Contacts of the strand formed by residues 899 - 904 (chain F) in PDB entry 6BAA


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 TRP 899 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707F  GLN*     3.2    33.2    -      -       +      +
    708F  LEU      3.1     6.1    +      -       -      +
    709F  THR*     3.4     6.0    -      -       +      -
    710F  MET*     2.4    37.9    +      -       -      +
    894F  LEU      6.1     1.6    -      -       -      -
    897F  ALA*     3.7     1.4    -      -       -      +
    898F  ASP*     1.3    99.6    +      -       +      +
    900F  ILE*     1.3    57.9    +      -       -      +
    911F  GLU*     6.1     0.9    -      -       +      -
    912F  GLY*     3.4    28.7    -      -       -      +
    913F  THR*     3.2    33.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 900 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    709F  THR*     5.6     0.7    -      -       -      -
    710F  MET*     3.4    16.2    -      -       +      -
    712F  VAL*     5.4     7.0    -      -       +      -
    894F  LEU*     5.4    13.0    -      -       +      +
    899F  TRP*     1.3    75.3    -      -       -      +
    901F  ILE*     1.3    62.0    +      -       -      +
    902F  ALA*     4.1     1.7    +      -       +      +
    910F  ARG      4.2     0.3    -      -       -      +
    911F  GLU*     3.5    23.3    -      -       -      +
    912F  GLY      3.6    16.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 901 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    709F  THR*     5.3     5.2    -      -       +      -
    710F  MET      2.7    17.5    +      -       -      +
    711F  ILE*     3.3     9.3    -      -       +      +
    712F  VAL*     2.4    38.1    +      -       -      +
    900F  ILE*     1.3    72.5    -      -       -      +
    902F  ALA*     1.3    57.2    +      -       -      +
    903F  MET*     3.9     1.0    +      -       -      +
    908F  ILE*     6.0     5.2    -      -       +      -
    910F  ARG      4.0     4.0    -      -       -      +
    911F  GLU*     4.6     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 902 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712F  VAL*     3.3    10.3    -      -       +      +
    713F  GLY*     5.8     1.1    -      -       -      -
    900F  ILE*     4.1     2.6    -      -       +      -
    901F  ILE*     1.3    72.3    -      -       -      +
    903F  MET*     1.3    61.1    +      -       -      +
    908F  ILE*     3.6     5.3    -      -       -      +
    909F  GLN*     2.8    30.8    +      -       +      -
    910F  ARG*     3.0    25.3    +      -       +      +
    922F  CYS*     6.5     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 903 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712F  VAL      2.6    17.2    +      -       -      +
    713F  GLY*     3.3    19.3    -      -       -      -
    714F  GLN*     4.1     1.7    +      -       -      +
    717F  CYS*     3.7    21.5    -      -       +      +
    718F  GLY      5.5     1.1    -      -       -      -
    719F  LYS*     5.2    11.2    -      -       +      +
    722F  LEU*     6.4     1.8    -      -       +      -
    901F  ILE      5.2     0.4    -      -       -      +
    902F  ALA*     1.3    74.8    -      -       -      +
    904F  LYS*     1.3    63.5    +      -       -      +
    907F  THR      3.3    13.5    -      -       -      +
    908F  ILE*     4.4     1.6    -      -       -      +
    909F  GLN*     4.9     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 904 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    714F  GLN*     6.3     1.8    -      -       +      -
    717F  CYS*     3.8     6.5    -      -       -      -
    903F  MET*     1.3    76.6    -      -       -      +
    905F  ASP*     1.3    65.8    +      -       +      +
    906F  GLY      3.2     2.2    -      -       -      -
    907F  THR*     2.9    29.6    +      -       -      +
    909F  GLN*     4.7    13.2    -      -       +      +
----------------------------------------------------------
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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