Contacts of the strand formed by residues 193 - 198 (chain C) in PDB entry 4IXU


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 193 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127C  ILE*     6.2     0.4    -      -       +      -
    139C  VAL*     3.2    22.0    -      -       +      +
    141C  TRP*     4.0    24.7    -      -       +      -
    164C  VAL*     4.0    16.6    -      -       +      -
    168C  LEU*     4.1    23.6    -      -       +      -
    188C  ILE*     4.3     5.6    -      -       +      -
    189C  SER      4.3     0.7    -      -       -      +
    190C  SER      3.9    18.2    -      -       -      +
    191C  ALA      3.5     2.0    -      -       -      -
    192C  SER*     1.3    82.5    -      -       -      +
    194C  VAL*     1.3    75.4    +      -       -      +
    195C  TYR*     4.0    23.3    -      -       +      -
    214C  ILE*     4.0    16.1    -      -       +      +
    215C  GLN*     3.7    10.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 194 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  VAL      2.9     6.7    +      -       -      -
    140C  VAL*     3.5     5.4    -      -       -      +
    141C  TRP*     2.9    23.7    +      -       -      +
    191C  ALA      5.5     0.9    -      -       -      +
    193C  ILE*     1.3    79.0    -      -       -      +
    195C  TYR*     1.3    76.4    +      -       -      +
    196C  ILE*     4.5     1.6    -      -       +      -
    215C  GLN*     3.3    11.4    -      -       +      +
    217C  PHE*     3.7    14.8    -      -       +      -
    234C  THR*     3.6    34.8    -      -       +      +
    237C  LEU*     4.1    22.2    -      -       +      -
    238C  LEU*     3.7    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 195 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141C  TRP*     3.2    40.2    -      +       +      -
    146C  ALA*     2.8    36.3    +      -       +      -
    148C  ILE*     3.7     8.8    -      -       +      +
    164C  VAL*     3.5    23.6    -      -       -      +
    193C  ILE*     4.0    11.0    -      -       +      -
    194C  VAL*     1.3    78.2    -      -       -      +
    196C  ILE*     1.3    66.0    +      -       -      +
    198C  LEU*     3.8    25.6    -      -       +      -
    209C  LEU*     3.8    13.5    -      -       +      -
    214C  ILE*     3.7    29.8    -      -       +      -
    215C  GLN      3.2     8.8    +      -       -      -
    216C  TYR*     3.4    18.4    -      -       +      -
    217C  PHE      2.8    25.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 196 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140C  VAL*     3.8    25.1    -      -       +      -
    141C  TRP      2.9     6.7    +      -       -      -
    142C  VAL*     3.3    16.7    -      -       +      +
    143C  ASP      3.0    23.9    +      -       -      -
    194C  VAL*     4.5     2.9    -      -       +      -
    195C  TYR*     1.3    81.4    -      -       -      +
    197C  GLY*     1.3    62.4    +      -       -      +
    198C  LEU      3.6     1.8    -      -       -      -
    217C  PHE*     3.4     4.0    -      -       +      +
    222C  ILE*     4.0    17.7    -      -       +      -
    227C  ILE*     4.4     1.1    -      -       +      -
    230C  VAL*     4.2    16.4    -      -       +      -
    231C  MET*     3.5    30.3    -      -       +      -
    234C  THR*     3.8    19.7    -      -       +      +
    271C  LEU*     4.9     0.9    -      -       +      -
    279C  ILE*     4.0    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 197 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143C  ASP      3.1    12.8    -      -       -      +
    144C  ALA*     3.7     0.2    -      -       -      -
    196C  ILE*     1.3    78.4    -      -       -      +
    198C  LEU*     1.3    65.5    +      -       -      +
    199C  ARG*     3.3    21.9    +      -       -      -
    217C  PHE      2.9    10.6    +      -       -      -
    219C  MET*     3.4    25.8    -      -       -      +
    222C  ILE*     4.3     2.6    -      -       -      +
    254C  ALA*     5.3     1.1    -      -       -      -
    271C  LEU*     4.7     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 198 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327B  ARG      3.1    10.1    -      -       -      +
    328B  GLU*     5.9     0.4    -      -       -      -
    143C  ASP*     3.3     7.2    +      -       +      +
    144C  ALA      3.5     2.7    -      -       -      -
    145C  HIS      3.3    34.8    -      -       -      +
    146C  ALA*     3.8     4.5    -      -       +      +
    195C  TYR*     3.8    30.3    -      -       +      -
    197C  GLY*     1.3    76.4    -      -       -      +
    199C  ARG*     1.3    58.5    +      -       -      +
    201C  VAL*     4.2    15.3    -      -       +      -
    209C  LEU*     4.0    19.5    -      -       +      -
    216C  TYR*     3.7    35.9    -      -       +      -
    217C  PHE      5.0     0.4    -      -       -      +
    218C  SER*     3.1    15.6    -      -       -      +
    219C  MET*     3.1    20.1    +      -       -      +
----------------------------------------------------------
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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