Contacts of the strand formed by residues 159 - 164 (chain C) in PDB entry 5JLH


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 159 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152C  MET*     3.3    32.8    -      -       +      -
    153C  ASP      3.2     6.3    -      -       -      +
    154C  SER*     3.1    18.6    -      -       -      +
    158C  VAL*     1.3    80.2    -      -       -      +
    160C  HIS*     1.3    72.9    +      -       -      +
    161C  THR*     4.7     2.0    -      -       -      +
    176C  ARG*     3.5     0.3    -      -       -      -
    177C  LEU*     2.8    56.7    +      -       +      +
    179C  LEU*     3.1    20.6    +      -       -      +
    180C  ALA*     4.6     1.2    +      -       -      -
    260C  LEU*     5.6     2.6    -      -       -      +
    273C  ILE*     4.7     2.9    -      -       +      +
    276C  THR*     5.7     0.7    -      -       -      +
    302C  THR*     5.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 160 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72C  HIS      5.5     0.2    +      -       -      -
     73C  GLY*     5.8     1.6    -      -       -      -
    107C  ALA*     3.2    26.9    -      -       +      +
    108C  PRO*     3.6    43.4    +      -       +      -
    136C  GLN*     4.3     2.7    +      -       -      -
    137C  ALA*     5.9     0.2    -      -       +      -
    152C  MET*     3.7     2.4    -      -       -      +
    153C  ASP*     2.5    61.8    +      -       +      +
    158C  VAL*     3.0    51.4    +      -       +      +
    159C  THR*     1.3    76.4    -      -       -      +
    161C  THR*     1.3    66.4    +      -       -      +
    162C  VAL*     5.2     1.1    -      -       +      -
    175C  LEU      3.5     7.9    -      -       -      +
    176C  ARG*     3.8    20.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 161 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150C  ILE*     3.7    26.5    -      -       +      -
    151C  VAL      3.4     7.9    -      -       -      +
    152C  MET*     3.6    19.0    -      -       +      +
    159C  THR*     4.7     2.3    -      -       -      +
    160C  HIS*     1.3    82.2    +      -       -      +
    162C  VAL*     1.3    66.1    +      -       -      +
    163C  PRO*     3.8     0.7    -      -       -      +
    174C  ILE*     3.3     4.9    -      -       -      -
    175C  LEU*     2.8    44.0    +      -       -      +
    177C  LEU*     6.1     0.5    -      -       -      +
    276C  THR*     4.5     9.3    +      -       -      -
    277C  THR*     4.7     9.4    -      -       -      +
    280C  SER*     3.3    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 162 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108C  PRO*     3.9    27.6    -      -       +      -
    135C  ILE*     5.3     4.0    -      -       +      -
    137C  ALA*     3.9    21.1    -      -       +      -
    138C  VAL*     5.0     6.1    -      -       +      -
    149C  GLY      4.0     0.7    -      -       -      +
    150C  ILE*     3.7     1.7    -      -       -      -
    151C  VAL*     3.0    35.7    +      -       -      +
    161C  THR*     1.3    81.0    -      -       -      +
    163C  PRO*     1.3    75.0    -      -       -      +
    164C  ILE*     3.7    19.1    +      -       +      +
    169C  ALA*     5.3     3.4    -      -       +      -
    170C  LEU      5.5     0.2    -      -       -      +
    174C  ILE*     3.7    31.6    -      -       +      -
    374C  PHE*     6.0     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 163 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149C  GLY      3.7     4.9    -      -       -      +
    150C  ILE*     3.9    15.9    -      -       +      -
    161C  THR      3.8     6.7    -      -       -      +
    162C  VAL*     1.3    94.4    -      -       +      +
    164C  ILE*     1.3    61.2    +      -       -      +
    170C  LEU*     3.8    25.3    +      -       +      +
    173C  ALA*     3.4    41.3    -      -       +      +
    174C  ILE*     4.1     3.6    -      -       +      +
    280C  SER*     4.6     4.7    -      -       -      -
    284C  CYS*     3.9    19.5    -      -       -      -
    292C  LEU*     4.0    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 164 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138C  VAL*     3.9    26.0    -      -       +      -
    141C  LEU*     3.2    35.2    -      -       +      -
    147C  THR      3.7     8.7    -      -       -      +
    148C  THR*     3.3     3.6    -      -       -      +
    149C  GLY      2.8    38.9    +      -       -      +
    151C  VAL*     5.7     1.8    -      -       +      -
    162C  VAL*     4.2    11.9    -      -       +      +
    163C  PRO*     1.3    76.3    -      -       -      +
    165C  TYR*     1.3    61.5    +      -       -      +
    167C  GLY*     3.2     9.9    -      -       -      +
    168C  TYR      3.2    26.9    -      -       -      +
    169C  ALA*     3.6    17.3    -      -       +      +
    170C  LEU*     6.0     0.7    -      -       -      -
    288C  ILE*     5.7     0.4    -      -       -      -
    292C  LEU*     3.7     5.2    -      -       -      +
----------------------------------------------------------
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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