Contacts of the strand formed by residues 718 - 728 (chain A) in PDB entry 3SQ4


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 THR 718 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    490A  LEU*     4.5     6.8    +      -       -      +
    493A  GLN*     2.7    42.8    +      -       +      +
    494A  ARG*     3.8    17.3    +      -       -      +
    497A  GLU*     3.7    28.3    -      -       +      -
    714A  ASP*     3.2     6.6    -      -       -      -
    715A  MET      2.9    33.2    +      -       -      -
    716A  GLU      3.3     0.9    +      -       -      -
    717A  GLY*     1.3    75.2    -      -       -      +
    719A  ARG*     1.3    61.6    +      -       -      +
    720A  TYR*     3.5    19.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 719 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494A  ARG*     5.5     0.2    -      -       -      +
    497A  GLU*     3.8    15.8    -      -       -      +
    645A  ASN*     2.7    44.9    +      -       -      +
    648A  VAL*     3.6    24.7    -      -       -      +
    649A  ASP*     2.7    30.9    +      -       -      -
    652A  ASP*     4.0    23.4    +      -       -      +
    713A  TRP*     3.6    15.3    -      -       -      -
    714A  ASP*     2.7    28.7    +      -       -      +
    717A  GLY      3.5     5.7    +      -       -      +
    718A  THR*     1.3    72.0    -      -       -      +
    720A  TYR*     1.3    68.3    +      -       -      +
    721A  ALA      3.7     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 720 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493A  GLN*     4.9     9.6    +      -       +      -
    497A  GLU*     3.7    21.3    -      -       -      +
    501A  GLU*     4.7     1.4    -      -       -      +
    712A  VAL*     3.7    35.6    -      -       +      +
    713A  TRP*     3.1    30.9    +      -       +      +
    714A  ASP      4.2     0.2    -      -       -      -
    715A  MET*     3.1    33.7    -      -       +      +
    718A  THR*     4.1    17.3    -      -       +      -
    719A  ARG*     1.3    80.9    -      -       -      +
    721A  ALA*     1.3    63.7    +      -       -      +
    722A  GLU*     3.1    23.0    +      -       -      +
    723A  PRO*     4.6     0.4    -      -       +      -
    724A  LYS*     3.9    39.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 721 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497A  GLU*     3.0    19.2    +      -       -      +
    500A  LYS*     4.1    20.2    -      -       +      -
    501A  GLU*     3.6    42.2    -      -       +      +
    504A  HIS*     4.8     7.3    +      -       -      +
    713A  TRP*     6.0     0.3    -      -       -      -
    719A  ARG      3.7     1.6    +      -       -      -
    720A  TYR*     1.3    72.2    -      -       -      +
    722A  GLU*     1.3    73.0    +      -       +      +
    723A  PRO*     4.6     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 722 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497A  GLU*     4.6     1.2    +      -       -      -
    500A  LYS*     6.1     1.3    -      -       +      +
    504A  HIS*     3.9    23.4    +      -       +      +
    720A  TYR*     3.1    20.6    -      -       -      +
    721A  ALA*     1.3    90.2    -      -       +      +
    723A  PRO*     1.3    81.8    -      -       +      +
    724A  LYS*     4.3     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 723 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    692A  PRO*     5.6     0.9    -      -       +      -
    711A  ASN*     3.5    20.6    -      -       -      +
    712A  VAL      3.5     9.9    -      -       -      +
    713A  TRP*     3.7    45.7    -      -       +      -
    720A  TYR*     4.7     1.6    -      -       +      -
    721A  ALA      4.6     1.8    -      -       -      +
    722A  GLU*     1.3   100.4    -      -       +      +
    724A  LYS*     1.3    59.3    +      -       -      +
    725A  LEU      4.4     0.2    +      -       -      -
    754A  GLN*     4.0    23.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 724 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711A  ASN*     4.6     0.2    -      -       -      -
    712A  VAL*     2.9    36.1    +      -       -      +
    720A  TYR*     3.9    46.2    -      -       +      +
    722A  GLU      3.5     3.8    +      -       -      +
    723A  PRO*     1.3    74.7    -      -       -      +
    725A  LEU*     1.3    77.5    +      -       -      +
    746A  LYS*     5.9     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 725 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710A  LEU      3.5     8.7    -      -       -      +
    711A  ASN*     3.7    21.3    -      -       -      +
    723A  PRO      5.8     0.4    -      -       -      +
    724A  LYS*     1.3    87.2    +      -       -      +
    726A  LYS*     1.3    60.3    +      -       -      +
    727A  ILE*     3.7    23.9    +      -       +      +
    746A  LYS*     3.9    41.1    +      -       +      +
    749A  ILE*     4.6     1.3    -      -       +      -
    750A  ARG*     3.8    34.8    -      -       +      +
    753A  LEU*     4.3    16.6    -      -       +      -
    754A  GLN*     4.0    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 726 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  SER*     5.7     1.4    +      -       -      -
    626A  TYR*     2.7    30.5    +      -       +      +
    686A  GLU*     4.8    10.1    +      -       -      -
    687A  ALA*     5.5     2.6    -      -       +      +
    708A  TYR*     3.1    25.4    +      -       +      +
    709A  ALA*     3.3     2.4    -      -       -      -
    710A  LEU*     2.8    46.7    +      -       +      +
    712A  VAL*     3.8    20.2    -      -       +      -
    715A  MET*     4.2    22.6    -      -       +      +
    724A  LYS      3.5     2.6    +      -       -      -
    725A  LEU*     1.3    72.5    -      -       -      +
    727A  ILE*     1.3    60.1    +      -       -      +
    728A  MET*     4.0    19.0    -      -       -      +
    115P  2DA      4.6     5.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 727 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708A  TYR      3.6     2.7    -      -       -      +
    709A  ALA*     4.1    10.3    -      -       +      -
    725A  LEU*     3.7    29.3    +      -       +      +
    726A  LYS*     1.3    79.8    -      -       -      +
    728A  MET*     1.3    74.8    +      -       -      +
    730A  LEU*     3.7    31.0    -      -       +      -
    732A  THR*     3.2    26.9    -      -       -      +
    733A  GLN*     3.3    31.3    +      -       +      +
    746A  LYS*     4.2    24.0    -      -       +      +
    749A  ILE*     4.2    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 728 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    706A  LYS      3.2     4.1    -      -       -      +
    708A  TYR*     2.9    78.0    +      -       +      +
    726A  LYS*     4.0    18.6    -      -       -      -
    727A  ILE*     1.3    88.7    -      -       -      +
    729A  GLY*     1.3    57.2    +      -       -      +
    730A  LEU      3.0    10.7    +      -       -      -
    733A  GLN*     5.6     0.9    -      -       -      +
    114P    G      3.2    55.9    -      -       +      +
    115P  2DA      3.3    10.8    -      -       -      +
----------------------------------------------------------
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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