Contacts of the strand formed by residues 323 - 330 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319H  LEU*     3.5     4.3    -      -       -      -
    320H  ARG*     2.9    32.8    +      -       +      +
    321H  ASN*     3.9    18.4    -      -       +      +
    322H  GLY*     1.3    83.7    +      -       -      +
    324H  PRO*     1.3    74.9    -      -       +      +
    325H  LEU*     3.8     7.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 324 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318H  LEU      3.6     8.7    -      -       -      +
    319H  LEU*     3.8    12.3    -      -       +      -
    322H  GLY      4.1     5.2    -      -       -      +
    323H  LYS*     1.3    90.7    -      -       +      +
    325H  LEU*     1.3    70.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 325 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317H  GLY*     3.8     1.9    -      -       -      -
    318H  LEU*     2.9    48.3    +      -       +      +
    320H  ARG*     3.7    50.9    -      -       +      +
    323H  LYS*     3.8     9.8    +      -       +      +
    324H  PRO*     1.3    83.6    -      -       -      +
    326H  GLU*     1.3    64.6    +      -       -      +
    327H  VAL*     4.7     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 326 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289H  SER*     5.2     0.9    -      -       -      -
    292H  GLY*     4.5    12.3    +      -       -      -
    315H  LYS*     3.4    45.6    -      -       -      +
    316H  LEU      3.4     4.3    -      -       -      +
    317H  GLY*     3.9    19.1    +      -       -      -
    325H  LEU*     1.3    75.5    -      -       -      +
    327H  VAL*     1.3    64.7    +      -       -      +
    123L  LYS*     5.5     6.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 327 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279H  ALA*     3.5    41.7    -      -       +      +
    280H  GLY      5.2     1.6    -      -       -      +
    281H  VAL*     4.0     9.9    -      -       +      -
    314H  VAL      3.6     0.9    -      -       -      +
    315H  LYS*     3.5     3.8    -      -       -      -
    316H  LEU*     2.7    44.5    +      -       +      +
    318H  LEU*     4.2    22.4    -      -       +      -
    320H  ARG*     5.1     7.6    -      -       -      +
    325H  LEU*     4.7    11.0    -      -       +      -
    326H  GLU*     1.3    79.1    -      -       -      +
    328H  GLU*     1.3    62.0    +      -       -      +
    329H  VAL*     3.8    10.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 328 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279H  ALA*     3.3    17.0    -      -       -      +
    313H  LYS*     3.6    40.5    +      -       +      +
    314H  VAL      3.3    10.5    -      -       -      +
    315H  LYS*     3.5    28.6    +      -       +      +
    326H  GLU      4.4     0.2    -      -       -      -
    327H  VAL*     1.3    71.8    -      -       -      +
    329H  VAL*     1.3    61.8    +      -       -      +
    330H  THR      4.4     0.3    +      -       -      -
    122L  SER*     3.7     7.3    +      -       -      -
    123L  LYS*     2.9    42.3    +      -       +      +
    124L  LEU      4.4     4.4    +      -       -      +
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Residues in contact with VAL 329 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242H  LEU*     3.8    20.0    -      -       +      +
    275H  GLY*     3.4    25.8    -      -       -      +
    276H  SER*     3.6    11.7    -      -       -      +
    279H  ALA*     3.8    17.7    -      -       +      -
    281H  VAL*     4.1     5.8    -      -       +      -
    312H  THR      3.6     1.0    -      -       -      +
    313H  LYS*     3.3     3.6    -      -       -      -
    314H  VAL*     2.8    40.1    +      -       +      +
    316H  LEU*     3.9    23.6    -      -       +      -
    327H  VAL*     3.8    13.5    -      -       +      +
    328H  GLU*     1.3    77.0    -      -       -      +
    330H  THR*     1.3    71.7    +      -       -      +
    331H  LEU*     4.8     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 330 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241H  LEU      4.8     0.2    -      -       -      +
    275H  GLY*     3.4    24.8    +      -       -      -
    278H  LYS*     4.5    14.6    +      -       -      +
    311H  GLY*     3.5    31.2    -      -       -      +
    312H  THR      3.6     3.1    -      -       -      -
    313H  LYS*     3.4    29.4    +      -       +      +
    328H  GLU      4.4     0.6    +      -       -      -
    329H  VAL*     1.3    74.9    -      -       -      +
    331H  LEU*     1.3    65.6    +      -       -      +
    332H  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