Contacts of the strand formed by residues 451 - 456 (chain A) in PDB entry 2H3W


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 451 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  GLN*     4.3     5.4    -      -       -      +
    437A  LEU*     5.1     1.1    -      -       +      -
    438A  GLN*     2.9    26.1    +      -       -      +
    449A  CYS      2.9    15.1    +      -       -      -
    450A  ALA*     1.3    72.9    +      -       -      +
    452A  TYR*     1.3    67.0    +      -       -      +
    469A  ARG*     3.5    31.6    -      -       -      +
    470A  SER*     3.4    28.9    -      -       -      +
    471A  ALA*     4.0     7.4    -      -       -      +
    549A  PHE*     3.7     4.0    -      -       -      -
    551A  LEU*     3.4    27.4    -      -       +      +
    553A  THR*     4.7     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 452 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  TRP*     4.5     4.4    -      +       -      -
    451A  THR*     1.3    75.3    -      -       -      +
    453A  GLU*     1.3    55.9    +      -       -      +
    454A  SER*     3.6    18.2    -      -       -      -
    465A  THR*     4.0     0.2    +      -       -      -
    466A  ASP      4.1     4.3    +      -       -      -
    467A  THR*     2.9    35.2    -      -       +      -
    468A  ILE      3.9     1.8    -      -       -      -
    518A  ARG*     2.8    24.4    +      -       -      -
    549A  PHE*     3.4    41.1    -      +       +      -
    551A  LEU      2.8    11.9    +      -       -      +
    552A  SER*     4.2     6.7    -      -       -      +
    553A  THR*     2.7    45.0    +      -       -      +
   1602A  HC5      2.7    49.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 453 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430A  ASP*     2.5    31.5    -      -       -      +
    434A  GLN*     3.1    13.6    -      -       -      +
    452A  TYR*     1.3    79.5    -      -       -      +
    454A  SER*     1.3    74.2    +      -       -      +
    455A  ALA      3.5     0.3    +      -       -      -
    466A  ASP      3.9     1.6    -      -       -      +
    467A  THR*     3.9     0.5    -      -       -      -
    468A  ILE*     3.0    51.5    +      -       +      +
    470A  SER*     4.0     5.6    -      -       -      +
    503A  HIS*     2.9    37.7    +      -       -      -
    553A  THR*     3.4    13.5    -      -       -      +
    554A  ALA*     4.9     3.6    -      -       -      -
    555A  GLN*     4.6     5.1    +      -       -      +
    578A  TYR*     3.3     4.5    +      -       -      -
   1601A  COA      4.3     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 454 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452A  TYR*     3.6     9.8    -      -       -      -
    453A  GLU*     1.3    84.5    -      -       -      +
    455A  ALA*     1.3    59.1    +      -       -      +
    465A  THR*     5.1     1.3    -      -       -      -
    466A  ASP      4.1     1.6    -      -       -      -
    468A  ILE*     4.3     1.9    -      -       -      +
    553A  THR      3.2     8.0    +      -       -      -
    554A  ALA*     3.2    12.0    -      -       -      +
    555A  GLN      5.3     0.3    +      -       -      -
   1601A  COA      3.7    40.9    -      -       -      +
   1602A  HC5      2.8    43.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 455 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  SER*     1.3    74.1    -      -       -      +
    456A  SER*     1.3    59.4    +      -       -      +
    457A  LEU*     3.3     4.2    -      -       +      +
    465A  THR*     3.0     9.0    -      -       -      -
    466A  ASP      2.8    40.6    +      -       -      +
    468A  ILE*     3.5    31.9    -      -       +      -
    510A  ALA*     3.8    15.7    -      -       +      -
    511A  ILE*     4.6     4.3    -      -       +      -
   1601A  COA      3.5     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  LEU*     3.9    17.4    -      -       -      +
    349A  PRO*     5.3     3.6    -      -       -      -
    455A  ALA*     1.3    71.2    -      -       -      +
    457A  LEU*     1.3    63.0    +      -       -      +
    458A  ARG*     3.2    34.4    +      -       -      +
    459A  MET      5.2     0.3    +      -       -      -
    464A  ARG      3.6     5.9    +      -       -      -
    511A  ILE*     3.5    24.8    -      -       -      +
   1601A  COA      2.8    40.4    +      -       -      -
----------------------------------------------------------
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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