Contacts of the strand formed by residues 64 - 69 (chain H) in PDB entry 1FPY


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 ASP 64 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48H  MET*     3.2    28.8    -      -       +      +
     49H  PHE*     3.5    15.6    +      -       -      +
     50H  ASP*     4.1     5.1    +      -       -      +
     62H  GLU      2.8    12.0    +      -       -      +
     63H  SER*     1.3    69.6    -      -       -      +
     65H  MET*     1.3    61.0    +      -       -      +
     94H  PRO*     3.3    22.5    -      -       -      +
    339I  ARG*     2.7    23.2    +      -       -      +
    344I  ARG*     3.5    21.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 65 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48H  MET*     3.4     5.2    -      -       -      +
     49H  PHE*     2.9    51.3    +      -       +      +
     51H  GLY*     4.7     3.1    -      -       -      +
     57H  TRP*     4.7     8.1    -      -       +      +
     62H  GLU      4.9     0.7    -      -       -      +
     63H  SER*     3.4    41.9    +      -       -      +
     64H  ASP*     1.3    74.6    -      -       -      +
     66H  VAL*     1.3    62.5    +      -       -      +
     91H  ILE*     3.8    21.1    -      -       +      -
     92H  LEU      3.3    20.2    -      -       -      +
     93H  GLU*     3.8    22.7    -      -       -      +
     94H  PRO*     4.1     5.6    -      -       +      -
    100H  TYR*     3.6    37.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 66 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45H  GLU      3.4    25.4    -      -       -      +
     46H  GLY*     4.2     0.9    -      -       -      -
     47H  LYS      3.5    10.5    -      -       -      +
     48H  MET*     4.1    12.1    -      -       -      -
     49H  PHE*     4.3     2.2    -      -       -      -
     65H  MET*     1.3    80.0    -      -       -      +
     67H  LEU*     1.3    71.6    +      -       -      +
     68H  MET*     3.5    10.0    +      -       +      +
     90H  ASP      3.2     4.5    -      -       -      +
     91H  ILE*     3.4     5.0    -      -       -      +
     92H  LEU*     3.0    38.2    +      -       +      +
     94H  PRO*     3.8    26.7    -      -       +      -
     95H  GLY      5.0     0.2    -      -       -      +
     97H  LEU*     4.2    14.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 67 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19H  LEU*     4.3    11.7    -      -       +      -
     21H  PHE*     3.6    23.6    -      -       +      -
     31H  VAL*     4.0    27.6    -      -       +      -
     42H  PHE*     5.2     0.4    -      -       +      -
     46H  GLY*     3.1    15.8    -      -       -      -
     47H  LYS*     2.9    22.7    +      -       +      +
     49H  PHE*     3.6    31.4    -      -       +      -
     66H  VAL*     1.3    70.3    -      -       -      +
     68H  MET*     1.3    60.9    +      -       -      +
     69H  PRO*     3.0    12.1    -      -       -      +
     89H  CYS*     3.7    22.7    -      -       +      -
     90H  ASP      3.7     0.4    -      -       -      -
     91H  ILE*     3.5    24.0    -      -       +      -
    180I  PHE*     5.9     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 68 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43H  PHE      3.4    24.5    -      -       -      +
     44H  GLU      3.6    11.2    -      -       -      +
     45H  GLU*     3.4    11.7    -      -       -      +
     46H  GLY*     3.4    22.9    -      -       -      +
     66H  VAL*     4.3     4.7    -      -       +      -
     67H  LEU*     1.3    72.5    -      -       -      +
     69H  PRO*     1.3    78.4    -      -       -      +
     70H  ASP      3.5     0.5    +      -       -      -
     89H  CYS*     3.3     2.2    -      -       -      +
     90H  ASP*     2.7    49.3    +      -       +      +
     92H  LEU*     3.5    38.1    -      -       +      -
     97H  LEU*     4.9     5.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 69 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42H  PHE*     3.6    45.1    -      -       +      +
     43H  PHE*     4.0    27.8    -      -       +      +
     46H  GLY*     3.8     6.1    -      -       -      -
     67H  LEU      3.0    13.2    -      -       -      +
     68H  MET*     1.3   101.9    -      -       -      +
     70H  ASP*     1.3    59.0    +      -       -      +
     71H  ALA      3.7     2.0    +      -       -      -
     87H  ILE*     3.9    13.0    -      -       +      -
     88H  ARG      3.9     0.7    -      -       -      +
     89H  CYS*     3.8    15.9    -      -       -      -
     90H  ASP*     5.2     0.3    -      -       -      +
----------------------------------------------------------
 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