Contacts of the strand formed by residues 53 - 60 (chain H) in PDB entry 6PSS


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 GLY 53 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51H  MET      3.4     3.2    +      -       -      -
     52H  PRO*     1.3    73.4    -      -       -      +
     54H  CYS*     1.3    56.2    +      -       -      -
    148H  ARG*     3.4     9.7    -      -       -      +
    149H  GLY*     2.6    40.2    +      -       -      +
    177H  TYR*     3.3    19.4    +      -       -      +
    179H  PRO*     5.2     3.8    -      -       -      -
    210H  THR*     5.7     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 54 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53H  GLY*     1.3    74.3    -      -       -      -
     55H  ALA*     1.3    63.6    +      -       -      +
     89H  ALA*     5.2     1.0    -      -       -      -
     90H  VAL*     3.2    36.7    +      -       -      +
     92H  VAL*     3.6    41.3    -      -       +      -
    146H  VAL*     5.1     1.6    -      -       +      -
    147H  GLN      3.3    21.5    -      -       -      +
    148H  ARG*     3.6    16.2    -      -       +      +
    176H  CYS      4.9     0.9    -      -       -      +
    177H  TYR*     3.9     4.4    +      -       -      +
    210H  THR*     5.3     5.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 55 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54H  CYS*     1.3    76.9    -      -       -      +
     56H  VAL*     1.3    72.8    +      -       +      +
     57H  THR*     3.5     3.1    +      -       -      -
     86H  LYS      5.3     4.3    -      -       -      +
     88H  LEU      4.2    17.5    -      -       -      +
     89H  ALA*     5.8     0.2    -      -       -      -
     90H  VAL*     5.4     4.3    -      -       -      -
    146H  VAL*     3.9     9.9    -      -       -      -
    147H  GLN      3.2    23.4    +      -       -      +
    175H  ALA*     5.0     0.2    -      -       -      -
    176H  CYS      3.7    30.5    -      -       -      +
    177H  TYR*     3.7     7.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 56 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55H  ALA*     1.3    79.7    -      -       +      +
     57H  THR*     1.3    59.4    +      -       -      +
     58H  GLU      4.8     3.4    -      -       -      +
     59H  VAL*     6.3     0.7    -      -       +      -
     85H  LEU*     3.3    37.0    -      -       +      +
     86H  LYS*     4.4     3.8    -      -       -      -
     88H  LEU*     4.8    10.5    +      -       +      +
     90H  VAL*     5.8     0.8    -      -       +      +
    144H  ILE*     4.1    28.3    -      -       +      -
    145H  LYS      3.3     9.4    -      -       -      +
    146H  VAL*     3.9    19.3    -      -       +      +
    173H  VAL*     3.6    21.0    -      -       +      +
    174H  ASP      5.1     0.4    -      -       -      +
    175H  ALA*     3.3    20.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 57 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55H  ALA      3.5     5.5    +      -       -      -
     56H  VAL*     1.3    74.9    -      -       -      +
     58H  GLU*     1.3    65.1    +      -       +      +
    145H  LYS*     2.9    26.3    +      -       -      +
    147H  GLN*     3.8    14.6    -      -       -      +
    158H  ARG*     3.4    38.5    +      -       -      +
    172H  LEU*     3.9     1.0    -      -       -      +
    173H  VAL*     3.0    32.0    +      -       -      +
    175H  ALA*     4.5     0.4    -      -       +      -
    177H  TYR*     3.2    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 58 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56H  VAL*     4.8     2.1    -      -       -      +
     57H  THR*     1.3    80.1    +      -       +      +
     59H  VAL*     1.3    65.5    +      -       -      +
    144H  ILE*     3.9     0.3    -      -       -      +
    145H  LYS*     3.1    68.9    +      -       +      +
    158H  ARG*     6.0     0.2    -      -       -      -
    171H  LEU      3.9    11.4    -      -       -      +
    172H  LEU*     4.2    22.7    -      -       +      +
    173H  VAL*     4.0     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 59 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56H  VAL*     6.3     1.3    -      -       +      -
     58H  GLU*     1.3    79.6    -      -       -      +
     60H  GLU*     1.3    74.9    +      -       -      +
     61H  ILE*     4.7     3.8    -      -       +      -
     82H  LEU*     3.7    28.9    -      -       +      -
     85H  LEU*     4.2    16.8    -      -       +      -
    142H  MET*     4.0    11.2    -      -       +      -
    143H  ARG      3.4    24.7    -      -       -      +
    144H  ILE*     3.7    18.4    -      -       +      -
    171H  LEU*     3.1    37.5    +      -       +      +
    173H  VAL*     5.9     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 60 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59H  VAL*     1.3    81.8    -      -       -      +
     61H  ILE*     1.3    64.7    +      -       -      +
     62H  ASP      3.4     7.0    +      -       -      +
     63H  GLY*     4.3    14.1    +      -       -      +
     64H  VAL      5.3     0.2    +      -       -      -
     65H  LEU      4.3     6.6    -      -       -      +
     66H  HIS*     3.4    35.0    +      -       -      -
    142H  MET*     3.3     1.6    -      -       -      +
    143H  ARG*     2.7    64.4    +      -       +      +
    171H  LEU*     3.8    12.9    +      -       -      +
----------------------------------------------------------
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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