Contacts of the strand formed by residues 121 - 127 (chain H) in PDB entry 2NVX


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 LEU 121 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537A  ARG*     3.9    11.0    -      -       +      +
    540A  PHE*     4.2    20.9    -      -       +      -
    564A  ALA*     6.2     0.2    -      -       +      -
    565A  ILE*     5.0     5.4    -      -       +      -
     23H  VAL*     3.8    36.6    -      -       +      -
     41H  ASP*     3.2    25.1    -      -       -      +
     43H  ASN      4.7     4.9    -      -       -      +
     95H  TYR*     4.6     5.4    -      -       -      +
     97H  MET*     3.9    22.9    -      -       -      -
    117H  SER*     3.4     4.2    -      -       -      -
    118H  PHE*     2.7    53.1    +      -       +      +
    119H  GLY      3.2     5.2    +      -       -      +
    120H  GLY*     1.3    79.0    -      -       -      +
    122H  LEU*     1.3    59.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 122 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537A  ARG*     3.6    20.4    -      -       -      +
    597A  LEU      4.2     1.1    -      -       -      +
    598A  LEU*     3.5    46.7    -      -       +      +
    599A  SER      4.2     0.9    -      -       -      +
    613A  ILE      4.6     6.1    -      -       -      +
    614A  PHE*     4.1    25.8    -      -       +      -
     25H  ARG*     4.1     3.1    -      -       -      +
     39H  THR      4.6     1.1    -      -       -      -
     40H  LEU*     3.6    16.7    -      -       -      +
     41H  ASP*     2.5    32.8    +      -       -      +
    102H  TYR*     3.0    33.0    -      -       +      +
    116H  TYR      3.2    11.9    -      -       -      +
    117H  SER*     4.7     0.7    -      -       -      -
    118H  PHE*     4.5     1.7    -      -       -      -
    120H  GLY      3.9     4.5    -      -       -      +
    121H  LEU*     1.3    77.6    -      -       -      +
    123H  MET*     1.3    62.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 123 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  LEU*     4.3     4.6    -      -       -      +
     38H  LEU*     3.3    29.2    -      -       +      -
     39H  THR      3.4     5.8    -      -       -      -
     40H  LEU*     3.6    29.4    -      -       +      -
     57H  VAL*     5.0     5.2    -      -       +      -
     59H  ILE*     4.9     3.6    -      -       -      -
    102H  TYR*     5.0     0.2    +      -       -      -
    114H  VAL      5.1     0.2    -      -       -      +
    115H  TYR*     3.2    15.9    -      -       -      -
    116H  TYR*     3.1    60.0    +      -       +      +
    118H  PHE*     3.9     5.8    -      -       +      -
    122H  LEU*     1.3    78.2    -      -       -      +
    124H  ARG*     1.3    69.8    +      -       -      +
    125H  LEU*     4.5     9.0    -      -       +      +
    142H  LEU*     3.5    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 124 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  LEU*     4.0    21.1    -      -       +      +
     37H  LYS*     4.6    12.4    +      -       -      +
     38H  LEU*     3.2    12.8    -      -       -      +
     39H  THR*     2.7    53.9    +      -       -      +
    105H  GLU*     5.2     3.8    +      -       -      -
    107H  VAL*     4.4    21.0    -      -       -      +
    113H  ALA*     4.7     7.9    -      -       +      +
    114H  VAL      3.6     4.0    -      -       -      +
    115H  TYR*     3.5    34.2    +      -       +      -
    123H  MET*     1.3    76.4    -      -       -      +
    125H  LEU*     1.3    62.9    +      -       -      +
    126H  GLU*     2.8    34.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 125 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  PHE*     3.6    31.2    -      -       +      -
     10H  PHE*     3.7    30.5    -      -       +      -
     36H  CYS*     4.5     2.2    -      -       -      -
     37H  LYS      3.8     6.5    -      -       -      +
     38H  LEU*     3.8    17.9    -      -       +      -
     57H  VAL*     6.1     1.6    -      -       +      -
     59H  ILE*     4.9     7.4    -      -       +      -
    113H  ALA*     3.0    30.5    -      -       -      +
    114H  VAL*     3.3    22.6    +      -       +      -
    116H  TYR*     5.8     0.4    -      -       +      -
    123H  MET*     4.9     8.3    -      -       +      -
    124H  ARG*     1.3    75.2    -      -       -      +
    126H  GLU*     1.3    63.1    +      -       -      +
    130H  ARG*     3.3    30.5    -      -       -      +
    134H  ASN*     4.5    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 126 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  GLN      3.5    17.0    -      -       -      +
     36H  CYS*     3.2    25.7    -      -       -      +
     37H  LYS*     3.4    39.2    +      -       -      +
    107H  VAL*     4.8    13.5    -      -       +      +
    111H  LEU*     4.3    17.0    -      -       +      +
    112H  ILE      3.4     8.3    -      -       -      +
    113H  ALA*     5.0     1.3    -      -       +      -
    124H  ARG*     2.8    37.8    +      -       -      +
    125H  LEU*     1.3    79.3    -      -       -      +
    127H  GLY*     1.3    59.9    +      -       -      +
    130H  ARG*     3.0    11.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 127 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  GLN*     4.3    18.5    -      -       -      +
     36H  CYS*     5.3     0.2    -      -       -      -
    110H  ASP      3.6     4.2    -      -       -      +
    111H  LEU*     3.6     5.0    -      -       -      +
    112H  ILE*     3.0    33.6    +      -       -      +
    126H  GLU*     1.3    75.5    -      -       -      +
    128H  ASN*     1.3    65.6    +      -       -      +
    129H  TYR*     5.4     1.6    -      -       -      -
    130H  ARG*     3.1    16.9    -      -       -      +
----------------------------------------------------------
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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