Contacts of the strand formed by residues 246 - 251 (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 246 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130C  HIS*     4.2     2.5    -      -       -      -
    138C  CYS*     3.6    17.9    -      -       -      +
    140C  VAL*     4.2    12.1    -      -       +      -
    235C  PHE*     4.2    13.5    -      -       +      -
    239C  ILE*     4.6     9.0    -      -       +      -
    244C  ARG      3.7    12.3    -      -       -      +
    245C  PRO*     1.3    73.0    -      -       -      +
    247C  HIS*     1.3    71.3    +      -       -      +
    248C  LEU      4.3     1.6    -      -       -      +
    283C  ILE*     4.1    23.1    -      -       +      +
    286C  THR*     3.5    37.9    -      -       +      +
    288C  LEU*     2.9    21.6    +      -       +      +
    289C  LEU*     3.7     7.8    -      -       +      +
    290C  SER*     2.9    24.6    +      -       -      +
    291C  ALA      3.3     6.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 247 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  THR*     3.4    29.0    +      -       -      -
    127C  ILE*     3.4    26.9    -      -       +      +
    130C  HIS*     2.9    27.8    +      -       +      +
    137C  LEU*     4.3     3.8    -      -       +      -
    138C  CYS      2.8    17.4    +      -       -      +
    139C  VAL*     3.3    12.2    -      -       +      +
    140C  VAL      2.9    25.8    +      -       -      +
    245C  PRO      4.0     0.2    +      -       -      -
    246C  ILE*     1.3    73.7    -      -       -      +
    248C  LEU*     1.3    70.2    +      -       -      +
    249C  SER*     3.6     5.5    +      -       -      -
    291C  ALA*     3.4    18.2    -      -       +      +
    293C  ASP*     2.7    34.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 248 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140C  VAL*     3.5    27.6    -      -       +      +
    142C  VAL*     3.7    24.9    -      -       +      -
    246C  ILE*     3.9     1.6    -      -       +      -
    247C  HIS*     1.3    72.0    -      -       -      +
    249C  SER*     1.3    60.0    +      -       -      +
    250C  PHE*     4.3    20.6    -      -       +      -
    279C  ILE*     4.9     1.8    -      -       +      -
    280C  ALA*     5.2     2.9    -      -       -      -
    283C  ILE*     4.2    28.3    -      -       +      -
    289C  LEU*     3.9    15.7    -      -       +      -
    291C  ALA      2.9     9.4    +      -       -      +
    292C  LEU*     3.1    16.3    -      -       +      -
    293C  ASP      2.8    25.6    +      -       -      +
    318C  VAL*     5.1     1.3    -      -       +      -
    322C  SER*     3.6    23.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 249 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  HIS*     2.8    28.1    +      -       -      -
    123C  ALA*     3.9     0.5    -      -       -      +
    139C  VAL*     4.7     1.1    -      -       -      -
    140C  VAL      2.9    11.1    +      -       -      -
    141C  TRP*     3.5    30.5    -      -       -      -
    142C  VAL      2.9    27.0    +      -       -      +
    247C  HIS*     3.6     8.3    +      -       -      -
    248C  LEU*     1.3    71.2    -      -       -      +
    250C  PHE*     1.3    59.8    +      -       -      +
    251C  ASP      3.9     0.6    +      -       -      -
    293C  ASP*     2.8    26.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 250 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  VAL*     3.6    37.7    -      -       +      -
    248C  LEU*     4.3    17.5    -      -       +      -
    249C  SER*     1.3    71.8    +      -       -      +
    251C  ASP*     1.3    80.6    +      -       -      +
    252C  ILE*     3.7     3.1    +      -       +      -
    254C  ALA*     4.3     2.0    -      -       +      -
    255C  PHE*     3.5    42.4    -      +       -      -
    271C  LEU*     4.4     6.7    -      -       +      -
    276C  GLY*     4.7     7.0    -      -       -      -
    279C  ILE*     4.6    12.1    -      -       +      -
    280C  ALA*     5.7     1.1    -      -       +      -
    292C  LEU*     5.5     0.9    -      -       +      -
    293C  ASP*     2.9    18.5    +      -       -      +
    294C  LEU*     3.4    18.2    -      -       +      +
    295C  VAL*     3.0    26.9    +      -       -      +
    318C  VAL*     3.7    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 251 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  HIS*     3.7     4.0    -      -       +      -
    142C  VAL      2.8     8.9    +      -       -      +
    143C  ASP*     3.2    22.4    -      -       -      +
    249C  SER      3.9     1.4    +      -       -      -
    250C  PHE*     1.3    74.1    -      -       -      +
    252C  ILE*     1.3    60.3    +      -       -      +
    253C  ASP*     3.0    20.1    +      -       -      +
    254C  ALA*     2.8    29.6    +      -       -      +
    295C  VAL*     3.7     6.5    -      -       -      +
    296C  GLU*     3.3    21.1    -      -       -      +
    401C   MN      2.3    32.1    +      -       -      -
    402C   MN      2.3    21.2    +      -       -      +
    406C  38I      2.8     4.7    +      -       -      -
----------------------------------------------------------
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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