Contacts of the strand formed by residues 897 - 900 (chain A) in PDB entry 5A7R


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 897 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  MET*     3.7     3.7    -      -       -      +
    716A  THR*     4.7     3.1    -      -       -      +
    717A  ARG      2.9    14.9    +      -       -      +
    718A  LEU*     3.3    22.6    -      -       +      -
    719A  HIS      3.0    24.8    +      -       -      +
    852A  PHE*     6.0     0.7    -      -       +      -
    865A  VAL*     3.7     6.1    -      -       +      +
    867A  THR*     4.2    19.3    -      -       +      -
    886A  GLN*     4.6     3.8    -      -       +      +
    887A  ILE*     4.5    21.8    -      -       +      +
    890A  ALA*     3.5    32.1    -      -       +      -
    895A  ARG      4.4     1.1    -      -       -      +
    896A  ASP*     1.3    74.3    -      -       -      +
    898A  VAL*     1.3    72.6    +      -       -      +
    899A  TYR*     4.0     8.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 898 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458A  ILE*     4.0    17.7    -      -       +      -
    461A  MET*     3.9    21.1    -      -       +      -
    719A  HIS*     3.3    19.5    -      -       +      -
    733A  MET*     3.7    32.1    -      -       +      -
    864A  ALA*     4.0     6.3    -      -       +      -
    865A  VAL      2.8    12.5    +      -       -      +
    866A  ALA*     3.5     2.0    -      -       -      -
    867A  THR*     2.9    27.9    +      -       -      +
    897A  VAL*     1.3    77.9    -      -       -      +
    899A  TYR*     1.3    59.2    +      -       -      +
    900A  PHE*     3.7    29.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 899 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718A  LEU*     4.1    13.0    -      -       +      -
    719A  HIS      2.9    11.0    +      -       -      +
    720A  VAL*     3.3    13.7    -      -       +      +
    721A  THR*     3.0    29.2    +      -       -      +
    867A  THR*     3.6    12.8    -      -       +      -
    868A  GLY*     3.3    27.9    +      -       -      -
    869A  ASN*     2.6    32.1    +      -       -      -
    879A  ALA*     4.2     7.6    +      -       -      +
    882A  LYS*     5.8     0.9    -      -       -      +
    883A  ALA*     3.7    29.4    +      -       +      +
    886A  GLN*     4.0     9.2    -      -       +      -
    887A  ILE*     6.0     1.8    -      -       +      -
    897A  VAL*     4.0     6.9    -      -       +      -
    898A  VAL*     1.3    71.6    -      -       -      +
    900A  PHE*     1.3    75.2    +      -       -      +
    901A  THR*     3.7    13.7    -      -       +      -
    911A  ILE*     3.7    23.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 900 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458A  ILE*     5.0     3.4    -      -       +      -
    721A  THR*     3.5    26.7    -      -       +      -
    723A  GLU      3.6    13.0    -      -       -      -
    724A  GLY      3.8    14.1    -      -       -      +
    725A  THR      3.8     9.4    -      -       -      -
    726A  ILE*     3.9    18.2    -      -       +      -
    729A  ASN*     3.6    40.6    -      -       +      -
    730A  GLY*     5.0     0.2    -      -       -      -
    866A  ALA*     4.2    10.3    -      -       +      -
    867A  THR      2.9    19.7    +      -       -      +
    868A  GLY*     3.3    19.4    -      -       -      -
    869A  ASN*     4.0     2.6    +      -       -      -
    898A  VAL*     3.7    31.0    -      -       +      -
    899A  TYR*     1.3    72.3    -      -       -      +
    901A  THR*     1.3    59.7    +      -       -      +
    902A  PHE      3.3     3.7    +      -       -      +
   1964A  AR6      4.1    19.6    +      -       +      -
----------------------------------------------------------
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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