Contacts of the strand formed by residues 457 - 464 (chain C) in PDB entry 2O2C


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 CYS 457 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389C  HIS*     4.7     0.4    -      -       -      -
    390C  ALA*     3.5    14.8    -      -       -      -
    392C  LEU*     3.8    21.1    -      -       +      -
    448C  ILE*     3.9    23.1    -      -       -      -
    455C  ILE      3.4    16.1    +      -       -      -
    456C  PRO*     1.3    74.5    -      -       -      +
    458C  ASP*     1.3    65.9    +      -       -      +
    459C  PHE*     3.5    24.7    -      -       +      -
    487C  LEU*     4.4     5.2    -      -       +      -
    525C  PRO      3.5    11.6    +      -       -      +
    526C  SER*     3.2     2.7    -      -       -      +
    527C  ASN*     2.8    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 458 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373C  LEU*     4.3     7.1    -      -       -      +
    389C  HIS*     3.0    26.0    +      -       -      -
    390C  ALA      2.8    14.3    +      -       -      +
    391C  ILE*     3.8     5.7    -      -       +      +
    392C  LEU*     2.8    31.5    +      -       -      +
    457C  CYS*     1.3    71.8    -      -       -      +
    459C  PHE*     1.3    63.0    +      -       -      +
    460C  ILE*     3.9     3.5    +      -       +      +
    527C  ASN*     3.0    36.3    +      -       -      +
    529C  LEU*     4.6     7.6    -      -       +      -
    546C  TYR*     2.7    37.6    +      -       -      +
    549C  LYS*     4.4     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 459 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392C  LEU*     3.5    20.2    -      -       +      -
    394C  TYR*     3.5    37.2    -      +       -      -
    445C  TYR*     3.8     8.3    -      +       -      -
    457C  CYS*     3.5    30.3    -      -       +      -
    458C  ASP*     1.3    71.2    -      -       -      +
    460C  ILE*     1.3    55.7    +      -       -      +
    480C  PHE*     3.6    19.6    -      +       +      -
    483C  GLN*     3.6    31.0    -      -       +      -
    484C  THR*     3.6    25.1    -      -       +      -
    487C  LEU*     3.9    20.6    -      -       +      -
    526C  SER*     4.2     5.2    -      -       -      -
    527C  ASN      2.8    13.4    +      -       -      +
    528C  THR*     3.4     3.4    -      -       -      +
    529C  LEU*     2.7    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 460 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391C  ILE*     4.4    11.2    -      -       +      -
    392C  LEU      3.2     6.3    +      -       -      -
    393C  PRO*     3.5     9.6    -      -       +      +
    394C  TYR*     2.6    35.2    +      -       -      +
    395C  ASP*     5.4     0.5    -      -       -      +
    398C  LEU*     4.3    13.5    -      -       +      -
    401C  LEU*     3.9    24.9    -      -       +      -
    458C  ASP      4.5     4.7    -      -       -      +
    459C  PHE*     1.3    74.6    -      -       -      +
    461C  GLY*     1.3    63.6    +      -       -      +
    480C  PHE*     3.5     4.2    -      -       -      -
    529C  LEU*     3.3    28.9    -      -       +      +
    531C  ILE*     5.5     3.8    -      -       +      -
    542C  ILE*     4.3    26.5    -      -       +      -
    546C  TYR*     3.6    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 461 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    394C  TYR      4.0    10.1    -      -       -      -
    395C  ASP*     5.8     1.8    -      -       -      -
    460C  ILE*     1.3    77.0    -      -       -      +
    462C  ALA*     1.3    59.7    +      -       -      -
    477C  MET*     4.5     4.0    -      -       -      -
    480C  PHE*     3.5    15.0    -      -       -      -
    529C  LEU      2.9     9.3    +      -       -      +
    530C  LEU*     3.4    10.3    -      -       -      -
    531C  ILE*     3.0    30.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 462 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    394C  TYR      4.5     5.6    +      -       -      +
    395C  ASP*     4.5    14.5    +      -       -      +
    461C  GLY*     1.3    74.5    -      -       -      -
    463C  ILE*     1.3    60.8    +      -       -      +
    464C  GLN      3.7    17.9    -      -       -      +
    473C  HIS*     3.1    24.1    +      -       -      +
    477C  MET*     3.2    13.7    -      -       -      +
    530C  LEU*     4.4     0.2    -      -       -      -
    531C  ILE*     3.4    19.3    -      -       +      -
    533C  SER*     4.1     9.0    -      -       -      -
    534C  LEU      4.2     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 463 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600B  MET*     3.9    19.3    -      -       +      +
    601B  PHE*     3.4    41.4    -      -       +      +
    604B  LEU*     3.7    15.0    -      -       +      +
    605B  SER*     3.6    22.9    -      -       -      +
     98C  PHE*     3.7    29.6    -      -       +      -
    462C  ALA*     1.3    72.9    -      -       -      +
    464C  GLN*     1.3    55.7    +      -       +      +
    473C  HIS*     2.8    21.6    +      -       -      -
    530C  LEU*     3.9    25.8    -      -       +      -
    531C  ILE      3.0    17.0    +      -       -      +
    532C  LYS*     3.6    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 464 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    604B  LEU      2.9    27.1    +      -       -      +
    605B  SER      4.0    14.5    +      -       -      +
    606B  HIS      4.7     6.1    +      -       -      +
    462C  ALA*     3.7    16.3    -      -       -      +
    463C  ILE*     1.3    81.1    -      -       +      +
    465C  SER*     1.3    61.7    +      -       -      +
    466C  GLN*     4.2     2.3    +      -       -      +
    468C  LYS*     4.0    13.2    +      -       -      +
    473C  HIS*     4.0     3.6    -      -       -      -
    532C  LYS*     2.8    41.1    +      -       +      +
    533C  SER*     3.9    24.5    +      -       -      -
    534C  LEU      4.6     0.5    +      -       -      -
----------------------------------------------------------
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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