Contacts of the strand formed by residues 783 - 792 (chain A) in PDB entry 4QUM


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 TYR 783 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    779A  CYS*     3.3     3.9    -      -       -      +
    780A  THR*     2.9    60.9    +      -       +      +
    781A  ILE      3.8     0.4    -      -       -      -
    782A  ALA*     1.3    86.4    -      -       +      +
    784A  VAL*     1.3    75.0    +      -       -      +
    785A  SER*     4.2    10.3    -      -       -      -
    804A  LEU*     4.6     1.8    -      -       +      -
    805A  GLN      3.1    14.1    -      -       -      +
    806A  TYR*     3.7     9.9    -      +       +      -
    807A  VAL*     4.3     2.0    -      -       -      +
    820A  ASP      5.6     1.3    -      -       -      -
    823A  GLU*     5.8     6.1    -      -       +      -
    824A  PHE*     3.5    40.8    -      +       +      -
    827A  TYR*     3.3    41.3    -      +       -      +
----------------------------------------------------------
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Residues in contact with VAL 784 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777A  GLU*     5.1     4.5    -      -       +      -
    778A  ASP      3.4    20.0    -      -       -      +
    779A  CYS*     4.0    11.9    -      -       +      -
    780A  THR      5.7     0.2    -      -       -      +
    783A  TYR*     1.3    79.0    -      -       -      +
    785A  SER*     1.3    59.3    +      -       -      +
    786A  ARG*     3.7    43.3    +      -       +      +
    803A  HIS      3.6     1.9    -      -       -      +
    804A  LEU*     3.5     3.1    -      -       -      -
    805A  GLN*     2.8    52.2    +      -       +      +
    807A  VAL*     4.6    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 785 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    776A  SER*     4.1     1.0    +      -       -      +
    777A  GLU*     3.8     1.7    -      -       -      -
    778A  ASP*     2.8    43.4    +      -       -      +
    783A  TYR*     4.1    13.0    -      -       -      -
    784A  VAL*     1.3    73.0    -      -       -      +
    786A  ARG*     1.3    60.9    +      -       -      +
    787A  GLU*     4.7     5.2    +      -       -      +
    802A  THR*     4.7     5.2    -      -       -      +
    803A  HIS      3.5     4.3    -      -       -      -
    804A  LEU*     3.6    16.6    -      -       -      +
    827A  TYR*     3.5    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 786 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    758A  TRP*     3.3    32.4    -      -       -      +
    760A  ASP*     5.1     4.0    +      -       -      -
    774A  CYS*     4.0     4.3    -      -       -      -
    776A  SER      3.3     4.9    -      -       -      +
    777A  GLU*     3.0    43.5    +      -       +      -
    784A  VAL*     3.7    28.3    +      -       +      +
    785A  SER*     1.3    76.7    +      -       -      +
    787A  GLU*     1.3    65.5    +      -       -      +
    788A  MET*     3.5    33.2    -      -       +      -
    802A  THR*     3.6     3.1    -      -       -      +
    803A  HIS*     2.8    47.7    +      -       -      +
    805A  GLN*     3.2    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 787 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    774A  CYS*     3.7     1.9    -      -       -      -
    775A  GLN*     2.9    38.5    +      -       +      +
    776A  SER*     3.2    29.7    +      -       -      +
    785A  SER*     4.7     4.9    +      -       -      +
    786A  ARG*     1.3    75.7    -      -       -      +
    788A  MET*     1.3    63.8    +      -       -      +
    800A  THR*     4.1    10.3    +      -       -      +
    801A  VAL      3.7     7.8    -      -       -      +
    802A  THR*     2.9    38.3    +      -       -      +
    827A  TYR*     5.6     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 788 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    729A  TRP*     4.2    20.6    -      -       +      -
    740A  ILE*     5.8     0.2    -      -       -      -
    757A  TYR*     5.6     0.2    -      -       -      -
    758A  TRP*     3.5    42.0    -      -       +      -
    772A  ILE*     4.8     6.3    -      -       +      -
    773A  GLN      3.5    10.8    -      -       -      +
    774A  CYS*     4.2     8.1    -      -       +      -
    775A  GLN*     4.7     3.1    -      -       -      -
    786A  ARG*     3.5    26.7    -      -       +      -
    787A  GLU*     1.3    79.7    -      -       -      +
    789A  LEU*     1.3    62.2    -      -       -      +
    790A  VAL*     4.1     1.3    -      -       +      -
    799A  HIS      3.8     0.2    -      -       -      +
    800A  THR*     3.3     8.4    +      -       -      -
    801A  VAL*     2.8    49.4    +      -       +      +
    803A  HIS*     3.7    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 789 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    771A  HIS      3.3     4.9    -      -       -      +
    772A  ILE*     3.5     2.6    -      -       -      +
    773A  GLN*     2.9    65.7    +      -       +      +
    775A  GLN*     3.4    32.0    -      -       -      +
    788A  MET*     1.3    73.4    -      -       -      +
    790A  VAL*     1.3    62.3    +      -       -      +
    791A  THR*     3.9     9.0    -      -       -      +
    798A  GLU*     3.8    41.1    -      -       +      +
    799A  HIS      3.7    15.7    -      -       -      +
    800A  THR*     4.6     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 790 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    729A  TRP*     3.5    35.9    -      -       +      -
    732A  VAL*     5.4     0.7    -      -       +      -
    733A  TRP*     3.8    25.5    -      -       +      -
    770A  PHE*     4.1    17.3    -      -       +      -
    771A  HIS      3.4     2.5    -      -       -      -
    772A  ILE*     3.8    18.8    -      -       +      -
    788A  MET*     5.0     1.3    -      -       +      +
    789A  LEU*     1.3    79.1    -      -       -      +
    791A  THR*     1.3    61.1    +      -       -      +
    798A  GLU*     3.5     2.9    -      -       -      +
    799A  HIS*     2.7    49.4    +      -       +      +
    801A  VAL*     4.3    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 791 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    770A  PHE*     3.5     5.1    -      -       -      -
    771A  HIS*     2.7    55.0    +      -       +      +
    773A  GLN*     4.3     6.6    +      -       -      -
    789A  LEU*     3.9    20.8    -      -       -      +
    790A  VAL*     1.3    77.0    +      -       -      +
    792A  ASN*     1.3    74.4    +      -       -      +
    793A  THR*     3.3     3.7    +      -       +      -
    796A  GLY*     4.2    13.7    -      -       -      +
    797A  GLU      3.5     9.0    -      -       -      +
    798A  GLU*     4.1    10.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 792 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    733A  TRP*     3.6    38.8    -      -       +      +
    769A  GLY      3.9    10.5    -      -       -      +
    770A  PHE*     4.3     9.7    -      -       +      -
    791A  THR*     1.3    70.5    -      -       -      +
    793A  THR*     1.3    63.5    +      -       -      +
    794A  GLN*     3.0    18.0    +      -       -      +
    795A  THR*     3.0    35.0    +      -       -      +
    796A  GLY*     2.8    30.7    +      -       -      -
    797A  GLU*     3.0     9.3    +      -       -      +
----------------------------------------------------------
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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