Contacts of the strand formed by residues 64 - 69 (chain J) 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 J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48J  MET*     3.2    29.4    -      -       +      +
     49J  PHE*     3.5    15.4    +      -       -      +
     50J  ASP*     4.1     5.0    +      -       -      +
     62J  GLU      2.8    11.5    +      -       -      +
     63J  SER*     1.3    71.1    -      -       -      +
     65J  MET*     1.3    60.1    +      -       -      +
     94J  PRO*     3.3    23.4    -      -       -      +
    336K  ALA      5.5     2.9    -      -       -      +
    339K  ARG*     2.7    22.2    +      -       -      +
    344K  ARG*     3.3    24.2    +      -       -      -
   4481K  ADP      5.7     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 65 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48J  MET*     3.4     5.1    -      -       -      +
     49J  PHE*     2.9    50.9    +      -       +      +
     51J  GLY*     4.7     3.1    -      -       -      +
     57J  TRP*     4.7     7.6    -      -       +      +
     62J  GLU      4.9     0.4    -      -       -      +
     63J  SER*     3.4    41.1    +      -       -      +
     64J  ASP*     1.3    75.3    -      -       -      +
     66J  VAL*     1.3    62.6    +      -       -      +
     91J  ILE*     3.8    22.0    -      -       +      -
     92J  LEU      3.3    19.3    -      -       -      +
     93J  GLU*     3.8    22.4    -      -       -      +
     94J  PRO*     4.1     6.1    -      -       +      -
    100J  TYR*     3.6    37.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45J  GLU      3.4    25.4    -      -       -      +
     46J  GLY*     4.2     1.1    -      -       -      -
     47J  LYS      3.5    10.8    -      -       -      +
     48J  MET*     4.1    11.7    -      -       -      -
     49J  PHE*     4.3     2.0    -      -       -      -
     65J  MET*     1.3    80.5    -      -       -      +
     67J  LEU*     1.3    73.0    +      -       -      +
     68J  MET*     3.5    10.2    +      -       +      +
     90J  ASP      3.2     4.5    -      -       -      +
     91J  ILE*     3.4     4.5    -      -       -      +
     92J  LEU*     3.0    37.4    +      -       +      +
     94J  PRO*     3.8    27.1    -      -       +      -
     97J  LEU*     4.2    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 67 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19J  LEU*     4.3    12.8    -      -       +      -
     21J  PHE*     3.6    24.5    -      -       +      -
     31J  VAL*     4.0    26.7    -      -       +      -
     42J  PHE*     5.2     0.4    -      -       +      -
     46J  GLY*     3.1    15.6    -      -       -      -
     47J  LYS*     2.9    21.6    +      -       +      +
     48J  MET      5.5     0.4    -      -       -      +
     49J  PHE*     3.6    30.9    -      -       +      -
     66J  VAL*     1.3    71.2    -      -       -      +
     68J  MET*     1.3    61.4    +      -       -      +
     69J  PRO*     3.0    13.1    -      -       +      +
     89J  CYS*     3.7    22.2    -      -       +      -
     90J  ASP      3.7     0.4    -      -       -      -
     91J  ILE*     3.5    24.2    -      -       +      -
    180K  PHE*     5.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 68 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43J  PHE      3.4    24.5    -      -       -      +
     44J  GLU      3.6    11.9    -      -       -      +
     45J  GLU*     3.4    10.8    -      -       -      +
     46J  GLY*     3.4    23.3    -      -       -      +
     66J  VAL*     3.5     5.3    +      -       +      -
     67J  LEU*     1.3    71.6    -      -       -      +
     69J  PRO*     1.3    77.1    -      -       -      +
     70J  ASP      3.5     0.3    +      -       -      -
     89J  CYS*     3.3     2.7    -      -       -      -
     90J  ASP*     2.7    51.3    +      -       +      +
     92J  LEU*     3.5    37.9    -      -       +      -
     97J  LEU*     4.9     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 69 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42J  PHE*     3.6    45.3    -      -       +      +
     43J  PHE*     4.0    27.2    -      -       +      +
     46J  GLY*     3.8     5.4    -      -       -      -
     67J  LEU      3.0    13.7    -      -       -      +
     68J  MET*     1.3   101.9    -      -       -      +
     70J  ASP*     1.3    60.2    +      -       -      +
     71J  ALA      3.7     2.4    +      -       -      -
     87J  ILE*     3.9    12.6    -      -       +      -
     88J  ARG      3.9     0.7    -      -       -      +
     89J  CYS*     3.8    14.6    -      -       -      -
     90J  ASP*     5.2     0.5    -      -       -      +
----------------------------------------------------------
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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