Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 1BU8


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 LYS 69 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ARG*     1.3    76.4    -      -       -      +
     70A  THR*     1.3    60.0    +      -       -      +
     71A  ARG*     3.6    35.0    -      -       +      +
     97A  GLU*     5.0     3.8    -      -       -      +
     98A  LYS      4.5     5.6    +      -       -      +
     99A  VAL*     3.3    13.4    -      -       +      +
    100A  ASN*     3.0    23.7    +      -       -      -
    141A  TYR*     3.5     3.4    -      -       -      -
    144A  GLU      4.5    14.5    +      -       -      -
    145A  ASN*     3.6    21.7    +      -       +      +
    146A  VAL      6.2     0.4    -      -       -      -
    147A  HIS*     5.8     3.5    -      -       -      +
    312A  ASP*     5.1     9.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  PHE*     3.3    12.9    -      -       +      -
     69A  LYS*     1.3    72.7    -      -       -      +
     71A  ARG*     1.3    66.6    -      -       -      +
     72A  PHE*     3.7    27.8    -      -       +      -
    100A  ASN*     3.2    28.7    +      -       +      +
    102A  ILE*     3.7    17.3    -      -       +      -
    135A  LEU*     5.5     1.3    -      -       +      -
    141A  TYR*     2.7    25.7    +      -       -      -
    145A  ASN      2.9     9.6    +      -       -      +
    146A  VAL*     3.4     6.7    -      -       +      +
    147A  HIS*     2.8    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LYS*     3.6    32.2    -      -       +      +
     70A  THR*     1.3    78.2    -      -       -      +
     72A  PHE*     1.3    63.4    +      -       -      +
     73A  ILE*     4.0     1.2    +      -       +      -
     93A  MET*     3.7    37.2    -      -       +      -
     97A  GLU*     2.9    38.0    +      -       -      -
     99A  VAL*     4.0    11.4    -      -       +      +
    100A  ASN      3.0     7.5    +      -       -      -
    101A  CYS*     3.5     7.7    -      -       -      -
    102A  ILE      3.0    22.6    +      -       -      +
    147A  HIS*     2.9    48.5    +      -       +      +
    149A  ILE*     4.7     1.6    -      -       +      -
    171A  ARG*     4.3     7.9    -      -       -      +
    309A  HIS*     3.4    17.3    +      -       -      -
    312A  ASP*     5.2     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  PHE*     4.2     6.1    -      +       -      -
     70A  THR*     3.7    24.7    -      -       +      -
     71A  ARG*     1.3    73.0    -      -       -      +
     73A  ILE*     1.3    61.0    +      -       -      +
     74A  VAL*     4.7     4.9    -      -       +      -
    102A  ILE*     3.2    30.3    -      -       +      -
    104A  VAL*     3.9    22.7    -      -       +      -
    128A  ILE*     4.0    17.9    -      -       +      -
    131A  LEU*     3.9    27.4    -      -       +      -
    132A  VAL*     4.2    16.6    -      -       +      -
    135A  LEU*     5.1     4.9    -      -       +      -
    146A  VAL*     3.8    18.8    -      -       +      -
    147A  HIS      2.8     6.7    +      -       -      +
    148A  LEU*     3.5    26.9    -      -       +      -
    149A  ILE*     2.8    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ARG      4.4     1.6    -      -       -      +
     72A  PHE*     1.3    75.8    -      -       -      +
     74A  VAL*     1.3    62.0    +      -       -      +
     85A  TRP*     3.7    19.3    -      -       +      -
     86A  LEU*     3.2    48.8    -      -       +      +
     89A  MET*     3.9    25.6    -      -       +      -
     90A  CYS*     3.8     1.6    -      -       -      +
     93A  MET*     4.0     6.3    -      -       +      -
    101A  CYS*     3.5    31.9    -      -       -      -
    102A  ILE      2.9    10.0    +      -       -      +
    103A  CYS*     3.5     2.9    -      -       -      -
    104A  VAL      2.8    27.9    +      -       -      -
    149A  ILE*     3.4    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  PHE*     4.7     2.9    -      -       +      -
     73A  ILE*     1.3    79.6    -      -       -      +
     75A  HIS*     1.3    71.2    +      -       -      +
     85A  TRP*     4.3     2.8    -      -       -      -
     86A  LEU*     4.2     3.1    -      -       -      -
    104A  VAL*     3.7    26.2    -      -       +      -
    106A  TRP*     3.7    19.5    -      -       +      +
    128A  ILE*     3.8     9.9    -      -       +      -
    149A  ILE      2.8    12.5    +      -       -      +
    150A  GLY*     3.6     0.2    -      -       -      -
    151A  HIS*     3.0    28.9    +      -       -      +
    154A  GLY*     4.0     7.9    -      -       -      +
    157A  VAL*     3.9    19.7    -      -       +      -
    158A  VAL*     3.6    27.4    -      -       +      -
----------------------------------------------------------
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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