Contacts of the strand formed by residues 407 - 414 (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 LEU 407 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ILE*     3.8    31.0    -      -       +      -
    309A  LEU*     3.6    20.0    -      -       +      -
    310A  HIS*     3.9    10.8    -      -       +      +
    403A  MET      3.2    10.7    +      -       -      +
    404A  ILE*     3.0    17.4    +      -       -      +
    405A  GLN      4.5     0.2    -      -       -      +
    406A  ASP*     1.3    76.9    -      -       -      +
    408A  ASP*     1.3    62.6    +      -       -      +
    409A  ILE*     3.5    38.4    +      -       +      +
    567A  GLY*     4.6     3.4    -      -       -      -
    568A  PRO*     4.6     0.2    -      -       +      -
    590A  SER*     4.3    13.7    -      -       -      -
    591A  ALA      3.7     9.0    -      -       -      +
    592A  TYR*     4.3    12.1    -      -       +      -
    593A  ASN*     3.9     6.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 408 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406A  ASP      3.7     0.2    +      -       -      -
    407A  LEU*     1.3    71.3    -      -       -      +
    409A  ILE*     1.3    67.6    +      -       -      +
    590A  SER*     3.2     5.2    -      -       -      -
    591A  ALA*     2.7    49.8    +      -       +      +
    592A  TYR      4.8     0.6    -      -       -      -
    593A  ASN*     3.4    25.1    -      -       -      +
    598A  THR      4.7     1.0    -      -       -      +
    599A  ASN*     3.7    13.8    +      -       -      -
    600A  ALA*     2.8    37.1    +      -       -      +
    601A  ALA*     4.8     1.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 409 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  ASN*     3.5    27.6    +      -       +      +
    305A  ALA*     4.3     8.7    -      -       +      -
    306A  GLY*     4.3    23.1    -      -       -      +
    309A  LEU*     4.3    12.3    -      -       +      -
    310A  HIS*     4.7     1.6    -      -       +      -
    407A  LEU*     3.5    37.5    +      -       +      +
    408A  ASP*     1.3    82.8    +      -       -      +
    410A  MET*     1.3    67.5    +      -       -      +
    411A  MET*     4.0    28.0    -      -       +      -
    565A  PHE*     5.6     5.4    -      -       +      -
    588A  SER*     5.9     0.7    -      -       -      -
    589A  VAL      3.4     7.6    -      -       -      +
    590A  SER*     4.6     7.6    -      -       -      -
    600A  ALA*     4.0     1.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  ASP      5.6     3.4    -      -       -      +
    302A  ASN*     3.5    17.5    -      -       -      +
    409A  ILE*     1.3    77.2    -      -       -      +
    411A  MET*     1.3    77.0    +      -       -      +
    412A  LEU*     3.8     2.6    +      -       +      -
    588A  SER      3.8     0.2    -      -       -      -
    589A  VAL*     2.8    39.7    +      -       +      +
    600A  ALA*     3.6    23.1    -      -       +      +
    601A  ALA*     3.3    37.7    -      -       +      +
    604A  ALA*     3.7    17.7    -      -       +      -
    605A  HIS*     5.0     8.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ILE*     3.7    15.7    -      -       +      -
    301A  ARG*     3.6    46.6    -      -       +      +
    302A  ASN*     2.7    26.8    +      -       -      +
    305A  ALA*     3.7    11.2    -      -       +      -
    409A  ILE*     4.0    10.8    -      -       +      -
    410A  MET*     1.3    81.4    -      -       -      +
    412A  LEU*     1.3    60.3    +      -       -      +
    413A  THR      4.2     1.4    +      -       -      -
    563A  VAL*     3.6    23.8    -      -       +      -
    565A  PHE*     3.6    24.5    -      -       +      -
    587A  PHE      3.7     3.8    -      -       -      +
    588A  SER*     3.7    21.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  ARG*     5.8     0.7    -      -       -      -
    410A  MET*     3.8     3.4    +      -       +      +
    411A  MET*     1.3    72.8    -      -       -      +
    413A  THR*     1.3    71.9    +      -       -      +
    414A  PHE*     3.5     9.9    +      -       +      +
    586A  ASN*     4.0     0.2    -      -       -      -
    587A  PHE*     2.8    69.3    +      -       +      +
    589A  VAL*     5.7     0.7    -      -       +      -
    604A  ALA*     3.6    43.3    -      -       +      +
    605A  HIS*     5.9     3.6    -      -       +      -
    607A  LEU*     4.8     4.3    -      -       +      -
    608A  GLU*     4.2    35.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  ARG*     4.1    22.7    +      -       -      -
    411A  MET      4.2     1.4    +      -       -      -
    412A  LEU*     1.3    80.0    -      -       -      +
    414A  PHE*     1.3    61.7    +      -       -      +
    415A  HIS*     3.1    23.5    +      -       +      +
    584A  HIS*     4.7     9.2    -      -       +      -
    585A  ILE      3.9     2.7    -      -       -      -
    586A  ASN*     4.2    20.9    +      -       -      +
    608A  GLU*     5.6     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    412A  LEU*     3.5     7.9    +      -       +      +
    413A  THR*     1.3    70.0    -      -       -      +
    415A  HIS*     1.3    57.8    +      -       -      +
    416A  HIS*     3.5    35.9    -      +       +      -
    417A  PHE*     3.2    55.6    -      +       -      -
    584A  HIS*     3.1     7.4    -      -       -      +
    585A  ILE*     2.9    44.5    +      -       +      +
    587A  PHE*     3.9    14.4    -      +       +      -
    608A  GLU*     3.4    36.1    -      -       +      -
    611A  LEU*     3.5    38.1    -      -       +      -
    612A  LEU*     3.9     5.4    -      -       +      -
----------------------------------------------------------
 Back to top of page


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