Contacts of the strand formed by residues 338 - 342 (chain F) in PDB entry 1P8J


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 338 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316F  SER      3.6     2.8    +      -       -      -
    317F  ILE*     3.4    14.8    -      -       +      +
    318F  SER      2.9    22.0    +      -       -      -
    336F  THR*     3.6     4.4    -      -       -      +
    337F  LEU*     1.3    80.2    -      -       -      +
    339F  THR*     1.3    66.8    +      -       -      +
    397F  VAL*     3.4    26.9    -      -       +      -
    401F  SER*     3.7     3.4    -      -       -      +
    424F  TYR      3.6     4.3    -      -       -      -
    427F  GLY      3.5    10.3    -      -       -      +
    429F  LEU*     3.5    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 339 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317F  ILE*     4.2     0.2    -      -       -      -
    318F  SER*     3.3    17.4    -      -       -      +
    319F  SER      3.4    19.7    -      -       -      +
    320F  ALA*     3.7    12.8    -      -       +      +
    338F  ALA*     1.3    74.2    +      -       -      +
    340F  THR*     1.3    88.7    +      -       -      +
    406F  LEU*     4.3     2.5    -      -       +      -
    424F  TYR*     2.9    38.5    +      -       +      +
    427F  GLY      2.7    18.6    +      -       -      -
    428F  LEU*     3.4     4.2    -      -       +      -
    429F  LEU*     2.9    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 340 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132F  LEU*     4.0    11.9    -      -       +      -
    317F  ILE*     3.9     3.1    -      -       +      -
    318F  SER      3.1     3.0    +      -       -      -
    319F  SER*     3.3     1.2    -      -       -      -
    320F  ALA      3.3    16.3    +      -       -      -
    339F  THR*     1.3    84.1    -      -       -      +
    341F  TYR*     1.3    65.3    +      -       -      +
    370F  SER*     2.9    52.2    +      -       -      +
    373F  LEU*     4.1     8.4    -      -       +      +
    374F  ALA*     3.9    11.0    -      -       +      +
    377F  ILE*     5.1     0.2    -      -       +      -
    428F  LEU*     3.7     8.7    -      -       -      -
    429F  LEU*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 341 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122F  TRP*     3.5    26.5    -      +       +      -
    123F  TYR*     3.9    15.7    -      -       +      -
    130F  ARG*     3.4    45.3    -      -       +      +
    131F  ASP*     3.6    13.9    -      -       -      -
    132F  LEU*     4.1     8.1    -      -       +      +
    320F  ALA*     3.4    16.4    -      -       +      +
    321F  THR      3.3    27.1    -      -       -      -
    322F  GLN      4.1     9.0    +      -       -      -
    324F  GLY*     4.6     4.8    +      -       -      -
    340F  THR*     1.3    77.4    -      -       -      +
    342F  SER*     1.3    62.5    +      -       -      +
    351F  ILE*     4.0     2.0    -      -       -      +
    370F  SER*     3.6     4.2    +      -       -      -
    373F  LEU*     3.6    20.5    -      -       +      +
    405F  HIS*     5.1     4.2    +      -       -      +
    406F  LEU*     4.5     9.8    -      -       +      +
    428F  LEU*     3.4    32.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 342 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122F  TRP*     3.8    15.2    -      -       -      -
    319F  SER*     3.7     4.0    -      -       -      -
    320F  ALA      3.0    12.8    +      -       -      +
    321F  THR*     3.9     3.5    -      -       -      -
    322F  GLN      4.1     1.0    +      -       -      -
    329F  TYR*     3.3    14.3    +      -       -      -
    341F  TYR*     1.3    78.1    -      -       -      +
    343F  SER*     1.3    72.5    +      -       -      +
    349F  LYS      4.1     0.7    -      -       -      +
    351F  ILE*     3.7    17.4    -      -       -      +
    365F  THR      4.0     0.3    -      -       -      -
    366F  GLY      2.7    25.2    +      -       -      -
    369F  ALA*     3.6    11.7    -      -       -      +
    370F  SER*     3.5    15.7    -      -       -      -
----------------------------------------------------------
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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