Contacts of the strand formed by residues 528 - 535 (chain C) in PDB entry 4OMC


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 PHE 528 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263C  VAL*     3.9    27.4    -      -       +      -
    305C  CYS*     4.6     4.7    -      -       -      -
    491C  LEU      3.9    13.2    -      -       -      +
    492C  THR*     3.2     6.1    -      -       -      +
    493C  LEU*     2.9    56.8    +      -       +      +
    498C  ARG*     3.7    27.8    -      -       +      -
    501C  LEU*     4.7     6.3    -      -       +      -
    503C  ILE*     4.7     1.6    -      -       +      -
    516C  LEU*     3.8    30.3    -      -       +      -
    522C  ASP*     5.3     0.7    -      -       -      -
    526C  ASP      4.8     1.6    -      -       -      -
    527C  GLY*     1.3    76.8    -      -       -      -
    529C  ASN*     1.3    60.0    +      -       -      +
    530C  ASP      3.8     0.4    -      -       -      -
    531C  TRP*     3.8    22.9    -      +       +      -
    533C  PHE*     3.7    27.6    -      +       +      -
    602C  FMT      3.8     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 529 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    492C  THR*     4.3    12.3    -      -       +      +
    526C  ASP      5.7     2.0    -      -       -      +
    528C  PHE*     1.3    70.9    -      -       -      +
    530C  ASP*     1.3    76.1    +      -       -      +
    531C  TRP*     3.2     2.6    +      -       -      -
    602C  FMT      3.0    23.0    +      -       -      +
    268D  ARG*     4.8    19.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 530 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    490C  ARG*     2.9    47.8    +      -       -      +
    491C  LEU      3.1     6.2    +      -       -      -
    492C  THR*     2.9    25.0    +      -       -      +
    529C  ASN*     1.3    78.2    +      -       -      +
    531C  TRP*     1.3    62.5    +      -       -      +
    532C  ALA      3.6     0.5    +      -       -      -
    565C  LYS*     3.0    25.8    +      -       -      +
    233D  ASP*     4.4     7.7    -      -       -      +
    267D  ALA*     5.2     2.6    -      -       -      +
    268D  ARG*     3.7    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 531 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263C  VAL*     3.7    27.8    -      -       +      -
    264C  ASP*     3.6    26.2    -      -       -      -
    265C  GLY*     4.5     2.2    -      -       -      -
    304C  ASN      2.8    28.8    +      -       -      -
    305C  CYS*     3.9     5.6    -      -       -      +
    307C  GLY*     3.8    24.5    -      -       -      -
    310C  ASN*     4.2    10.6    -      -       -      +
    489C  ALA      3.3     3.8    -      -       -      +
    490C  ARG*     3.3     1.1    -      -       -      -
    491C  LEU      2.9    26.2    +      -       -      +
    528C  PHE*     3.8    27.6    -      +       +      -
    529C  ASN      3.2     1.3    -      -       -      -
    530C  ASP*     1.3    77.1    -      -       -      +
    532C  ALA*     1.3    60.9    +      -       -      +
    533C  PHE*     3.3    39.1    +      +       +      -
    602C  FMT      4.0    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 532 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310C  ASN*     2.6    30.6    +      -       -      +
    488C  GLN*     3.7    21.4    +      -       +      +
    489C  ALA      3.9     4.5    -      -       -      -
    490C  ARG*     3.5    38.1    -      -       +      +
    530C  ASP      3.6     2.2    +      -       -      -
    531C  TRP*     1.3    76.4    -      -       -      +
    533C  PHE*     1.3    60.3    +      -       -      +
    534C  MET*     3.2     3.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 533 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304C  ASN*     4.1    11.2    -      -       +      +
    305C  CYS*     5.1     0.7    -      -       -      -
    310C  ASN*     4.0     4.9    -      -       -      +
    488C  GLN*     3.1     5.0    -      -       -      -
    489C  ALA*     2.8    45.1    +      -       -      +
    491C  LEU*     3.8    29.4    -      -       +      -
    503C  ILE*     4.3     7.0    -      -       +      -
    515C  LEU*     3.2    52.9    -      -       +      +
    516C  LEU*     4.0    15.0    -      -       +      -
    528C  PHE*     3.7    33.0    -      +       -      -
    531C  TRP*     3.5    35.8    -      +       +      -
    532C  ALA*     1.3    71.6    -      -       -      +
    534C  MET*     1.3    58.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 534 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304C  ASN*     3.6     3.5    +      -       -      +
    310C  ASN*     3.0    48.3    +      -       -      +
    311C  SER      3.7    16.2    -      -       -      +
    312C  ILE*     4.0    16.6    -      -       +      -
    314C  THR      5.5     0.2    -      -       -      +
    334C  SER*     2.7    17.4    +      -       -      -
    335C  SER*     3.3    38.3    +      -       -      +
    486C  HIS*     4.1    17.5    -      -       +      -
    487C  ALA      3.3    11.0    -      -       -      +
    488C  GLN*     4.1     7.0    -      -       +      -
    515C  LEU*     4.7     1.6    -      -       -      -
    532C  ALA      4.0     3.1    -      -       -      +
    533C  PHE*     1.3    75.2    -      -       -      +
    535C  THR*     1.3    92.3    +      -       -      +
    536C  THR*     3.7    12.8    -      -       +      -
    608C   NA      4.1     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 535 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334C  SER*     3.4    17.5    -      -       -      -
    485C  GLU      4.4     1.0    -      -       -      +
    486C  HIS*     3.9     3.3    -      -       -      -
    487C  ALA*     3.0    42.0    +      -       +      +
    505C  LEU*     4.5    14.6    -      -       +      -
    513C  SER*     2.7    34.0    +      -       -      +
    515C  LEU*     4.5     3.6    -      -       +      -
    534C  MET*     1.3    82.6    -      -       -      +
    536C  THR*     1.3    62.0    +      -       -      +
    537C  HIS*     3.0    13.0    +      -       -      +
    538C  SER*     5.1     8.1    +      -       -      +
    547C  TRP*     5.7     1.8    -      -       +      -
----------------------------------------------------------
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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