Contacts of the strand formed by residues 319 - 323 (chain C) in PDB entry 2ODE


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 319 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250C  PHE*     4.0    17.0    -      -       +      -
    254C  CYS*     3.5    29.2    -      -       -      -
    264C  ILE*     3.6    24.2    -      -       +      +
    266C  LEU*     3.8    22.4    -      -       +      -
    308C  GLU*     4.3    25.3    -      -       +      +
    311C  ASN*     4.2    21.2    -      -       +      +
    317C  LYS*     4.3     3.8    +      -       +      -
    318C  GLU*     1.3    90.5    -      -       -      +
    320C  TYR*     1.3    64.2    +      -       -      +
    321C  THR*     3.5    20.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 320 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263C  SER*     4.5     7.4    -      -       -      -
    264C  ILE      2.9    27.7    +      -       -      +
    265C  ILE*     3.3    22.5    -      -       +      +
    266C  LEU      2.9    21.2    +      -       -      -
    318C  GLU*     3.4    57.9    +      -       +      +
    319C  ILE*     1.3    69.4    -      -       -      +
    321C  THR*     1.3    62.6    +      -       -      +
    322C  HIS*     3.8     9.7    -      -       -      +
    342C  VAL*     3.8    39.5    -      -       +      -
    346C  ASN*     3.3    28.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 321 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266C  LEU*     3.3    16.4    -      -       +      +
    268C  LEU*     3.5    31.6    -      -       +      -
    304C  GLN*     3.6    21.5    +      -       +      +
    308C  GLU*     2.6    26.8    +      -       -      -
    319C  ILE*     3.5    19.3    +      -       -      +
    320C  TYR*     1.3    73.0    -      -       -      +
    322C  HIS*     1.3    76.7    +      -       -      +
    323C  PHE*     4.8     4.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 322 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265C  ILE*     4.5     3.6    -      -       +      -
    266C  LEU      2.8    10.1    +      -       -      +
    267C  PHE*     3.4     7.0    -      -       +      -
    268C  LEU*     2.8    25.8    +      -       -      +
    320C  TYR*     3.8    19.6    +      -       +      +
    321C  THR*     1.3    84.7    +      -       -      +
    323C  PHE*     1.3    66.2    +      -       -      +
    324C  THR*     3.8     1.5    +      -       +      +
    335C  VAL*     3.6    35.5    -      -       +      +
    338C  ALA*     3.6    32.5    +      -       +      +
    339C  VAL*     4.4    15.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 323 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227C  LEU*     4.1    12.8    -      -       +      -
    268C  LEU*     3.4    37.5    -      -       +      +
    271C  LYS*     3.9    12.6    -      -       +      -
    296C  TYR*     3.9    21.5    -      +       -      +
    300C  ALA*     3.7    34.8    -      -       +      -
    301C  ALA*     4.5     1.8    -      -       -      -
    304C  GLN*     3.3    29.8    -      -       -      -
    321C  THR*     4.8     3.8    -      -       +      -
    322C  HIS*     1.3    75.9    -      -       -      +
    324C  THR*     1.3    63.5    +      -       -      +
    331C  ASN*     4.0     4.5    +      -       -      +
    335C  VAL*     4.1     9.4    -      -       -      +
----------------------------------------------------------
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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