Contacts of the strand formed by residues 64 - 69 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  MET*     3.2    30.1    -      -       +      +
     49A  PHE      3.5    15.2    +      -       -      +
     50A  ASP*     4.1     5.9    +      -       -      +
     62A  GLU      2.8    11.3    +      -       -      +
     63A  SER*     1.3    70.0    -      -       -      +
     65A  MET*     1.3    59.7    +      -       -      +
     94A  PRO*     3.3    22.9    -      -       -      +
    336F  ALA      5.6     1.6    -      -       -      +
    339F  ARG*     2.8    21.7    +      -       -      +
    344F  ARG*     3.3    24.5    +      -       -      -
   4476F  ADP      5.6     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  MET*     3.4     5.1    -      -       -      +
     49A  PHE*     2.9    50.5    +      -       +      +
     51A  GLY*     5.4     2.7    -      -       -      +
     57A  TRP*     4.7     8.3    -      -       +      +
     62A  GLU      4.9     0.4    -      -       -      +
     63A  SER*     3.4    41.2    +      -       -      +
     64A  ASP*     1.3    75.1    -      -       -      +
     66A  VAL*     1.3    62.3    +      -       -      +
     91A  ILE*     3.8    20.4    -      -       +      -
     92A  LEU      3.3    20.6    -      -       -      +
     93A  GLU*     3.8    22.9    -      -       -      +
     94A  PRO*     4.2     5.6    -      -       +      -
    100A  TYR*     3.6    38.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLU      3.4    25.1    -      -       -      +
     46A  GLY*     4.2     0.9    -      -       -      -
     47A  LYS      3.5    11.0    -      -       -      +
     48A  MET*     4.1    12.6    -      -       -      -
     49A  PHE*     4.3     1.6    -      -       -      -
     65A  MET*     1.3    79.2    -      -       -      +
     67A  LEU*     1.3    73.5    +      -       -      +
     68A  MET*     3.5     9.8    +      -       +      +
     90A  ASP      3.2     4.9    -      -       -      +
     91A  ILE*     3.4     4.5    -      -       -      +
     92A  LEU*     3.0    37.9    +      -       +      +
     93A  GLU      4.3     0.2    -      -       -      +
     94A  PRO*     3.8    27.8    -      -       +      -
     97A  LEU*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LEU*     4.3    12.3    -      -       +      -
     21A  PHE*     3.6    23.3    -      -       +      -
     31A  VAL*     4.0    27.1    -      -       +      -
     42A  PHE*     5.2     0.4    -      -       +      -
     46A  GLY*     3.1    15.2    -      -       -      -
     47A  LYS*     2.9    22.7    +      -       +      +
     48A  MET      5.5     0.2    -      -       -      +
     49A  PHE*     3.6    30.7    -      -       +      -
     66A  VAL*     1.3    70.5    -      -       -      +
     68A  MET*     1.3    60.7    +      -       -      +
     69A  PRO*     3.0    13.0    -      -       -      +
     89A  CYS*     3.7    23.1    -      -       +      -
     90A  ASP      3.7     0.4    -      -       -      -
     91A  ILE*     3.5    24.0    -      -       +      -
    180F  PHE*     5.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  PHE      3.4    24.9    -      -       -      +
     44A  GLU      3.6    11.7    -      -       -      +
     45A  GLU*     3.4    11.7    -      -       -      +
     46A  GLY*     3.4    22.9    -      -       -      +
     66A  VAL*     3.5     4.7    +      -       +      +
     67A  LEU*     1.3    72.9    -      -       -      +
     69A  PRO*     1.3    77.8    -      -       -      +
     70A  ASP      3.5     0.2    +      -       -      -
     89A  CYS*     3.3     2.4    -      -       -      +
     90A  ASP*     2.7    49.8    +      -       +      +
     92A  LEU*     3.5    39.5    -      -       +      -
     97A  LEU*     4.9     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     3.6    46.0    -      -       +      +
     43A  PHE*     4.0    28.5    -      -       +      +
     46A  GLY*     3.8     6.5    -      -       -      -
     67A  LEU*     3.0    13.0    -      -       +      +
     68A  MET*     1.3   101.1    -      -       -      +
     70A  ASP*     1.3    60.4    +      -       -      +
     71A  ALA      3.7     2.1    +      -       -      -
     87A  ILE*     3.9    13.2    -      -       +      -
     88A  ARG      3.9     0.7    -      -       -      +
     89A  CYS*     3.8    14.3    -      -       -      -
     90A  ASP*     5.2     0.3    -      -       -      +
----------------------------------------------------------
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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