Contacts of the strand formed by residues 789 - 799 (chain A) in PDB entry 4YOC


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 GLY 789 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    784A  GLU*     3.8    10.5    -      -       -      -
    785A  ASP*     2.3    52.4    +      -       -      -
    786A  SER*     4.6     1.1    +      -       -      -
    788A  ASN*     1.3    71.3    -      -       -      +
    790A  GLN*     1.3    61.5    +      -       -      -
    791A  MET*     3.5     6.8    +      -       -      +
    824A  GLN*     4.8     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 790 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    731A  ILE*     3.3    53.8    +      -       -      +
    732A  SER*     4.8     0.2    -      -       -      +
    733A  TRP*     3.7    29.1    -      -       +      +
    783A  TRP      3.9     3.8    -      -       -      -
    784A  GLU*     3.3    20.0    +      -       -      +
    789A  GLY*     1.3    70.2    -      -       -      -
    791A  MET*     1.3    60.6    +      -       -      +
    824A  GLN*     3.5     9.8    -      -       -      +
    825A  LEU*     3.1    32.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with MET 791 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    733A  TRP*     4.2     4.0    -      -       -      -
    782A  LEU*     3.7     1.0    -      -       -      -
    783A  TRP*     2.7    78.3    +      -       +      +
    788A  ASN*     3.6    30.3    -      -       +      +
    789A  GLY      3.6    17.0    -      -       -      +
    790A  GLN*     1.3    77.2    -      -       -      +
    792A  PHE*     1.3    62.0    +      -       -      +
    822A  ASP*     3.9    21.1    -      -       +      +
    823A  MET*     3.6    10.3    -      -       -      +
    824A  GLN*     3.5    36.1    -      -       -      -
    825A  LEU*     4.2     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 792 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    763A  VAL*     4.1    12.3    -      -       +      -
    765A  VAL*     5.1     4.0    -      -       +      -
    779A  VAL*     3.9    29.2    -      -       +      -
    781A  ALA      3.1    14.1    -      -       -      +
    782A  LEU*     3.6    16.2    -      -       +      -
    783A  TRP*     3.5     8.0    -      -       -      -
    791A  MET*     1.3    74.9    -      -       -      +
    793A  HIS*     1.3    65.8    +      -       -      +
    794A  ALA*     3.7    30.1    +      -       +      -
    822A  ASP*     3.6     1.4    -      -       -      -
    823A  MET*     2.9    83.6    +      -       +      +
    824A  GLN      4.1     3.6    -      -       -      -
    825A  LEU*     3.7    17.0    -      -       +      -
    828A  ILE*     4.0    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 793 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    778A  ARG      3.3     1.7    -      -       -      +
    779A  VAL*     3.7     2.4    -      -       -      -
    780A  THR*     3.0    55.0    +      -       +      +
    781A  ALA*     3.0    15.0    +      -       +      -
    783A  TRP*     3.5     9.1    -      -       +      -
    792A  PHE*     1.3    73.8    -      -       -      +
    794A  ALA*     1.3    59.4    +      -       -      +
    820A  CYS*     3.5     7.4    -      -       +      +
    821A  GLU*     3.2    34.5    +      -       -      -
    822A  ASP*     2.8    25.2    +      -       -      +
    891A  LYS      5.2     1.3    -      -       -      -
    893A  CYS*     3.7     9.9    -      -       +      -
    896A  CYS*     3.1     9.7    -      -       -      -
   1702A   ZN      2.1    35.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 794 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777A  ALA*     3.7    16.2    -      -       +      -
    778A  ARG      3.6     3.8    -      -       -      -
    792A  PHE*     3.7    27.9    +      -       +      -
    793A  HIS*     1.3    71.6    -      -       -      +
    795A  HIS*     1.3    61.1    +      -       -      +
    796A  TRP*     3.7    21.7    +      -       +      -
    820A  CYS*     3.1     6.8    -      -       -      +
    821A  GLU      2.9    41.3    +      -       -      +
    823A  MET*     5.0     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 795 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777A  ALA*     3.4     0.8    -      -       -      -
