Contacts of the strand formed by residues 842 - 849 (chain A) in PDB entry 6M0X


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 GLU 842 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    831A  ARG      3.4     0.7    -      -       -      +
    832A  GLN*     3.1    11.3    -      -       -      +
    833A  ALA      2.8    37.1    +      -       -      +
    838A  ASP*     4.1    16.3    -      -       -      +
    840A  ALA*     4.3     7.7    -      -       -      +
    841A  ASP*     1.3    76.2    -      -       -      +
    843A  THR*     1.3    64.6    +      -       -      +
    844A  TYR*     3.6    13.9    +      -       +      -
    941A  LYS*     3.7    37.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 843 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    830A  THR*     3.9    21.1    -      -       -      +
    831A  ARG      3.4     4.3    -      -       -      +
    832A  GLN*     3.0    26.3    +      -       -      +
    842A  GLU*     1.3    75.3    -      -       -      +
    844A  TYR*     1.3    61.5    +      -       -      +
    941A  LYS*     3.6     7.1    -      -       -      +
    942A  LEU*     3.0    53.5    +      -       +      +
    956A  LYS*     5.9     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 844 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    830A  THR*     3.2     5.3    -      -       -      -
    831A  ARG      2.8    37.3    +      -       -      +
    833A  ALA*     3.8    18.2    -      -       +      -
    835A  VAL*     3.5    40.1    +      -       +      +
    838A  ASP*     3.1    19.7    +      -       -      -
    842A  GLU*     3.8    20.4    -      -       +      -
    843A  THR*     1.3    78.1    -      -       -      +
    845A  VAL*     1.3    63.2    +      -       -      +
    846A  LEU*     3.6     1.7    +      -       -      +
    871A  LYS*     6.0     0.2    -      -       -      -
    938A  TYR*     4.1    29.8    -      -       +      -
    939A  ASP      4.3     7.0    -      -       -      -
    940A  SER*     3.4    22.2    -      -       -      -
    941A  LYS*     3.3    31.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 845 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    828A  TYR*     3.7    28.7    -      -       +      -
    829A  ALA      3.6     4.0    -      -       -      +
    830A  THR*     4.1     7.4    -      -       +      -
    843A  THR      4.1     0.2    +      -       -      -
    844A  TYR*     1.3    71.9    -      -       -      +
    846A  LEU*     1.3    73.4    +      -       -      +
    939A  ASP*     2.9    32.4    +      -       +      +
    940A  SER*     2.7    19.7    +      -       -      +
    941A  LYS      4.6     0.7    -      -       -      +
    942A  LEU*     3.7    40.6    -      -       +      -
    958A  VAL*     4.7     1.3    -      -       +      -
    960A  GLN*     3.7    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 846 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    828A  TYR*     3.6    13.7    -      -       -      -
    829A  ALA*     2.9    29.9    +      -       +      +
    830A  THR*     4.5     0.2    -      -       -      -
    831A  ARG*     3.8    44.0    -      -       +      +
    844A  TYR      4.1     4.0    -      -       -      +
    845A  VAL*     1.3    90.1    -      -       -      +
    847A  GLY*     1.3    63.1    +      -       -      +
    873A  LEU*     3.7    24.7    -      -       +      -
    936A  LYS*     4.5    11.7    -      -       +      -
    937A  TYR      3.4    10.3    -      -       -      +
    938A  TYR*     3.5    33.0    -      -       +      -
    939A  ASP*     4.2     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 847 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    828A  TYR*     5.6     3.8    -      -       -      -
    845A  VAL      4.1     0.2    +      -       -      -
    846A  LEU*     1.3    74.8    -      -       -      +
    848A  LYS*     1.3    64.5    +      -       -      +
    936A  LYS*     3.4     4.0    -      -       -      +
    937A  TYR*     3.0    50.1    +      -       -      +
    939A  ASP*     4.1     7.5    -      -       -      +
     23B    U      5.7     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 848 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    847A  GLY*     1.3    76.5    -      -       -      +
    849A  ILE*     1.3    66.9    +      -       -      +
    850A  LYS*     3.5     8.0    +      -       +      +
    934A  SER*     3.4    37.0    +      -       -      +
    935A  LEU      3.4     8.5    -      -       -      +
    936A  LYS*     3.9    28.9    -      -       +      +
    937A  TYR*     3.6     6.8    +      -       -      -
     22B    U      2.8    34.9    +      -       -      -
     23B    U      3.1    35.6    +      -       -      +
     43B    A      6.1     0.2    -      -       -      -
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Residues in contact with ILE 849 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    848A  LYS*     1.3    71.2    -      -       -      +
    850A  LYS*     1.3    65.0    +      -       -      +
    851A  ASP      3.5    10.9    +      -       -      +
    852A  ILE*     4.1     8.1    -      -       +      -
    857A  GLY*     3.5    32.1    -      -       -      +
    860A  ALA*     4.2    13.2    -      -       +      -
    861A  PHE*     3.9    36.1    -      -       +      +
    864A  ILE*     4.3     4.5    -      -       +      -
    872A  PHE*     4.1    20.2    -      -       +      -
    934A  SER*     3.2    23.2    -      -       -      -
    935A  LEU*     2.9    19.5    +      -       +      +
    937A  TYR*     4.0    11.4    -      -       +      -
----------------------------------------------------------
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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