Contacts of the strand formed by residues 59 - 66 (chain A) in PDB entry 2DVI


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 GLU 59 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  SER*     4.7     3.1    +      -       -      -
     48A  TYR*     4.3     6.5    -      -       -      +
     53A  TRP*     5.3     2.2    -      -       -      +
     57A  SER      3.3     8.4    +      -       -      +
     58A  LEU*     1.3    80.6    -      -       -      +
     60A  ILE*     1.3    65.8    +      -       -      +
     61A  ASP*     3.7     2.6    -      -       -      +
    101A  HIS*     3.8    17.0    -      -       +      -
    108A  GLU*     3.6    24.5    -      -       +      +
    109A  VAL      4.7     0.4    -      -       -      +
    110A  ASP*     3.2    26.8    -      -       -      +
    504A  CTP      4.3     3.5    +      -       -      +
    602A   MG      2.8    38.4    -      -       -      -
     34B    C      3.9     9.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  GLY*     3.9    21.3    -      -       -      +
     27A  ALA*     4.3     5.6    -      -       +      -
     28A  GLU*     4.3    13.0    -      -       -      +
     31A  LEU*     4.9     2.7    -      -       +      -
     44A  PHE*     3.7    31.6    -      -       +      -
     48A  TYR*     3.7    35.4    -      -       +      -
     58A  LEU*     4.4     1.3    -      -       +      -
     59A  GLU*     1.3    72.8    -      -       -      +
     61A  ASP*     1.3    62.1    +      -       -      +
     62A  VAL*     3.9     9.9    -      -       +      -
    107A  VAL*     4.2    21.8    -      -       +      -
    108A  GLU      3.1    10.0    +      -       -      +
    109A  VAL*     3.5    12.7    -      -       +      +
    110A  ASP*     2.8    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  PHE*     3.6     7.3    -      -       -      -
     45A  VAL*     3.2    45.8    +      -       +      +
     46A  GLY*     3.8     6.9    -      -       -      -
     47A  SER      4.5     0.3    +      -       -      -
     48A  TYR*     4.9     1.3    +      -       -      +
     59A  GLU*     3.7     2.3    -      -       -      +
     60A  ILE*     1.3    72.9    -      -       -      +
     62A  VAL*     1.3    63.1    +      -       -      +
     63A  PHE*     4.1     2.7    -      -       +      -
    110A  ASP*     3.7    14.1    -      -       -      +
    504A  CTP      3.0    21.7    +      -       -      -
    602A   MG      2.9    22.3    -      -       -      -
     34B    C      2.8    38.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     4.3    10.3    -      -       +      -
     35A  LEU*     3.8    26.0    -      -       +      -
     42A  TYR*     4.0    19.7    -      -       +      -
     43A  VAL      3.8     4.5    -      -       -      +
     44A  PHE*     3.7    27.1    -      -       +      +
     60A  ILE*     3.9     9.4    -      -       +      -
     61A  ASP*     1.3    75.5    -      -       -      +
     63A  PHE*     1.3    67.8    +      -       -      +
     64A  LEU*     4.8     5.2    -      -       +      -
    109A  VAL*     4.3    13.9    -      -       +      -
    110A  ASP      3.0     8.4    +      -       -      +
    111A  VAL*     3.6    10.4    -      -       +      +
    112A  VAL      2.8    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  TYR*     3.0     7.3    -      -       -      +
     43A  VAL*     2.9    56.0    +      -       +      +
     45A  VAL*     3.8    20.6    -      -       +      -
     61A  ASP*     4.6     1.1    -      -       +      -
     62A  VAL*     1.3    81.7    -      -       -      +
     64A  LEU*     1.3    62.4    +      -       -      +
     65A  LEU*     3.7     5.4    +      -       +      +
    112A  VAL*     3.2    23.3    -      -       +      -
    114A  CYS*     3.5    23.1    -      -       +      -
    127A  VAL*     3.5    32.5    -      -       +      -
    130A  THR*     3.7    11.4    -      -       +      -
    131A  PRO*     4.0     8.3    -      -       +      -
     34B    C      3.2    44.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     4.3     6.7    -      -       +      -
     40A  VAL*     3.8    25.8    -      -       +      -
     41A  GLU      3.6     4.0    -      -       -      +
     42A  TYR*     4.2     9.4    -      -       +      -
     62A  VAL*     4.8     3.6    -      -       +      -
     63A  PHE*     1.3    75.2    -      -       -      +
     65A  LEU*     1.3    61.2    +      -       -      +
     66A  PHE*     3.4    17.0    -      -       +      -
     79A  GLY*     4.0    21.1    -      -       -      +
     82A  ILE*     3.9    31.9    -      -       +      -
    111A  VAL*     3.7    29.4    -      -       +      -
    112A  VAL      2.7    16.4    +      -       -      +
    113A  PRO*     4.1     4.5    -      -       +      -
    114A  CYS*     3.0    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  GLU*     3.0    54.0    +      -       +      +
     42A  TYR      4.4     8.7    -      -       -      +
     43A  VAL*     3.8    38.1    -      -       +      -
     63A  PHE      3.9     2.7    -      -       -      +
     64A  LEU*     1.3    74.9    -      -       -      +
     66A  PHE*     1.3    64.2    +      -       -      +
     67A  PRO*     4.6     1.7    -      -       -      +
    114A  CYS*     3.6    23.8    -      -       -      -
    116A  LYS*     3.6    27.4    -      -       +      -
    131A  PRO*     4.8     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LEU*     3.4    34.8    -      -       +      -
     65A  LEU*     1.3    76.4    -      -       -      +
     67A  PRO*     1.3    72.7    -      -       +      +
     70A  PHE*     3.6    28.7    -      +       +      -
     75A  LEU*     3.4    33.7    -      -       +      -
     78A  ARG*     3.7    36.6    -      -       +      -
     79A  GLY*     4.1     9.4    -      -       -      -
     82A  ILE*     4.6     9.6    -      -       +      -
    113A  PRO*     4.0    14.1    -      -       +      -
    114A  CYS      3.0    12.6    +      -       -      +
    115A  TYR*     3.4     3.6    -      -       +      -
    116A  LYS*     2.9    27.5    +      -       -      +
----------------------------------------------------------
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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