Contacts of the strand formed by residues 133 - 139 (chain C) in PDB entry 5NVL


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 133 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  TRP*     3.8     7.8    -      -       -      -
    132C  GLY*     1.3    75.0    -      -       -      -
    134C  LYS*     1.3    61.6    +      -       -      -
    183C  TRP*     3.2     6.1    -      -       -      +
    184C  ASN*     2.8    30.7    +      -       -      +
    187C  ALA*     4.2     0.4    -      -       -      +
    214C  TYR*     3.2    24.2    +      -       -      -
    215C  LYS      3.5    13.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 134 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  TRP*     3.7    42.6    -      -       +      +
    133C  GLY*     1.3    73.5    -      -       -      -
    135C  TRP*     1.3    61.1    +      -       -      +
    136C  ILE*     3.8    31.1    -      -       +      +
    181C  SER*     4.2     7.2    +      -       -      -
    182C  ILE      3.2     7.2    -      -       -      +
    183C  TRP*     3.3    46.2    -      -       +      +
    213C  GLU      3.7     0.5    -      -       -      +
    214C  TYR*     3.4    10.6    -      -       -      -
    215C  LYS*     3.0    34.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 135 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134C  LYS*     1.3    71.1    -      -       -      +
    136C  ILE*     1.3    58.1    +      -       -      +
    180C  ILE      4.6     0.2    -      -       -      -
    181C  SER*     3.0    28.8    -      -       -      -
    182C  ILE*     3.1    15.6    +      -       +      +
    184C  ASN*     5.5     0.2    -      -       -      -
    193C  THR*     2.8    29.4    +      -       -      -
    194C  ALA*     5.3     0.9    -      -       -      -
    196C  ILE*     3.7    25.8    -      -       +      -
    197C  ARG*     3.5    36.7    -      -       +      +
    200C  LEU*     4.0    23.6    -      -       +      +
    212C  MET*     3.9    20.2    -      -       +      -
    213C  GLU      3.3    32.8    -      -       -      -
    214C  TYR*     3.5    47.0    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134C  LYS*     3.8    26.7    -      -       +      -
    135C  TRP*     1.3    78.1    -      -       -      +
    137C  ILE*     1.3    70.9    +      -       -      +
    138C  ARG*     4.1    16.4    -      -       +      -
    179C  ILE*     3.4    27.8    -      -       +      -
    180C  ILE      3.5     2.9    -      -       -      +
    181C  SER*     4.4     2.9    -      -       -      -
    212C  MET*     3.5     2.9    -      -       -      +
    213C  GLU*     2.5    45.3    +      -       +      +
    215C  LYS*     3.3    53.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 137 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  TRP      5.3     0.2    -      -       -      -
    136C  ILE*     1.3    79.4    -      -       -      +
    138C  ARG*     1.3    62.5    -      -       -      +
    139C  LEU*     3.5    31.5    +      -       +      +
    178C  ASP      3.8     0.2    -      -       -      +
    179C  ILE*     3.3     3.3    -      -       -      -
    180C  ILE*     2.8    50.7    +      -       +      +
    200C  LEU*     3.8    15.5    -      -       +      -
    204C  LEU*     3.3    34.5    -      -       +      -
    206C  LEU*     4.5     2.5    -      -       +      -
    210C  THR*     4.5    11.2    -      -       +      -
    211C  ILE      4.0    14.1    -      -       -      +
    212C  MET*     3.7    28.7    -      -       +      -
     97D  ASN*     4.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 138 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  ILE*     4.1    17.0    -      -       +      -
    137C  ILE*     1.3    72.5    -      -       -      +
    139C  LEU*     1.3    61.2    +      -       -      +
    177C  GLU*     2.8    35.3    +      -       -      +
    178C  ASP      3.7     4.0    -      -       -      -
    179C  ILE*     4.2    13.0    -      -       +      +
    211C  ILE      5.0     0.6    +      -       -      -
    213C  GLU*     4.6    12.9    +      -       +      +
    215C  LYS*     5.9     5.1    -      -       -      +
     97D  ASN*     3.3    18.0    +      -       -      +
     98D  SER*     3.1    26.4    +      -       -      +
    100D  ALA*     3.3    21.2    +      -       -      +
    101D  VAL*     3.9    36.5    -      -       +      +
    103D  ARG*     5.2     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 139 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  ILE*     3.5    30.5    -      -       +      +
    138C  ARG*     1.3    76.1    -      -       -      +
    140C  ARG*     1.3    67.1    +      -       -      +
    143C  LEU*     4.5     8.1    -      -       +      -
    144C  ALA*     4.5    10.5    -      -       +      +
    147C  CYS*     4.1    20.0    -      -       +      -
    177C  GLU*     3.3     8.8    -      -       -      +
    178C  ASP*     2.6    40.2    +      -       +      +
    180C  ILE*     3.6    32.1    -      -       +      -
    204C  LEU*     6.3     0.4    -      -       +      -
    206C  LEU*     4.7     6.3    -      -       +      -
     96D  VAL*     3.4    31.4    -      -       +      +
     98D  SER*     3.6     4.7    -      -       -      -
----------------------------------------------------------
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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