Contacts of the strand formed by residues 78 - 81 (chain A) in PDB entry 2YYO


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 78 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  GLY*     3.2     0.9    -      -       -      -
     60A  LEU*     2.9    42.4    +      -       +      +
     71A  PRO*     5.0     0.2    -      -       -      +
     72A  GLY*     4.1     1.7    +      -       -      -
     77A  SER*     1.3    77.3    +      -       -      +
     79A  ALA*     1.3    67.7    +      -       -      +
     87A  LEU*     3.5    25.8    -      -       +      -
     88A  TYR      3.3     8.3    -      -       -      +
     89A  ASN*     3.8     9.0    -      -       +      -
    123A  ILE*     3.5    31.0    -      -       +      -
    125A  PHE*     3.9    15.9    -      -       +      -
    135A  THR*     4.0    12.6    -      -       +      -
    137A  MSE      3.9    10.8    -      -       -      -
    139A  MSE      4.5     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  VAL      3.3    21.1    -      -       -      +
     59A  GLY*     3.9     1.8    -      -       -      +
     71A  PRO*     3.2    33.0    -      -       +      +
     72A  GLY*     4.0     0.4    -      -       -      -
     78A  VAL*     1.3    78.6    -      -       -      +
     80A  TYR*     1.3    59.9    +      -       -      +
     81A  HIS*     3.9    10.0    +      -       +      +
     86A  LYS      3.7     0.7    -      -       -      +
     87A  LEU*     3.4     5.4    -      -       -      +
     88A  TYR*     2.8    39.9    +      -       -      -
    125A  PHE*     3.9     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ILE      4.1     0.2    -      -       -      +
     57A  ALA*     3.6     0.9    -      -       -      -
     58A  VAL*     2.9    31.6    +      -       -      +
     79A  ALA*     1.3    71.4    -      -       -      +
     81A  HIS*     1.3    68.8    +      -       -      +
     82A  ALA      3.9     0.7    +      -       -      -
     85A  GLY*     3.5    22.2    -      -       -      -
     86A  LYS      3.6     2.9    -      -       -      -
     87A  LEU*     4.7     0.9    -      -       -      +
     97A  PHE*     3.5    31.0    -      +       -      -
     98A  GLY*     3.7     5.5    -      -       -      -
     99A  SER      2.6    34.9    +      -       -      -
    101A  CYS*     3.7    25.4    -      -       -      -
    107A  ILE*     3.5    30.4    -      -       +      +
    125A  PHE*     3.7    24.8    -      +       +      -
    126A  THR      5.4     1.1    -      -       -      -
    127A  LYS*     4.2     9.3    -      -       +      +
    132A  VAL*     4.2    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  THR      6.3     0.4    -      -       -      -
     56A  ILE      3.7     4.3    -      -       -      +
     57A  ALA*     3.4    20.9    -      -       +      +
     70A  GLN*     3.9    10.0    -      -       +      +
     71A  PRO      3.1    27.0    +      -       -      -
     73A  TRP*     3.7    23.0    +      +       -      -
     79A  ALA*     3.9     4.3    +      -       +      -
     80A  TYR*     1.3    79.4    -      -       -      +
     82A  ALA*     1.3    55.0    +      -       -      +
     83A  ASP*     3.6    13.7    -      -       -      +
     84A  ASP*     3.4    15.9    -      -       -      +
     85A  GLY*     2.7    37.1    +      -       -      -
     86A  LYS      3.0     6.3    +      -       -      -
     88A  TYR*     3.4    41.7    -      +       +      -
----------------------------------------------------------
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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