Contacts of the strand formed by residues 194 - 198 (chain C) in PDB entry 5MLE


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 194 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162C  ASN*     2.9    24.0    +      -       -      +
    163C  SER*     3.5     1.7    -      -       -      -
    164C  PHE      3.1    25.3    +      -       -      -
    188C  ILE*     3.7     4.5    -      -       -      +
    193C  ALA*     1.3    79.2    -      -       -      +
    195C  ALA*     1.3    64.8    +      -       -      +
    196C  GLN*     3.5     3.1    +      -       +      +
    249C  PRO*     4.1    21.8    -      -       +      +
    250C  LEU      4.9     0.4    -      -       -      +
    251C  TYR*     3.8    29.6    -      -       +      +
    275C  TYR*     5.6     2.5    -      -       +      -
    391C  VAL*     3.8    33.2    -      -       +      +
    392C  PHE*     4.2    19.7    -      -       +      -
    475C  PRO*     3.9    20.9    -      -       +      -
    478C  VAL*     5.0     5.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 195 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164C  PHE      3.9     3.1    -      -       -      -
    166C  VAL*     6.1     0.2    -      -       +      -
    185C  LEU*     3.9    22.4    -      -       +      -
    188C  ILE*     3.7    15.9    -      -       +      +
    194C  ILE*     1.3    73.4    -      -       -      +
    196C  GLN*     1.3    62.8    +      -       -      +
    248C  CYS*     3.9    18.4    -      -       -      -
    249C  PRO      3.1    16.9    +      -       -      +
    250C  LEU*     3.5    10.4    -      -       +      +
    251C  TYR      3.0    24.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 196 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107C  HIS*     3.1    26.4    -      -       -      -
    138C  HIS*     3.6    24.8    +      -       -      +
    163C  SER*     5.2     0.9    -      -       -      -
    164C  PHE      2.7    19.6    +      -       -      +
    165C  LEU*     3.5    16.1    -      -       +      +
    166C  VAL*     3.2    21.0    +      -       -      +
    194C  ILE*     3.5     7.4    +      -       +      +
    195C  ALA*     1.3    77.2    -      -       -      +
    197C  VAL*     1.3    68.0    +      -       -      +
    251C  TYR*     3.2    46.3    -      -       +      +
    253C  THR*     3.9     4.2    -      -       +      +
    392C  PHE*     4.0     5.2    -      -       +      -
    608C   NI      3.2    19.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 197 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165C  LEU*     4.4     3.8    -      -       -      -
    166C  VAL*     3.5    25.6    -      -       +      -
    168C  MET*     4.2    13.5    -      -       -      -
    181C  ILE*     5.6     2.7    -      -       +      -
    185C  LEU*     5.6     3.8    -      -       +      -
    195C  ALA      5.4     0.2    -      -       -      -
    196C  GLN*     1.3    82.2    -      -       -      +
    198C  HIS*     1.3    58.3    +      -       -      +
    199C  ALA*     3.5    30.2    +      -       +      +
    239C  ALA*     4.4    14.4    -      -       +      -
    250C  LEU*     4.0    21.8    -      -       +      -
    251C  TYR      3.1    10.1    +      -       -      +
    252C  ILE*     4.3     7.6    -      -       +      +
    253C  THR*     2.8    33.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 198 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  ARG*     6.1     1.6    -      -       -      -
    165C  LEU*     4.5     5.7    -      -       +      +
    166C  VAL      3.2     9.3    +      -       -      +
    167C  TYR*     3.8    36.8    -      +       +      -
    168C  MET*     3.2    22.9    +      -       -      +
    169C  ALA*     4.1    12.8    +      -       +      +
    170C  PHE*     4.1    15.5    -      +       -      -
    197C  VAL*     1.3    71.7    -      -       -      +
    199C  ALA*     1.3    59.7    +      -       -      +
    200C  GLU*     2.9    36.5    +      -       +      -
    253C  THR*     3.8     8.1    -      -       -      +
    254C  LYS*     4.4    14.8    +      -       +      -
    304C  SER*     3.1    26.6    +      -       -      -
    305C  PRO*     4.0     8.0    -      -       +      +
----------------------------------------------------------
 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