Contacts of the strand formed by residues 244 - 247 (chain C) in PDB entry 1LUA


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 244 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209C  TRP*     3.6    46.4    -      -       +      +
    210C  GLN*     3.8    17.7    -      -       +      -
    212C  GLU      2.8    30.8    +      -       -      -
    213C  SER*     3.8    10.1    +      -       -      +
    215C  ILE*     2.8    31.7    +      -       +      +
    216C  GLU      3.5    10.3    -      -       -      +
    217C  ILE*     5.5     0.2    -      -       -      -
    218C  VAL*     6.3     0.2    -      -       +      -
    240C  GLU*     3.0     8.2    -      -       -      +
    241C  TYR*     2.6    44.1    +      -       -      +
    242C  GLY      3.1     1.2    +      -       -      -
    243C  GLY*     1.3    84.8    -      -       -      +
    245C  ARG*     1.3    64.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 245 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113C  ALA*     3.1    36.6    +      -       +      +
    114C  ALA*     4.8     2.2    -      -       -      +
    209C  TRP*     5.7     0.4    -      -       -      -
    216C  GLU*     3.1    19.2    +      -       -      +
    217C  ILE*     3.3    34.8    -      -       +      +
    218C  VAL*     3.1    25.7    +      -       -      +
    238C  GLY*     3.4    28.9    -      -       -      +
    239C  LYS      3.3     3.4    -      -       -      -
    240C  GLU*     3.8    25.1    -      -       +      -
    241C  TYR*     5.3     0.7    -      -       -      -
    243C  GLY      5.3     2.6    +      -       -      -
    244C  LYS*     1.3    75.7    -      -       -      +
    246C  ALA*     1.3    61.1    +      -       -      +
    247C  PHE*     4.7     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 246 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209C  TRP*     4.7     0.9    -      -       +      -
    218C  VAL*     3.6    14.8    -      -       +      -
    232C  ILE*     3.7    31.9    -      -       +      -
    236C  ASP*     3.7    10.1    -      -       +      +
    238C  GLY      2.8    28.1    +      -       -      -
    239C  LYS      2.9    11.8    +      -       -      -
    241C  TYR*     3.9    19.5    -      -       +      -
    245C  ARG*     1.3    76.4    -      -       -      +
    247C  PHE*     1.3    59.4    +      -       -      +
    248C  GLY      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 247 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  LEU*     3.8    49.4    -      -       +      -
    110C  VAL*     4.4     6.1    -      -       +      -
    113C  ALA*     3.9    19.5    -      -       +      -
    217C  ILE*     3.8    27.1    -      -       +      -
    218C  VAL*     3.0    10.9    +      -       -      +
    219C  ALA*     3.3     5.9    -      -       +      -
    220C  ASP*     3.0    26.3    +      -       -      +
    232C  ILE*     4.4     4.8    -      -       -      +
    236C  ASP      3.5     2.5    -      -       -      -
    237C  LYS*     3.7    24.5    -      -       +      -
    238C  GLY*     3.5    30.7    -      -       -      -
    245C  ARG*     4.7     2.5    -      -       +      -
    246C  ALA*     1.3    75.2    -      -       -      +
    248C  GLY*     1.3    59.8    +      -       -      +
    251C  GLY      5.7     0.4    -      -       -      -
    252C  ILE*     4.1    17.4    -      -       +      +
----------------------------------------------------------
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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