Contacts of the strand formed by residues 299 - 308 (chain A) in PDB entry 1X8B


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 PHE 299 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ARG*     4.7     5.2    -      -       -      -
    295A  TYR*     3.2    26.4    +      -       +      +
    296A  THR*     3.2     9.9    -      -       -      +
    297A  THR      3.5     0.4    -      -       -      -
    298A  GLU*     1.3    94.0    -      -       +      +
    300A  HIS*     1.3    59.7    +      -       -      +
    301A  GLU      3.9     1.3    +      -       -      -
    316A  CYS*     4.1    16.6    -      -       +      -
    317A  VAL      3.3     6.1    -      -       -      +
    318A  LYS*     3.5    44.9    -      -       +      -
    319A  ARG*     3.1    19.7    +      -       -      +
    325A  TYR*     4.2     4.7    -      +       -      -
    327A  ILE*     3.7    24.9    -      -       +      -
    366A  TRP*     3.7    22.7    -      +       -      -
    375A  GLN*     3.6    33.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  PHE*     1.3    72.0    -      -       -      +
    301A  GLU*     1.3    74.4    +      -       -      +
    302A  LEU*     3.3    35.4    +      -       +      +
    316A  CYS*     3.3     2.7    -      -       -      -
    317A  VAL*     2.8    48.6    +      -       +      +
    319A  ARG*     3.7    26.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  TYR*     2.7    43.7    +      -       +      +
    299A  PHE      3.9     3.6    +      -       -      -
    300A  HIS*     1.3    86.7    +      -       -      +
    302A  LEU*     1.3    62.5    +      -       -      +
    303A  GLU*     4.7     3.7    -      -       -      +
    314A  PHE*     3.5    40.9    -      -       +      -
    316A  CYS*     4.0     7.0    -      -       -      -
    329A  ARG*     5.7     0.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  HIS*     3.3    33.2    -      -       +      +
    301A  GLU*     1.3    75.0    -      -       -      +
    303A  GLU*     1.3    66.6    +      -       +      +
    315A  LYS*     2.8    49.7    +      -       +      +
    316A  CYS      4.7     0.4    -      -       -      -
    317A  VAL*     3.5    30.3    -      -       +      +
    324A  ILE*     4.9     4.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 303 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  GLU*     3.9     2.5    -      -       -      +
    302A  LEU*     1.3    84.1    -      -       -      +
    304A  LYS*     1.3    64.2    +      -       -      +
    305A  ILE*     4.1    20.4    -      -       +      +
    314A  PHE*     3.3     9.8    -      -       -      +
    315A  LYS*     2.8    50.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  GLU*     1.3    81.4    -      -       -      +
    305A  ILE*     1.3    63.0    +      -       -      +
    306A  GLY      3.6    21.3    -      -       -      +
    307A  SER*     4.4    12.9    +      -       -      -
    312A  SER*     3.8    15.0    +      -       -      -
    313A  VAL      3.6     7.6    -      -       -      +
    314A  PHE*     3.7    34.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  GLU*     4.1    15.7    -      -       +      +
    304A  LYS*     1.3    80.1    -      -       -      +
    306A  GLY*     1.3    58.7    +      -       -      +
    313A  VAL*     2.8    33.1    +      -       +      +
    314A  PHE      4.2     0.9    -      -       -      -
    315A  LYS*     3.9    31.6    -      -       +      +
    326A  ALA*     4.3     2.9    -      -       +      -
    378A  TYR*     4.0    19.1    -      -       +      +
    901A  824      3.5    62.6    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 306 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  LYS*     3.6     5.9    -      -       -      +
    305A  ILE*     1.3    80.2    -      -       -      +
    307A  SER*     1.3    63.3    +      -       -      -
    312A  SER*     3.3     4.9    -      -       -      -
    313A  VAL*     2.9    40.1    +      -       -      +
    901A  824      4.7     5.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  LYS*     4.4    13.8    +      -       -      +
    306A  GLY*     1.3    74.8    -      -       -      -
    308A  GLY*     1.3    68.8    +      -       -      +
    311A  GLY      3.5     7.1    -      -       -      -
    312A  SER*     3.7    13.5    +      -       -      -
    313A  VAL*     6.0     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 308 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  SER*     1.3    84.6    +      -       -      +
    309A  GLU*     1.3    58.5    +      -       -      -
    310A  PHE*     2.9    11.8    +      -       -      -
    311A  GLY*     2.8    17.6    +      -       -      +
----------------------------------------------------------
 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