Contacts of the strand formed by residues 792 - 805 (chain A) in PDB entry 6S1M


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 792 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601A  LEU*     3.6    25.4    -      -       +      +
    602A  ASP*     3.5    36.3    -      -       -      +
    603A  PHE*     3.9    28.3    -      -       +      +
    731A  THR*     4.7    11.0    -      -       +      -
    779A  ALA*     3.8    24.1    -      -       -      +
    780A  ASP*     4.8     4.2    -      -       -      +
    782A  VAL*     3.7    34.1    -      -       +      -
    783A  SER*     2.7    27.0    +      -       -      +
    791A  ARG*     1.3    76.6    -      -       -      +
    793A  GLU*     1.3    62.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 793 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601A  LEU*     3.4     2.6    -      -       -      -
    602A  ASP*     2.9    46.2    +      -       -      +
    604A  SER*     4.4    21.9    +      -       -      +
    779A  ALA*     3.8     7.9    -      -       -      -
    780A  ASP*     5.7     1.1    -      -       -      -
    791A  ARG*     4.8    10.7    +      -       +      +
    792A  LEU*     1.3    76.6    -      -       -      +
    794A  PHE*     1.3    68.3    +      -       -      +
    795A  GLU*     3.3    26.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 794 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599A  ALA*     4.0    10.8    -      -       +      -
    600A  THR      3.8     4.0    -      -       -      -
    601A  LEU*     4.0     9.6    -      -       +      -
    772A  MET*     3.9    31.4    -      -       +      -
    775A  GLY*     3.4    36.6    -      -       -      -
    776A  ARG*     3.6    36.8    -      -       +      +
    779A  ALA*     3.5    13.3    -      -       +      +
    793A  GLU*     1.3    83.2    -      -       -      +
    795A  GLU*     1.3    67.5    -      -       -      +
    796A  LYS*     3.3    33.7    -      -       -      -
    797A  VAL*     3.6    15.0    -      -       +      -
    814A  PHE      5.7     0.2    -      -       -      -
    815A  SER      5.5     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 795 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600A  THR*     3.0    17.5    +      -       +      +
    602A  ASP*     2.9    39.7    -      -       -      +
    604A  SER*     6.1     0.5    -      -       -      -
    793A  GLU*     3.3    25.5    -      -       -      +
    794A  PHE*     1.3    79.3    -      -       -      +
    796A  LYS*     1.3   100.5    +      -       +      +
    814A  PHE      4.8     1.6    -      -       -      +
    815A  SER*     5.6     2.8    -      -       -      -
    101T  TTP      5.1     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 796 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600A  THR*     3.4    42.6    +      -       +      +
    794A  PHE*     3.3    21.8    -      -       -      -
    795A  GLU*     1.3   113.1    +      -       -      +
    797A  VAL*     1.3    63.1    +      -       -      +
    798A  TYR*     3.6    34.3    -      -       +      +
    813A  LEU*     3.7    31.2    -      -       +      -
    814A  PHE      3.8     8.3    -      -       -      +
    825A  ASP*     4.6     2.5    -      -       -      -
    827A  LYS*     6.3     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 797 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597A  PRO*     3.8    26.7    -      -       +      -
    598A  ILE      3.5     4.7    -      -       -      +
    599A  ALA*     4.2    13.5    -      -       +      -
    768A  VAL*     4.1    18.4    -      -       +      -
    771A  ALA*     4.4    12.8    -      -       +      -
    772A  MET*     4.0    15.7    -      -       +      -
    794A  PHE*     3.6    19.3    -      -       +      -
    796A  LYS*     1.3    80.2    -      -       -      +
    798A  TYR*     1.3    65.7    +      -       -      +
    799A  PHE*     4.6     4.0    -      -       +      -
    812A  LEU      3.4    10.4    -      -       -      +
    813A  LEU*     4.3     0.7    -      -       -      -
    814A  PHE*     3.4    30.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 798 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    596A  VAL      4.6     1.2    -      -       -      +
    597A  PRO*     3.4     3.8    -      -       -      +
    598A  ILE*     3.0    37.5    +      -       +      +
    600A  THR*     3.9    16.4    -      -       -      -
    760A  MET*     4.5    16.6    -      -       +      -
    796A  LYS*     3.6    28.0    -      -       +      +
    797A  VAL*     1.3    72.0    -      -       -      +
    799A  PHE*     1.3    64.1    +      -       -      +
    800A  PRO      3.9     9.1    -      -       -      +
    801A  TYR*     4.2    21.8    -      +       +      -
    809A  TYR*     4.3    14.2    +      +       -      -
    810A  ALA      5.1     1.1    -      -       -      -
    811A  GLY*     3.6    25.1    -      -       -      -
    812A  LEU      3.3    11.4    -      -       -      -
    813A  LEU*     4.6     4.0    -      -       +      -
    825A  ASP*     2.6    46.5    +      -       +      +
    827A  LYS*     4.4     8.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 799 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    595A  ASP*     3.5    29.6    -      -       -      -
