Contacts of the strand formed by residues 160 - 167 (chain C) in PDB entry 4LL1


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 VAL 160 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155C  ASP      5.9     0.4    -      -       -      +
    158C  ALA      3.7    10.8    -      -       -      +
    159C  PRO*     1.3    77.4    -      -       -      +
    161C  SER*     1.3    66.2    +      -       -      +
    183C  ARG*     3.2     2.5    -      -       -      +
    184C  ILE*     2.8    48.9    +      -       +      +
    186C  ARG      4.1     1.1    -      -       -      -
    187C  LYS*     3.7    35.0    -      -       +      +
    292C  LEU*     4.0    31.2    -      -       +      +
    293C  PRO*     4.7    10.5    -      -       +      +
----------------------------------------------------------
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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  PRO      4.4     1.1    +      -       -      -
    160C  VAL*     1.3    81.9    -      -       -      +
    162C  ALA*     1.3    64.8    +      -       -      +
    182C  ALA      3.2    14.6    -      -       -      -
    183C  ARG*     3.7    16.6    -      -       -      -
    292C  LEU*     4.2     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 162 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161C  SER*     1.3    80.3    +      -       -      +
    163C  LYS*     1.3    63.8    +      -       -      +
    181C  SER*     3.2     3.5    -      -       -      -
    182C  ALA      3.0    27.8    +      -       -      +
    290C  LEU*     3.7    20.7    -      -       +      +
    291C  ASP      5.6     1.3    -      -       -      +
    292C  LEU*     3.7    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 163 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162C  ALA*     1.3    77.6    -      -       -      +
    164C  LYS*     1.3    64.9    +      -       -      +
    180C  VAL      3.2     7.6    -      -       -      +
    181C  SER*     3.6    19.5    -      -       -      -
    290C  LEU*     3.7     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 164 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163C  LYS*     1.3    77.4    -      -       -      +
    165C  GLU*     1.3    68.1    +      -       -      +
    166C  LYS*     5.9     0.9    -      -       +      -
    178C  VAL      4.2     0.3    -      -       -      +
    179C  SER*     3.2     3.5    -      -       -      -
    180C  VAL*     2.8    32.6    +      -       -      +
    288C  VAL*     4.1    21.6    -      -       +      +
    289C  ILE*     3.2    29.3    +      -       -      +
    290C  LEU*     3.6    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 165 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164C  LYS*     1.3    81.2    -      -       -      +
    166C  LYS*     1.3    64.5    +      -       -      +
    167C  LYS      4.4     0.2    -      -       -      -
    177C  ARG*     3.5    50.7    +      -       +      +
    178C  VAL      3.5     6.2    -      -       -      +
    179C  SER*     3.9    18.8    -      -       -      +
    202C  GLU*     5.0     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 166 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164C  LYS*     5.9     1.3    -      -       +      -
    165C  GLU*     1.3    75.4    -      -       -      +
    167C  LYS*     1.3    76.7    +      -       -      +
    168C  VAL*     3.5    12.0    +      -       +      +
    177C  ARG*     3.2     8.1    -      -       -      +
    178C  VAL      2.8    42.1    +      -       -      +
    282C  VAL*     4.5     4.0    -      -       -      +
    285C  SER*     3.2    22.4    +      -       -      -
    286C  LYS*     2.4    45.2    +      -       +      +
    287C  LYS      4.2    10.8    +      -       -      +
    288C  VAL*     4.1    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 167 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166C  LYS*     1.3    84.1    -      -       -      +
    168C  VAL*     1.3    64.3    +      -       -      +
    169C  SER*     3.9    26.0    +      -       -      +
    174C  PRO      4.6     8.4    +      -       -      +
    175C  ASP*     5.5     1.8    -      -       -      -
    176C  GLY      3.6    11.4    -      -       -      +
    177C  ARG*     4.0    27.4    -      -       -      +
----------------------------------------------------------
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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