Contacts of the strand formed by residues 152 - 159 (chain D) in PDB entry 6H25


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 PHE 152 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101D  THR*     4.1    14.6    -      -       +      -
    102D  CYS*     4.2    19.7    -      -       -      -
    105D  VAL*     3.6    29.6    -      -       +      -
    106D  VAL*     6.2     0.2    -      -       +      -
    134D  LEU*     3.5    43.2    -      -       +      +
    137D  ALA*     4.3     2.7    -      -       +      -
    138D  CYS*     3.3    40.3    -      -       +      +
    141D  LEU*     5.6     2.0    -      -       +      -
    148D  MET*     4.6    10.1    -      -       -      -
    150D  ALA      4.5     2.5    -      -       -      -
    151D  LEU*     1.3    79.9    -      -       -      +
    153D  CYS*     1.3    65.0    +      -       -      +
    184D  ALA*     5.3     2.0    -      -       +      -
    185D  LEU      3.2    15.7    -      -       -      +
    193D  LEU*     4.0    15.7    -      -       +      -
    221D  PHE*     3.7     5.2    -      -       -      -
    224D  TYR*     3.0    16.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 153 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134D  LEU*     4.9     2.9    -      -       -      -
    135D  ASN*     3.3    17.0    -      -       -      +
    152D  PHE*     1.3    75.7    -      -       -      +
    154D  GLY*     1.3    64.2    +      -       -      +
    155D  VAL*     4.9     2.5    -      -       -      -
    183D  PHE      4.0     0.5    -      -       -      +
    184D  ALA*     3.3     5.3    -      -       -      +
    185D  LEU*     2.8    34.2    +      -       -      +
    217D  SER*     3.9    28.7    -      -       -      -
    220D  VAL*     3.7    22.7    -      -       +      -
    221D  PHE*     3.6    27.8    -      -       +      -
    224D  TYR*     3.8     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 154 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  GLN*     5.1     2.6    +      -       -      -
    131D  ALA*     3.3    29.2    +      -       -      +
    134D  LEU*     4.5     8.9    -      -       -      +
    135D  ASN*     3.1    20.0    +      -       -      +
    153D  CYS*     1.3    77.4    -      -       -      +
    155D  VAL*     1.3    67.4    +      -       -      +
    182D  THR*     5.9     0.2    -      -       -      -
    183D  PHE      3.3     8.3    -      -       -      -
    184D  ALA*     4.2     3.8    -      -       -      -
    220D  VAL*     5.4     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 155 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  LEU*     4.6     4.7    -      -       +      -
    131D  ALA*     4.0     4.3    -      -       -      -
    153D  CYS*     4.9     5.2    -      -       -      -
    154D  GLY*     1.3    78.8    -      -       -      +
    156D  ALA*     1.3    67.4    +      -       -      +
    167D  LEU*     5.5     3.6    -      -       +      -
    168D  ASP*     3.9    12.1    -      -       -      +
    182D  THR*     3.5     5.5    -      -       -      +
    183D  PHE*     2.9    34.1    +      -       +      +
    185D  LEU*     4.2     5.2    -      -       +      -
    213D  ALA*     3.7    37.7    -      -       +      +
    216D  ALA*     3.7    31.2    -      -       +      -
    217D  SER      4.6     1.3    -      -       -      +
    220D  VAL*     4.6    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 156 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128D  SER*     3.5    29.8    -      -       -      +
    131D  ALA*     5.0     0.7    -      -       +      -
    155D  VAL*     1.3    77.9    -      -       -      +
    157D  CYS*     1.3    60.5    +      -       -      +
    167D  LEU*     3.4     9.2    -      -       -      +
    168D  ASP*     2.7    36.0    +      -       -      +
    169D  PRO*     4.1     5.8    -      -       +      -
    180D  VAL*     5.3     3.1    -      -       +      -
    181D  LEU      3.1    14.6    -      -       -      +
    182D  THR*     3.9    13.0    -      -       +      +
    183D  PHE*     4.8     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156D  ALA*     1.3    74.3    -      -       -      +
    158D  ALA*     1.3    61.7    +      -       -      +
    159D  LEU*     4.2     2.2    -      -       +      -
    165D  LEU*     4.4     7.9    -      -       +      -
    166D  VAL      3.2     7.9    -      -       -      +
    167D  LEU*     4.2    14.6    -      -       +      -
    169D  PRO*     4.7     2.9    -      -       -      -
    179D  ALA      4.7     0.2    -      -       -      -
    180D  VAL*     3.6     4.9    -      -       -      +
    181D  LEU*     2.9    51.7    +      -       -      +
    183D  PHE*     4.4     6.0    -      -       -      -
    209D  CYS*     3.0    49.4    -      -       +      +
    213D  ALA*     6.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 158 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157D  CYS*     1.3    76.3    -      -       -      +
    159D  LEU*     1.3    63.5    +      -       -      +
    160D  ASP*     3.8     3.2    +      -       -      +
    164D  THR      3.6     3.6    -      -       -      +
    165D  LEU*     3.3     4.5    -      -       -      -
    166D  VAL*     2.9    35.3    +      -       +      +
    169D  PRO*     3.8    30.3    -      -       +      -
    173D  GLN*     4.4     5.2    -      -       +      +
    177D  ALA*     4.2    14.1    -      -       +      -
    179D  ALA      3.4     8.5    -      -       -      +
    180D  VAL*     4.8     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 159 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157D  CYS*     4.4     4.7    -      -       -      -
    158D  ALA*     1.3    75.0    -      -       -      +
    160D  ASP*     1.3    64.2    +      -       -      +
    163D  GLY*     3.4    36.1    -      -       -      +
    164D  THR      4.3     0.2    -      -       -      -
    165D  LEU*     4.1    12.1    -      -       +      -
    177D  ALA*     3.3     2.7    -      -       -      +
    178D  ARG*     3.0     9.7    +      -       +      +
    179D  ALA*     2.9    46.0    +      -       +      -
    181D  LEU*     4.7     8.7    -      -       +      -
    201D  TYR*     5.4     1.1    -      -       +      -
    205D  GLU*     4.4    30.7    -      -       +      +
    209D  CYS*     2.9    37.2    -      -       -      -
----------------------------------------------------------
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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