Contacts of the strand formed by residues 153 - 156 (chain E) in PDB entry 5LK5


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 153 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148E  PHE      3.6     0.7    -      -       -      +
    149E  ASN*     3.1     7.4    +      -       -      -
    150E  TYR      2.8    35.5    +      -       -      +
    151E  LYS      3.1     5.6    +      -       -      +
    152E  GLY*     1.3    83.5    -      -       -      +
    154E  ASN*     1.3    64.3    +      -       -      +
    155E  VAL*     3.6    14.4    +      -       +      +
    203E  LEU*     4.5    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 154 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126E  SER      5.8     0.6    +      -       -      -
    127E  GLU*     6.0     0.4    -      -       -      +
    128E  TYR*     3.2    48.3    +      -       -      +
    147E  ILE*     3.8     7.0    -      -       +      -
    148E  PHE      3.7     2.9    -      -       -      -
    149E  ASN*     3.1    23.0    +      -       -      +
    153E  LYS*     1.3    74.6    -      -       -      +
    155E  VAL*     1.3    60.9    +      -       -      +
    156E  LEU*     3.5    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 155 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147E  ILE*     3.3     5.7    -      -       -      +
    148E  PHE      2.7    42.8    +      -       -      +
    150E  TYR*     4.5     6.1    -      -       +      +
    153E  LYS*     3.9    24.9    -      -       +      +
    154E  ASN*     1.3    75.0    -      -       -      +
    156E  LEU*     1.3    65.0    +      -       -      +
    200E  TRP*     3.3    26.6    -      -       +      -
    201E  ASP*     3.8    28.5    -      -       +      +
    202E  PHE*     4.0    23.3    -      -       +      -
    203E  LEU      5.9     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 156 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143E  LYS*     5.0     8.3    -      -       -      +
    145E  HIS*     4.4    22.2    -      -       +      +
    146E  VAL      4.0     2.9    -      -       -      -
    147E  ILE*     4.0    24.9    -      -       +      -
    154E  ASN*     3.5    20.0    -      -       +      +
    155E  VAL*     1.3    78.5    -      -       -      +
    157E  ILE*     1.3    70.6    +      -       -      +
    158E  ASN*     3.4     3.6    +      -       -      +
    199E  ASP      4.5     0.2    -      -       -      +
    200E  TRP*     3.4    10.4    -      -       -      -
    201E  ASP      5.2     0.7    +      -       -      -
    366G  ARG*     5.9     4.9    -      -       -      +
----------------------------------------------------------
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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