Contacts of the strand formed by residues 323 - 330 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319E  LEU*     3.5     3.5    -      -       -      -
    320E  ARG*     2.9    33.5    +      -       +      +
    321E  ASN*     3.8    18.4    -      -       +      +
    322E  GLY*     1.3    85.1    +      -       -      +
    324E  PRO*     1.4    73.7    -      -       +      +
    325E  LEU*     3.8     7.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 324 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318E  LEU      3.6     8.7    -      -       -      +
    319E  LEU*     3.8    13.4    -      -       +      -
    322E  GLY      4.1     4.5    -      -       -      +
    323E  LYS*     1.4    90.1    -      -       +      +
    325E  LEU*     1.4    70.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 325 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316E  LEU      3.6     0.2    -      -       -      +
    317E  GLY*     3.8     2.1    -      -       -      -
    318E  LEU*     2.9    47.7    +      -       +      +
    320E  ARG*     3.7    49.6    -      -       +      +
    323E  LYS*     4.2     9.2    -      -       +      +
    324E  PRO*     1.4    82.7    -      -       -      +
    326E  GLU*     1.3    63.8    +      -       -      +
    327E  VAL*     4.8     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 326 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289E  SER*     5.2     0.7    -      -       -      -
    292E  GLY*     4.5    12.5    +      -       -      -
    315E  LYS*     3.4    45.2    -      -       -      +
    316E  LEU      3.4     3.8    -      -       -      +
    317E  GLY*     3.8    19.0    +      -       -      -
    325E  LEU*     1.3    75.9    -      -       -      +
    327E  VAL*     1.3    66.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 327 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279E  ALA*     3.6    39.5    -      -       +      +
    280E  GLY      5.4     1.1    -      -       -      -
    281E  VAL*     4.2    13.5    -      -       +      +
    314E  VAL      3.6     0.5    -      -       -      +
    315E  LYS*     3.4     4.2    -      -       -      -
    316E  LEU*     2.7    44.6    +      -       +      +
    318E  LEU*     4.2    22.0    -      -       +      -
    320E  ARG*     5.3     4.9    -      -       -      +
    325E  LEU*     4.8     9.9    -      -       +      -
    326E  GLU*     1.3    82.7    -      -       -      +
    328E  GLU*     1.3    61.5    +      -       -      +
    329E  VAL*     3.8    10.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 328 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  ASN*     3.5    28.5    +      -       -      -
    121B  PRO*     5.3     4.0    -      -       -      +
    279E  ALA*     3.5    17.3    -      -       -      +
    313E  LYS*     3.6    41.2    +      -       +      +
    314E  VAL      3.3    10.8    -      -       -      +
    315E  LYS*     3.5    31.1    -      -       +      +
    327E  VAL*     1.3    71.4    -      -       -      +
    329E  VAL*     1.3    61.8    +      -       -      +
    330E  THR*     4.5     0.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 329 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242E  LEU*     3.8    20.6    -      -       +      +
    275E  GLY*     3.5    25.8    -      -       -      -
    276E  SER*     3.6    10.8    -      -       -      +
    279E  ALA*     3.7    17.0    -      -       +      -
    281E  VAL*     4.2     5.2    -      -       +      -
    312E  THR      3.6     1.0    -      -       -      +
    313E  LYS*     3.3     3.1    -      -       -      -
    314E  VAL*     2.8    40.6    +      -       +      +
    316E  LEU*     3.8    23.8    -      -       +      -
    327E  VAL*     3.8    13.5    -      -       +      +
    328E  GLU*     1.3    77.5    -      -       -      +
    330E  THR*     1.3    71.1    +      -       -      +
    331E  LEU*     4.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 330 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241E  LEU      4.8     0.3    -      -       -      +
    275E  GLY*     3.4    27.4    +      -       -      -
    311E  GLY*     3.5    31.0    -      -       -      +
    312E  THR      3.6     2.9    -      -       -      -
    313E  LYS*     3.4    29.2    -      -       +      +
    328E  GLU      5.7     0.2    -      -       -      -
    329E  VAL*     1.3    74.6    -      -       -      +
    331E  LEU*     1.3    64.4    +      -       -      +
    332E  ASP*     3.7     2.9    +      -       -      +
----------------------------------------------------------
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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