Contacts of the strand formed by residues 114 - 119 (chain D) in PDB entry 6VSU


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 LEU 114 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  THR*     3.4    20.0    -      -       +      -
     67D  LEU*     3.8    31.6    -      -       +      -
     93D  ILE*     4.5    12.8    -      -       +      -
     94D  TRP*     4.0    25.6    -      -       +      -
    108D  LEU*     3.7    39.1    -      -       +      +
    109D  LYS      5.4     0.3    -      -       -      -
    110D  ASP      3.2     2.8    +      -       -      +
    111D  PRO*     3.2    23.3    +      -       -      +
    113D  VAL*     1.3    80.4    -      -       -      +
    115D  THR*     1.3    75.4    +      -       -      +
    116D  ASP*     6.1     0.2    -      -       +      -
    333D  VAL*     5.4     2.7    -      -       +      -
    334D  ARG*     5.8     1.1    -      -       +      -
    337D  ALA*     4.1     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 115 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51D  LYS*     3.9    33.0    -      -       +      +
     54D  LEU*     4.9     2.9    -      -       +      -
     55D  VAL*     4.2     6.5    -      -       +      -
     65D  THR      2.9     7.2    +      -       -      +
     66D  SER*     2.8    29.7    +      -       -      -
     67D  LEU*     2.9    26.5    +      -       -      +
    111D  PRO*     3.4    33.5    +      -       +      +
    114D  LEU*     1.3    78.3    -      -       -      +
    116D  ASP*     1.3    63.7    +      -       -      +
    152D  LEU*     4.0     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 116 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ASP*     4.0    16.1    -      -       -      +
     51D  LYS*     3.2    24.2    +      -       -      +
     67D  LEU*     3.4    22.6    -      -       +      +
     90D  ARG*     2.7    43.4    +      -       -      +
     94D  TRP*     5.8     1.7    +      -       -      -
    115D  THR*     1.3    78.7    -      -       -      +
    117D  VAL*     1.3    62.7    +      -       -      +
    118D  GLY*     2.7    30.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 117 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44D  ILE*     3.8    12.0    -      -       +      +
     47D  ARG*     2.5    40.4    +      -       +      +
     48D  ALA*     3.7    38.8    -      -       +      +
     51D  LYS*     4.1     8.1    -      -       +      -
     66D  SER*     3.5    17.9    -      -       -      +
     67D  LEU      2.9    21.1    +      -       -      +
     68D  LEU*     3.8    23.3    -      -       +      -
    116D  ASP*     1.3    72.8    -      -       -      +
    118D  GLY*     1.3    50.5    +      -       -      +
    146D  VAL*     3.9    20.4    -      -       +      -
    152D  LEU*     4.9     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 118 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  GLU*     4.1     7.9    -      -       -      -
     47D  ARG*     3.1     8.7    -      -       -      -
     68D  LEU*     3.6     8.5    -      -       -      +
     69D  GLY      2.8    26.9    +      -       -      -
     90D  ARG*     3.3    13.1    +      -       -      -
    116D  ASP*     2.7    17.5    +      -       -      -
    117D  VAL*     1.3    80.8    -      -       -      +
    119D  ASP*     1.3    53.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  GLU*     3.8    13.3    +      -       -      +
     44D  ILE*     3.7    10.3    -      -       -      +
     47D  ARG*     3.2    11.2    +      -       -      +
     69D  GLY*     2.9    24.0    -      -       -      +
     71D  PRO*     4.2    13.1    -      -       +      +
     86D  PRO*     3.6    10.9    -      -       -      +
     87D  PRO*     4.0    14.2    -      -       -      +
     90D  ARG*     2.7    32.6    +      -       -      -
    118D  GLY*     1.3    71.0    -      -       -      -
    120D  VAL*     1.3    68.4    +      -       -      +
    121D  PRO*     3.3     9.9    -      -       +      +
----------------------------------------------------------
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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