Contacts of the strand formed by residues 109 - 114 (chain A) in PDB entry 4ZDV


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 109 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ILE*     4.4     3.8    -      -       +      -
     32A  PRO      3.0    14.3    +      -       -      +
     33A  VAL*     3.3     9.8    -      -       +      +
     34A  ILE      2.9    22.8    +      -       -      -
     83A  VAL*     4.1    11.9    -      -       +      -
     95A  ILE*     4.0    23.3    -      -       +      -
     98A  ILE*     4.1    15.7    -      -       +      +
     99A  TYR*     4.0    19.0    -      -       +      -
    102A  GLU*     3.8    40.2    -      -       +      +
    103A  LYS*     4.1     2.5    -      -       -      +
    107A  GLY      4.0     0.6    +      -       -      -
    108A  PHE*     1.3    71.9    -      -       -      +
    110A  TYR*     1.3    61.0    +      -       -      +
    111A  MET*     3.5    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PHE*     3.7     9.5    -      +       +      -
      8A  LYS*     3.5    39.0    -      -       +      +
     16A  ARG*     3.5     9.7    -      -       -      -
     34A  ILE*     3.6    31.6    -      -       +      -
     36A  GLU*     4.5     8.7    -      -       -      -
     82A  LEU      4.2     3.1    -      -       -      +
     83A  VAL*     4.2    14.7    -      -       -      +
     84A  ASN      4.8     2.8    +      -       -      -
    102A  GLU      5.4     1.4    +      -       -      -
    104A  ASP*     3.5    23.3    -      -       +      +
    106A  ASP*     2.6    31.7    +      -       -      -
    108A  PHE*     3.4    24.2    +      -       +      -
    109A  LEU*     1.3    75.2    -      -       -      +
    111A  MET*     1.3    65.0    +      -       -      +
    112A  VAL*     5.7     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  VAL*     3.6    22.2    -      -       +      -
     34A  ILE      2.8    12.2    +      -       -      +
     35A  ILE*     4.3     6.5    -      -       +      -
     36A  GLU*     3.2    25.0    +      -       -      +
     60A  MET*     3.5    30.7    -      -       +      -
     63A  LEU*     3.6    24.0    -      -       +      -
     81A  LEU*     3.8    29.6    -      -       +      -
     82A  LEU      3.3     9.2    -      -       -      +
     83A  VAL*     3.7    11.9    -      -       +      -
     88A  MET*     5.8     0.2    -      -       -      -
     95A  ILE*     4.1     1.8    -      -       +      -
    109A  LEU*     3.5    24.5    -      -       +      +
    110A  TYR*     1.3    79.6    -      -       -      +
    112A  VAL*     1.3    68.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  GLU*     3.2    17.7    -      -       +      +
     37A  ARG      5.2     0.4    -      -       -      +
     38A  TYR*     3.4    44.2    -      -       +      -
     81A  LEU*     3.6     4.6    -      -       -      -
     82A  LEU*     2.7    49.1    +      -       +      +
    110A  TYR*     5.7     2.5    -      -       +      -
    111A  MET*     1.3    80.1    -      -       -      +
    113A  TYR*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ILE*     4.0    13.9    -      -       +      -
     36A  GLU      3.0    23.7    +      -       -      -
     37A  ARG*     3.5    34.4    +      -       +      +
     38A  TYR*     2.8    25.7    +      -       -      +
     44A  LEU*     4.0    15.0    -      -       +      -
     45A  PRO      2.6    29.8    +      -       -      -
     46A  VAL*     3.5     2.6    -      -       -      -
     47A  LEU*     2.9    40.4    +      -       +      +
     67A  ILE*     4.9     1.1    -      -       +      -
     71A  LEU*     3.7    15.6    -      -       +      +
     79A  PHE*     3.5    30.1    -      +       +      -
     80A  PHE      3.1    12.3    -      -       -      +
     81A  LEU*     4.0     4.9    -      -       +      -
     82A  LEU*     5.7     0.2    -      -       -      -
    112A  VAL*     1.3    74.8    -      -       -      +
    114A  ALA*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  TYR*     3.8    24.5    -      -       +      -
     41A  GLU*     3.6    12.6    -      -       -      +
     44A  LEU*     3.5    13.6    -      -       -      +
     79A  PHE*     3.8     0.2    -      -       -      -
     80A  PHE*     2.9    31.2    +      -       -      +
     82A  LEU*     5.0     7.2    -      -       +      +
    113A  TYR*     1.3    77.3    -      -       -      +
    115A  SER*     1.3    62.2    +      -       -      +
    116A  GLN*     3.3    21.6    +      -       -      +
----------------------------------------------------------
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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