Contacts of the strand formed by residues 639 - 643 (chain B) in PDB entry 1OFD


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 639 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    521B  PHE      3.6     5.4    +      -       -      -
    522B  LEU*     3.3    22.2    -      -       -      -
    523B  GLY      2.8    35.2    +      -       -      -
    596B  GLU      2.9     7.3    +      -       -      -
    597B  ILE*     3.5     4.0    -      -       -      -
    598B  LEU*     2.9    25.8    +      -       -      +
    635B  ARG*     4.3     4.3    -      -       -      +
    638B  ALA*     1.3    75.2    +      -       -      +
    640B  LEU*     1.3    67.0    +      -       -      +
    641B  ILE      4.2     0.2    +      -       -      -
    662B  SER*     3.7    15.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 640 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598B  LEU*     3.5    26.5    -      -       +      +
    600B  LEU*     4.6     6.3    -      -       +      -
    622B  VAL*     3.9    22.2    -      -       +      -
    625B  VAL*     3.5    34.3    -      -       +      -
    626B  HIS*     4.0    15.3    -      -       +      +
    629B  LEU*     3.9    11.0    -      -       +      -
    635B  ARG*     3.9    17.0    -      -       -      +
    638B  ALA*     5.3     1.8    -      -       +      +
    639B  SER*     1.3    82.4    -      -       -      +
    641B  ILE*     1.3    61.5    +      -       -      +
    642B  VAL      4.3     0.2    -      -       -      -
    660B  GLY      3.7    19.4    +      -       -      +
    661B  ALA*     3.6     2.2    -      -       -      -
    662B  SER*     2.8    37.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 641 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    522B  LEU*     3.9    32.3    -      -       +      -
    546B  VAL*     4.7     2.9    -      -       +      -
    551B  LEU*     4.3    21.3    -      -       +      -
    554B  ILE*     4.0    20.4    -      -       +      -
    597B  ILE*     3.7    25.4    -      -       +      -
    598B  LEU      2.8    10.9    +      -       -      +
    599B  VAL*     3.5    12.8    -      -       +      -
    600B  LEU*     2.8    35.8    +      -       -      +
    622B  VAL*     6.2     0.2    -      -       -      -
    640B  LEU*     1.3    77.1    -      -       -      +
    642B  VAL*     1.3    66.4    +      -       -      +
    643B  ASP      3.8     0.4    +      -       -      +
    661B  ALA*     5.5     0.2    -      -       -      -
    663B  ALA*     3.4    23.1    -      -       +      +
    664B  ILE      4.6     0.9    -      -       -      +
    665B  CYS      4.7     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 642 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600B  LEU*     3.6    10.8    -      -       +      +
    618B  PRO*     3.7    20.9    -      -       +      +
    622B  VAL*     5.2     8.1    -      -       +      -
    640B  LEU      4.3     0.2    -      -       -      -
    641B  ILE*     1.3    72.7    -      -       -      +
    643B  ASP*     1.3    58.3    +      -       -      +
    644B  THR*     3.5    29.9    +      -       +      -
    656B  LEU*     4.0    10.3    -      -       +      -
    661B  ALA*     3.9    12.5    -      -       +      +
    663B  ALA      3.0     4.3    +      -       -      +
    664B  ILE*     3.1    41.8    -      -       +      +
    665B  CYS      2.8    25.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 643 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551B  LEU*     3.8    12.0    -      -       +      +
    555B  LYS*     5.0     4.2    +      -       -      -
    599B  VAL*     3.7    13.5    -      -       +      +
    600B  LEU      2.8     8.5    +      -       -      +
    601B  THR*     2.9    56.5    +      -       -      +
    602B  ASP*     3.2     7.1    +      -       -      +
    603B  ARG*     2.8    36.9    +      -       -      +
    641B  ILE      3.8     0.8    +      -       -      -
    642B  VAL*     1.3    70.9    -      -       -      +
    644B  THR*     1.3    57.8    +      -       -      +
    665B  CYS*     3.4    21.2    -      -       +      +
    667B  TYR*     3.5     5.5    -      -       -      -
----------------------------------------------------------
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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