Contacts of the strand formed by residues 571 - 575 (chain H) in PDB entry 2A07


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 ALA 571 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564H  ARG*     3.4    39.0    -      -       +      +
    565H  VAL      3.8     4.7    -      -       -      +
    566H  GLU*     3.8    20.2    -      -       +      +
    570H  GLY*     1.3    74.7    -      -       -      -
    572H  VAL*     1.3    68.5    +      -       -      +
    573H  TRP*     5.1     2.0    -      -       -      +
    526I  THR*     3.7    18.5    -      -       -      +
    527I  LEU      4.7     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 572 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564H  ARG*     3.4     5.4    -      -       -      +
    565H  VAL*     2.7    62.6    +      -       +      +
    567H  ASN*     4.3    20.9    -      -       -      +
    569H  LYS      6.0     0.2    -      -       -      +
    570H  GLY      5.5     0.4    -      -       -      -
    571H  ALA*     1.3    79.9    -      -       -      +
    573H  TRP*     1.3    62.1    +      -       -      +
    574H  THR*     4.6     1.1    -      -       +      -
    524I  GLN*     4.0    35.2    -      -       +      +
    525I  LEU*     3.4    13.0    -      -       -      +
    526I  THR*     3.9    18.4    -      -       +      +
    529I  GLU*     5.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 573 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556H  LEU*     3.6    63.0    -      -       +      +
    557H  SER*     4.6     5.4    -      -       -      -
    562H  PHE*     3.7    15.9    -      -       +      -
    563H  VAL      3.6     5.6    -      -       -      -
    564H  ARG*     3.7    52.2    -      -       +      +
    571H  ALA*     5.1     2.1    +      -       -      +
    572H  VAL*     1.3    75.7    -      -       -      +
    574H  THR*     1.3    64.3    +      -       -      +
    602H   MG      4.4     0.9    -      -       -      -
    517I  ILE*     3.5    13.0    -      -       +      +
    524I  GLN*     3.4     6.2    -      -       -      -
    525I  LEU      2.6    38.1    +      -       -      +
    527I  LEU*     4.1    25.5    -      -       -      +
    530I  ILE*     4.0    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 574 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562H  PHE*     3.4     7.4    -      -       -      +
    563H  VAL*     2.8    47.5    +      -       -      +
    565H  VAL*     3.6    27.6    -      -       +      +
    572H  VAL*     4.6     0.7    -      -       +      -
    573H  TRP*     1.3    80.7    -      -       -      +
    575H  VAL*     1.3    70.2    +      -       -      +
    517I  ILE*     4.1     7.0    -      -       -      +
    523I  ARG      4.1     4.5    -      -       -      +
    524I  GLN*     3.8    31.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 575 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    561H  CYS      3.3     7.9    -      -       -      +
    562H  PHE*     4.0    11.0    -      -       +      -
    563H  VAL*     5.7     0.4    -      -       -      -
    574H  THR*     1.3    84.4    +      -       -      +
    576H  ASP*     1.3    71.0    +      -       -      +
    577H  GLU*     3.4    22.5    +      -       +      +
    580H  TYR*     4.3    11.9    -      -       +      -
    514I  ARG*     4.0    26.5    -      -       +      -
    517I  ILE*     3.7    33.8    -      -       +      +
    518I  MET*     3.9    16.8    -      -       +      +
    523I  ARG      4.9     0.2    +      -       -      -
----------------------------------------------------------
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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