Contacts of the strand formed by residues 105 - 110 (chain D) 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 105 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  GLN*     3.9    12.0    +      -       -      +
      8D  SER      4.1     9.4    +      -       -      -
      9D  PRO*     2.8    33.4    +      -       +      +
     10D  GLN      3.7     6.1    -      -       -      +
     11D  PHE      4.8     0.4    -      -       -      +
     12D  LEU*     4.9     5.8    -      -       +      +
     22D  VAL*     3.9    34.5    -      -       +      +
     23D  TYR      4.9     0.7    +      -       -      -
     86D  GLY      3.7     0.9    -      -       -      +
     87D  LEU*     3.7     3.5    -      -       -      +
     88D  TYR*     3.0    38.7    +      -       +      +
    104D  GLY*     1.3    73.2    +      -       -      -
    106D  LYS*     1.3    67.6    +      -       -      +
    107D  LEU*     3.7     6.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 106 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  GLN      3.1    15.0    +      -       -      +
     11D  PHE*     3.6    30.7    -      -       +      +
     12D  LEU      3.2    24.2    +      -       -      +
     86D  GLY*     3.9    10.3    -      -       -      +
     87D  LEU*     4.1    17.5    -      -       +      +
    104D  GLY      4.2     0.2    -      -       -      -
    105D  THR*     1.3    71.0    -      -       -      +
    107D  LEU*     1.3    64.6    +      -       -      +
    108D  SER*     4.2    11.0    +      -       -      +
     42E  GLY*     6.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 107 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  LEU*     3.3    39.7    -      -       +      +
     14D  ILE*     4.1    12.6    -      -       +      -
     20D  LEU*     4.1    17.9    -      -       +      -
     22D  VAL*     6.0     2.2    -      -       +      -
     77D  ILE*     4.0    18.8    -      -       +      -
     84D  ASP      3.5    23.6    -      -       -      +
     85D  THR*     3.4     5.7    -      -       -      +
     86D  GLY*     3.1    35.7    +      -       -      +
     88D  TYR*     3.9    14.4    -      -       +      -
    105D  THR*     3.7     4.9    +      -       +      +
    106D  LYS*     1.3    75.8    -      -       -      +
    108D  SER*     1.3    63.0    +      -       -      +
    109D  VAL*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 108 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  LEU      3.0     9.4    +      -       -      +
     13D  SER*     3.5    16.6    +      -       -      -
     14D  ILE*     3.1    29.1    +      -       -      +
     85D  THR*     4.1     9.1    -      -       -      +
    106D  LYS*     5.1    11.3    +      -       -      -
    107D  LEU*     1.3    76.1    +      -       -      +
    109D  VAL*     1.3    64.7    +      -       -      +
    110D  LYS*     4.2     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 109 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14D  ILE*     3.5    19.3    -      -       +      -
     16D  GLU*     3.8    27.6    -      -       +      +
     80D  ALA*     4.1    13.5    -      -       +      +
     81D  GLN      4.0    29.6    -      -       -      +
     82D  PRO*     4.2    13.7    -      -       +      +
     84D  ASP*     4.5     0.9    -      -       +      -
     85D  THR*     3.2    22.8    +      -       -      +
    107D  LEU*     3.8    24.5    -      -       +      -
    108D  SER*     1.3    76.2    -      -       -      +
    110D  LYS*     1.3    64.2    +      -       -      +
    111D  PRO*     4.3     2.6    -      -       -      +
    160D  VAL*     6.0     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 110 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13D  SER*     3.6    22.2    +      -       -      +
     14D  ILE      2.9    18.0    +      -       -      +
     15D  GLN*     3.5    23.4    +      -       -      +
     16D  GLU*     2.7    31.8    +      -       -      +
     82D  PRO*     5.4     0.9    -      -       -      -
    108D  SER*     5.2     6.1    -      -       -      +
    109D  VAL*     1.3    75.4    -      -       -      +
    111D  PRO*     1.3    71.1    -      -       +      +
    141D  SER*     2.8    36.4    +      -       -      +
    142D  GLN*     5.4     0.6    +      -       -      -
    158D  LYS*     3.8    18.1    -      -       -      +
      6I  GLU*     3.3    32.3    +      -       -      -
----------------------------------------------------------
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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