Contacts of the strand formed by residues 126 - 131 (chain C) in PDB entry 5ODS


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 ALA 126 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121C  LEU      4.0     0.3    -      -       -      +
    122C  VAL*     3.8     1.7    -      -       -      -
    123C  THR*     3.0    34.6    +      -       -      +
    125C  ASN*     1.3    82.4    -      -       +      +
    127C  VAL*     1.3    66.5    +      -       -      +
    128C  TYR*     4.0    22.2    -      -       +      +
    140C  LYS*     4.0    14.6    -      -       +      -
    142C  PHE      3.4    13.9    -      -       -      +
    143C  ASP*     3.9    11.2    -      -       -      +
    144C  ARG*     3.9     5.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  ALA*     5.1     5.2    -      -       +      -
    121C  LEU      3.4     7.4    -      -       -      +
    122C  VAL*     4.2    25.6    -      -       +      -
    126C  ALA*     1.3    81.2    -      -       -      +
    128C  TYR*     1.3    71.7    +      -       -      +
    129C  HIS*     4.6    11.4    -      -       +      +
    140C  LYS*     3.7     2.6    -      -       -      +
    141C  MET*     2.8    28.8    +      -       +      +
    142C  PHE*     3.0    50.8    +      -       +      +
    144C  ARG*     4.6     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104C  MET*     4.6    18.9    -      -       +      +
    105C  THR*     5.5     0.7    +      -       -      -
    106C  ASP*     4.4    11.1    +      -       -      -
    120C  ALA*     3.2     1.6    -      -       -      +
    121C  LEU*     2.7    56.6    +      -       +      +
    123C  THR*     3.5    35.3    +      -       +      -
    125C  ASN*     6.1     0.2    -      -       -      +
    126C  ALA*     4.0    17.9    -      -       +      +
    127C  VAL*     1.3    73.6    -      -       -      +
    129C  HIS*     1.3    73.2    +      -       -      +
    130C  TRP      4.1     0.2    -      -       -      -
    138C  PRO*     4.2    23.6    -      -       +      -
    139C  VAL      3.3     7.0    -      -       -      +
    140C  LYS*     3.4    41.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 129 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114C  ILE*     4.2    25.3    -      -       +      +
    118C  THR*     4.7    17.2    -      -       +      +
    119C  VAL      4.0     2.2    -      -       -      -
    120C  ALA*     4.0    13.2    -      -       +      +
    127C  VAL*     4.6     6.5    -      -       +      +
    128C  TYR*     1.3    85.2    -      -       -      +
    130C  TRP*     1.3    60.2    +      -       -      +
    131C  SER      4.0     1.4    +      -       -      -
    137C  GLN      4.4     0.2    -      -       -      +
    138C  PRO*     3.8     0.8    -      -       -      +
    139C  VAL*     2.8    38.1    +      -       -      +
    141C  MET*     3.4    41.4    -      -       +      +
    142C  PHE*     6.1     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 130 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  LEU*     3.6    39.3    -      -       +      -
     89C  GLN      4.2     2.5    -      -       -      -
     90C  ILE*     3.9    30.7    -      -       +      -
    100C  LYS*     3.3    16.4    -      -       +      +
    101C  ALA*     3.7    32.8    -      -       -      -
    102C  HIS*     3.7    20.4    -      -       +      +
    111C  TRP*     5.1     4.5    -      +       -      -
    118C  THR*     4.4     2.0    -      -       -      -
    119C  VAL*     2.9    58.6    +      -       +      +
    121C  LEU*     4.1     8.1    -      -       +      -
    128C  TYR      4.1     0.2    -      -       -      -
    129C  HIS*     1.3    72.9    -      -       -      +
    131C  SER*     1.3    63.3    +      -       -      +
    132C  MET      3.7     0.2    +      -       -      -
    136C  SER      3.2    27.0    +      -       -      -
    137C  GLN*     3.8     1.0    +      -       -      +
    138C  PRO*     3.5    36.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 131 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  ILE*     4.3     1.4    -      -       -      +
    100C  LYS*     3.2    26.7    -      -       -      +
    117C  ASN      3.2    14.9    +      -       -      -
    118C  THR*     4.3     8.0    -      -       -      +
    129C  HIS      4.0     2.6    +      -       -      -
    130C  TRP*     1.3    80.2    -      -       -      +
    132C  MET*     1.3    62.8    +      -       -      +
    133C  GLU*     3.4    19.0    +      -       -      +
    136C  SER*     3.6    19.4    +      -       -      -
    137C  GLN      5.4     0.8    +      -       -      -
----------------------------------------------------------
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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