Contacts of the strand formed by residues 145 - 150 (chain C) in PDB entry 6KQH


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 145 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143C  SER      3.7     0.6    +      -       -      -
    144C  PRO*     1.3    74.9    -      -       -      +
    146C  VAL*     1.3    65.9    +      -       -      -
    147C  TYR*     3.8    10.6    -      -       -      -
    161C  SER      3.5     2.3    -      -       -      +
    162C  ILE*     3.6     2.8    -      -       -      +
    163C  ILE      2.9    34.2    +      -       -      -
    269C  LEU*     4.4     4.4    -      -       -      +
    273C  GLY*     3.9    17.0    -      -       -      -
    276C  LYS*     4.7     3.6    -      -       -      -
    277C  ALA*     4.7     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145C  GLY*     1.3    76.1    -      -       -      +
    147C  TYR*     1.3    68.7    +      -       -      +
    148C  PHE*     3.7    28.6    -      -       +      -
    161C  SER      3.4     7.6    -      -       -      +
    162C  ILE*     4.3    12.6    -      -       +      -
    269C  LEU*     6.1     1.3    -      -       +      -
    276C  LYS*     5.2     6.4    +      -       -      +
    277C  ALA*     4.0    20.8    -      -       +      +
    280C  LYS*     4.0    20.5    -      -       +      +
    281C  LEU*     3.9    26.7    -      -       +      -
    302C  VAL*     4.4    10.5    -      -       +      -
    306C  THR*     3.8    23.6    -      -       +      +
    323C  ASP*     4.4     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 147 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  ARG*     3.9    32.3    -      -       -      +
    143C  SER*     2.3    42.4    +      -       -      -
    144C  PRO      3.9     0.2    +      -       -      -
    145C  GLY      3.8    20.0    -      -       -      -
    146C  VAL*     1.3    76.9    -      -       -      +
    148C  PHE*     1.3    72.5    +      -       -      +
    149C  THR*     5.0     5.4    -      -       +      -
    159C  ILE      4.5     0.2    -      -       -      -
    160C  ALA*     3.4     0.9    -      -       -      +
    161C  SER*     2.9    41.7    +      -       -      +
    163C  ILE*     4.3    11.2    -      -       +      -
    276C  LYS*     3.6    16.6    -      -       -      -
    323C  ASP*     3.6    23.3    -      -       +      +
    325C  ILE*     4.6     4.9    -      -       +      -
    330C  ASN*     3.4    41.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 148 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146C  VAL*     3.7    28.9    -      -       +      -
    147C  TYR*     1.3    73.9    -      -       -      +
    149C  THR*     1.3    63.3    +      -       -      +
    158C  TYR*     5.4     0.2    -      -       +      -
    159C  ILE      3.4     5.8    -      -       -      +
    160C  ALA*     3.5    28.9    -      -       +      -
    280C  LYS*     3.9    16.2    -      -       +      -
    281C  LEU*     4.2     5.8    -      -       +      -
    306C  THR*     3.7    17.9    -      -       +      -
    309C  TYR*     3.4    45.1    -      +       +      -
    310C  LEU*     3.7    24.0    -      -       +      -
    313C  LEU*     3.7    20.9    -      -       +      -
    321C  GLU      4.6     3.1    -      -       -      +
    322C  VAL*     3.2     4.8    -      -       -      +
    323C  ASP*     2.9    35.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 149 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  ARG*     5.4     1.8    -      -       -      +
    147C  TYR*     5.0     4.7    -      -       +      -
    148C  PHE*     1.3    81.3    -      -       -      +
    150C  PRO*     1.3    73.4    +      -       +      +
    158C  TYR*     3.3     5.2    -      -       -      +
    159C  ILE*     2.9    47.4    +      -       -      +
    161C  SER*     4.7     6.0    +      -       -      +
    322C  VAL*     3.6     4.7    -      -       -      -
    323C  ASP      4.3     8.1    -      -       -      +
    325C  ILE*     4.3    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 150 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149C  THR*     1.3    93.5    +      -       +      +
    151C  ASP*     1.3    67.3    +      -       -      +
    152C  PRO*     3.3     9.5    -      -       -      +
    157C  ARG      4.0     0.9    -      -       -      +
    158C  TYR*     3.8    17.9    -      -       +      -
    159C  ILE*     4.9     1.2    -      -       -      +
    322C  VAL*     3.4    26.2    -      -       +      -
    323C  ASP      5.5     0.9    -      -       -      +
----------------------------------------------------------
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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