Contacts of the strand formed by residues 138 - 148 (chain R) in PDB entry 1VQM


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 SER 138 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   20530    G      2.5    23.1    +      -       -      -
     22R  GLN*     3.5    27.1    +      -       -      -
    121R  GLU*     3.0     7.8    -      -       -      -
    122R  GLN*     2.6    54.0    +      -       -      -
    136R  TRP      5.2     0.5    +      -       -      -
    137R  ASN*     1.3    72.7    -      -       -      +
    139R  PRO*     1.3    69.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 139 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   13700    G      3.4    29.8    -      -       +      +
   20530    G      4.2    10.5    -      -       -      +
   20540    A      5.7     1.8    -      -       -      +
     21R  ARG      3.4     0.7    -      -       -      +
     22R  GLN*     3.4    25.2    -      -       -      +
     23R  MET*     3.5    22.6    +      -       -      +
     25R  PHE*     4.3    14.4    -      -       +      +
    118R  LYS*     4.2    22.7    -      -       +      +
    120R  GLY      3.8     4.7    -      -       -      +
    121R  GLU*     4.5     2.2    -      -       +      +
    137R  ASN      4.3     2.7    -      -       -      +
    138R  SER*     1.3    88.7    -      -       -      +
    140R  GLN*     1.3    60.8    +      -       -      +
    141R  VAL*     4.1     1.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 140 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20R  GLU*     4.0    37.6    +      -       +      +
     21R  ARG      3.3     3.8    -      -       -      -
     22R  GLN*     4.6    12.0    -      -       +      +
    118R  LYS*     3.5     5.7    -      -       -      +
    119R  VAL*     2.8    30.2    +      -       +      +
    120R  GLY*     2.7    27.4    +      -       -      +
    121R  GLU      3.5    16.9    +      -       -      +
    122R  GLN*     3.9    32.1    +      -       +      +
    138R  SER      4.1     0.2    -      -       -      +
    139R  PRO*     1.3    77.0    -      -       -      +
    141R  VAL*     1.3    62.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 141 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18R  LEU*     4.2     1.7    -      -       -      +
     19R  ARG      3.8     1.4    -      -       -      -
     20R  GLU      3.3     2.4    +      -       -      -
     21R  ARG*     2.7    43.3    +      -       -      +
     23R  MET*     3.7    48.0    -      -       +      +
     25R  PHE*     3.7    30.1    -      -       +      -
     28R  SER*     4.2     2.0    -      -       -      +
    116R  ALA*     4.1    17.3    -      -       +      -
    117R  HIS      3.5     6.1    -      -       -      +
    139R  PRO*     4.6     0.4    -      -       +      -
    140R  GLN*     1.3    81.1    -      -       -      +
    142R  ASP*     1.3    77.7    +      -       -      +
    143R  VAL*     4.4     0.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 142 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1R  GLY*     3.2     5.1    -      -       -      -
      2R  ILE*     3.2    37.2    +      -       +      -
     18R  LEU      3.2    11.0    -      -       -      +
     19R  ARG*     3.2    16.5    +      -       -      -
     20R  GLU*     2.7    35.9    +      -       -      +
    117R  HIS*     2.8    30.5    +      -       -      +
    119R  VAL*     3.2    31.3    -      -       +      +
    141R  VAL*     1.3    78.1    -      -       -      +
    143R  VAL*     1.3    61.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 143 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2R  ILE*     4.3     4.0    -      -       -      -
     17R  MET*     3.3     6.8    -      -       -      +
     18R  LEU*     3.0    71.6    +      -       +      -
     23R  MET*     4.7     7.4    -      -       +      -
     88R  PHE*     3.9    24.9    -      -       +      -
     91R  LEU*     3.8    19.6    -      -       +      +
    114R  VAL*     4.3     1.8    -      -       +      -
    115R  ALA      3.3    20.9    -      -       -      +
    116R  ALA*     4.2     6.3    -      -       +      -
