Contacts of the strand formed by residues 54 - 58 (chain A) in PDB entry 1R2Y


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 GLY 54 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     4.1    12.6    -      -       -      -
     52A  VAL*     3.6     9.1    -      -       -      +
     53A  ARG*     1.3    80.7    -      -       -      +
     55A  LEU*     1.3    60.7    +      -       -      +
     64A  PHE*     3.6     2.4    -      -       -      -
     65A  LEU*     2.7    47.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ARG*     3.0    58.5    +      -       +      +
     14A  LEU*     3.8    23.1    -      -       +      -
     15A  LEU*     3.7    36.7    -      -       +      +
     18A  ILE*     4.3     5.6    -      -       +      -
     54A  GLY*     1.3    74.1    -      -       -      +
     56A  GLU*     1.3    65.7    +      -       -      +
     62A  LEU*     4.5     5.6    -      -       +      -
     63A  LYS      3.5    13.2    -      -       -      +
     64A  PHE*     3.5    42.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ARG*     3.5     8.8    -      -       -      +
     55A  LEU*     1.3    79.7    -      -       -      +
     57A  ARG*     1.3    61.5    +      -       -      +
     62A  LEU*     3.5     5.5    -      -       -      +
     63A  LYS*     2.6    65.5    +      -       +      +
     65A  LEU*     3.4    29.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     3.6    25.6    -      -       -      +
      7A  VAL*     3.8    10.8    -      -       +      -
      8A  GLU*     2.7    57.5    +      -       -      +
     11A  ARG*     3.6    10.5    -      -       +      +
     56A  GLU*     1.3    80.2    -      -       -      +
     58A  ARG*     1.3    64.1    +      -       -      +
     59A  GLY      3.0    38.2    +      -       -      +
     61A  PHE      3.3    13.7    -      -       -      +
     62A  LEU*     4.9     0.2    -      -       +      -
     63A  LYS*     4.6     2.0    -      -       -      +
    137A  GLU*     2.9    34.7    +      -       -      +
    139A  LEU*     5.7     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  ARG*     1.3    76.9    -      -       -      +
     59A  GLY*     1.3    59.8    +      -       -      +
     60A  LYS      3.2     0.3    +      -       -      -
     61A  PHE*     2.9    36.1    +      -       +      +
     63A  LYS*     5.4     7.5    -      -       +      +
    126A  ASP*     5.7     3.6    -      -       -      +
    131A  LEU*     4.2    27.4    +      -       +      -
    134A  LEU*     3.2    34.8    +      -       +      +
    135A  GLY      2.8    29.7    +      -       -      -
    136A  PRO*     4.4     3.4    -      -       -      +
    137A  GLU*     3.0    35.5    +      -       -      +
    170A  ALA*     3.8     9.9    -      -       -      +
----------------------------------------------------------
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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