Contacts of the strand formed by residues 24 - 33 (chain A) in PDB entry 6XYY


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 24 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  VAL      3.6     0.2    -      -       -      +
     20A  THR*     3.3     5.8    -      -       -      +
     21A  VAL      2.9    34.0    +      -       -      +
     22A  GLN      4.4     4.7    -      -       -      +
     23A  GLY*     1.3    81.6    -      -       -      +
     25A  GLU*     1.3    67.9    +      -       -      +
     26A  VAL*     3.6     3.5    +      -       -      +
    101A  PRO*     5.1     8.1    -      -       -      +
    102A  ALA*     5.6     7.2    -      -       -      +
    168A  ALA      5.0     0.7    -      -       -      -
    169A  ALA*     3.0    37.4    +      -       +      +
    170A  VAL      5.6     0.2    +      -       -      -
    172A  ASN*     3.5    43.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ARG*     6.0     1.2    -      -       -      +
      5A  LEU*     4.9     1.2    -      -       -      +
     18A  SER*     2.7    30.6    +      -       -      +
     19A  VAL      3.2     9.2    -      -       -      +
     20A  THR*     4.4     9.3    -      -       -      +
     24A  ARG*     1.3    74.2    -      -       -      +
     26A  VAL*     1.3    55.6    +      -       -      +
     27A  HIS*     3.4    24.5    +      -       -      +
    101A  PRO*     3.8     2.1    -      -       -      +
    102A  ALA*     2.8    46.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  SER*     3.4     2.6    -      -       -      -
     19A  VAL*     2.8    48.7    +      -       +      +
     21A  VAL*     4.9     1.1    -      -       +      -
     24A  ARG*     4.1     5.2    -      -       +      +
     25A  GLU*     1.3    78.1    -      -       -      +
     27A  HIS*     1.3    69.6    +      -       -      +
     28A  VAL*     4.0     4.5    -      -       +      -
     99A  TRP*     4.1    11.7    -      -       +      -
    100A  ALA      3.3    30.3    -      -       -      +
    101A  PRO*     4.0     4.7    -      -       +      -
    165A  ASP*     4.4     4.9    -      -       -      +
    168A  ALA*     4.1    11.2    -      -       +      -
    169A  ALA*     3.8    36.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ARG*     3.9    18.9    +      -       +      +
      5A  LEU*     3.3    33.3    -      -       +      +
     17A  ARG      3.4     4.3    -      -       -      +
     18A  SER*     3.8     9.2    -      -       -      -
     25A  GLU*     3.4    25.4    +      -       +      -
     26A  VAL*     1.3    79.9    -      -       -      +
     28A  VAL*     1.3    61.0    +      -       -      +
     29A  TYR*     3.4    39.7    +      -       +      +
     98A  VAL      3.6     0.3    -      -       -      +
    100A  ALA*     2.7    38.3    +      -       +      +
    101A  PRO      5.3     0.8    +      -       -      -
    102A  ALA*     4.7    17.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  GLY*     3.5     1.2    -      -       -      -
     17A  ARG*     2.7    62.6    +      -       -      +
     19A  VAL*     3.8    24.9    -      -       +      -
     26A  VAL*     4.3     2.7    -      -       +      +
     27A  HIS*     1.3    73.8    -      -       -      +
     29A  TYR*     1.3    62.7    +      -       -      +
     30A  THR*     4.0    20.9    +      -       +      -
     59A  ALA      3.7     4.7    -      -       -      +
     98A  VAL      3.8     3.1    -      -       -      +
     99A  TRP*     3.5    39.5    -      -       +      +
    165A  ASP*     3.8     9.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  LEU*     3.1    32.0    +      -       -      -
      6A  VAL      4.9     0.5    -      -       -      -
      7A  VAL*     3.9    22.9    -      -       +      +
     14A  VAL*     4.1     8.3    -      -       +      -
     15A  ARG      4.0     3.6    -      -       -      -
     16A  GLY*     3.4    21.3    -      -       -      -
     27A  HIS*     3.4    48.1    +      -       +      +
     28A  VAL*     1.3    70.7    -      -       -      +
     30A  THR*     1.3    60.9    +      -       -      +
     32A  ILE*     3.9    21.0    -      -       +      +
     59A  ALA*     3.6     7.6    -      -       +      -
     96A  ILE      4.2     0.7    -      -       -      +
     97A  ASN*     3.2     3.3    -      -       -      +
     98A  VAL*     2.8    44.9    +      -       -      +
    100A  ALA*     4.5     5.2    -      -       +      -
    225A  PHE*     3.6    29.8    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ARG*     4.0    10.4    +      -       -      +
     28A  VAL*     4.0    18.0    +      -       +      -
     29A  TYR*     1.3    75.3    -      -       -      +
     31A  GLY*     1.3    59.3    +      -       -      +
     32A  ILE      3.7     1.1    -      -       -      -
     58A  ASP      4.4     0.7    -      -       -      +
     59A  ALA*     2.8    40.0    +      -       -      +
     60A  THR      3.8     4.9    -      -       -      -
     61A  GLY      2.9    29.6    +      -       -      +
     62A  LEU*     4.5    15.7    -      -       +      -
     97A  ASN*     3.2    26.7    -      -       +      +
     99A  TRP*     4.7     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  THR*     1.3    74.4    -      -       -      +
     32A  ILE*     1.3    63.0    +      -       -      +
     33A  PRO*     3.8     4.7    -      -       -      +
     57A  LEU*     4.2    12.4    -      -       -      +
     58A  ASP      4.7     1.8    -      -       -      +
     61A  GLY      4.1     3.6    +      -       -      -
     63A  SER*     4.0    25.5    -      -       -      -
     95A  TYR*     3.5    15.8    -      -       -      -
     96A  ILE      3.2     2.5    +      -       -      -
     97A  ASN*     3.1    12.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  VAL*     4.0    31.2    -      -       +      -
     29A  TYR*     3.9    27.6    -      -       +      +
     31A  GLY*     1.3    79.6    -      -       -      +
     33A  PRO*     1.3    79.5    -      -       +      +
     34A  TYR*     3.5     0.7    +      -       +      -
     53A  TRP*     4.1    13.5    -      -       +      -
     57A  LEU*     5.2     1.8    -      -       +      -
     59A  ALA*     4.2     7.0    -      -       +      -
     95A  TYR*     3.1     3.0    -      -       -      -
     96A  ILE*     2.6    45.3    +      -       +      +
     98A  VAL*     4.9     6.3    -      -       +      -
    217A  TRP*     4.0    27.6    -      -       +      -
    225A  PHE*     4.4    13.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  SER*     5.0     0.7    +      -       -      -
     31A  GLY      3.8     4.7    -      -       -      +
     32A  ILE*     1.3    92.4    -      -       +      +
     34A  TYR*     1.3    60.7    +      -       -      +
     35A  ALA      4.4    10.8    -      -       -      +
     37A  PRO*     6.4     0.4    -      -       +      -
     50A  ALA*     4.0     9.6    -      -       +      +
     53A  TRP*     3.5    29.9    -      -       +      -
     57A  LEU*     3.5    26.0    -      -       +      -
     94A  LEU      3.6     3.8    -      -       -      +
     95A  TYR*     3.6    25.1    -      -       +      -
    217A  TRP*     4.6     4.9    +      -       -      -
----------------------------------------------------------
 Back to top of page


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