Contacts of the strand formed by residues 17 - 26 (chain D) in PDB entry 1VQ7


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 ARG 17 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30309    C      3.1    27.1    +      -       -      -
   30319    C      5.0     6.9    +      -       -      -
   30449    A      6.3     1.4    -      -       -      -
     15D  GLU      4.6     2.2    -      -       -      +
     16D  PRO*     1.3    77.9    -      -       -      +
     18D  ILE*     1.3    70.4    +      -       -      +
     19D  GLU*     4.4    19.9    +      -       -      +
    134D  LEU*     3.5     9.5    -      -       -      +
    135D  VAL*     3.2    37.6    +      -       -      +
    136D  ARG      4.2    10.0    +      -       -      -
    137D  PRO*     3.8    17.2    -      -       +      +
    139D  TYR*     4.0    23.6    -      -       -      +
    140D  ARG*     5.0     2.4    -      -       -      +
    165D  PHE*     4.1     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 18 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  ARG*     1.3    81.0    -      -       -      +
     19D  GLU*     1.3    64.6    +      -       -      +
     20D  LYS*     3.9     7.6    -      -       -      +
     21D  VAL*     3.7    24.9    -      -       +      -
     77D  ASP*     5.0     8.2    +      -       -      +
     80D  ALA*     4.5     9.2    -      -       +      -
     81D  GLU*     5.1    14.1    -      -       +      +
     84D  LEU*     3.2    31.2    -      -       +      -
    132D  VAL*     4.2     5.8    -      -       +      -
    133D  ASN      3.8     7.2    -      -       -      +
    134D  LEU*     3.3    19.5    -      -       +      -
    165D  PHE*     4.3    13.4    -      -       +      -
    166D  ILE*     6.2     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 19 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30449    A      4.2    18.6    +      -       -      +
     17D  ARG*     3.8    18.2    +      -       -      +
     18D  ILE*     1.3    74.6    -      -       -      +
     20D  LYS*     1.3    72.6    +      -       +      +
     75D  LEU      4.1     0.2    -      -       -      +
     76D  ARG*     3.4    36.8    +      -       -      +
     77D  ASP      4.9     0.3    +      -       -      -
    133D  ASN*     3.0    29.3    +      -       -      +
    135D  VAL*     4.3    15.1    -      -       +      +
    139D  TYR*     2.8    48.1    -      -       -      +
    143D  LYS*     4.5     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 20 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   23480    C      2.8    34.1    +      -       -      -
   23490    G      2.6    26.6    +      -       -      -
     18D  ILE*     3.6     2.4    -      -       -      -
     19D  GLU*     1.3    86.3    -      -       +      +
     21D  VAL*     1.3    64.6    +      -       -      +
     22D  VAL*     4.1    13.8    -      -       +      +
     74D  THR*     5.2     4.6    -      -       +      +
     75D  LEU      3.2     9.6    -      -       -      +
     76D  ARG*     3.6    34.9    -      -       -      +
    131D  THR      4.1     0.3    -      -       -      +
    133D  ASN*     2.8    56.6    +      -       +      +
    143D  LYS*     5.6     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 21 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  ILE*     3.7    20.9    -      -       +      -
     20D  LYS*     1.3    78.1    -      -       -      +
     22D  VAL*     1.3    60.9    +      -       -      +
     23D  VAL*     3.9     3.6    +      -       +      +
     73D  VAL      3.4     2.8    -      -       -      +
     75D  LEU*     3.0    34.2    +      -       +      +
     80D  ALA*     3.8    18.2    -      -       +      -
     83D  PHE*     4.3    13.2    -      -       +      -
     84D  LEU*     3.8    22.4    -      -       +      -
    130D  VAL*     4.0    17.7    -      -       +      -
    131D  THR      3.0    14.8    -      -       -      +
    132D  VAL*     3.9    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 22 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   23470    C      3.4    24.9    +      -       -      +
   23480    C      3.8    26.5    -      -       -      -
     20D  LYS*     4.1    17.9    +      -       +      -
     21D  VAL*     1.3    74.8    -      -       -      +
     23D  VAL*     1.3    64.2    +      -       -      +
     24D  HIS      3.9     0.7    +      -       -      -
     72D  LYS*     4.0    28.5    -      -       +      -
     73D  VAL      3.2     9.9    -      -       -      +
     74D  THR*     3.9    19.3    -      -       +      -
    129D  ASP*     3.9     1.2    -      -       -      +
    130D  VAL*     3.6     0.9    -      -       -      -
    131D  THR*     2.9    39.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 23 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21D  VAL*     4.6     5.6    -      -       +      +
     22D  VAL*     1.3    73.7    -      -       -      +
     24D  HIS*     1.3    59.7    +      -       -      +
     41D  LEU*     3.9    18.5    -      -       +      +
     44D  ILE*     5.5     0.9    -      -       +      -
     45D  THR*     3.3    29.8    -      -       +      -
     72D  LYS*     3.3     2.4    -      -       -      -
     73D  VAL*     3.1    35.0    +      -       +      +
     75D  LEU*     5.0     2.7    -      -       +      -
     83D  PHE*     3.4    41.5    -      -       +      -
    128D  LEU*     5.4     2.7    -      -       +      -
    129D  ASP      3.2     8.1    -      -       -      +
    130D  VAL*     3.6    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 24 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   23380    G      3.1    15.7    -      -       -      -
   23460    C      2.9    52.9    +      -       -      -
   23470    C      3.1    30.8    +      -       -      +
     22D  VAL*     3.9     2.2    +      -       +      -
     23D  VAL*     1.3    75.6    -      -       -      +
     25D  MET*     1.3    71.2    +      -       -      +
     26D  GLY*     3.1    18.9    +      -       -      -
     41D  LEU*     5.1     0.2    -      -       -      -
     71D  ALA      3.0    20.2    -      -       -      +
     72D  LYS*     3.5    13.5    -      -       +      -
    128D  LEU*     5.0     0.4    -      -       -      +
    129D  ASP*     3.0    47.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 25 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  HIS*     1.3    78.4    -      -       -      +
     26D  GLY*     1.3    60.4    +      -       -      +
     27D  ILE*     2.9    17.3    +      -       +      +
     37D  ALA*     3.1    55.1    -      -       +      +
     40D  ILE*     3.5    22.9    -      -       +      -
     41D  LEU*     3.1    35.0    -      -       +      +
     70D  GLY*     3.3    16.6    -      -       -      -
     71D  ALA      2.9    10.8    +      -       -      +
    128D  LEU*     4.4    27.6    -      -       +      +
    129D  ASP*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 26 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   23450    A      4.3    15.0    +      -       -      +
   23460    C      4.3    16.6    -      -       -      -
     24D  HIS*     3.1    30.0    +      -       -      -
     25D  MET*     1.3    68.4    -      -       -      +
     27D  ILE*     1.3    66.0    +      -       -      +
     69D  ILE*     4.5     2.9    -      -       -      -
     70D  GLY*     4.5     0.9    -      -       -      -
    129D  ASP*     4.5     2.6    +      -       -      -
----------------------------------------------------------
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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