Contacts of the strand formed by residues 78 - 84 (chain H) in PDB entry 2R4S


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 THR 78 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21H  SER*     5.5     2.2    -      -       -      -
     22H  CYS      3.4    10.8    -      -       -      -
     23H  LYS*     3.4    35.7    -      -       +      -
     29H  PHE*     3.5     6.1    -      -       -      -
     73H  ASP*     2.9    26.2    +      -       -      +
     76H  SER*     3.0    32.5    -      -       -      +
     77H  SER*     1.3    77.4    -      -       -      +
     79H  ALA*     1.3    62.1    +      -       -      +
     80H  TYR*     3.1    29.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 79 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21H  SER*     3.3     4.0    -      -       -      -
     22H  CYS      3.0    29.9    +      -       -      +
     29H  PHE*     3.7     9.4    -      -       +      -
     34H  ILE*     3.2    35.4    -      -       +      -
     36H  TRP*     3.7     8.9    -      -       +      +
     51H  ILE*     5.3     2.5    -      -       +      -
     71H  THR      3.5    11.7    -      -       -      +
     72H  ALA*     4.1     5.6    -      -       +      +
     78H  THR*     1.3    75.2    -      -       -      +
     80H  TYR*     1.3    66.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 80 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19H  LYS*     3.9    32.5    -      -       +      -
     20H  LEU      3.3     9.2    -      -       -      +
     21H  SER*     3.8    24.2    -      -       -      -
     36H  TRP*     4.0    10.9    +      -       -      -
     70H  LEU*     3.5     4.0    -      -       -      +
     71H  THR*     2.6    58.1    +      -       +      +
     73H  ASP*     4.1    17.9    -      -       +      +
     76H  SER*     4.9     5.4    +      -       -      -
     78H  THR*     3.1    32.8    +      -       -      +
     79H  ALA*     1.3    76.5    -      -       -      +
     81H  MET*     1.3    64.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 81 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18H  VAL      4.0     0.2    -      -       -      +
     19H  LYS*     3.6     5.6    -      -       -      -
     20H  LEU*     3.1    63.2    +      -       +      +
     36H  TRP*     3.7    37.7    -      -       +      -
     48H  ILE*     3.9    28.5    -      -       -      -
     68H  ALA*     4.1    11.2    -      -       +      -
     69H  THR      3.8     3.8    -      -       -      -
     70H  LEU*     4.0    12.6    -      -       +      -
     80H  TYR*     1.3    78.4    -      -       -      +
     82H  GLN*     1.3    62.6    +      -       -      +
     83H  LEU*     3.3    15.8    +      -       +      +
     94H  TYR*     3.5    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 82 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17H  SER*     3.3    22.2    +      -       -      -
     18H  VAL      4.2     2.0    -      -       -      -
     19H  LYS*     3.3    34.8    -      -       +      +
     67H  LYS      3.2     3.5    -      -       -      +
     68H  ALA*     2.9    27.1    -      -       -      -
     69H  THR*     2.8    37.8    +      -       -      +
     71H  THR*     5.3     1.7    -      -       +      +
     81H  MET*     1.3    69.5    -      -       -      +
     83H  LEU*     1.3    58.8    +      -       -      +
     84H  SER*     4.0    15.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 83 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17H  SER*     3.3    18.9    +      -       -      -
     18H  VAL*     3.1    21.2    +      -       +      -
     20H  LEU*     4.8     0.9    -      -       +      -
     38H  ARG*     5.6     0.4    -      -       -      +
     48H  ILE*     5.3     0.2    -      -       +      -
     64H  PHE*     5.2     3.1    -      -       +      -
     67H  LYS*     3.3    41.3    -      -       +      +
     68H  ALA*     3.6    14.4    -      -       +      -
     81H  MET*     3.3    22.7    +      -       +      +
     82H  GLN*     1.3    69.8    -      -       -      +
     84H  SER*     1.3    58.5    +      -       -      +
     86H  LEU*     3.0    30.0    -      -       +      +
     90H  ASP*     4.8     2.0    -      -       -      +
     94H  TYR*     3.5    37.7    -      -       +      +
    109H  LEU*     4.4     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 84 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17H  SER*     4.0     9.6    +      -       -      -
     66H  ASP      5.1     4.7    -      -       -      -
     67H  LYS*     2.9    35.6    +      -       -      +
     69H  THR*     5.5     0.2    +      -       -      -
     82H  GLN*     3.7    17.7    +      -       -      +
     83H  LEU*     1.3    70.9    -      -       -      +
     85H  SER*     1.3    79.1    +      -       -      +
     86H  LEU      3.3     2.5    -      -       -      -
----------------------------------------------------------
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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