Contacts of the strand formed by residues 298 - 305 (chain A) in PDB entry 3HO5


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 LYS 298 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  PHE      3.9     0.2    -      -       -      -
    290A  HIS*     3.0    34.3    +      -       +      +
    293A  TYR*     3.4     9.1    -      -       -      -
    296A  ASN*     2.9    37.1    +      -       -      +
    297A  GLY*     1.3    72.8    -      -       -      +
    299A  LEU*     1.3    59.7    +      -       -      +
    300A  TYR*     4.2    10.0    -      -       +      +
    323A  GLU*     2.7    38.5    +      -       -      +
    324A  TYR      3.5     3.6    -      -       -      +
    325A  THR*     2.8    28.4    +      -       -      +
    338A  THR      5.8     0.2    +      -       -      -
    340A  ARG*     4.1     2.2    -      -       -      +
    617A  CYS*     3.1    28.7    +      -       -      +
    618A  THR      3.8     1.1    -      -       -      -
    619A  PRO*     3.6    28.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  TYR*     3.4    44.0    -      -       +      +
    266A  LEU*     4.7     6.3    -      -       +      -
    287A  LEU*     4.1    18.8    -      -       +      -
    288A  ALA      3.7     5.2    -      -       -      -
    289A  PHE*     4.4     9.4    -      -       +      +
    293A  TYR*     4.2     1.1    -      -       +      -
    297A  GLY      4.0     4.0    -      -       -      +
    298A  LYS*     1.3    72.0    -      -       -      +
    300A  TYR*     1.3    77.5    +      -       -      +
    301A  VAL*     4.6     7.0    -      -       +      -
    323A  GLU*     3.4     4.2    -      -       -      +
    324A  TYR*     2.8    55.4    +      -       +      +
    325A  THR*     3.9     4.9    -      -       -      +
    326A  VAL      3.9    12.8    -      -       -      +
    334A  VAL*     3.8    12.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  LEU*     3.3     5.4    -      -       -      +
    288A  ALA*     2.8    50.5    +      -       +      +
    290A  HIS*     3.9    14.9    -      +       -      -
    298A  LYS*     4.2    11.5    -      -       +      +
    299A  LEU*     1.3    81.7    -      -       -      +
    301A  VAL*     1.3    62.7    +      -       -      +
    321A  VAL*     5.3     2.9    -      -       +      -
    322A  VAL      3.4     4.7    -      -       -      +
    323A  GLU*     2.8    45.1    +      -       +      -
    342A  PHE*     3.7    22.4    -      +       -      -
    357A  LEU*     3.4    18.2    -      -       +      +
    359A  PHE*     3.6    29.6    -      +       -      -
    365A  LEU*     4.4    13.7    -      -       +      -
    397A  VAL*     3.5    25.2    -      -       +      +
    619A  PRO*     4.0     4.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  LEU*     4.7    14.6    -      -       +      -
    268A  ILE*     5.2     2.0    -      -       +      -
    284A  LEU*     3.4    31.0    -      -       +      -
    286A  SER      3.4     4.9    -      -       -      +
    287A  LEU*     4.1    17.3    -      -       +      -
    299A  LEU*     4.6     9.4    -      -       +      -
    300A  TYR*     1.3    79.0    -      -       -      +
    302A  SER*     1.3    61.9    +      -       -      +
    303A  TYR*     3.8    21.2    +      -       +      -
    320A  ARG      3.9     0.3    -      -       -      +
    321A  VAL*     3.3     3.1    -      -       -      +
    322A  VAL*     2.8    35.1    +      -       -      +
    324A  TYR*     4.1    24.7    -      -       +      -
    357A  LEU*     3.8     2.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  LEU*     4.0     2.3    -      -       -      +
    285A  LEU*     3.0    23.1    +      -       -      +
    286A  SER*     2.9    23.9    +      -       -      +
    301A  VAL*     1.3    72.6    -      -       -      +
    303A  TYR*     1.3    61.8    +      -       -      +
    319A  LEU*     4.5     7.2    -      -       -      -
    320A  ARG      3.2    11.4    -      -       -      -
    321A  VAL*     4.1     6.1    -      -       -      -
    355A  GLY*     2.6    32.4    +      -       -      -
    357A  LEU*     3.7    15.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 303 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  ILE*     4.1    20.9    -      -       +      +
    271A  LEU*     3.9    29.0    -      -       +      +
    272A  VAL*     3.9    14.8    -      -       +      -
    283A  GLY      3.9    10.8    -      -       -      +
    284A  LEU*     4.1    15.3    -      -       +      -
    285A  LEU*     4.2     6.9    -      -       -      +
    301A  VAL*     3.8    20.6    -      -       +      -
    302A  SER*     1.3    73.7    -      -       -      +
    304A  THR*     1.3    70.9    +      -       -      +
    305A  THR*     3.8    22.2    -      -       +      -
    319A  LEU*     3.6     1.7    -      -       -      +
    320A  ARG*     2.7    69.6    +      -       +      +
    322A  VAL*     3.6    27.6    -      -       +      +
    324A  TYR*     4.6     1.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  VAL*     3.2    11.3    -      -       -      +
    273A  GLN*     2.9    24.4    +      -       +      +
    282A  ARG*     2.9    41.6    +      -       +      +
    283A  GLY      3.2     7.4    +      -       -      -
    285A  LEU*     4.0     8.0    -      -       -      +
    303A  TYR*     1.3    75.6    +      -       -      +
    305A  THR*     1.3    62.9    +      -       -      +
    317A  HIS*     3.1    35.6    +      -       +      +
    318A  ILE      3.8     3.6    -      -       -      -
    319A  LEU*     4.6     4.0    -      -       -      +
    353A  LEU*     3.8    17.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  LEU*     2.9    23.7    +      -       -      +
    273A  GLN*     4.1     4.0    -      -       -      +
    303A  TYR*     3.8     8.1    -      -       -      -
    304A  THR*     1.3    74.8    -      -       -      +
    306A  ASN*     1.3    85.2    +      -       -      +
    317A  HIS*     3.4     1.8    -      -       -      +
    318A  ILE*     3.1    49.9    +      -       +      +
    320A  ARG*     3.5    44.9    +      -       +      +
----------------------------------------------------------
 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