Contacts of the strand formed by residues 182 - 186 (chain C) in PDB entry 1TLF


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 ILE 182 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171C  VAL*     5.6     0.4    -      -       +      -
    174C  LEU*     4.2    18.2    -      -       +      -
    175C  VAL*     4.8     3.1    -      -       +      -
    179C  HIS*     4.0    29.4    -      -       +      +
    180C  GLN      3.4    12.2    +      -       -      +
    181C  GLN*     1.3    79.4    -      -       -      +
    183C  ALA*     1.3    71.0    +      -       -      +
    205C  LEU*     3.9    32.1    -      -       +      -
    210C  ILE*     4.3     8.7    -      -       +      -
    211C  GLN      5.2     0.8    +      -       -      -
    212C  PRO*     3.4     6.0    -      -       -      +
    213C  ILE*     3.0    29.7    +      -       -      +
    239C  PRO*     4.1     0.4    -      -       -      -
    241C  ALA*     3.3    14.6    -      -       +      +
    243C  LEU*     3.9    25.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 183 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  ILE*     1.3    77.2    -      -       -      +
    184C  LEU*     1.3    64.0    +      -       -      +
    213C  ILE*     4.8     0.4    -      -       +      -
    214C  ALA*     3.2    16.8    -      -       +      +
    232C  MET*     3.6    30.3    -      -       +      -
    239C  PRO*     3.7    20.4    -      -       +      -
    241C  ALA      3.0     7.2    +      -       -      +
    242C  MET*     3.3     6.2    -      -       +      +
    243C  LEU*     2.9    26.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 184 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  ILE*     4.9     0.7    -      -       +      -
    183C  ALA*     1.3    78.9    -      -       -      +
    185C  LEU*     1.3    60.3    +      -       -      +
    186C  ALA      3.9     0.9    -      -       -      -
    198C  LEU*     3.3    29.8    -      -       +      -
    201C  TRP*     3.7    37.2    -      -       +      -
    202C  HIS*     3.8    22.0    -      -       +      +
    205C  LEU*     4.1    10.5    -      -       +      -
    212C  PRO*     3.8    22.0    -      -       +      -
    214C  ALA      2.8     9.7    +      -       -      +
    215C  GLU*     3.1    12.6    -      -       +      -
    216C  ARG*     3.0    26.6    +      -       -      +
    232C  MET*     4.9     0.9    -      -       -      +
    242C  MET*     5.6     0.2    -      -       -      -
    243C  LEU*     3.6    22.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 185 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  LEU*     1.3    72.8    -      -       -      +
    186C  ALA*     1.3    58.6    +      -       -      +
    201C  TRP*     3.8     3.3    -      -       -      -
    216C  ARG*     3.1    21.8    -      -       +      +
    217C  GLU*     4.5     0.4    -      -       -      -
    225C  GLY*     3.8    20.2    -      -       -      -
    228C  GLN*     3.4    33.2    -      -       +      -
    229C  THR*     4.0    12.3    -      -       -      +
    242C  MET*     4.6    11.4    -      -       +      -
    243C  LEU      3.1    12.0    +      -       -      +
    244C  VAL*     3.7    26.4    -      -       +      -
    245C  ALA*     3.0    25.6    +      -       -      +
    249C  MET*     3.5    27.5    -      -       +      +
    253C  ALA*     4.7     1.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 186 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  LEU      3.9     0.6    -      -       -      -
    185C  LEU*     1.3    77.0    -      -       -      +
    187C  GLY*     1.3    61.2    +      -       -      +
    189C  LEU*     4.2     2.2    -      -       +      -
    194C  ALA      4.9     3.1    -      -       -      +
    198C  LEU*     3.9    27.4    -      -       +      -
    201C  TRP*     4.2     4.5    -      -       +      -
    215C  GLU*     5.7     0.9    -      -       +      -
    216C  ARG      2.7     9.2    +      -       -      +
    217C  GLU*     3.0    33.7    -      -       +      +
    218C  GLY      3.0    25.3    +      -       -      -
    245C  ALA*     3.8     6.1    -      -       -      -
    249C  MET*     3.6     3.6    -      -       -      +
----------------------------------------------------------
 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