Contacts of the strand formed by residues 162 - 167 (chain C) in PDB entry 1LNU


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 TYR 162 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  LEU*     4.2    16.6    -      -       +      -
    122C  TRP*     5.3     2.0    -      -       +      -
    123C  LEU      3.0     7.2    -      -       -      +
    124C  ARG*     3.4    47.7    +      -       +      -
    125C  ASN      5.3     0.2    -      -       -      -
    152C  LEU*     4.2    20.4    -      -       +      -
    154C  PHE*     3.0    48.8    -      +       -      +
    155C  ILE      3.6     9.6    +      -       -      -
    156C  PRO*     5.8     0.7    -      -       +      -
    160C  ASP*     4.1    20.0    +      -       -      -
    161C  ILE*     1.3    81.5    -      -       -      +
    163C  ASP*     1.3    61.8    +      -       -      +
    178C  HIS*     3.0    25.1    -      -       -      -
    179C  TRP*     3.2    47.3    +      +       +      +
    181C  PRO*     5.9     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 163 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122C  TRP*     4.5     1.8    -      -       -      -
    123C  LEU*     2.7    51.5    +      -       +      +
    126C  SER      6.1     1.1    -      -       -      +
    162C  TYR*     1.3    76.8    -      -       -      +
    164C  CYS*     1.3    64.3    +      -       -      +
    176C  LEU*     2.9    40.8    -      -       +      +
    177C  LYS      3.0    28.3    +      -       -      +
    178C  HIS*     3.1    26.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 164 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  ALA*     5.5     0.4    -      -       -      -
     92C  VAL*     3.7    10.1    -      -       +      -
    108C  CYS*     2.0    49.6    -      -       -      -
    120C  ILE*     3.7    21.8    -      -       -      -
    121C  THR      3.8     4.3    -      -       -      -
    122C  TRP*     3.4    23.0    -      -       +      -
    163C  ASP*     1.3    70.3    -      -       -      +
    165C  LYS*     1.3    57.4    +      -       -      +
    166C  VAL*     3.9     7.8    +      -       -      +
    175C  VAL*     3.5     5.9    -      -       -      +
    176C  LEU*     3.8     1.7    -      -       -      -
    177C  LYS*     3.0    31.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 165 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119C  ASN      3.4     1.6    -      -       -      +
    120C  ILE*     3.2     6.1    -      -       -      +
    121C  THR*     2.6    63.0    +      -       -      +
    123C  LEU*     3.8    27.8    -      -       +      +
    128C  SER*     5.8     0.7    -      -       -      +
    163C  ASP      3.4     0.6    +      -       -      -
    164C  CYS*     1.3    71.1    -      -       -      +
    166C  VAL*     1.3    62.6    +      -       -      +
    167C  GLU*     4.6    14.7    -      -       +      +
    174C  PRO*     3.6    32.2    -      -       +      +
    175C  VAL      3.8     2.7    -      -       -      -
    176C  LEU*     4.0    18.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 166 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  PRO*     4.2    17.3    -      -       +      +
     89C  GLN      5.3     1.3    -      -       -      +
     90C  ALA*     4.9     7.6    -      -       +      -
    110C  VAL*     4.2    21.8    -      -       +      -
    118C  ILE*     3.8    21.5    -      -       +      -
    119C  ASN      3.3     1.6    -      -       -      -
    120C  ILE*     3.9    23.3    -      -       +      -
    164C  CYS*     4.4     8.5    -      -       -      +
    165C  LYS*     1.3    80.0    -      -       -      +
    167C  GLU*     1.3    67.1    +      -       -      +
    171C  LEU*     3.4     8.4    -      -       +      +
    174C  PRO*     3.1     5.5    -      -       -      +
    175C  VAL*     2.8    48.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 167 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118C  ILE*     3.3     5.4    -      -       -      +
    119C  ASN*     3.0    56.0    +      -       +      +
    121C  THR*     4.5    16.3    +      -       -      +
    165C  LYS*     4.6    12.7    -      -       +      +
    166C  VAL*     1.3    78.0    -      -       -      +
    168C  HIS*     1.3    61.6    +      -       -      +
    171C  LEU*     3.8     6.7    -      -       +      -
    174C  PRO*     3.7    24.5    -      -       +      +
    305C  NAG      3.6    27.3    +      -       +      +
----------------------------------------------------------
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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