Contacts of the strand formed by residues 143 - 149 (chain L) in PDB entry 6AHU


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 143 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2J  ALA*     4.1    17.3    -      -       +      -
    101L  ILE      3.3    19.8    +      -       -      +
    102L  ASP*     4.3    16.1    -      -       +      +
    103L  GLU      5.1     0.6    -      -       -      -
    104L  ASP      3.1    28.9    +      -       -      +
    118L  SER*     3.6    18.2    +      -       -      +
    119L  LEU      3.5    26.8    -      -       -      +
    120L  ASP*     3.5     9.0    -      -       -      +
    134L  SER*     3.9    21.6    +      -       -      -
    135L  GLN*     5.2    12.3    +      -       +      +
    141L  ILE*     3.7    11.0    -      -       -      +
    142L  MET*     1.3    90.8    -      -       +      +
    144L  PHE*     1.3    72.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 144 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118L  SER*     3.5     2.8    +      -       -      -
    119L  LEU*     2.7    40.5    +      -       -      +
    120L  ASP      4.5     4.7    -      -       -      -
    121L  LYS*     4.5    23.1    -      -       +      -
    124L  TYR*     3.6    61.5    -      +       +      -
    125L  GLU*     5.9     0.7    -      -       +      -
    132L  HIS*     3.7     5.8    -      -       -      +
    133L  PRO*     3.7    37.7    -      -       +      -
    134L  SER      5.0     0.7    -      -       -      +
    141L  ILE*     3.7    33.7    -      -       +      -
    143L  LYS*     1.3    79.0    -      -       -      +
    145L  ILE*     1.3    61.1    +      -       -      +
    146L  VAL*     4.3     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 145 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101L  ILE*     6.3     0.4    -      -       +      -
    116L  ILE*     3.7    24.9    -      -       +      -
    117L  LEU      3.4     8.5    -      -       -      +
    118L  SER*     3.7    23.1    -      -       -      +
    131L  GLY*     3.4     1.8    -      -       -      -
    132L  HIS*     3.2    45.2    +      -       +      +
    134L  SER*     3.4    28.9    -      -       -      +
    144L  PHE*     1.3    78.1    -      -       -      +
    146L  VAL*     1.3    64.8    +      -       -      +
    147L  SER*     4.9     1.3    -      -       -      +
    321L  PRO*     5.5     4.9    -      -       +      +
    322L  VAL*     5.2     6.1    -      -       +      -
    328L  GLU*     3.6    30.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 146 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115L  LEU      3.6     0.2    -      -       -      +
    116L  ILE*     3.4     1.9    -      -       -      -
    117L  LEU*     3.0    46.4    +      -       +      +
    119L  LEU*     4.9     8.3    -      -       +      -
    124L  TYR*     3.7    36.1    -      -       +      -
    129L  LEU*     3.7    30.5    -      -       +      +
    130L  GLN      3.3    17.7    -      -       -      +
    131L  GLY*     3.8     3.6    -      -       -      -
    144L  PHE      4.3     0.9    -      -       -      -
    145L  ILE*     1.3    75.5    -      -       -      +
    147L  SER*     1.3    61.4    +      -       -      +
    148L  ILE*     3.8    22.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 147 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114L  LYS*     4.5    11.8    -      -       -      +
    115L  LEU      4.0     2.2    -      -       -      -
    116L  ILE*     3.4    29.5    -      -       -      +
    130L  GLN      4.5     4.5    +      -       -      +
    132L  HIS*     5.9     5.7    -      -       -      -
    145L  ILE*     4.2     3.2    +      -       -      -
    146L  VAL*     1.3    74.5    -      -       -      +
    148L  ILE*     1.3    63.7    +      -       -      +
    149L  ASP*     4.1     2.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 148 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78L  ILE*     6.0     0.2    -      -       +      -
    114L  LYS*     3.3     1.5    -      -       -      -
    115L  LEU*     2.5    57.1    +      -       +      +
    117L  LEU*     4.1    14.8    -      -       +      -
    129L  LEU*     3.8    30.1    -      -       +      -
    146L  VAL*     3.8    11.0    -      -       +      -
    147L  SER*     1.3    76.5    +      -       -      +
    149L  ASP*     1.3    58.4    +      -       -      +
    150L  LEU*     3.4    21.8    +      -       +      -
    153L  LEU*     4.2     5.4    -      -       +      -
    165L  ILE*     3.8    41.1    -      -       +      -
    169L  PHE*     4.6     5.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 149 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112L  ASN      3.8     6.1    -      -       -      +
    113L  GLY      3.1    20.6    -      -       -      +
    114L  LYS*     3.7    27.1    -      -       +      +
    147L  SER*     4.0     3.2    +      -       -      +
    148L  ILE*     1.3    70.6    -      -       -      +
    150L  LEU*     1.3    62.0    +      -       -      +
    151L  MET*     3.4     8.9    +      -       -      +
    152L  GLU*     3.3    42.8    +      -       -      +
    153L  LEU*     3.4    24.1    +      -       -      +
----------------------------------------------------------
 Back to top of page


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