Contacts of the strand formed by residues 157 - 163 (chain C) in PDB entry 1AXC


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 ALA 157 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156C  ASP*     1.3    79.9    +      -       +      +
    158C  VAL*     1.3    61.8    +      -       -      +
    159C  VAL*     5.6     1.2    -      -       +      +
    170C  SER      3.6     0.2    -      -       -      +
    171C  ALA*     3.6    24.9    -      -       -      +
    172C  SER      4.5     2.8    +      -       -      -
    206C  THR*     3.8    22.4    -      -       +      -
    207C  PHE      3.2    11.2    -      -       -      +
    208C  ALA*     4.4     0.4    -      -       -      +
    209C  LEU*     3.8     2.5    -      -       -      +
    254C  LYS*     4.0    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 158 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147C  ILE*     5.6     0.2    -      -       +      -
    148C  CYS*     6.5     0.2    -      -       -      -
    151C  LEU*     3.4    28.5    -      -       +      -
    157C  ALA*     1.3    76.1    -      -       -      +
    159C  VAL*     1.3    68.4    +      -       -      +
    160C  ILE*     3.8     5.9    +      -       +      +
    169C  PHE*     4.0    21.5    -      -       +      -
    170C  SER      3.1     4.5    -      -       -      +
    205C  LEU      3.5     1.2    -      -       -      +
    206C  THR*     3.3     3.5    -      -       -      -
    207C  PHE*     2.7    47.0    +      -       +      +
    209C  LEU*     3.8    18.6    -      -       +      -
    212C  LEU*     3.6    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 159 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157C  ALA*     5.6     1.6    -      -       +      +
    158C  VAL*     1.3    73.7    -      -       -      +
    160C  ILE*     1.3    59.9    +      -       -      +
    161C  SER*     4.1     6.8    +      -       -      +
    168C  LYS      3.2     7.3    -      -       -      +
    170C  SER*     2.8    46.3    +      -       -      +
    171C  ALA*     6.3     0.2    -      -       -      -
    204C  GLN*     3.6    35.9    -      -       +      +
    205C  LEU      3.1     6.5    -      -       -      +
    206C  THR*     4.0    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 160 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144C  PHE*     5.5     2.0    -      -       +      -
    158C  VAL*     4.3    13.5    -      -       +      -
    159C  VAL*     1.3    73.0    -      -       -      +
    161C  SER*     1.3    62.3    +      -       -      +
    162C  CYS      4.2     0.2    +      -       -      -
    167C  VAL*     3.7    23.6    -      -       +      -
    168C  LYS      3.3     2.5    -      -       -      -
    169C  PHE*     3.8    31.0    -      -       +      +
    203C  VAL      3.8     1.6    -      -       -      +
    204C  GLN*     3.2     3.2    -      -       -      -
    205C  LEU*     2.8    39.0    +      -       -      +
    207C  PHE*     3.5    34.3    -      -       +      -
    212C  LEU*     5.0     5.2    -      -       +      -
    227C  LEU*     4.9     5.4    -      -       +      -
    229C  MET*     3.7    27.9    -      -       +      +
    235C  LEU*     4.2    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 161 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159C  VAL*     4.1     6.6    +      -       -      +
    160C  ILE*     1.3    71.7    -      -       -      +
    162C  CYS*     1.3    61.4    +      -       -      +
    163C  ALA*     4.2     0.6    +      -       -      -
    166C  GLY      4.4     0.2    -      -       -      +
    167C  VAL*     3.1     6.0    -      -       -      +
    168C  LYS*     2.7    65.9    +      -       -      -
    170C  SER*     5.4     0.3    +      -       -      -
    203C  VAL      3.4     6.5    -      -       -      -
    204C  GLN*     3.6    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 162 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  CYS*     3.2    40.0    -      -       +      -
    137C  VAL*     3.8    15.3    -      -       -      -
    160C  ILE      4.1     0.4    -      -       -      -
    161C  SER*     1.3    73.9    -      -       -      +
    163C  ALA*     1.3    61.8    +      -       -      +
    166C  GLY      4.3     1.8    -      -       -      -
    167C  VAL*     4.3     3.1    -      -       +      -
    197C  ILE*     3.5    31.2    -      -       -      -
    202C  PRO*     3.4     9.7    -      -       -      +
    203C  VAL*     2.8    31.8    +      -       +      +
    229C  MET*     4.0    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 163 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161C  SER      4.2     0.6    -      -       -      -
    162C  CYS*     1.3    75.4    -      -       -      +
    164C  LYS*     1.3    65.0    +      -       -      +
    165C  ASP*     3.4    11.7    -      -       -      +
    166C  GLY      2.9    22.4    +      -       -      +
    197C  ILE*     3.3    15.1    -      -       -      +
    199C  MET*     3.9    13.2    -      -       +      -
    202C  PRO*     5.0     6.7    -      -       +      -
----------------------------------------------------------
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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