    778A  ARG*     2.9    44.9    +      -       +      +
    780A  THR*     3.6    23.2    -      -       +      +
    793A  HIS      3.7     0.8    +      -       -      -
    794A  ALA*     1.3    70.3    -      -       -      +
    796A  TRP*     1.3    73.0    +      -       -      +
    797A  PHE*     4.7     2.8    -      -       -      -
    816A  LEU*     5.3    15.9    -      -       +      +
    817A  VAL      3.0    24.4    +      -       -      -
    818A  ASP*     5.7     0.4    -      -       -      -
    819A  GLU      3.6    13.0    -      -       -      -
    820A  CYS*     4.1     1.8    -      -       -      -
    868A  TRP*     6.5     0.2    -      +       -      -
    893A  CYS*     4.1    14.5    -      -       -      -
    894A  VAL*     4.3    16.3    +      -       +      +
    895A  SER*     3.6    24.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 796 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    719A  HIS*     3.1    40.3    +      +       +      +
    723A  LYS*     3.9    22.7    -      -       +      -
    765A  VAL*     4.3    12.6    -      -       +      -
    775A  TYR*     3.6    25.8    -      +       +      -
    776A  LEU      3.1    29.6    -      -       -      -
    777A  ALA*     3.5    16.8    -      -       +      -
    794A  ALA*     4.0    14.5    +      -       +      -
    795A  HIS*     1.3    83.2    +      -       -      +
    797A  PHE*     1.3    62.6    +      -       -      +
    816A  LEU*     4.9     0.7    -      -       -      -
    817A  VAL*     3.4    18.6    +      -       +      +
    819A  GLU*     3.1    37.7    +      -       +      +
    820A  CYS*     3.9     4.5    -      -       -      -
    821A  GLU*     3.0    40.6    +      -       +      +
    823A  MET*     3.9    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 797 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    719A  HIS*     3.2    23.3    +      -       -      -
    762A  CYS*     3.8    16.2    -      -       +      -
    776A  LEU*     2.9    40.0    +      -       +      +
    777A  ALA*     3.7    22.4    -      -       -      -
    778A  ARG*     3.1    35.0    -      -       +      -
    795A  HIS      5.0     1.1    -      -       -      -
    796A  TRP*     1.3    78.0    -      -       -      +
    798A  CYS*     1.3    60.8    +      -       -      +
    799A  ALA      4.2     0.9    +      -       -      -
    814A  LEU*     3.9    33.0    -      -       +      -
    815A  PHE      3.9     5.2    -      -       -      -
    816A  LEU*     3.7    27.6    -      -       +      -
    817A  VAL*     4.5     1.8    -      -       -      -
    834A  VAL*     4.1    18.6    -      -       +      -
    865A  TYR*     4.6     5.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with CYS 798 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718A  MET*     3.6    22.9    -      -       +      -
    719A  HIS*     5.2     0.2    -      -       -      -
    797A  PHE*     1.3    75.0    -      -       -      +
    799A  ALA*     1.3    78.8    +      -       -      +
    802A  ASP*     4.1    15.7    -      -       -      -
    803A  THR*     3.8    17.0    -      -       +      -
    814A  LEU*     3.4     6.6    -      -       -      -
    815A  PHE*     2.9    45.2    +      -       +      +
    817A  VAL*     3.5    19.5    -      -       +      -
    869A  TYR*     4.5     4.7    -      -       -      -
    871A  GLN*     4.7     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 799 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718A  MET*     5.8     0.6    -      -       -      -
    719A  HIS*     5.9     0.4    +      -       -      -
    773A  PRO*     6.0     4.7    -      -       +      -
    797A  PHE      4.2     1.0    +      -       -      -
    798A  CYS*     1.3    86.5    -      -       -      +
    800A  GLY*     1.3    60.7    +      -       -      +
    801A  THR*     3.9    11.0    -      -       +      -
    802A  ASP*     2.8    41.1    +      -       -      +
    803A  THR*     3.5     2.3    +      -       -      +
    813A  GLU      4.5     3.1    -      -       -      -
    814A  LEU*     4.6     8.0    -      -       +      +
----------------------------------------------------------
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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