    597A  PRO*     3.6    35.0    -      -       +      -
    766A  SER*     4.1    17.0    -      -       -      -
    768A  VAL*     4.0    15.0    -      -       +      -
    797A  VAL*     4.6     3.6    -      -       +      -
    798A  TYR*     1.3    75.6    -      -       -      +
    800A  PRO*     1.3    70.1    +      -       +      +
    812A  LEU*     3.4    16.2    +      -       -      +
    814A  PHE*     3.7    37.5    -      +       +      -
    817A  ARG*     5.7     2.7    -      -       -      -
    855A  ARG*     4.0    20.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 800 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    593A  TYR*     4.3    12.8    -      -       +      +
    594A  TYR      3.3    14.6    -      -       -      +
    595A  ASP*     3.5    22.0    -      -       -      +
    596A  VAL      5.6     0.9    -      -       -      +
    798A  TYR      3.9     0.7    -      -       -      -
    799A  PHE*     1.3    94.4    +      -       +      +
    801A  TYR*     1.3    62.8    +      -       -      +
    811A  GLY*     3.7     4.0    -      -       -      -
    812A  LEU*     3.6    33.7    +      -       +      -
    852A  LEU*     3.8    32.9    -      -       +      +
    855A  ARG*     4.3    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 801 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    593A  TYR*     3.6     6.5    -      -       -      -
    594A  TYR*     2.9    45.0    +      +       +      +
    598A  ILE*     3.6    39.0    -      -       +      -
    752A  VAL*     4.4    17.0    -      -       +      -
    753A  TYR*     4.2     6.4    -      -       -      -
    760A  MET*     2.8    33.8    -      -       -      -
    798A  TYR*     4.2    24.5    -      +       +      +
    800A  PRO*     1.3    75.2    -      -       -      +
    802A  LEU*     1.3    64.1    +      -       -      +
    803A  LEU*     4.3    16.2    -      -       +      +
    809A  TYR*     3.2    41.4    -      +       +      +
    810A  ALA      3.1    18.2    -      -       -      -
    811A  GLY*     5.2     0.2    -      -       -      -
    852A  LEU*     5.6     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 802 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    592A  GLY      3.4    16.8    -      -       -      +
    593A  TYR*     4.1    24.9    -      -       +      -
    801A  TYR*     1.3    77.8    -      -       -      +
    803A  LEU*     1.3    59.0    +      -       -      +
    804A  ILE*     3.7    24.7    +      -       +      +
    809A  TYR*     3.2     6.0    -      -       -      +
    810A  ALA*     2.9    52.2    +      -       +      +
    829A  LEU*     5.6     3.1    -      -       +      -
    848A  LEU*     5.0    11.2    -      -       +      -
    851A  LEU*     5.6     6.5    -      -       +      -
    852A  LEU*     5.1    12.8    -      -       +      -
    969A  ILE*     4.8    22.4    -      -       +      +
    972A  PRO*     4.9     8.1    -      -       +      -
    973A  ILE*     5.1     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 803 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    589A  PRO*     3.7    28.3    -      -       +      -
    590A  LEU      3.9    15.7    -      -       -      +
    591A  LYS*     3.3     8.4    +      -       -      +
    592A  GLY*     2.9    36.4    +      -       -      +
    594A  TYR*     5.4     4.4    -      -       +      -
    752A  VAL*     4.2    13.9    -      -       +      +
    753A  TYR*     4.4    22.4    -      -       +      -
    801A  TYR*     4.3    22.8    -      -       +      +
    802A  LEU*     1.3    72.3    -      -       -      +
    804A  ILE*     1.3    62.5    +      -       -      +
    805A  SER      3.7    22.0    -      -       -      +
    809A  TYR*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 804 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    591A  LYS*     3.2    35.0    -      -       -      +
    802A  LEU*     3.7    36.1    -      -       +      +
    803A  LEU*     1.3    81.6    -      -       -      +
    805A  SER*     1.3    70.1    +      -       -      +
    808A  ARG*     3.1    21.0    +      -       +      +
    809A  TYR*     4.9     0.9    -      -       -      -
    829A  LEU*     4.4    18.8    -      -       +      -
    968A  ARG*     4.5    33.9    -      -       +      +
    969A  ILE*     5.2     6.7    -      -       +      -
    972A  PRO*     4.5    15.9    -      -       +      -
      6T    T      5.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 805 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    589A  PRO*     4.8    12.4    -      -       -      +
    591A  LYS*     5.5     0.7    -      -       -      -
    753A  TYR*     4.6     1.7    +      -       -      -
    803A  LEU*     3.7    15.6    -      -       -      +
    804A  ILE*     1.3    83.2    -      -       -      +
    806A  LYS*     1.3    66.8    +      -       -      +
    807A  LYS      3.7     1.2    +      -       -      -
    808A  ARG*     3.3    37.1    +      -       -      +
      5T    T      4.3    12.4    -      -       -      -
      6T    T      4.5    10.6    +      -       -      -
----------------------------------------------------------
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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