Contacts of the strand formed by residues 464 - 471 (chain A) in PDB entry 4OMD


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 ARG 464 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460A  ASP      5.0     0.9    -      -       -      +
    461A  ILE*     3.2    11.5    +      -       -      +
    463A  LYS*     1.3    86.0    +      -       +      +
    465A  LEU*     1.3    65.1    +      -       -      +
    466A  GLU*     2.5    43.2    +      -       -      +
    512A  ARG*     5.0     0.2    -      -       -      +
    550A  GLU*     3.3    35.1    +      -       -      +
    551A  ILE      3.3    12.8    -      -       -      +
    552A  GLU*     4.1    21.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 465 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459A  LYS*     3.8    29.4    -      -       +      -
    460A  ASP      3.8    15.7    -      -       -      +
    461A  ILE*     4.0    17.0    -      -       +      +
    464A  ARG*     1.3    80.2    +      -       -      +
    466A  GLU*     1.3    77.1    +      -       -      +
    467A  VAL*     4.1     7.9    -      -       +      -
    549A  LEU      3.8     0.7    -      -       -      +
    550A  GLU*     3.6     4.0    -      -       -      -
    551A  ILE*     2.7    51.2    +      -       +      +
    563A  LEU*     3.8    35.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 466 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459A  LYS*     5.6     1.2    +      -       -      -
    464A  ARG*     2.5    35.0    +      -       -      +
    465A  LEU*     1.3    81.5    -      -       -      +
    467A  VAL*     1.3    67.5    +      -       -      +
    468A  ARG*     2.9    39.1    +      -       +      +
    548A  VAL*     3.7    22.1    -      -       +      +
    549A  LEU      3.4     4.9    -      -       -      +
    550A  GLU*     4.4     4.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 467 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ILE*     4.0    28.0    -      -       +      -
    455A  LEU*     4.2    14.1    -      -       +      -
    459A  LYS*     4.6    13.5    -      -       +      +
    465A  LEU*     4.1    25.1    -      -       +      -
    466A  GLU*     1.3    79.2    -      -       -      +
    468A  ARG*     1.3    66.9    +      -       -      +
    547A  TRP      3.7     0.7    -      -       -      +
    548A  VAL*     3.4     3.9    -      -       -      -
    549A  LEU*     2.9    46.6    +      -       +      +
    563A  LEU*     4.3    14.1    -      -       +      -
    566A  PHE*     4.2    11.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 468 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ILE*     4.7     1.0    -      -       -      +
    466A  GLU*     2.9    35.6    +      -       -      +
    467A  VAL*     1.3    82.6    -      -       -      +
    469A  LYS*     1.3    68.1    +      -       -      +
    546A  GLU*     2.9    43.2    +      -       -      +
    547A  TRP      3.5     3.8    -      -       -      -
    548A  VAL*     3.4    23.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452A  ILE*     4.7     7.9    -      -       -      -
    453A  ASP      5.2     2.7    +      -       -      -
    454A  ILE*     3.4    54.4    +      -       +      +
    467A  VAL*     5.4     0.7    -      -       +      +
    468A  ARG*     1.3    79.6    -      -       -      +
    470A  THR*     1.3    75.7    +      -       -      +
    471A  VAL*     3.7    12.8    +      -       +      +
    545A  GLY      3.5     0.7    -      -       -      +
    546A  GLU*     3.3     4.6    -      -       -      +
    547A  TRP*     2.8    40.1    +      -       +      +
    566A  PHE*     5.7     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 470 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    469A  LYS*     1.3    89.7    +      -       -      +
    471A  VAL*     1.3    68.0    +      -       -      +
    472A  THR*     5.6     3.5    -      -       +      +
    545A  GLY*     3.2    19.5    -      -       -      +
    546A  GLU*     3.9    15.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452A  ILE*     3.8    39.9    -      -       +      -
    454A  ILE*     4.5     3.8    -      -       +      -
    469A  LYS*     3.8    24.9    -      -       +      +
    470A  THR*     1.3    82.5    -      -       -      +
    472A  THR*     1.3    64.6    +      -       -      +
    473A  ALA*     3.9     8.3    -      -       +      +
    543A  PRO      3.5    23.6    -      -       -      +
    544A  SER*     3.6     1.9    -      -       -      -
    545A  GLY*     2.8    30.7    +      -       -      +
    547A  TRP*     3.5    21.1    -      -       +      +
    568A  LEU*     4.5     1.3    -      -       +      -
    570A  LEU*     4.9     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page


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