Contacts of the strand formed by residues 416 - 419 (chain A) in PDB entry 2ODP


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 416 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390A  ALA      3.3     6.5    -      -       -      +
    400A  TRP*     3.3    21.2    -      -       +      -
    403A  LEU*     3.5    34.1    -      -       +      +
    404A  ASN*     3.8    13.0    -      -       -      +
    407A  GLY*     5.3     0.7    -      -       -      -
    414A  ARG*     2.8    32.0    +      -       -      +
    415A  HIS*     1.3    79.6    -      -       -      +
    417A  PHE*     1.3    57.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389A  TYR*     4.1    16.2    -      +       -      -
    390A  ALA      3.2     6.5    +      -       -      -
    391A  ILE*     3.4    19.0    -      -       +      +
    392A  GLY      3.1    23.9    +      -       -      -
    400A  TRP*     4.0     1.5    -      -       -      -
    403A  LEU*     3.4     7.0    -      -       -      +
    414A  ARG*     3.5    69.5    -      -       +      +
    415A  HIS      4.3     0.4    -      -       -      -
    416A  ALA*     1.3    78.9    -      -       -      +
    418A  ILE*     1.3    64.0    +      -       -      +
    419A  LEU*     4.0    22.4    -      -       +      -
    428A  VAL*     3.8    39.9    -      -       +      -
    431A  HIS*     6.6     0.2    -      -       +      -
    432A  MET*     4.2     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392A  GLY      3.5     7.2    -      -       -      +
    394A  GLY      5.9     2.0    -      -       -      +
    396A  LEU      6.1     0.2    -      -       -      +
    398A  VAL*     3.9    36.3    -      -       +      +
    400A  TRP*     3.4    44.8    -      -       +      -
    403A  LEU*     3.9     0.9    -      -       +      -
    414A  ARG*     4.9     2.0    -      -       -      +
    417A  PHE*     1.3    76.3    -      -       -      +
    419A  LEU*     1.3    71.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391A  ILE*     3.9    14.6    -      -       +      -
    392A  GLY      2.9    10.0    +      -       -      +
    393A  VAL*     3.2     8.5    -      -       +      -
    394A  GLY      2.8    34.9    +      -       -      +
    417A  PHE*     4.0    16.4    -      -       +      -
    418A  ILE*     1.3    87.0    -      -       -      +
    420A  GLN*     1.3    55.1    +      -       -      +
    421A  ASP      4.4     2.7    -      -       -      +
    424A  ALA*     4.2    18.2    -      -       +      +
    425A  LEU*     3.6    41.3    -      -       +      -
    428A  VAL*     3.7    29.8    -      -       +      -
----------------------------------------------------------
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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