Contacts of the strand formed by residues 716 - 728 (chain A) in PDB entry 6DBT


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 LEU 716 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    604A  ASP*     3.6    27.6    -      -       +      +
    605A  SER*     4.9     3.1    -      -       -      +
    608A  THR*     4.4     8.7    -      -       +      -
    711A  ILE      3.6     0.7    -      -       -      +
    712A  SER*     4.3     1.8    -      -       -      -
    713A  VAL*     2.8    35.2    +      -       -      +
    714A  GLY      3.7     8.5    -      -       -      +
    715A  GLY*     1.3    85.5    -      -       -      +
    717A  LEU*     1.3    62.2    +      -       -      +
    718A  ARG*     3.4    40.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 717 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    608A  THR*     4.1     9.4    +      -       -      -
    710A  ILE*     4.1    24.5    -      -       +      -
    711A  ILE      3.3    10.8    -      -       -      +
    712A  SER*     4.1     8.0    -      -       -      +
    715A  GLY      4.1     1.8    +      -       -      -
    716A  LEU*     1.3    73.1    -      -       -      +
    718A  ARG*     1.3    63.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 718 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    593A  ILE*     4.9     3.8    -      -       -      +
    594A  MET*     3.0    40.4    -      -       -      +
    597A  LEU*     4.3    15.5    -      -       -      +
    604A  ASP*     4.7     6.7    +      -       -      +
    607A  CYS*     3.9    18.2    +      -       -      -
    608A  THR*     3.2    25.1    -      -       +      +
    611A  PHE*     4.2    13.2    -      -       +      -
    710A  ILE*     3.3     8.0    -      -       -      +
    711A  ILE      2.9    31.1    +      -       -      +
    713A  VAL*     3.7    30.0    +      -       +      +
    714A  GLY      4.6     2.0    +      -       -      -
    716A  LEU*     3.4    39.8    -      -       -      +
    717A  LEU*     1.3    80.1    -      -       -      +
    719A  SER*     1.3    60.5    +      -       -      +
    720A  PHE*     3.5    18.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 719 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    608A  THR      3.0     7.8    +      -       -      -
    609A  SER*     2.3    52.9    +      -       -      +
    611A  PHE*     3.6    13.9    +      -       -      +
    708A  ARG*     2.9    31.6    +      -       -      -
    709A  LEU      3.1     6.5    -      -       -      -
    710A  ILE*     3.5    17.2    -      -       -      +
    718A  ARG*     1.3    70.7    -      -       -      +
    720A  PHE*     1.3    67.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 720 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  LEU*     3.5    31.9    -      -       +      -
    593A  ILE*     4.9     8.5    -      -       +      -
    609A  SER      5.6     0.2    -      -       -      -
    611A  PHE*     3.4    46.7    -      +       +      +
    613A  VAL*     4.4     9.9    -      -       +      -
    649A  ILE*     4.5     4.0    -      -       +      -
    708A  ARG*     3.4     8.0    -      -       -      +
    709A  LEU*     2.8    46.2    +      -       +      +
    711A  ILE*     3.2    33.0    -      -       +      -
    713A  VAL*     4.7     9.6    -      -       +      -
    718A  ARG*     3.5    22.2    -      -       +      -
    719A  SER*     1.3    77.7    -      -       -      +
    721A  ARG*     1.3    67.7    +      -       -      +
    722A  PHE*     4.3     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 721 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    609A  SER      6.0     1.8    -      -       -      +
    610A  GLY*     6.5     0.9    -      -       -      -
    611A  PHE      2.9    16.4    +      -       -      +
    612A  THR*     4.8     8.7    -      -       -      +
    613A  VAL*     3.6    15.4    +      -       -      +
    652A  ARG*     6.5     1.6    -      -       -      -
    705A  MET      4.1    11.0    +      -       -      -
    706A  GLU*     3.6    19.8    +      -       -      +
    707A  SER      5.0     3.1    -      -       -      -
    708A  ARG*     3.1    49.1    -      -       +      +
    720A  PHE*     1.3    73.7    -      -       -      +
    722A  PHE*     1.3    81.0    +      -       -      +
    723A  PHE*     4.5    23.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 722 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538A  TRP*     5.2     8.1    -      +       -      -
    582A  LEU*     4.3    28.9    -      -       +      -
    586A  LEU*     4.6     9.0    -      -       +      -
    613A  VAL*     3.6    39.9    -      -       +      +
