Contacts of the strand formed by residues 2 - 10 (chain Q) in PDB entry 1NVU


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 THR 2 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1Q  MET*     1.3    73.5    -      -       -      +
      3Q  GLU*     1.3    70.2    +      -       -      +
      4Q  TYR*     3.5    39.1    +      -       +      +
     49Q  GLU*     5.4     6.9    +      -       -      +
     50Q  THR      3.8     5.7    +      -       -      -
     51Q  CYS*     3.5     5.0    -      -       -      -
     52Q  LEU*     2.9    23.9    +      -       -      -
    164Q  ARG*     5.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 3 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1Q  MET      3.8     2.7    +      -       -      +
      2Q  THR*     1.3    82.6    -      -       -      +
      4Q  TYR*     1.3    65.1    +      -       -      +
      5Q  LYS*     3.1    21.8    +      -       +      +
     41Q  ARG*     3.3    26.2    +      -       -      -
     52Q  LEU*     3.2    21.7    -      -       +      +
     54Q  ASP*     2.3    33.4    -      -       -      +
     76Q  GLU*     3.8    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 4 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2Q  THR*     3.5    31.8    +      -       +      +
      3Q  GLU*     1.3    78.3    -      -       -      +
      5Q  LYS*     1.3    62.8    +      -       -      +
      6Q  LEU*     3.6    17.5    +      -       +      +
     51Q  CYS*     3.6    37.9    -      -       +      -
     52Q  LEU      2.9     8.0    +      -       -      +
     53Q  LEU*     3.7     9.8    -      -       +      -
     54Q  ASP*     2.8    30.3    +      -       -      +
     76Q  GLU*     3.3     4.9    -      -       -      +
    160Q  VAL*     3.8    17.0    -      -       +      -
    163Q  ILE*     3.6    31.4    -      -       +      -
    164Q  ARG*     2.9    47.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 5 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3Q  GLU*     3.1    27.0    +      -       +      +
      4Q  TYR*     1.3    72.9    -      -       -      +
      6Q  LEU*     1.3    63.8    +      -       -      +
      7Q  VAL*     5.8     0.7    -      -       +      -
     54Q  ASP*     3.5    17.3    +      -       +      +
     74Q  THR*     3.8    26.0    -      -       -      +
     75Q  GLY*     3.8     4.8    -      -       -      -
     76Q  GLU*     2.8    58.5    +      -       -      +
     77Q  GLY      3.3     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 6 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Q  TYR*     4.0    16.2    -      -       +      +
      5Q  LYS*     1.3    76.9    -      -       -      +
      7Q  VAL*     1.3    64.3    +      -       -      +
      8Q  VAL*     5.7     0.9    -      -       +      -
     53Q  LEU*     4.1    23.1    -      -       +      -
     54Q  ASP      2.8    14.8    +      -       -      +
     55Q  ILE*     4.4    12.6    -      -       +      -
     56Q  LEU*     2.8    26.6    +      -       -      +
     77Q  GLY      3.5     3.4    -      -       -      -
    156Q  PHE*     3.9    28.7    -      -       +      +
    159Q  LEU*     4.1    20.4    -      -       +      -
    160Q  VAL*     4.2    14.1    -      -       +      -
    163Q  ILE*     3.3    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 7 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5Q  LYS*     5.0     0.7    -      -       +      -
      6Q  LEU*     1.3    81.0    -      -       -      +
      8Q  VAL*     1.3    64.1    +      -       -      +
      9Q  VAL*     3.7    21.7    +      -       +      -
     56Q  LEU*     3.5    15.5    -      -       +      +
     58Q  THR*     3.8    17.9    -      -       +      -
     71Q  TYR*     3.9    20.6    -      -       +      +
     74Q  THR*     4.9     1.3    -      -       -      +
     75Q  GLY*     3.7    28.0    -      -       -      +
     77Q  GLY      2.9     7.0    +      -       -      +
     78Q  PHE*     3.2    23.6    -      -       +      +
     79Q  LEU*     2.8    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 8 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6Q  LEU*     5.7     0.7    -      -       +      -
      7Q  VAL*     1.3    75.1    -      -       -      +
      9Q  VAL*     1.3    64.9    +      -       -      +
     16Q  LYS*     3.6    39.4    -      -       +      +
     19Q  LEU*     5.5     1.6    -      -       +      -
     20Q  THR*     3.9    10.8    -      -       -      +
     55Q  ILE*     3.9    26.5    -      -       +      -
     56Q  LEU      2.9     9.4    +      -       -      +
     57Q  ASP*     4.6     3.8    -      -       -      -
     58Q  THR*     2.9    26.7    +      -       -      +
     79Q  LEU*     3.6    13.7    -      -       +      +
     81Q  VAL*     3.9    16.8    -      -       +      -
    156Q  PHE*     4.1    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 9 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Q  VAL*     3.7    20.6    -      -       +      -
      8Q  VAL*     1.3    80.1    -      -       -      +
     10Q  GLY*     1.3    59.8    +      -       -      +
     16Q  LYS*     3.3    11.9    -      -       -      +
     58Q  THR*     3.8    11.4    -      -       +      +
     68Q  ARG*     6.2     0.7    -      -       -      -
     71Q  TYR*     6.0     0.4    -      -       +      -
     72Q  MET*     4.5    15.7    -      -       +      -
     78Q  PHE*     4.4    10.5    -      -       +      -
     79Q  LEU      2.9    14.8    +      -       -      +
     80Q  CYS*     4.0    21.3    -      -       -      -
     81Q  VAL*     2.9    27.4    +      -       -      +
     96Q  TYR*     4.0    24.5    -      -       +      -
    100Q  ILE*     4.5     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 10 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9Q  VAL*     1.3    79.3    -      -       -      +
     11Q  ALA*     1.3    68.0    +      -       -      -
     14Q  VAL*     4.5     0.4    -      -       -      -
     16Q  LYS*     3.0    14.9    +      -       -      +
     58Q  THR*     5.0     0.6    +      -       -      -
     60Q  GLY*     3.1    14.4    -      -       -      -
     81Q  VAL      3.5    15.0    -      -       -      -
     93Q  ILE*     5.4     1.1    -      -       -      -
     96Q  TYR*     3.3    26.0    +      -       -      -
----------------------------------------------------------
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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