Contacts of the strand formed by residues 319 - 324 (chain A) in PDB entry 6MXO


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 ILE 319 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316A  PRO*     5.4     3.6    -      -       +      -
    318A  THR*     1.3    78.9    -      -       -      +
    320A  GLY*     1.3    59.2    +      -       -      +
    348A  LEU*     3.4    24.2    -      -       +      +
    351A  ARG*     3.7    37.7    -      -       +      +
    352A  LEU*     4.0    17.5    -      -       +      -
    355A  ASP*     3.8    37.0    -      -       +      +
    361A  ARG*     4.5     5.6    -      -       -      +
    425A  CYS*     4.2     1.3    -      -       -      -
    426A  ALA      2.8    37.3    +      -       -      +
    429A  PHE*     3.9    11.4    -      -       +      -
      7T    C      3.8     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  THR*     5.3     0.4    +      -       -      -
    319A  ILE*     1.3    74.6    -      -       -      +
    321A  CYS*     1.4    58.9    +      -       -      -
    351A  ARG*     2.8    27.3    +      -       -      -
    423A  PHE*     4.2    13.2    -      -       -      -
    424A  LEU      3.4     7.6    -      -       -      -
    425A  CYS*     4.1     7.2    -      -       -      -
      6T    T      3.3    12.8    -      -       -      +
      7T    C      2.8    14.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LYS*     4.7     2.7    -      -       -      -
    320A  GLY*     1.4    72.0    -      -       -      -
    322A  SER*     1.3    62.1    +      -       -      +
    344A  LEU*     3.8    30.6    -      -       +      +
    347A  GLU*     4.1     9.9    -      -       -      -
    348A  LEU*     3.7    42.0    -      -       +      -
    351A  ARG*     3.5    21.8    -      -       -      -
    423A  PHE*     3.5     1.1    -      -       -      -
    424A  LEU*     2.8    35.3    +      -       +      +
      6T    T      3.4     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LYS*     3.5    14.8    -      -       -      +
    321A  CYS*     1.3    77.0    -      -       -      +
    323A  LYS*     1.3    63.8    +      -       -      +
    344A  LEU*     4.3     4.0    -      -       -      -
    421A  MET*     4.9     5.1    -      -       -      +
    422A  LEU      3.3    11.2    -      -       -      -
    423A  PHE*     3.4    24.7    -      -       -      -
      5T    C      3.6    30.5    +      -       -      +
      6T    T      3.0    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  TYR*     3.1    30.5    +      -       -      -
     85A  GLY      3.2    21.2    +      -       -      +
     86A  LYS*     4.1    11.4    -      -       +      -
    322A  SER*     1.3    76.2    -      -       -      +
    324A  ASN*     1.3    72.2    +      -       -      +
    325A  PHE*     3.1    47.8    -      -       +      -
    340A  TRP*     3.7    27.4    -      -       +      -
    344A  LEU*     4.5    13.4    -      -       +      +
    421A  MET*     3.5     1.4    -      -       -      -
    422A  LEU      2.9    26.7    +      -       -      +
      5T    C      3.6     9.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  SER*     5.8     0.2    +      -       -      -
    323A  LYS*     1.3    88.9    +      -       -      +
    325A  PHE*     1.3    67.0    +      -       -      +
    326A  PRO*     3.4    16.1    -      -       +      +
    420A  THR      3.4     7.2    -      -       -      +
    421A  MET*     3.2    25.2    -      -       -      +
      5T    C      2.8    26.7    +      -       -      +
----------------------------------------------------------
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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