    615A  VAL*     4.9     1.3    -      -       +      -
    646A  ILE*     5.8     0.4    -      -       +      -
    704A  MET*     4.9    17.5    -      -       +      +
    705A  MET*     3.8    27.4    +      -       -      +
    707A  SER      5.4     5.0    +      -       -      -
    709A  LEU*     4.1    38.4    -      -       +      -
    720A  PHE*     4.3     9.9    -      -       +      -
    721A  ARG*     1.3    94.0    -      -       -      +
    723A  PHE*     1.3    74.2    +      -       -      +
    724A  PHE*     3.6    26.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with PHE 723 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612A  THR*     3.6    39.7    -      -       +      -
    613A  VAL      3.2    16.9    +      -       -      +
    614A  VAL*     3.7    11.6    -      -       +      -
    615A  VAL      3.4    13.7    +      -       -      -
    705A  MET*     5.5     2.5    -      -       -      -
    721A  ARG*     4.5    26.7    -      -       +      -
    722A  PHE*     1.3    87.8    -      -       -      +
    724A  PHE*     1.3    69.9    +      -       -      +
    725A  ARG*     5.2     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 724 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578A  TYR*     3.3    39.0    -      +       -      -
    582A  LEU*     4.4    14.4    -      -       +      -
    615A  VAL*     3.8    19.5    -      -       +      -
    617A  GLU*     3.3    24.5    -      -       +      +
    701A  ARG*     3.4    24.5    -      -       +      +
    704A  MET*     4.7    12.3    -      -       +      -
    705A  MET*     4.5    20.7    -      -       +      +
    722A  PHE*     3.6    31.4    -      +       +      -
    723A  PHE*     1.3    88.9    -      -       -      +
    725A  ARG*     1.3    67.3    +      -       -      +
    726A  GLY      4.0     1.9    +      -       -      -
    808A  GLU*     4.4    13.7    -      -       -      +
    810A  GLN*     5.0     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 725 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614A  VAL*     3.6    35.9    -      -       +      +
    615A  VAL      3.0    10.5    +      -       -      +
    616A  LYS*     3.3     4.0    -      -       -      -
    617A  GLU*     3.1    25.7    +      -       -      -
    723A  PHE*     5.2     7.5    -      -       -      +
    724A  PHE*     1.3    81.9    -      -       -      +
    726A  GLY*     1.3    61.9    +      -       -      +
    727A  THR*     3.5    11.4    +      -       +      +
    810A  GLN*     2.8    51.5    +      -       -      +
    971A  ARG*     5.0     7.5    +      -       -      +
    972A  ASP*     4.4    29.2    +      -       -      +
    978A  TRP*     4.2    19.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 726 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617A  GLU*     4.4    13.4    +      -       -      +
    701A  ARG*     5.9     1.1    -      -       -      +
    724A  PHE      4.0     3.0    +      -       -      -
    725A  ARG*     1.3    70.3    -      -       -      +
    727A  THR*     1.3    58.4    +      -       -      -
    729A  TYR*     3.8    18.2    -      -       -      -
    808A  GLU*     4.4    12.4    +      -       -      +
    809A  THR*     3.8     4.3    +      -       -      -
    810A  GLN*     2.8    41.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 727 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616A  LYS*     3.6     9.8    -      -       +      +
    617A  GLU      4.0     2.0    +      -       -      -
    725A  ARG*     3.5    24.5    +      -       +      +
    726A  GLY*     1.3    78.0    -      -       -      +
    728A  GLY*     1.3    59.4    +      -       -      +
    729A  TYR*     2.6    29.1    +      -       -      +
    810A  GLN*     4.3     7.0    -      -       -      +
    812A  THR*     3.6    28.5    -      -       +      +
    978A  TRP*     2.9    53.4    +      -       +      +
    980A  SER*     4.9     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 728 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616A  LYS*     5.6     0.9    -      -       -      -
    617A  GLU      3.2    17.0    +      -       -      -
    618A  SER*     3.3    10.0    +      -       -      -
    619A  CYS      3.0    31.4    +      -       -      +
    620A  ASP*     5.1     0.3    -      -       -      +
    727A  THR*     1.3    78.1    +      -       -      +
    729A  TYR*     1.3    61.6    +      -       -      -
    980A  SER*     3.7    26.5    +      -       -      -
----------------------------------------------------------
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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