Contacts of the strand formed by residues 339 - 344 (chain A) 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 ILE 339 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  SER*     5.0    12.1    -      -       -      -
    288A  PRO*     4.5    16.6    -      -       +      -
    289A  LEU*     4.0    35.4    -      -       +      -
    334A  PHE*     4.9     2.9    -      -       +      -
    335A  SER*     2.7    25.2    +      -       -      -
    336A  ASP*     3.2    18.6    +      -       +      +
    338A  LYS*     1.3    87.0    -      -       +      +
    340A  VAL*     1.3    66.9    +      -       -      +
    341A  GLY      4.5     1.8    -      -       -      +
    391A  ALA*     4.6     1.1    -      -       +      -
    392A  VAL      3.2    15.0    -      -       -      +
    393A  ASP*     4.3    19.1    -      -       +      +
    394A  LEU*     4.8     0.9    -      -       -      -
    400A  LEU*     5.0     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PHE*     3.7    35.4    -      -       +      -
      7A  ALA*     4.3     7.4    -      -       +      -
    200A  PHE*     4.2    18.8    -      -       +      -
    202A  VAL*     4.0    13.0    -      -       +      -
    334A  PHE      3.3    11.4    -      -       -      +
    335A  SER*     3.9     8.5    -      -       -      +
    339A  ILE*     1.3    76.9    -      -       -      +
    341A  GLY*     1.3    62.7    +      -       -      +
    391A  ALA*     3.3     0.7    -      -       -      -
    392A  VAL*     2.8    47.5    +      -       +      +
    394A  LEU*     4.2    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PHE*     4.0     7.6    -      -       -      -
    333A  VAL*     3.4     7.6    -      -       -      +
    334A  PHE*     2.9    49.4    +      -       -      -
    340A  VAL*     1.3    78.1    -      -       -      +
    342A  ALA*     1.3    61.6    +      -       -      +
    390A  ILE      3.2    11.9    -      -       -      -
    391A  ALA*     3.9     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PHE*     4.0     7.6    -      -       +      -
    331A  LEU*     4.2     7.0    -      -       +      -
    332A  LEU      3.0    13.0    -      -       -      +
    333A  VAL*     4.2     3.8    -      -       +      -
    334A  PHE*     3.7     9.2    -      -       -      -
    341A  GLY*     1.3    75.9    -      -       -      +
    343A  GLY*     1.3    59.4    +      -       -      +
    364A  LEU*     3.9    35.0    -      -       +      -
    384A  LEU*     4.2     4.0    -      -       +      -
    389A  MET*     3.1     7.4    -      -       -      +
    390A  ILE      2.9    30.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292A  ALA*     6.3     2.0    -      -       -      -
    330A  ALA      3.9     0.3    -      -       -      +
    331A  LEU*     3.6     4.3    -      -       -      +
    332A  LEU*     2.9    39.2    +      -       -      +
    334A  PHE*     4.1     6.1    -      -       -      -
    342A  ALA*     1.3    76.0    -      -       -      +
    344A  LEU*     1.3    64.6    -      -       -      -
    384A  LEU*     4.3     1.6    -      -       -      -
    388A  GLN      3.3    11.4    -      -       -      -
    389A  MET*     3.8    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  VAL*     4.3    12.1    -      -       -      +
    330A  ALA*     3.3    15.3    -      -       -      +
    331A  LEU*     3.8    25.6    -      -       +      -
    332A  LEU*     6.0     0.9    -      -       -      -
    343A  GLY*     1.3    75.0    -      -       -      -
    345A  ASP*     1.3    71.6    +      -       -      +
    348A  GLY*     3.8    14.8    -      -       -      +
    350A  ARG*     3.3    28.9    -      -       +      +
    352A  ALA*     4.1     7.4    -      -       +      +
    383A  ARG*     5.8     0.4    -      -       -      +
    384A  LEU*     3.3    40.2    -      -       +      +
    385A  ALA      3.7    10.3    -      -       -      +
    387A  GLY*     3.7    19.3    -      -       -      +
    388A  GLN      3.1     8.4    +      -       -      +
    389A  MET*     6.1     0.2    -      -       -      +
   1381A  GLU*     5.5     0.9    -      -       -      +
----------------------------------------------------------
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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