Contacts of the strand formed by residues 683 - 689 (chain A) in PDB entry 4DTR


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 MET 683 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410A  PHE*     3.6    34.5    -      -       +      +
    411A  ASP      3.5     8.1    -      -       -      +
    412A  LEU*     3.8    22.4    -      -       +      +
    594A  LEU*     5.1     0.9    -      -       +      -
    597A  ILE*     4.0    25.8    -      -       +      -
    623A  ASP      3.4    28.3    -      -       -      +
    624A  SER      4.5     0.7    -      -       -      -
    625A  ILE*     3.9    19.7    -      -       +      +
    660A  GLU*     4.0    12.0    -      -       -      +
    663A  ILE*     3.8    37.8    -      -       +      +
    664A  ASP*     5.0     6.5    +      -       -      +
    667A  PHE*     4.1     2.9    -      -       +      -
    681A  MET      3.8     2.6    +      -       -      -
    682A  PHE*     1.3    72.0    -      -       -      +
    684A  ASP*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 684 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410A  PHE*     3.3     4.3    -      -       -      -
    411A  ASP*     3.0    32.4    +      -       -      +
    413A  THR*     4.3    11.6    +      -       -      +
    660A  GLU*     3.6    19.1    -      -       -      +
    682A  PHE*     3.8    10.4    +      -       -      +
    683A  MET*     1.3    78.6    +      -       -      +
    685A  ARG*     1.3    71.8    +      -       -      +
    686A  GLU*     3.4     0.7    +      -       -      +
    716A  GLU*     6.1     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 685 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    408A  MET*     4.6     3.4    -      -       +      -
    409A  SER      3.4    11.2    -      -       -      +
    410A  PHE*     3.6    15.1    -      -       +      -
    652A  ASP*     2.7    33.9    +      -       -      +
    655A  ALA*     3.8    20.8    -      -       +      +
    660A  GLU*     2.9    19.3    +      -       -      +
    684A  ASP*     1.3    78.4    -      -       -      +
    686A  GLU*     1.3    87.2    +      -       -      +
    687A  ALA      3.8     3.6    -      -       -      +
    688A  ILE*     3.7    27.5    -      -       +      +
    714A  ASP*     2.9    43.2    +      -       -      +
    716A  GLU*     3.7    17.5    -      -       -      +
    717A  GLY*     4.4     8.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 686 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  SER*     2.7    25.6    +      -       -      +
    410A  PHE      5.1     0.3    -      -       -      -
    411A  ASP*     3.5    38.7    -      -       +      +
    486A  LYS*     5.9     0.2    +      -       -      -
    624A  SER*     5.2     3.5    -      -       -      -
    626A  TYR*     4.8     9.0    +      -       -      -
    684A  ASP      3.4     1.0    +      -       -      +
    685A  ARG*     1.3    84.9    +      -       -      +
    687A  ALA*     1.3    59.7    +      -       +      +
    715A  MET*     3.4    30.9    -      -       +      +
    716A  GLU*     2.8    45.7    +      -       +      +
    726A  LYS*     5.4     3.6    -      -       -      -
   1001A  DTP      5.2     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 687 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  VAL*     4.4     0.7    -      -       +      +
    408A  MET*     3.3     5.4    -      -       -      -
    409A  SER*     2.8    44.0    +      -       -      +
    685A  ARG*     3.8     2.8    -      -       -      -
    686A  GLU*     1.3    74.6    -      -       -      +
    688A  ILE*     1.3    67.0    +      -       -      +
    689A  ALA*     4.1     1.1    -      -       +      +
    710A  LEU*     5.0    10.8    -      -       +      -
    712A  VAL*     4.3    19.5    -      -       +      -
    714A  ASP      3.5     3.8    -      -       -      -
    715A  MET*     4.0    16.6    -      -       +      -
    726A  LYS*     5.0     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 688 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  VAL      3.7     2.5    -      -       -      -
    408A  MET*     3.9     9.4    -      -       +      -
    647A  TRP*     3.8    24.5    -      -       +      -
    648A  VAL*     3.7    20.4    -      -       +      +
    651A  LEU*     3.8    19.1    -      -       +      +
    652A  ASP*     3.4    40.4    -      -       +      +
    685A  ARG*     3.7    26.5    -      -       -      +
    687A  ALA*     1.3    77.2    -      -       -      +
    689A  ALA*     1.3    62.5    +      -       -      +
    712A  VAL*     3.6     2.6    -      -       -      -
    713A  TRP*     3.0    28.6    +      -       -      +
    714A  ASP*     3.0    17.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 689 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    405A  LYS      4.2     1.3    -      -       -      -
    406A  TYR*     3.5     3.8    -      -       -      +
    407A  VAL*     2.8    37.0    +      -       +      +
    647A  TRP*     3.9    10.5    -      -       -      -
    651A  LEU*     5.1     0.5    -      -       -      +
    687A  ALA*     5.4     0.9    -      -       +      -
    688A  ILE*     1.3    76.3    -      -       -      +
    690A  GLY*     1.3    58.9    +      -       -      +
    699A  GLY      5.0     0.9    -      -       -      +
    710A  LEU*     3.9    39.7    -      -       +      -
    711A  ASN      3.2    15.9    -      -       -      +
    712A  VAL*     4.4     3.6    -      -       +      -
    713A  TRP*     4.4     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