Contacts of the helix formed by residues 507 - 515 (chain B) 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 SER 507 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505B  GLU*     3.3    13.4    +      -       -      +
    506B  ARG*     1.3    75.9    -      -       -      +
    508B  ALA*     1.3    64.8    +      -       -      +
    509B  GLU*     3.4    11.6    +      -       -      +
    510B  LYS*     3.8    24.0    +      -       -      +
    511B  ILE*     3.3    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 508 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497B  ARG*     5.4     3.0    +      -       -      +
    506B  ARG      3.2     7.1    +      -       -      +
    507B  SER*     1.3    74.2    +      -       -      +
    509B  GLU*     1.3    57.1    +      -       -      +
    511B  ILE*     3.5     8.2    +      -       -      +
    512B  ASN*     3.0    34.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 509 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    507B  SER*     3.3     7.9    +      -       -      +
    508B  ALA*     1.3    77.7    -      -       -      +
    510B  LYS*     1.3    70.1    +      -       +      +
    512B  ASN*     3.8     6.7    -      -       +      +
    513B  ALA*     2.9    41.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 510 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    500B  LEU*     5.0     0.2    -      -       -      +
    505B  GLU*     4.1    29.6    -      -       +      +
    507B  SER*     3.5    22.3    +      -       -      +
    508B  ALA      3.4     0.6    -      -       -      -
    509B  GLU*     1.3    82.3    +      -       +      +
    511B  ILE*     1.3    63.0    +      -       -      +
    513B  ALA*     4.1     4.9    -      -       -      +
    514B  LEU*     3.4    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 511 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497B  ARG*     3.9    30.7    -      -       +      +
    500B  LEU*     3.2    56.1    -      -       +      +
    501B  GLU*     4.2    15.5    -      -       +      +
    505B  GLU*     3.7    18.2    -      -       +      +
    506B  ARG      5.4     0.9    -      -       -      -
    507B  SER      3.3    16.8    +      -       -      +
    508B  ALA*     3.7     9.9    -      -       -      +
    509B  GLU      3.2     0.2    -      -       -      -
    510B  LYS*     1.3    77.6    -      -       -      +
    512B  ASN*     1.3    57.4    +      -       -      +
    514B  LEU*     3.2     3.1    +      -       -      +
    515B  LEU*     2.9    41.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 512 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497B  ARG*     3.5    27.9    +      -       -      +
    508B  ALA*     3.0    20.0    +      -       -      +
    509B  GLU*     3.5     8.9    +      -       +      +
    511B  ILE*     1.3    76.5    -      -       -      +
    513B  ALA*     1.3    59.7    +      -       -      +
    515B  LEU*     4.0     8.3    +      -       -      +
    516B  PRO*     3.7    15.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 513 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509B  GLU*     2.9    30.0    +      -       -      +
    510B  LYS*     4.1     7.2    -      -       -      +
    511B  ILE      3.2     0.2    -      -       -      -
    512B  ASN*     1.3    78.0    -      -       -      +
    514B  LEU*     1.3    62.4    +      -       +      +
    516B  PRO*     3.9     4.5    -      -       -      +
    517B  HIS*     3.3    23.0    +      -       -      -
    421C  GLY*     5.2     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 514 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    500B  LEU*     4.1    20.9    -      -       +      -
    510B  LYS      3.4    17.6    +      -       -      +
    511B  ILE      3.2     4.1    +      -       -      +
    513B  ALA*     1.3    82.5    -      -       +      +
    515B  LEU*     1.3    64.8    +      -       -      +
    516B  PRO      3.6     0.2    -      -       -      -
    517B  HIS*     3.1    19.5    +      -       +      +
    518B  LYS*     3.3    30.8    +      -       +      +
    141C  THR*     3.7    32.5    -      -       -      +
    565C  TRP*     3.9    31.0    -      -       +      +
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Residues in contact with LEU 515 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493B  PRO*     3.4    33.0    -      -       +      +
    496B  VAL*     3.5    26.2    -      -       +      +
    497B  ARG*     3.2    53.2    -      -       -      +
    500B  LEU*     4.5     1.1    -      -       +      +
    511B  ILE*     2.9    28.3    +      -       +      +
    512B  ASN*     4.2    11.7    -      -       -      +
    514B  LEU*     1.3    75.7    -      -       -      +
    516B  PRO*     1.4    69.7    -      -       +      +
    517B  HIS      3.3     0.2    +      -       -      -
    518B  LYS*     3.3     8.3    +      -       -      -
    519B  THR*     2.8    19.9    +      -       -      -
----------------------------------------------------------
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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