Contacts of the strand formed by residues 122 - 126 (chain A) in PDB entry 2DH3


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 ALA 122 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  GLY*     1.3    73.4    -      -       -      -
    123A  LEU*     1.3    62.8    -      -       -      +
    154A  LYS      4.5     5.1    +      -       -      -
    155A  VAL*     3.6    19.5    -      -       +      +
    156A  LYS*     3.4    21.1    +      -       -      -
    157A  GLY      3.9     3.5    +      -       -      -
    357A  PHE*     4.0    19.7    -      -       +      -
    363A  PRO*     3.4    26.6    -      -       +      +
    365A  PHE*     4.0    13.5    -      -       +      -
    422A  PHE*     5.4     0.4    -      -       +      -
    426A  SER*     4.8     4.6    +      -       -      +
    429A  ARG*     5.1     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  TRP*     4.0    16.8    -      -       +      -
    118A  TRP*     5.1     2.7    -      -       +      -
    121A  GLY      5.3     1.1    -      -       -      +
    122A  ALA*     1.3    78.7    -      -       -      +
    124A  TYR*     1.3    59.5    -      -       -      +
    155A  VAL*     4.9     0.4    -      -       -      -
    156A  LYS*     6.0     0.4    -      -       +      -
    157A  GLY*     3.3    29.4    -      -       -      +
    159A  VAL*     4.5     6.7    -      -       +      -
    204A  ILE*     4.1    10.1    -      -       +      -
    274A  LEU*     4.4    11.2    -      -       +      -
    276A  ILE*     4.3    21.8    -      -       +      -
    298A  LEU*     4.8     4.7    -      -       +      -
    362A  THR*     3.6    25.6    -      -       +      -
    363A  PRO      2.9    10.6    +      -       -      +
    364A  VAL*     3.5    22.4    -      -       +      -
    365A  PHE*     2.9    32.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  ALA      4.2     0.2    +      -       -      -
    123A  LEU*     1.3    72.3    -      -       -      +
    125A  ARG*     1.3    56.8    +      -       -      +
    126A  ILE*     3.7    26.7    +      -       +      -
    132A  PHE*     3.8    12.6    -      +       -      -
    149A  TYR*     4.3     1.4    -      -       -      -
    150A  LEU*     3.5    31.2    -      -       +      -
    153A  LEU*     3.8    10.5    -      -       +      -
    155A  VAL*     3.9    31.4    -      -       +      -
    157A  GLY      3.1     7.8    +      -       -      +
    158A  LEU*     3.2     7.1    -      -       +      +
    159A  VAL*     2.6    32.6    +      -       -      -
    365A  PHE*     3.6     8.3    -      +       +      -
    366A  SER      4.6     3.8    -      -       -      -
    367A  TYR*     3.5    32.3    -      -       +      +
    368A  GLY      3.9     0.7    +      -       -      -
    370A  GLU*     2.5    41.8    +      -       +      -
    388A  MET*     4.2     1.4    -      -       -      +
    422A  PHE*     5.4     5.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  TYR*     1.3    72.0    -      -       -      +
    126A  ILE*     1.3    61.1    +      -       -      +
    127A  GLY      3.8     2.5    -      -       -      +
    159A  VAL*     3.7    22.2    -      -       +      +
    245A  GLN*     4.0    15.8    +      -       -      +
    300A  THR*     4.4     7.3    -      -       -      +
    333A  SER*     4.5     1.0    -      -       -      -
    335A  SER*     3.1    27.1    +      -       -      +
    336A  GLN*     3.2    26.8    +      -       -      +
    337A  ALA*     3.9     5.6    -      -       -      +
    338A  ARG      3.8    11.1    +      -       -      -
    364A  VAL*     3.2    43.3    +      -       +      +
    365A  PHE*     2.7    17.7    +      -       -      +
    366A  SER*     3.1    33.1    +      -       -      +
    367A  TYR*     2.8    35.0    +      -       -      +
    369A  ASP*     5.3     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  TYR*     3.7    32.8    -      -       +      +
    125A  ARG*     1.3    75.5    -      -       -      +
    127A  GLY*     1.3    61.4    +      -       -      +
    128A  ASP      4.4     8.7    -      -       -      +
    129A  LEU*     4.6    14.6    +      -       +      +
    132A  PHE*     4.0    36.6    -      -       +      -
    143A  LEU*     4.3    18.6    -      -       +      -
    150A  LEU*     4.5     2.2    -      -       +      -
    158A  LEU*     4.1    29.4    -      -       +      -
    159A  VAL      2.8    20.4    +      -       -      +
    160A  LEU*     3.9     5.8    -      -       +      +
    161A  GLY      3.5    15.2    +      -       -      -
    367A  TYR*     3.9     7.4    -      -       +      -
----------------------------------------------------------
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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