Contacts of the strand formed by residues 302 - 315 (chain L) 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 L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319J  HIS*     3.1    11.6    -      -       -      -
    320J  LYS*     2.9    31.6    +      -       -      +
    227L  GLU*     3.7    12.5    -      -       -      +
    269L  VAL*     3.6    18.8    -      -       +      +
    300L  ARG*     2.9    44.5    +      -       +      +
    301L  ASN*     1.3    75.3    -      -       -      +
    303L  TYR*     1.3    84.3    +      -       -      +
    347L  THR      3.9     0.5    -      -       -      -
    348L  VAL*     2.9    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 303 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105J  HIS*     2.6    46.4    +      +       +      +
    106J  ASN*     3.1    14.0    +      -       -      -
    319J  HIS*     3.5    11.8    -      -       -      +
    320J  LYS*     4.0    32.8    +      -       +      +
    227L  GLU*     3.2    27.7    +      -       +      +
    269L  VAL*     4.0     0.3    -      -       -      +
    302L  ASP*     1.3    92.0    +      -       -      +
    304L  VAL*     1.3    65.7    +      -       -      +
    305L  HIS*     3.8    22.9    -      +       +      -
    345L  TYR*     3.7    25.1    -      +       +      -
    346L  LEU      3.3     5.6    -      -       -      +
    347L  THR*     3.8    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 304 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225L  ALA*     3.9    18.2    -      -       +      -
    226L  ILE      3.4     4.9    -      -       -      +
    269L  VAL*     3.9    30.1    -      -       +      -
    303L  TYR*     1.3    78.4    -      -       -      +
    305L  HIS*     1.3    64.0    +      -       -      +
    306L  ALA      3.8    21.8    -      -       -      +
    307L  LEU*     5.2     1.6    -      -       +      -
    342L  LEU*     4.2    15.3    -      -       +      +
    345L  TYR*     3.2     4.2    -      -       -      -
    346L  LEU*     2.8    54.8    +      -       +      +
    348L  VAL*     4.1    13.0    -      -       +      -
    354L  ILE*     4.6     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 305 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226L  ILE      2.9     5.5    +      -       -      -
    227L  GLU*     3.8    10.0    -      -       +      +
    228L  ASP*     3.2    33.3    +      -       +      +
    229L  ARG*     3.1    41.9    -      -       +      +
    232L  LYS*     4.2    23.5    +      -       +      +
    303L  TYR*     3.8    25.1    -      +       +      -
    304L  VAL*     1.3    74.6    -      -       -      +
    306L  ALA*     1.3    61.3    +      -       +      +
    341L  TYR*     4.0     4.4    -      -       +      -
    342L  LEU*     3.0    31.6    +      -       -      +
    345L  TYR*     3.6    34.2    -      +       +      +
----------------------------------------------------------
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Residues in contact with ALA 306 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225L  ALA*     3.4     4.3    -      -       -      -
    226L  ILE*     3.0    36.9    +      -       +      +
    228L  ASP*     5.4     0.2    -      -       +      -
    304L  VAL*     3.6     7.9    -      -       -      +
    305L  HIS*     1.3    82.1    -      -       +      +
    307L  LEU*     1.3    66.5    +      -       -      +
    339L  VAL*     3.8    25.4    -      -       +      -
    340L  PHE      3.2    18.2    -      -       -      +
    341L  TYR*     4.0     9.9    -      -       +      -
    342L  LEU*     4.1     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 307 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223L  VAL*     4.6    15.5    -      -       +      -
    224L  VAL      3.4     7.2    -      -       -      +
    225L  ALA*     3.9    18.2    -      -       +      -
    294L  PHE*     4.0    19.1    -      -       +      -
    296L  LEU*     4.2    11.7    -      -       +      -
    304L  VAL*     5.2     4.0    -      -       +      -
    306L  ALA*     1.3    82.8    -      -       -      +
    308L  VAL*     1.3    65.1    +      -       -      +
    339L  VAL*     3.5     0.3    -      -       -      -
    340L  PHE*     2.7    45.8    +      -       +      +
    342L  LEU*     4.7     7.9    -      -       +      -
    354L  ILE*     5.2     2.7    -      -       +      -
    358L  ILE*     6.3     1.1    -      -       +      -
    374L  VAL*     3.7    32.5    -      -       +      -
    376L  LEU*     4.3    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 308 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223L  VAL*     3.3     4.2    -      -       -      -
    224L  VAL*     2.8    42.9    +      -       +      +
    226L  ILE*     3.6    40.2    -      -       +      -
    263L  VAL*     4.2     7.4    -      -       +      -
    307L  LEU*     1.3    79.6    -      -       -      +
    309L  THR*     1.3    70.0    +      -       -      +
    310L  TYR*     5.0     2.2    -      -       +      -
    328L  PRO*     4.8     8.7    -      -       +      -
    337L  GLN*     3.6    31.9    -      -       +      -
    338L  THR      3.2    10.1    -      -       -      +
    339L  VAL*     4.1    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 309 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190L  CYS*     3.3    18.2    -      -       -      +
