Contacts of the strand formed by residues 708 - 713 (chain E) 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 LEU 708 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    706E  GLY      3.7     2.7    +      -       -      +
    707E  GLN*     1.3    74.1    -      -       -      +
    709E  THR*     1.3    61.0    +      -       -      +
    710E  MET      4.2     0.2    -      -       -      -
    876E  LEU*     6.3     3.1    -      -       +      -
    884E  VAL*     3.4    10.1    -      -       +      +
    897E  ALA*     4.2    11.4    -      -       +      -
    898E  ASP*     3.2    27.7    +      -       +      +
    899E  TRP      3.1    22.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 709 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703E  ILE*     4.9     8.4    -      -       +      +
    707E  GLN*     3.1    37.9    +      -       -      +
    708E  LEU*     1.3    72.3    -      -       -      +
    710E  MET*     1.3    73.3    +      -       -      +
    711E  ILE*     5.5     1.2    -      -       +      +
    884E  VAL      3.6     8.3    +      -       -      -
    885E  VAL*     3.8    12.9    -      -       +      +
    886E  LEU*     3.1    25.8    +      -       -      +
    887E  VAL      4.3     0.2    +      -       -      -
    897E  ALA*     5.3     1.5    -      -       -      +
    899E  TRP*     3.4     9.2    -      -       +      +
    900E  ILE      5.6     0.2    -      -       -      -
    901E  ILE*     5.3     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 710 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708E  LEU      4.2     0.4    +      -       -      -
    709E  THR*     1.3    80.2    -      -       -      +
    711E  ILE*     1.3    57.5    +      -       -      +
    712E  VAL*     5.7     1.6    -      -       +      -
    886E  LEU      3.2    12.1    -      -       -      +
    888E  THR*     4.4    13.7    -      -       +      -
    894E  LEU*     5.6     9.2    -      -       +      -
    897E  ALA*     5.0    12.0    -      -       +      +
    899E  TRP      2.4    21.9    +      -       -      +
    900E  ILE*     3.4    14.9    -      -       +      -
    901E  ILE*     2.7    31.0    +      -       -      +
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Residues in contact with ILE 711 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    709E  THR*     5.5     1.3    -      -       +      +
    710E  MET*     1.3    74.6    -      -       -      +
    712E  VAL*     1.3    60.7    +      -       -      +
    719E  LYS*     5.3    13.3    -      -       +      +
    722E  LEU*     6.1     4.5    -      -       +      -
    887E  VAL*     3.6    25.8    -      -       +      +
    888E  THR      2.8    26.0    +      -       -      +
    901E  ILE*     3.3    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 712 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710E  MET*     4.2     2.0    -      -       +      -
    711E  ILE*     1.3    70.9    -      -       -      +
    713E  GLY*     1.3    53.5    +      -       -      +
    719E  LYS*     5.7     4.9    -      -       -      -
    888E  THR*     3.3    17.5    -      -       +      +
    889E  HIS*     5.3     3.4    -      -       -      -
    890E  LYS      5.8     2.5    -      -       -      +
    900E  ILE*     5.4     8.5    -      -       +      -
    901E  ILE      2.4    26.8    +      -       -      +
    902E  ALA*     4.1     5.6    -      -       +      -
    903E  MET*     2.6    38.2    +      -       -      +
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Residues in contact with GLY 713 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712E  VAL*     1.3    78.3    -      -       -      +
    714E  GLN*     1.3    69.9    -      -       -      +
    715E  VAL      3.7     1.0    +      -       -      -
    717E  CYS*     4.5     0.7    -      -       -      -
    719E  LYS*     5.8     4.6    -      -       -      +
    888E  THR      4.6     1.4    +      -       -      -
    889E  HIS*     4.7    16.8    +      -       -      +
    902E  ALA*     5.3     1.1    -      -       -      -
    903E  MET*     3.3    18.6    -      -       -      -
----------------------------------------------------------
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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