Contacts of the strand formed by residues 823 - 827 (chain A) in PDB entry 2XY7


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 ARG 823 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491A  ALA*     4.1    26.7    +      -       -      +
    643A  SER*     3.0    21.6    +      -       -      -
    644A  GLU*     2.8    28.5    +      -       -      -
    647A  TRP*     3.8    14.5    -      -       -      -
    815A  LEU*     4.9     1.8    -      -       -      -
    821A  GLN      3.3     7.0    +      -       -      +
    822A  ALA*     1.3    75.2    -      -       -      +
    824A  LEU*     1.3    65.1    +      -       -      +
    825A  LEU*     3.6     5.8    +      -       +      +
    834A  LEU*     3.2     7.7    -      -       -      -
    835A  GLU*     2.8    58.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 824 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484A  ILE*     4.0    23.8    -      -       +      -
    488A  MET*     3.5    36.5    -      -       +      +
    491A  ALA*     4.8     1.2    -      -       -      +
    808A  MET*     4.7    13.0    -      -       +      +
    811A  LEU*     3.7    36.3    -      -       +      -
    812A  ASN*     4.6    10.3    -      -       -      +
    815A  LEU*     4.9     5.6    -      -       +      +
    823A  ARG*     1.3    78.7    -      -       -      +
    825A  LEU*     1.3    66.0    +      -       -      +
    826A  LEU      4.3     4.9    -      -       -      +
    832A  LEU*     4.1    24.5    -      -       +      -
    833A  ILE      3.7    13.7    -      -       -      +
    834A  LEU*     4.1     6.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 825 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488A  MET*     3.3    32.5    -      -       -      +
    491A  ALA*     4.3     6.3    -      -       +      -
    492A  GLY      3.6    21.1    -      -       -      +
    493A  VAL*     3.8    28.0    -      -       +      -
    494A  LYS      5.9     0.2    -      -       -      +
    606A  PHE*     4.1     3.3    -      -       -      -
    641A  VAL      5.6     1.6    -      -       -      +
    649A  ILE*     4.6     9.2    -      -       +      -
    823A  ARG*     4.0    10.8    -      -       +      +
    824A  LEU*     1.3    82.4    -      -       -      +
    826A  LEU*     1.3    65.9    +      -       +      +
    833A  ILE*     2.9    21.5    +      -       +      +
    834A  LEU      4.5     3.6    -      -       -      +
    835A  GLU*     3.5    53.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 826 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488A  MET*     4.2     4.3    -      -       -      -
    493A  VAL*     4.2    19.5    -      -       +      -
    604A  THR*     4.7     1.3    -      -       +      -
    606A  PHE*     3.8    21.1    -      -       +      -
    623A  LEU*     3.4    46.0    -      -       +      +
    640A  PHE*     6.2     0.2    -      -       +      -
    824A  LEU*     4.3     4.0    -      -       -      +
    825A  LEU*     1.3    84.5    -      -       +      +
    827A  GLN*     1.3    64.3    +      -       -      +
    828A  VAL*     5.0     2.0    -      -       +      -
    832A  LEU*     3.5     4.2    -      -       -      +
    833A  ILE*     2.9    45.2    +      -       +      +
    872A  TRP*     3.9    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 827 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488A  MET*     4.3    10.5    -      -       +      +
    606A  PHE*     4.1    11.8    -      -       +      -
    616A  LEU*     4.3    23.5    -      -       +      +
    624A  GLN*     3.1    27.5    +      -       -      +
    804A  ILE*     3.5    21.8    -      -       +      +
    805A  LYS*     5.3     1.0    -      -       -      +
    808A  MET*     3.2    27.5    -      -       +      +
    826A  LEU*     1.3    74.8    -      -       -      +
    828A  VAL*     1.3    68.9    +      -       -      +
    829A  HIS*     2.7    33.6    +      -       -      +
    831A  GLU      3.4     6.3    -      -       -      +
    832A  LEU*     3.3    26.7    -      -       +      -
----------------------------------------------------------
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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