Contacts of the strand formed by residues 109 - 118 (chain F) in PDB entry 2VLR


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 PHE 109 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  CYS*     4.9     0.7    -      -       +      -
    102F  ASP      3.9     6.1    -      -       -      -
    103F  VAL*     4.2     1.6    -      -       -      +
    107F  TRP      4.3     0.2    +      -       -      -
    108F  ARG*     1.3    75.2    -      -       -      +
    110F  LEU*     1.3    73.1    +      -       -      +
    111F  ARG*     3.6    33.4    -      -       -      -
    112F  GLY*     3.7     6.1    -      -       -      -
    130F  LEU*     4.0    11.0    -      -       +      -
    160F  LEU      3.8    26.0    -      -       -      -
    161F  GLU*     3.8    40.8    -      -       +      +
    165F  VAL*     3.8    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 110 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2F  SER*     4.3    10.5    -      -       -      +
    102F  ASP*     3.0    22.4    +      -       +      +
    103F  VAL*     3.5    26.2    -      -       -      +
    104F  GLY*     3.8    12.8    -      -       -      +
    106F  ASP*     6.1     0.2    -      -       -      +
    108F  ARG      3.4     1.5    +      -       -      +
    109F  PHE*     1.3    85.8    -      -       -      +
    111F  ARG*     1.3    65.3    +      -       +      +
    128F  GLU*     5.3     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 111 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  CYS*     3.3     2.3    -      -       -      -
    102F  ASP*     2.7    45.7    +      -       +      +
    109F  PHE*     3.6    14.9    -      -       -      -
    110F  LEU*     1.3    83.1    -      -       +      +
    112F  GLY*     1.3    66.1    +      -       -      +
    113F  TYR*     3.6    42.9    +      -       +      +
    128F  GLU*     3.5    50.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 112 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100F  GLY      3.5     8.7    -      -       -      -
    101F  CYS*     4.4     0.7    -      -       -      -
    109F  PHE*     3.7    13.7    -      -       -      -
    111F  ARG*     1.3    82.3    +      -       -      +
    113F  TYR*     1.3    68.4    +      -       -      -
    126F  LEU      5.4     1.7    -      -       -      +
    127F  LYS      5.3     0.7    -      -       -      +
    128F  GLU*     5.2     5.6    +      -       -      +
    130F  LEU*     3.7    26.2    -      -       -      +
    160F  LEU*     4.3     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 113 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  ARG*     3.4    40.4    +      -       -      -
     98F  MET*     4.0    32.3    -      -       +      -
     99F  TYR*     3.5     4.6    -      -       -      +
    100F  GLY      3.0    27.9    +      -       -      +
    102F  ASP*     3.3    20.3    +      -       -      -
    111F  ARG*     3.6    51.4    +      -       +      -
    112F  GLY*     1.3    75.8    -      -       -      -
    114F  HIS*     1.4    64.1    +      -       -      +
    115F  GLN*     4.6    13.7    -      -       -      +
    126F  LEU*     5.3     4.3    -      -       -      -
    130F  LEU*     5.3     0.7    -      -       -      -
    160F  LEU*     3.5    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 114 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97F  ARG*     3.1    31.7    +      -       -      -
     98F  MET      3.5     8.1    -      -       -      -
     99F  TYR*     4.0    20.6    -      +       +      -
    113F  TYR*     1.4    75.7    -      -       -      +
    115F  GLN*     1.4    62.7    +      -       -      +
    116F  TYR*     3.7    25.3    -      +       -      -
    124F  ILE      4.5     0.2    -      -       -      +
    125F  ALA*     3.8     0.7    -      -       -      -
    126F  LEU*     3.0    45.2    +      -       +      +
    133F  TRP*     3.8    20.0    -      +       -      -
    147F  TRP*     4.4     1.6    -      +       -      -
    156F  LEU*     3.8    28.5    -      -       +      -
    160F  LEU*     4.7     4.7    -      -       +      -
      7H  PHE*     3.9    12.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 115 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97F  ARG*     3.5     3.9    -      -       -      +
     98F  MET*     3.1    61.5    +      -       +      +
    113F  TYR*     4.6    16.4    -      -       -      +
    114F  HIS*     1.4    78.5    +      -       -      +
    116F  TYR*     1.3    65.3    +      -       -      +
    124F  ILE      3.4     4.9    -      -       -      +
    125F  ALA*     3.7    26.7    -      -       +      +
    126F  LEU      4.8     5.5    +      -       -      -
     58G  LYS      5.4     4.0    -      -       -      +
     60G  TRP*     3.4    26.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 116 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74F  HIS*     4.1    17.1    +      +       -      -
     77F  ASP*     4.8     0.7    +      -       -      -
     95F  VAL*     4.2    10.1    -      -       +      -
     96F  GLN      3.3    12.8    -      -       -      -
     97F  ARG*     3.1    43.0    +      -       +      -
    114F  HIS*     3.7    18.2    -      +       -      -
    115F  GLN*     1.3    81.1    -      -       -      +
    117F  ALA*     1.3    53.9    +      -       -      +
    122F  ASP*     3.8     1.0    -      -       -      -
    123F  TYR*     2.8    40.6    +      -       +      +
    124F  ILE*     2.8    33.7    +      -       +      +
    133F  TRP*     6.3     0.2    -      +       -      -
    147F  TRP*     3.6    25.0    -      +       -      -
     60G  TRP*     3.8    10.3    -      -       -      -
      7H  PHE*     4.2    10.4    +      -       -      -
      9H  LEU*     4.1    27.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 117 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95F  VAL*     3.4    11.2    -      -       -      +
     96F  GLN*     2.9    43.6    +      -       +      +
    116F  TYR*     1.3    74.1    -      -       -      +
    118F  TYR*     1.3    59.0    +      -       -      +
    120F  GLY      4.6     0.7    -      -       -      -
    121F  LYS      3.3    20.4    -      -       -      +
    123F  TYR*     4.1     3.4    -      -       -      +
     60G  TRP*     3.5    37.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 118 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78F  LEU*     4.8     5.7    +      -       +      -
     81F  LEU*     3.4    39.7    -      -       +      +
     82F  ARG*     4.1     4.7    +      -       -      +
     85F  TYR*     3.6    40.4    -      +       -      +
     87F  GLN*     2.8    27.3    +      -       -      -
     93F  HIS*     3.4    26.0    -      -       +      +
     94F  THR      3.3    17.3    -      -       -      -
     95F  VAL*     4.0     8.7    -      -       +      -
    117F  ALA*     1.3    73.2    -      -       -      +
    119F  ASP*     1.3    86.2    +      -       +      +
    120F  GLY      3.2     2.6    +      -       -      -
    121F  LYS*     3.1    26.2    +      -       -      +
    123F  TYR*     4.2    17.3    -      -       +      +
----------------------------------------------------------
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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