Contacts of the strand formed by residues 31 - 37 (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 THR 31 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27F  TYR*     3.3     4.6    -      -       -      -
     28F  VAL*     3.0    36.8    +      -       -      +
     29F  ASP      3.5     0.6    -      -       -      -
     30F  ASP*     1.3    78.4    +      -       -      +
     32F  GLN*     1.3    73.2    +      -       -      +
     33F  PHE*     3.8     2.3    +      -       -      +
     49F  ALA*     4.7     4.3    -      -       +      -
     51F  TRP*     4.4    15.0    -      -       +      +
    178F  THR*     4.7    11.1    -      -       +      +
    179F  LEU*     4.0    20.0    -      -       +      +
    181F  ARG*     5.3     2.6    +      -       -      -
    209F  TYR*     3.1    22.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 32 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25F  VAL*     3.5    18.9    -      -       +      +
     26F  GLY      3.5    14.1    -      -       -      +
     27F  TYR*     3.6    33.6    +      -       +      +
     30F  ASP      4.2     0.8    +      -       -      -
     31F  THR*     1.3    78.1    -      -       -      +
     33F  PHE*     1.3    62.5    +      -       -      +
     34F  VAL      3.1    20.6    +      -       -      +
     35F  ARG*     4.0     0.4    -      -       -      +
     48F  ARG*     3.6    31.3    +      -       +      +
     49F  ALA*     3.6     8.3    -      -       -      +
     52G  SER*     5.7     2.1    -      -       -      -
     53G  ASP*     2.9    36.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 33 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5F  MET*     4.5     4.3    -      -       +      -
      7F  TYR*     3.6    24.7    -      +       -      -
     26F  GLY*     3.0    31.0    +      -       -      -
     27F  TYR      3.7    22.4    -      -       -      -
     28F  VAL*     4.0    13.9    -      -       +      -
     31F  THR      4.6     0.2    -      -       -      +
     32F  GLN*     1.3    74.2    -      -       -      +
     34F  VAL*     1.3    77.3    +      -       +      +
     48F  ARG*     3.0    20.8    +      -       -      -
     49F  ALA*     4.1    10.3    -      -       +      +
     51F  TRP*     3.7    24.5    -      +       +      -
     52F  ILE*     3.3    36.3    -      -       +      +
     59F  TYR*     4.1     1.6    -      -       -      -
    171F  TYR*     3.8    33.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 34 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7F  TYR*     3.9    19.3    -      -       +      +
     25F  VAL*     3.6     1.4    -      -       -      -
     26F  GLY*     3.5    32.5    +      -       -      +
     32F  GLN*     3.1    19.6    +      -       -      -
     33F  PHE*     1.3    99.8    -      -       +      +
     35F  ARG*     1.3    60.6    +      -       -      +
     45F  MET*     4.0    21.1    -      -       +      -
     46F  GLU      3.2    13.2    -      -       -      +
     48F  ARG*     4.1     3.9    -      -       -      +
     52F  ILE*     4.7     0.2    -      -       +      -
     59F  TYR*     4.4     8.1    -      -       +      +
     60F  TRP*     4.0    22.4    -      -       +      -
     63F  GLU*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 35 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24F  ALA      3.2    11.4    -      -       -      +
     25F  VAL*     4.3     3.4    -      -       +      -
     32F  GLN*     4.0     2.2    -      -       -      +
     34F  VAL*     1.3    76.2    -      -       -      +
     36F  PHE*     1.3    65.7    +      -       -      +
     37F  ASP*     5.4     7.4    -      -       -      +
     44F  ARG      4.0     1.2    -      -       -      +
     45F  MET*     3.3    10.5    -      -       -      +
     46F  GLU*     2.8    69.0    +      -       +      +
     48F  ARG*     3.7    38.1    -      -       +      +
     53G  ASP*     3.0    38.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 36 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22F  PHE*     3.5    39.3    -      +       -      -
     23F  ILE*     3.2     8.0    -      -       -      +
     24F  ALA*     2.8    40.3    +      -       +      +
     35F  ARG*     1.3    77.9    -      -       -      +
     37F  ASP*     1.3    64.3    +      -       -      +
     38F  SER*     3.9    18.4    -      -       -      -
     43F  GLN*     3.9    43.1    -      -       -      -
     44F  ARG*     3.7    23.1    -      -       -      -
     45F  MET*     4.1    13.0    -      -       -      -
     64F  THR*     5.8     0.2    -      -       +      -
     67F  VAL*     3.9    25.4    -      -       +      -
     68F  LYS*     4.6    15.5    -      -       +      -
     71F  SER*     4.5     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 37 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21F  ARG*     3.1    36.9    +      -       -      -
     22F  PHE      3.5     3.0    -      -       -      +
     23F  ILE*     4.2    10.0    -      -       +      +
     35F  ARG*     5.4     9.8    -      -       -      +
     36F  PHE*     1.3    84.0    -      -       -      +
     38F  SER*     1.3    65.5    +      -       -      +
     39F  ASP*     2.9    17.7    +      -       -      +
     40F  ALA*     3.3    29.4    +      -       +      +
     43F  GLN*     4.0     6.4    +      -       -      -
     44F  ARG      5.3     0.8    +      -       -      -
----------------------------------------------------------
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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