    221L  LEU*     4.1    10.8    -      -       +      -
    222L  TYR      3.1    17.0    -      -       -      +
    223L  VAL*     3.6    20.9    -      -       +      -
    275L  ILE*     4.6     8.7    -      -       +      -
    308L  VAL*     1.3    76.2    -      -       -      +
    310L  TYR*     1.3    61.3    +      -       -      +
    337L  GLN*     3.9     4.0    -      -       -      -
    338L  THR*     2.9    48.5    +      -       -      -
    340L  PHE*     3.8    18.4    -      -       +      -
    358L  ILE*     4.9     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 310 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190L  CYS*     6.4     0.2    -      -       -      +
    221L  LEU*     3.5     6.6    -      -       -      +
    222L  TYR*     2.8    62.7    +      +       +      -
    224L  VAL*     4.2    26.7    -      -       +      -
    272L  ALA*     3.2    22.3    -      -       -      +
    308L  VAL*     5.0     1.8    -      -       +      -
    309L  THR*     1.3    77.4    -      -       -      +
    311L  PHE*     1.3    66.3    +      -       -      +
    312L  ASN*     3.9    17.7    -      -       -      -
    326L  THR*     3.5    15.5    -      -       -      +
    327L  ALA*     3.5    38.1    -      -       +      -
    328L  PRO*     3.8    18.4    -      -       +      -
    329L  ASP*     5.8     0.9    -      -       -      -
    336L  LYS      5.3     0.7    -      -       -      -
    337L  GLN*     4.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 311 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187L  MET*     4.2     9.6    -      -       +      -
    188L  GLY      3.8     5.8    -      -       -      -
    190L  CYS*     4.4     6.5    -      -       -      -
    191L  LEU*     3.5    46.9    -      -       +      -
    220L  ALA      3.1    17.0    -      -       -      +
    221L  LEU*     4.1     7.9    -      -       +      -
    310L  TYR*     1.3    78.1    -      -       -      +
    312L  ASN*     1.3    67.5    +      -       -      +
    313L  ILE*     3.7    30.3    -      -       +      -
    324L  PHE*     4.5     2.9    -      +       -      -
    326L  THR*     2.9    52.9    +      -       +      +
    335L  TRP*     3.6    43.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASN 312 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218L  ARG*     5.8     3.8    +      -       -      +
    219L  ALA*     3.4     4.3    -      -       -      -
    220L  ALA*     2.9    33.8    +      -       +      +
    222L  TYR*     3.3    27.1    +      -       +      -
    310L  TYR*     3.9    10.9    -      -       -      -
    311L  PHE*     1.3    79.3    +      -       -      +
    313L  ILE*     1.3    68.8    +      -       -      +
    324L  PHE      3.4     7.0    -      -       -      +
    325L  SER*     2.7    36.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 313 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186L  TRP*     5.0     0.7    -      -       +      -
    187L  MET*     3.8    29.6    -      -       +      -
    191L  LEU*     4.4     0.4    -      -       +      -
    216L  PRO*     3.4    32.5    -      -       +      -
    218L  ARG*     3.6     3.4    -      -       -      +
    219L  ALA*     3.7    21.1    -      -       +      -
    311L  PHE*     3.7    23.1    -      -       +      -
    312L  ASN*     1.3    83.5    -      -       -      +
    314L  GLU*     1.3    65.3    +      -       -      +
    315L  PHE*     4.2     5.6    -      -       +      -
    321L  LYS*     4.7     2.6    +      -       -      -
    323L  GLY*     3.0    20.8    -      -       -      -
    324L  PHE*     2.9    45.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 314 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216L  PRO*     3.3     2.9    -      -       -      +
    217L  ASP*     3.2     8.1    +      -       -      +
    218L  ARG*     2.9    68.4    +      -       +      +
    313L  ILE*     1.3    76.8    -      -       -      +
    315L  PHE*     1.3    72.8    +      -       -      +
    316L  THR*     3.7    16.2    -      -       +      +
    321L  LYS*     3.8    30.4    +      -       -      +
    322L  MET      3.3    14.1    -      -       -      +
    323L  GLY*     4.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 315 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98L  THR*     3.5    28.5    -      -       +      -
     99L  TYR*     4.0    36.8    -      +       -      -
    102L  SER*     3.8    15.7    -      -       -      -
    214L  MET      5.5     0.7    -      -       -      -
    215L  PHE*     3.6    27.1    -      +       +      -
    216L  PRO*     3.4    40.6    -      -       +      -
    217L  ASP*     4.0     3.1    -      -       -      -
    313L  ILE*     4.2    10.5    -      -       +      -
    314L  GLU*     1.3    73.0    -      -       -      +
    316L  THR*     1.3    62.2    -      -       -      +
    317L  LYS      3.3     2.8    +      -       -      -
    318L  CYS*     3.5    31.5    +      -       -      +
    320L  LYS      4.8     0.5    -      -       -      +
    321L  LYS*     5.6     0.2    -      -       -      -
    322L  MET*     2.9    30.5    +      -       +      +
    323L  GLY*     4.3     1.8    -      -       -      -
    324L  PHE*     4.6     2.7    -      +       -      -
----------------------------------------------------------
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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