Contacts of the strand formed by residues 55 - 59 (chain A) in PDB entry 2Y96


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 55 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  THR*     3.0    15.3    +      -       -      -
     54A  HIS*     1.3    77.6    -      -       -      +
     56A  ASN*     1.3    67.5    +      -       -      +
     63A  TYR*     3.8    31.9    -      -       +      -
     64A  ILE      3.4    13.2    -      -       -      +
     65A  GLY*     3.8     7.9    -      -       -      -
     69A  THR*     3.6    29.2    -      -       +      +
     81A  PHE*     5.3     2.9    -      -       +      -
    144A  LEU*     3.9     3.4    -      -       +      -
    181A  ARG*     3.5     0.2    -      -       -      +
   1208A  SO4      3.1    17.7    +      -       -      +
   1211A  SO4      3.9     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  GLN*     3.6    18.8    +      -       -      +
     53A  THR*     2.9    20.1    +      -       -      +
     55A  VAL*     1.3    72.2    -      -       -      +
     57A  GLU*     1.3    66.0    +      -       -      +
     58A  VAL*     3.5     2.1    +      -       -      +
     63A  TYR*     3.2     6.8    -      -       -      -
     64A  ILE      3.0    30.9    +      -       -      +
    151A  ARG*     4.7     0.2    +      -       -      -
    180A  ASN      3.1    27.0    +      -       -      +
    181A  ARG*     2.8    44.4    +      -       +      +
   1211A  SO4      2.8    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ASN*     1.3    71.3    -      -       -      +
     58A  VAL*     1.3    57.7    +      -       -      +
     59A  TRP      3.3    18.6    -      -       -      +
     60A  PRO*     3.7     6.1    -      -       -      +
     61A  LYS*     3.0    28.2    +      -       -      +
     62A  LEU      3.6     6.5    -      -       -      +
     63A  TYR*     3.5    32.2    +      -       +      -
    180A  ASN*     3.3    21.8    -      -       -      +
   1211A  SO4      3.1    24.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ASN      3.7    10.5    -      -       -      +
     57A  GLU*     1.3    76.4    -      -       -      +
     59A  TRP*     1.3    64.1    -      -       +      +
     62A  LEU*     2.9    25.8    +      -       +      +
     64A  ILE*     3.8    34.5    -      -       +      +
    158A  VAL*     4.1    10.5    -      -       +      -
    162A  LEU*     5.4     0.2    -      -       -      +
    176A  GLN*     3.0    27.3    +      -       -      +
    177A  VAL*     4.4    14.1    -      -       +      +
    180A  ASN*     3.4    27.0    +      -       +      +
    181A  ARG*     3.9    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  GLU*     3.3     8.6    -      -       -      +
     58A  VAL*     1.3    77.2    -      -       +      +
     60A  PRO*     1.3   103.1    -      -       +      +
     61A  LYS      3.1     1.0    +      -       -      -
     62A  LEU*     2.9    37.4    +      -       +      +
    136A  LEU*     4.2    17.3    -      -       +      +
    158A  VAL*     5.9     0.2    -      -       +      -
    161A  TYR*     4.5     4.5    +      +       -      -
    162A  LEU*     3.9    15.5    -      -       +      -
    166A  LYS*     3.7    40.7    -      -       +      +
    168A  MET*     3.4    29.6    -      -       +      -
    176A  GLN*     3.6    32.5    -      -       +      +
----------------------------------------------------------
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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