    141R  VAL*     4.9     1.6    -      -       +      -
    142R  ASP*     1.3    76.6    -      -       -      +
    144R  GLU*     1.3    65.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 144 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2R  ILE*     3.9    12.7    -      -       +      +
      3R  SER      4.6     0.7    -      -       -      -
      4R  TYR*     3.3    24.7    -      -       +      +
      5R  SER*     2.6    43.9    +      -       -      -
      6R  VAL      4.6     0.3    +      -       -      -
     16R  ALA      3.8     3.8    -      -       -      -
     17R  MET*     4.0     2.9    -      -       +      -
    113R  HIS*     2.9    28.3    +      -       +      +
    114R  VAL*     3.1    26.9    -      -       -      +
    115R  ALA*     3.0    14.5    +      -       -      +
    117R  HIS*     3.0    24.1    -      -       +      -
    143R  VAL*     1.3    75.2    -      -       -      +
    145R  LEU*     1.3    62.7    +      -       -      +
    146R  ILE*     4.9     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 145 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4R  TYR*     3.9     1.5    -      -       -      -
     14R  ALA      4.0     0.3    -      -       -      +
     15R  LYS*     3.4     4.7    -      -       -      -
     16R  ALA*     3.0    37.0    +      -       +      +
     35R  ILE*     5.6     1.6    -      -       +      -
     91R  LEU*     3.7    26.7    -      -       +      -
     92R  LEU*     3.5    29.2    -      -       +      -
     95R  ALA*     3.8    23.3    -      -       +      -
    111R  ILE*     3.3    32.3    -      -       +      -
    113R  HIS      3.2    15.3    -      -       -      +
    114R  VAL*     3.7    10.8    -      -       +      -
    144R  GLU*     1.3    77.2    -      -       -      +
    146R  ILE*     1.3    69.4    +      -       -      +
    147R  LEU*     4.4     7.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 146 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4R  TYR*     4.0    23.8    -      -       +      -
      6R  VAL*     4.1    29.8    -      -       +      +
      7R  GLU      4.8     0.2    -      -       -      +
      8R  ALA*     4.2    11.4    -      -       +      -
     13R  THR*     3.4    33.9    -      -       +      +
     14R  ALA      3.5     2.7    -      -       -      +
     15R  LYS*     4.4     4.3    -      -       +      -
    111R  ILE*     3.8     1.9    -      -       -      -
    112R  LYS*     2.9    40.2    +      -       +      +
    113R  HIS*     2.8    42.6    +      -       +      +
    144R  GLU*     4.9     0.2    -      -       -      +
    145R  LEU*     1.3    79.4    -      -       -      +
    147R  LEU*     1.3    61.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 147 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13R  THR*     3.3    10.6    +      -       -      -
     14R  ALA*     2.7    36.1    +      -       +      +
     40R  ALA*     4.3     6.3    -      -       +      -
     92R  LEU*     5.0     0.9    -      -       +      -
     95R  ALA*     3.6    34.8    -      -       +      +
     96R  VAL*     3.9    23.6    -      -       +      +
     99R  ALA*     4.5     7.9    -      -       +      -
    106R  GLY      4.5     7.0    -      -       -      +
    109R  MET*     3.9    22.2    -      -       +      +
    110R  THR      3.2    13.0    -      -       -      +
    111R  ILE*     3.9    24.7    -      -       +      -
    145R  LEU*     4.4    10.8    -      -       +      -
    146R  ILE*     1.3    75.2    -      -       -      +
    148R  GLU*     1.3    59.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 148 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12R  THR*     3.6    19.1    +      -       -      +
     13R  THR*     4.0     7.3    +      -       -      +
    109R  MET*     3.6     6.0    -      -       -      +
    110R  THR*     2.8    38.4    +      -       -      +
    112R  LYS*     3.7    46.2    +      -       +      +
    147R  LEU*     1.3    77.5    -      -       -      +
    149R  GLU*     1.3    78.7    +      -       +      +
----------------------------------------------------------
 Back to top of page


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