Contacts of the strand formed by residues 774 - 780 (chain A) in PDB entry 5VLR


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 VAL 774 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    739A  THR*     4.3    19.5    -      -       +      +
    740A  LEU      4.7    10.3    -      -       -      +
    741A  LEU*     4.1    18.6    -      -       +      -
    762A  MET*     3.5     6.4    -      -       -      +
    763A  TYR*     2.8    55.2    +      -       +      +
    764A  SER*     5.6     2.0    -      -       -      -
    765A  ASN*     5.0     8.3    -      -       -      +
    773A  SER*     1.3    84.0    +      -       -      +
    775A  GLY*     1.3    55.1    +      -       -      +
    826A  GLU*     6.1     0.9    -      -       -      +
    827A  VAL      6.1     0.2    -      -       -      -
    829A  LEU*     4.8     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 775 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    761A  ILE      3.2    11.7    -      -       -      -
    762A  MET*     3.6    17.9    -      -       -      +
    763A  TYR*     4.7     0.9    -      -       -      -
    774A  VAL*     1.3    75.0    -      -       -      +
    776A  ILE*     1.3    69.5    +      -       -      +
    826A  GLU*     4.2     5.0    -      -       -      +
    827A  VAL*     3.2    34.2    +      -       -      +
    829A  LEU*     5.4     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 776 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    692A  LEU*     5.2     6.3    -      -       +      -
    733A  SER*     4.7     4.3    -      -       -      +
    734A  PRO*     5.7     0.2    -      -       +      -
    735A  LEU*     4.4    17.5    -      -       +      -
    741A  LEU*     3.9    32.1    -      -       +      -
    759A  LEU      3.5     1.4    -      -       -      +
    760A  TRP*     4.0     0.2    -      -       -      -
    761A  ILE*     2.8    53.0    +      -       +      +
    763A  TYR*     4.2    12.3    -      -       +      +
    775A  GLY*     1.3    76.6    -      -       -      +
    777A  ILE*     1.3    65.1    +      -       -      +
    778A  PHE      5.3     0.2    -      -       -      +
    824A  LEU*     4.5    24.5    -      -       +      -
    825A  ILE      3.9     5.4    -      -       -      +
    826A  GLU*     5.1     0.2    -      -       -      +
    827A  VAL*     3.8     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 777 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    752A  MET*     5.0     4.9    -      -       -      -
    758A  PRO*     3.7    26.9    -      -       +      +
    759A  LEU      3.3     8.3    -      -       -      +
    760A  TRP*     3.9    22.4    -      -       +      -
    776A  ILE*     1.3    73.2    -      -       -      +
    778A  PHE*     1.3    62.5    +      -       -      +
    779A  LYS      3.6     1.8    +      -       -      +
    824A  LEU*     3.2    10.6    -      -       -      -
    825A  ILE*     2.8    42.5    +      -       +      +
    826A  GLU      4.2     0.2    -      -       -      +
    827A  VAL*     3.6    19.7    -      -       +      -
   4001A  9EM      3.3    66.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 778 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    689A  LEU*     3.8    25.8    -      -       +      -
    692A  LEU*     3.7    39.3    -      -       +      -
    693A  LYS*     3.7    33.2    -      -       +      -
    696A  ASN*     4.0    11.8    -      -       +      +
    757A  LYS      4.8     0.2    -      -       -      +
    758A  PRO*     3.4     3.6    -      -       -      +
    759A  LEU*     2.9    44.9    +      -       +      +
    761A  ILE*     5.1     2.2    -      -       +      -
    776A  ILE*     4.1     1.4    +      -       +      -
    777A  ILE*     1.3    69.7    -      -       -      +
    779A  LYS*     1.3    58.3    +      -       -      +
    780A  ASN*     3.7    22.1    +      -       +      -
    822A  THR*     3.3    32.8    -      -       +      -
    823A  GLY      3.8     3.6    -      -       -      -
    824A  LEU*     3.8    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 779 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    754A  SER*     5.2     6.7    +      -       -      +
    756A  MET*     4.5     8.7    -      -       +      -
    758A  PRO*     3.9    21.5    -      -       +      +
    777A  ILE*     3.6     1.4    +      -       +      -
    778A  PHE*     1.3    73.4    -      -       -      +
    780A  ASN*     1.3    65.0    +      -       -      +
    782A  ASP*     3.4    33.4    +      -       +      +
    784A  LEU*     4.4    19.2    -      -       +      +
    821A  ARG      4.0     0.6    -      -       -      +
    822A  THR*     3.4     3.6    -      -       -      +
    823A  GLY      3.0    34.1    +      -       -      +
    825A  ILE*     3.9    19.5    -      -       +      -
    911A  ASP*     3.4    18.0    +      -       -      -
   4001A  9EM      3.0    41.5    -      -       -      -
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Residues in contact with ASN 780 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    693A  LYS*     3.4    33.9    -      -       -      +
    696A  ASN*     3.0    28.3    +      -       -      +
    697A  ASP*     3.6     3.8    -      -       -      +
    700A  LYS*     3.7    14.5    +      -       -      -
    756A  MET*     3.3    26.1    +      -       -      +
    758A  PRO*     5.6     0.2    -      -       -      +
    778A  PHE*     3.7    16.2    +      -       +      -
    779A  LYS*     1.3    74.8    -      -       -      +
    781A  GLY*     1.3    62.4    +      -       -      +
    782A  ASP      3.8     2.0    -      -       -      -
    820A  ASP      4.0     4.8    +      -       -      -
    821A  ARG*     3.3     6.8    +      -       -      +
    822A  THR*     3.2    20.5    +      -       -      +
----------------------------------------------------------
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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