALA*     3.5     5.0    -      -       -      +
    226H  ILE*     2.9    40.1    +      -       +      +
    228H  ASP*     5.4     0.2    -      -       +      -
    304H  VAL*     3.6     4.0    -      -       -      +
    305H  HIS*     1.3    82.7    -      -       +      +
    307H  LEU*     1.3    61.9    +      -       -      +
    339H  VAL*     3.8    25.4    -      -       +      -
    340H  PHE      3.2    18.2    -      -       -      +
    341H  TYR*     3.9    11.2    -      -       +      -
    342H  LEU*     4.2     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 307 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223H  VAL*     4.7    15.0    -      -       +      -
    224H  VAL      3.4     4.0    -      -       -      +
    225H  ALA*     3.9    23.3    -      -       +      -
    294H  PHE*     4.0    18.8    -      -       +      -
    296H  LEU*     4.1    14.4    -      -       +      -
    304H  VAL*     5.1     4.3    -      -       +      -
    306H  ALA*     1.3    75.1    -      -       -      +
    308H  VAL*     1.3    62.1    +      -       -      +
    340H  PHE*     2.6    52.7    +      -       +      +
    342H  LEU*     4.7     7.6    -      -       +      -
    354H  ILE*     5.1     2.5    -      -       +      -
    358H  ILE*     6.4     1.3    -      -       +      -
    374H  VAL*     3.8    32.8    -      -       +      -
    376H  LEU*     4.3    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 308 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223H  VAL*     3.4     4.0    -      -       -      -
    224H  VAL*     2.8    43.1    +      -       +      +
    226H  ILE*     3.7    39.3    -      -       +      -
    263H  VAL*     4.1     8.3    -      -       +      -
    307H  LEU*     1.3    81.1    -      -       -      +
    309H  THR*     1.3    67.3    +      -       -      +
    310H  TYR*     4.2     3.5    +      -       +      -
    328H  PRO*     4.8     8.3    -      -       +      -
    337H  GLN*     3.6    30.7    -      -       +      -
    338H  THR      3.2    10.8    -      -       -      +
    339H  VAL*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 309 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190H  CYS*     3.1    30.6    -      -       -      +
    221H  LEU*     4.1     7.4    -      -       +      -
    222H  TYR      3.1    13.9    -      -       -      +
    223H  VAL*     3.7    17.3    -      -       +      -
    275H  ILE*     4.7     8.7    -      -       +      -
    308H  VAL*     1.3    79.0    -      -       -      +
    310H  TYR*     1.3    61.5    -      -       -      +
    337H  GLN*     3.8     3.8    -      -       -      +
    338H  THR*     2.9    41.0    +      -       -      -
    340H  PHE*     3.7    20.6    -      -       +      -
    358H  ILE*     4.9     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 310 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190H  CYS*     6.4     0.2    -      -       -      +
    221H  LEU*     3.6     4.3    -      -       -      +
    222H  TYR*     2.8    63.5    +      +       +      +
    224H  VAL*     4.2    22.4    -      -       +      -
    272H  ALA*     3.3    21.1    -      -       -      +
    308H  VAL*     4.9     6.5    -      -       +      -
    309H  THR*     1.3    74.8    -      -       -      +
    311H  PHE*     1.3    66.5    +      -       -      +
    312H  ASN*     3.8    19.5    -      -       -      -
    326H  THR*     3.5    25.4    -      -       -      +
    327H  ALA*     3.6    28.0    -      -       +      -
    328H  PRO*     3.9    17.9    -      -       +      -
    329H  ASP*     5.6     1.8    -      -       -      -
    336H  LYS      5.3     0.4    -      -       -      -
    337H  GLN*     4.4     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 311 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187H  MET*     4.2     7.6    -      -       +      -
    188H  GLY      3.7     8.1    -      -       -      -
    190H  CYS*     4.4     7.0    -      -       -      -
    191H  LEU*     3.5    49.4    -      -       +      -
    220H  ALA      3.1    19.5    -      -       -      +
    221H  LEU*     4.0     8.5    -      -       +      -
    310H  TYR*     1.3    79.0    -      -       -      +
    312H  ASN*     1.3    62.7    +      -       -      +
    313H  ILE*     3.8    26.5    -      -       +      -
    324H  PHE*     4.4     2.6    -      +       -      +
    326H  THR*     2.9    52.5    +      -       +      +
    335H  TRP*     3.7    42.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASN 312 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218H  ARG*     5.8     3.9    +      -       -      +
    219H  ALA*     3.4     4.5    -      -       -      +
    220H  ALA*     2.9    34.9    +      -       +      +
    222H  TYR*     3.3    28.0    +      -       +      -
    310H  TYR*     3.8    11.1    -      -       -      -
    311H  PHE*     1.3    78.7    +      -       -      +
    313H  ILE*     1.3    68.3    +      -       -      +
    324H  PHE      3.4     6.7    -      -       -      +
    325H  SER*     2.6    37.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 313 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186H  TRP*     4.9     0.9    -      -       +      -
    187H  MET*     3.9    29.2    -      -       +      -
    216H  PRO*     3.5    32.5    -      -       +      -
    218H  ARG      3.8     2.7    -      -       -      +
    219H  ALA*     3.7    21.3    -      -       +      -
    311H  PHE*     3.8    18.8    -      -       +      -
    312H  ASN*     1.3    83.7    -      -       -      +
    314H  GLU*     1.3    65.2    +      -       -      +
    315H  PHE*     4.0    12.6    -      -       +      -
    321H  LYS*     4.6     3.1    +      -       -      -
    323H  GLY*     3.1    20.9    -      -       -      -
    324H  PHE*     2.8    42.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 314 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216H  PRO*     3.3     2.8    -      -       -      +
    217H  ASP*     3.2     8.1    +      -       -      +
    218H  ARG*     2.8    73.9    +      -       +      +
    313H  ILE*     1.3    77.5    -      -       -      +
    315H  PHE*     1.3    69.7    +      -       -      +
    316H  THR*     3.8    21.5    -      -       +      +
    321H  LYS*     4.0    30.2    +      -       +      +
    322H  MET      3.6    11.7    -      -       -      +
----------------------------------------------------------
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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