Contacts of the strand formed by residues 353 - 357 (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 ARG 353 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  PRO*     5.6     3.6    -      -       +      -
    352A  ALA*     1.3    77.0    -      -       -      +
    354A  TYR*     1.3    61.5    +      -       -      +
    364A  LEU*     3.3     2.9    -      -       -      +
    365A  GLY      2.9    34.2    +      -       -      +
    366A  SER      4.9     4.5    -      -       -      +
    367A  GLU      4.6     2.0    -      -       -      +
    368A  ALA*     3.6    48.9    -      -       +      +
    382A  GLY      3.7     8.3    -      -       -      -
    383A  ARG*     4.4     8.4    -      -       -      +
   1328A  GLU*     4.4     6.5    +      -       -      +
   1329A  ALA      2.3    31.8    +      -       -      -
   1330A  ASN*     3.3    13.2    +      -       -      +
   1331A  ASP*     4.6     2.6    +      -       -      -
   1358A  VAL*     3.7    28.6    -      -       -      +
   1359A  ILE*     4.1     8.7    +      -       -      +
   1360A  ILE      3.9     4.9    -      -       -      -
   1361A  GLY*     3.0    30.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  ARG*     1.3    77.0    -      -       -      +
    355A  CYS*     1.3    63.6    +      -       -      +
    356A  ILE*     3.8    22.4    -      -       +      -
    362A  ILE*     4.5     3.8    -      -       +      -
    363A  VAL      3.1    13.2    -      -       -      +
    364A  LEU*     3.9    22.7    -      -       +      -
    380A  GLU*     3.1    27.6    +      -       +      -
    381A  LYS*     3.5     5.2    -      -       -      +
    382A  GLY*     2.8    49.3    +      -       -      +
    383A  ARG*     3.2    35.5    +      -       -      -
    384A  LEU*     4.5     7.2    -      -       +      -
    390A  ILE*     3.7    29.1    -      -       +      +
    401A  LYS*     3.5    12.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  TYR*     1.3    75.2    -      -       -      +
    356A  ILE*     1.3    62.9    +      -       -      +
    361A  TYR      3.8     0.3    -      -       -      +
    362A  ILE*     3.3     6.2    -      -       -      +
    363A  VAL*     2.9    42.6    +      -       +      +
    368A  ALA      5.8     3.8    -      -       -      -
    371A  VAL      6.0     0.4    -      -       -      -
    373A  LEU*     3.6    26.1    -      -       +      +
    378A  ILE*     4.0    24.9    -      -       -      -
    380A  GLU      3.6     4.9    -      -       -      -
    381A  LYS*     4.8     9.6    -      -       -      +
   1328A  GLU*     5.8     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  TYR*     3.8    20.2    -      -       +      -
    355A  CYS*     1.3    79.5    -      -       -      +
    357A  THR*     1.3    68.9    +      -       -      +
    360A  ASP*     3.9     8.5    -      -       -      +
    361A  TYR      3.4     6.7    -      -       -      +
    362A  ILE*     3.8    19.7    -      -       +      -
    378A  ILE*     3.6     4.5    -      -       -      +
    379A  VAL*     2.8    37.6    +      -       +      -
    380A  GLU*     3.0    40.0    +      -       +      +
    399A  ILE*     3.7    31.0    -      -       +      -
    401A  LYS*     4.3    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  ILE*     1.3    83.9    -      -       -      +
    358A  LYS*     1.3    60.5    +      -       -      +
    359A  ASP*     3.0    16.7    +      -       -      +
    360A  ASP*     2.9    18.9    +      -       -      +
    361A  TYR*     2.9    41.2    +      -       +      +
    373A  LEU*     4.2    29.6    -      -       +      -
    377A  ASP*     3.2    26.5    -      -       -      +
    378A  ILE*     4.2     4.0    -      -       +      +
    379A  VAL*     4.0     7.4    -      -       -      +
----------------------------------------------------------
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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