Contacts of the strand formed by residues 322 - 326 (chain A) in PDB entry 4L0D


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 322 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  ARG*     4.3    16.2    -      -       -      +
    277A  ILE      3.3     2.4    +      -       -      -
    278A  ILE*     3.4    19.1    -      -       +      -
    279A  GLY      2.9    23.9    +      -       -      -
    320A  VAL*     3.3     4.6    -      -       -      +
    321A  ASP*     1.3    81.8    -      -       -      +
    323A  TRP*     1.3    77.9    +      -       -      +
    324A  PHE*     3.5    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  VAL*     3.9    37.5    -      -       +      -
    279A  GLY*     3.6    17.5    -      -       -      -
    280A  VAL      4.4     0.2    -      -       -      -
    281A  ASP*     4.2    16.4    -      -       +      -
    287A  LEU*     3.8    21.1    -      -       +      -
    288A  ALA*     3.5    34.3    -      -       +      -
    289A  GLU*     3.4    49.8    +      -       +      +
    293A  LEU*     4.2    11.3    -      -       +      +
    315A  LEU*     4.7     7.6    -      -       +      -
    317A  ARG*     4.4    14.1    +      -       +      -
    320A  VAL*     3.5    39.4    +      -       +      +
    322A  LYS*     1.3    91.5    -      -       -      +
    324A  PHE*     1.3    71.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278A  ILE*     3.7    19.1    -      -       +      -
    279A  GLY      2.9     8.1    +      -       -      +
    280A  VAL*     3.4     3.5    -      -       -      +
    281A  ASP*     2.9    27.0    +      -       -      +
    293A  LEU*     5.5     0.9    -      -       -      -
    322A  LYS*     3.5    42.0    -      -       +      -
    323A  TRP*     1.3    83.4    -      -       -      +
    325A  LYS*     1.3    66.4    +      -       -      +
    326A  SER      3.9     0.2    +      -       -      -
    356A  VAL*     3.6    33.7    -      -       +      -
    359A  LYS*     4.3    22.4    -      -       +      -
    360A  ALA*     3.7    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  ASP*     3.1    38.4    -      -       +      +
    282A  PRO      3.2    16.6    +      -       -      +
    283A  GLU*     3.3    34.9    -      -       +      +
    284A  GLY      3.8     2.6    -      -       -      +
    285A  SER      3.3    10.7    +      -       -      -
    288A  ALA*     4.0     5.4    -      -       +      -
    293A  LEU*     4.0    36.1    +      -       +      +
    294A  ASN*     3.4    26.9    +      -       -      +
    296A  THR*     5.5     0.8    -      -       -      +
    324A  PHE*     1.3    79.8    -      -       -      +
    326A  SER*     1.3    59.5    +      -       -      +
    330A  GLU*     4.0     7.6    -      -       -      +
    356A  VAL*     4.8     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  VAL*     3.8    22.8    -      -       -      +
    281A  ASP      2.9    13.6    +      -       -      -
    282A  PRO*     3.3     9.9    -      -       -      +
    283A  GLU*     2.9    29.6    +      -       -      +
    306A  ILE*     4.6     1.2    -      -       -      +
    324A  PHE      3.9     0.2    +      -       -      -
    325A  LYS*     1.3    75.4    -      -       -      +
    327A  ASN*     1.3    63.1    +      -       -      +
    330A  GLU*     3.1    13.5    -      -       -      -
    352A  SER*     3.8    24.0    +      -       -      -
    356A  VAL*     4.4     7.2    -      -       -      -
----------------------------------------------------------
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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