Contacts of the strand formed by residues 77 - 83 (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 GLY 77 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5Q  LYS      3.3     4.5    +      -       -      +
      6Q  LEU*     3.5     2.8    -      -       -      -
      7Q  VAL*     2.9    26.5    +      -       -      +
     75Q  GLY      3.6     0.2    -      -       -      -
     76Q  GLU*     1.3    82.6    -      -       -      +
     78Q  PHE*     1.3    67.1    +      -       -      -
    110Q  PRO      3.2    10.8    -      -       -      -
    159Q  LEU*     3.9    10.3    -      -       -      +
    163Q  ILE*     3.7    16.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 78 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Q  VAL*     3.2    30.1    -      -       +      +
      9Q  VAL*     4.4     5.2    -      -       +      -
     72Q  MET*     3.4    53.2    -      -       +      -
     75Q  GLY*     4.0    15.5    -      -       -      -
     77Q  GLY*     1.3    79.7    -      -       -      -
     79Q  LEU*     1.3    62.3    +      -       -      +
     80Q  CYS*     3.8     3.8    -      -       -      -
    100Q  ILE*     3.6    33.7    -      -       +      -
    104Q  LYS*     3.7    11.2    -      -       +      -
    109Q  VAL*     3.6    31.6    -      -       +      -
    110Q  PRO      3.0     5.4    +      -       -      -
    111Q  MET*     3.0    13.1    -      -       +      +
    112Q  VAL      3.0    24.3    +      -       -      -
    159Q  LEU*     3.7     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 79 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Q  VAL      2.8    11.3    +      -       -      +
      8Q  VAL*     3.6    15.9    -      -       +      -
      9Q  VAL*     2.9    29.6    +      -       -      +
     19Q  LEU*     5.3     4.7    -      -       +      -
     78Q  PHE*     1.3    72.5    -      -       -      +
     80Q  CYS*     1.3    60.4    +      -       -      +
     81Q  VAL*     3.7     4.7    +      -       +      +
    112Q  VAL*     3.6    17.7    -      -       +      -
    114Q  VAL*     3.7    19.5    -      -       +      -
    155Q  ALA*     3.7    26.9    -      -       +      +
    156Q  PHE*     3.7    44.9    -      -       +      -
    159Q  LEU*     3.5    24.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 80 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9Q  VAL*     3.7    20.2    -      -       +      -
     78Q  PHE*     4.4     4.3    -      -       -      -
     79Q  LEU*     1.3    73.2    -      -       -      +
     81Q  VAL*     1.3    60.3    +      -       -      +
     93Q  ILE*     4.0    20.9    -      -       +      -
     96Q  TYR*     4.9     6.1    -      -       +      -
     97Q  ARG*     5.3     3.8    -      -       -      -
    100Q  ILE*     4.1    12.6    -      -       -      -
    111Q  MET*     3.8    29.4    -      -       -      -
    112Q  VAL      2.9    12.7    +      -       -      +
    113Q  LEU*     3.6    15.5    -      -       +      +
    114Q  VAL      2.8    24.1    +      -       -      +
    139Q  ILE*     6.0     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 81 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8Q  VAL*     3.9    23.1    -      -       +      -
      9Q  VAL      2.9    17.9    +      -       -      +
     10Q  GLY*     3.5    19.8    -      -       -      -
     11Q  ALA      4.1     2.4    +      -       -      -
     14Q  VAL*     3.7    25.2    -      -       +      +
     16Q  LYS*     4.3     2.9    -      -       +      +
     19Q  LEU*     4.0    17.0    -      -       +      -
     79Q  LEU*     4.0     8.3    -      -       +      +
     80Q  CYS*     1.3    76.9    -      -       -      +
     82Q  PHE*     1.3    74.0    +      -       -      +
     89Q  SER      4.9     0.5    -      -       -      +
     93Q  ILE*     3.7     6.8    -      -       -      +
    114Q  VAL*     3.4    18.2    -      -       +      +
    116Q  ASN*     3.9    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 82 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14Q  VAL*     4.0    10.1    -      -       -      -
     81Q  VAL*     1.3    74.7    -      -       -      +
     83Q  ALA*     1.3    65.4    +      -       -      +
     84Q  ILE*     4.1     9.6    -      -       +      -
     89Q  SER*     3.5    29.2    -      -       -      +
     90Q  PHE*     3.7    33.0    -      +       +      -
     93Q  ILE*     4.0     4.5    -      -       +      -
    113Q  LEU*     3.9    22.2    -      -       +      -
    114Q  VAL      3.0    25.2    +      -       -      +
    115Q  GLY*     3.6     9.2    -      -       -      -
    116Q  ASN*     2.7    33.8    +      -       -      +
    125Q  VAL*     3.8    23.8    -      -       +      -
    130Q  ALA*     3.7     7.0    -      -       +      -
    141Q  TYR*     3.5    37.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with ALA 83 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14Q  VAL*     3.9    16.0    -      -       +      +
     82Q  PHE*     1.3    81.1    -      -       -      +
     84Q  ILE*     1.3    59.0    +      -       -      +
     85Q  ASN*     2.9    26.8    +      -       -      +
     86Q  ASN*     3.0    29.3    +      -       +      +
     89Q  SER*     3.1     6.4    +      -       -      +
    116Q  ASN      3.5     5.8    -      -       -      -
    117Q  LYS*     3.9    24.0    -      -       +      +
    125Q  VAL*     4.3     0.3    -      -       -      +
----------------------------------------------------------
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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