Contacts of the strand formed by residues 323 - 330 (chain F) in PDB entry 3STJ


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 LYS 323 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319F  LEU*     3.5     3.9    -      -       -      -
    320F  ARG*     2.9    31.5    +      -       +      +
    321F  ASN*     3.8    18.2    -      -       +      +
    322F  GLY*     1.3    85.6    +      -       -      +
    324F  PRO*     1.4    75.9    -      -       +      +
    325F  LEU*     3.8     7.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 324 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318F  LEU      3.6     9.4    -      -       -      +
    319F  LEU*     3.8    13.4    -      -       +      -
    322F  GLY      4.1     4.7    -      -       -      +
    323F  LYS*     1.4    90.7    -      -       +      +
    325F  LEU*     1.3    70.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 325 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317F  GLY*     3.8     2.3    -      -       -      -
    318F  LEU*     2.9    47.5    +      -       +      +
    320F  ARG*     3.7    50.3    -      -       +      +
    323F  LYS*     4.2     9.6    -      -       +      +
    324F  PRO*     1.3    81.2    -      -       -      +
    326F  GLU*     1.3    62.1    +      -       -      +
    327F  VAL*     4.7     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 326 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289F  SER*     5.2     0.9    -      -       -      -
    292F  GLY*     4.6    12.3    +      -       -      -
    315F  LYS*     3.4    44.7    -      -       -      +
    316F  LEU      3.4     4.0    -      -       -      +
    317F  GLY*     3.8    18.1    +      -       -      -
    325F  LEU*     1.3    76.1    -      -       -      +
    327F  VAL*     1.3    65.6    +      -       -      +
    328F  GLU      4.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 327 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279F  ALA*     3.4    44.0    -      -       +      +
    280F  GLY      5.2     5.2    -      -       -      +
    281F  VAL*     4.0    11.2    -      -       +      -
    314F  VAL      3.6     0.9    -      -       -      +
    315F  LYS*     3.5     4.4    -      -       -      -
    316F  LEU*     2.7    44.5    +      -       +      +
    318F  LEU*     4.3    21.8    -      -       +      -
    320F  ARG*     5.3     2.5    -      -       -      +
    325F  LEU*     4.7     9.2    -      -       +      -
    326F  GLU*     1.3    81.7    -      -       -      +
    328F  GLU*     1.3    57.9    +      -       -      +
    329F  VAL*     3.8    10.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 328 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279F  ALA*     3.3    17.2    -      -       -      +
    313F  LYS*     3.6    44.6    +      -       +      +
    314F  VAL      3.3    11.4    -      -       -      +
    315F  LYS*     3.6    31.3    +      -       +      +
    327F  VAL*     1.3    71.4    -      -       -      +
    329F  VAL*     1.3    61.1    +      -       -      +
    330F  THR*     5.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 329 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242F  LEU*     3.8    20.4    -      -       +      +
    275F  GLY*     3.5    25.6    -      -       -      -
    276F  SER*     3.5    12.3    -      -       -      +
    279F  ALA*     3.8    17.0    -      -       +      -
    281F  VAL*     4.3     5.8    -      -       +      -
    312F  THR      3.6     1.2    -      -       -      +
    313F  LYS*     3.3     3.5    -      -       -      -
    314F  VAL*     2.8    38.2    +      -       +      +
    316F  LEU*     3.8    24.5    -      -       +      -
    327F  VAL*     3.8    13.5    -      -       +      +
    328F  GLU*     1.3    76.4    -      -       -      +
    330F  THR*     1.3    73.0    +      -       -      +
    331F  LEU*     4.8     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 330 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275F  GLY*     3.4    26.8    +      -       -      -
    311F  GLY*     3.5    31.6    -      -       -      +
    312F  THR      3.6     2.9    -      -       -      -
    313F  LYS*     3.4    29.5    -      -       +      +
    328F  GLU      4.4     0.6    +      -       -      -
    329F  VAL*     1.3    74.3    -      -       -      +
    331F  LEU*     1.3    64.5    +      -       -      +
    332F  ASP*     3.6     3.1    +      -       -      +
----------------------------------------------------------
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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