Contacts of the strand formed by residues 609 - 613 (chain A) in PDB entry 2XRG


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 609 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546A  GLU*     3.3    21.0    +      -       -      -
    548A  SER*     3.8    20.4    -      -       -      -
    549A  ARG      4.6     3.0    +      -       -      +
    550A  PRO*     3.5    38.9    -      -       +      +
    551A  ASN*     3.2    25.8    +      -       -      +
    600A  ARG*     3.7     6.1    +      -       -      -
    601A  PRO      4.6     2.6    +      -       -      -
    603A  VAL*     3.6    30.1    -      -       +      +
    607A  THR*     4.4    13.2    -      -       +      -
    608A  SER*     1.3    73.7    -      -       -      +
    610A  ASP*     1.3    69.5    +      -       -      +
    611A  ILE*     3.7    14.1    -      -       +      +
    620A  GLY*     4.4    17.7    -      -       -      -
    621A  TYR      3.4    17.3    -      -       -      +
    622A  SER*     4.1     5.4    -      -       -      -
    629A  LEU*     4.4    12.6    -      -       +      -
    630A  TRP*     5.0     6.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with ASP 610 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  ASN*     3.4    24.6    -      -       +      +
    553A  PRO*     3.6    26.2    -      -       +      +
    609A  TYR*     1.3    79.0    -      -       -      +
    611A  ILE*     1.3    66.3    +      -       -      +
    612A  LEU*     3.9    12.8    +      -       -      +
    620A  GLY      3.7     0.3    -      -       -      -
    621A  TYR*     3.0    38.1    +      -       -      +
    623A  GLU*     3.5    32.0    -      -       -      +
    658A  VAL*     4.2    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 611 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    550A  PRO*     3.7    23.1    -      -       +      -
    551A  ASN      3.1     6.4    +      -       -      +
    552A  TYR*     4.0    24.8    -      -       +      +
    553A  PRO*     3.7    13.0    -      -       -      +
    600A  ARG*     4.6    13.9    -      -       -      -
    609A  TYR*     3.7    26.9    -      -       +      -
    610A  ASP*     1.3    71.9    -      -       -      +
    612A  LEU*     1.3    71.6    +      -       -      +
    613A  TYR*     3.8    27.2    -      -       +      +
    618A  GLU*     3.6    23.3    -      -       -      +
    619A  SER      3.5     8.5    -      -       -      +
    620A  GLY*     4.8     0.2    -      -       -      -
    630A  TRP*     4.2    20.2    -      -       +      -
    657A  ARG*     5.5     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 612 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553A  PRO*     4.7     3.4    -      -       +      -
    610A  ASP*     3.9    21.3    -      -       -      +
    611A  ILE*     1.3    83.1    -      -       -      +
    613A  TYR*     1.4    63.2    +      -       -      +
    614A  HIS*     3.9    11.2    +      -       +      -
    618A  GLU*     3.4    10.6    -      -       -      +
    619A  SER*     3.3    39.5    +      -       -      +
    621A  TYR*     3.9    22.0    -      -       +      -
    655A  ASP*     4.6     0.2    -      -       -      +
    657A  ARG*     3.4    48.5    -      -       +      +
    658A  VAL*     4.6     3.6    -      -       +      -
    699A  THR*     4.0    27.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 613 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552A  TYR*     3.5    31.9    -      +       +      -
    592A  GLU*     3.7    30.1    -      -       +      -
    611A  ILE*     3.8    17.8    -      -       +      +
    612A  LEU*     1.4    73.0    -      -       -      +
    614A  HIS*     1.3    64.5    +      -       -      +
    617A  PHE      4.4     1.1    -      -       -      -
    618A  GLU*     3.6    33.3    +      -       +      -
    657A  ARG*     2.9    26.4    +      -       -      +
----------------------------------------------------------
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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