Contacts of the strand formed by residues 720 - 727 (chain A) in PDB entry 6TD3


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 SER 720 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  GLY      5.2     0.2    -      -       -      -
    381A  ALA*     4.3     7.2    -      -       -      +
    382A  PHE*     3.1    40.4    +      -       -      +
    719A  GLU*     1.3    68.4    -      -       -      +
    721A  PRO*     1.4    67.2    -      -       -      +
    722A  ARG*     4.1    18.2    +      -       -      +
    737A  SER*     3.3     3.0    -      -       -      -
    738A  SER*     2.9    46.8    +      -       -      -
    740A  ILE*     5.8     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 721 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  VAL*     3.0    22.2    -      -       -      +
    378A  CYS*     3.8    18.8    -      -       +      -
    379A  SER      3.8    12.6    -      -       -      +
    380A  GLY      3.7    16.8    -      -       -      +
    385A  GLY*     3.9     6.3    -      -       -      -
    386A  SER      3.6    22.9    -      -       -      +
    387A  LEU*     4.6     0.4    -      -       +      -
    717A  LEU*     4.0    19.7    -      -       +      -
    719A  GLU      3.4     7.4    -      -       -      +
    720A  SER*     1.4    84.0    -      -       -      +
    722A  ARG*     1.3    64.5    +      -       -      +
    735A  VAL*     4.2     6.7    -      -       +      -
    736A  LEU      3.6     5.6    -      -       -      +
    737A  SER*     4.3     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 722 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  VAL*     3.5    22.4    -      -       -      +
    361A  ASP*     3.5     5.4    -      -       -      +
    378A  CYS*     4.5     0.7    -      -       -      -
    720A  SER*     4.1    17.6    +      -       -      +
    721A  PRO*     1.3    79.3    -      -       -      +
    723A  LYS*     1.3    73.6    +      -       +      +
    736A  LEU*     2.8    24.5    +      -       +      +
    737A  SER*     4.5     5.6    -      -       -      -
    738A  SER*     3.3    21.5    +      -       -      +
    787A  GLU*     3.0    35.0    +      -       -      -
    789A  HIS*     3.2    24.1    -      -       +      +
    812A  TYR*     4.6     7.3    -      -       -      -
    813A  ALA      4.6    12.8    +      -       -      +
    814A  LEU*     5.8     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 723 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  VAL      4.9     4.0    +      -       -      -
    361A  ASP*     3.6    27.9    +      -       -      +
    378A  CYS*     3.8     3.8    -      -       -      -
    722A  ARG*     1.3    88.8    +      -       +      +
    724A  ILE*     1.3    60.4    +      -       -      +
    734A  GLY      4.0     0.2    -      -       -      +
    735A  VAL*     3.3     7.1    -      -       -      +
    736A  LEU*     2.9    48.2    +      -       +      +
    814A  LEU      3.5    26.7    -      -       -      +
    815A  SER*     4.6     5.8    -      -       -      +
    816A  LEU*     4.1    12.9    -      -       +      +
    871A  TYR      5.2     4.7    +      -       -      -
    913A  TYR*     6.3     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 724 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361A  ASP*     3.0    24.1    +      -       -      +
    362A  MET*     3.8    31.0    -      -       -      +
    363A  CYS*     4.1     9.6    -      -       -      +
    376A  VAL*     3.5    37.2    -      -       +      +
    378A  CYS*     3.6    17.7    -      -       -      +
    387A  LEU*     4.6     8.3    -      -       +      -
    723A  LYS*     1.3    75.1    -      -       -      +
    725A  CYS*     1.3    81.8    +      -       -      +
    733A  PHE*     3.9    15.3    -      -       +      -
    734A  GLY      3.5     4.9    -      -       -      +
    735A  VAL*     3.7    20.2    -      -       +      -
    816A  LEU*     4.4     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 725 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  CYS*     4.6     6.7    -      -       -      -
    724A  ILE*     1.3    82.0    -      -       -      +
    726A  TYR*     1.3    60.1    +      -       -      +
    733A  PHE*     3.3     9.2    -      -       -      +
    734A  GLY      2.9    31.4    +      -       -      -
    816A  LEU*     3.7    33.0    -      -       +      +
    817A  VAL*     4.1     1.1    -      -       -      -
    818A  SER*     3.8    22.7    -      -       -      +
    829A  PHE*     3.6    26.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 726 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  CYS*     4.6     4.3    -      -       +      +
    365A  VAL*     3.5    33.7    -      -       +      -
    366A  ASP      5.5     2.9    -      -       -      -
    367A  LEU*     4.5     5.6    -      -       +      +
    369A  ARG*     4.2     3.7    +      -       -      -
    725A  CYS*     1.3    76.3    -      -       -      +
    727A  GLN*     1.4    64.7    +      -       -      +
    728A  GLU*     3.3    50.9    +      -       +      +
    731A  GLN*     3.8     1.0    +      -       -      -
    732A  CYS      3.7     9.9    -      -       -      -
    733A  PHE*     3.5    26.9    -      +       +      -
    796A  GLN*     2.5    44.6    +      -       +      -
    818A  SER*     3.7    15.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 727 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    725A  CYS      4.2     0.4    +      -       -      -
    726A  TYR*     1.4    71.8    -      -       -      +
    728A  GLU*     1.4    63.6    +      -       -      +
    729A  VAL*     4.3     1.8    -      -       +      +
    730A  SER*     2.7    30.4    +      -       -      +
    731A  GLN      3.2    13.2    +      -       -      -
    732A  CYS      2.9    22.4    +      -       -      +
    818A  SER*     2.8    26.8    +      -       -      +
    827A  THR*     3.5    31.3    +      -       +      +
    828A  TYR      3.4    16.8    +      -       -      -
    829A  PHE*     3.3    44.1    -      -       +      -
    853A  TYR*     4.1     7.4    +      -       -      +
----------------------------------------------------------
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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