Contacts of the strand formed by residues 16 - 22 (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 PHE 16 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14J  VAL*     2.9     9.3    -      -       -      +
     15J  LYS*     1.3    95.4    -      -       +      +
     17J  VAL*     1.3    60.9    -      -       -      +
     32J  THR*     3.6    24.9    -      -       +      -
     33J  ILE      3.4     2.5    -      -       -      -
     34J  PRO*     3.9    22.9    -      -       +      -
     35J  ALA      3.9     0.4    -      -       -      +
     82J  ASP*     4.0    13.5    -      -       +      -
     83J  SER      3.3     3.0    +      -       -      -
     84J  THR*     3.3    14.7    -      -       +      -
     85J  LEU      2.8    29.4    +      -       -      -
    193K  SER*     3.5    45.5    -      -       -      -
    196K  CYS*     3.9    23.3    -      -       +      -
    197K  LEU*     3.7    25.6    -      -       +      -
    209K  HIS*     4.5     2.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 17 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5J  VAL*     6.4     0.4    -      -       +      -
      9J  LEU*     4.3    17.7    -      -       +      -
     16J  PHE*     1.3    80.7    -      -       -      +
     18J  ASP*     1.3    63.3    +      -       -      +
     19J  LEU*     3.6    24.4    +      -       +      -
     31J  VAL      3.5     1.6    -      -       -      +
     32J  THR*     3.3     4.8    -      -       -      +
     33J  ILE*     2.6    50.4    +      -       +      +
     35J  ALA*     4.3    10.5    -      -       -      -
     38J  VAL*     3.9    24.7    -      -       +      -
     42J  PHE*     5.2     0.4    -      -       +      -
     85J  LEU*     3.0    14.4    -      -       +      +
     87J  ILE*     3.8    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 18 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16J  PHE      4.2     0.4    -      -       -      -
     17J  VAL*     1.3    73.7    -      -       -      +
     19J  LEU*     1.3    64.8    +      -       -      +
     20J  ARG*     2.8    32.7    +      -       -      +
     30J  HIS*     2.9    29.7    -      -       -      +
     31J  VAL      3.3     4.2    -      -       -      +
     32J  THR*     2.7    29.6    +      -       +      -
     80J  PHE*     4.0     9.7    -      -       +      -
     84J  THR*     4.1    13.0    +      -       -      +
     85J  LEU      2.6    13.1    +      -       -      +
     86J  ILE*     3.3    10.1    -      -       +      +
     87J  ILE      2.8    26.9    +      -       -      +
    189K  GLN*     3.9     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 19 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17J  VAL*     3.6    27.1    -      -       +      +
     18J  ASP*     1.3    72.2    -      -       -      +
     20J  ARG*     1.3    60.9    +      -       -      +
     21J  PHE*     4.8     2.5    -      -       -      -
     30J  HIS*     2.9     5.5    -      -       -      -
     31J  VAL*     2.7    62.3    +      -       +      +
     33J  ILE*     4.6    20.2    -      -       +      -
     42J  PHE*     4.1    28.9    -      -       +      -
     47J  LYS*     5.1     6.1    -      -       +      -
     67J  LEU*     4.3    15.7    -      -       +      -
     87J  ILE*     3.4     9.0    -      -       +      +
     89J  CYS*     3.6    23.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 20 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18J  ASP*     2.8    23.0    +      -       -      +
     19J  LEU*     1.3    80.4    -      -       -      +
     21J  PHE*     1.3    59.7    +      -       -      +
     28J  GLU*     3.4    31.1    +      -       -      +
     29J  GLN      3.0     7.2    -      -       -      +
     30J  HIS*     3.6    12.6    -      -       +      +
     77J  ASP*     2.6    27.3    +      -       -      -
     80J  PHE*     3.6     8.7    -      -       -      -
     86J  ILE*     3.5    41.3    -      -       +      +
     87J  ILE      2.9     9.3    +      -       -      +
     88J  ARG*     3.2    15.4    -      -       -      +
     89J  CYS*     2.6    34.2    +      -       -      -
    202J  MET*     5.2     0.8    -      -       -      +
    240J  TYR*     3.4    39.8    +      -       -      -
    182K  VAL*     4.1     5.1    -      -       -      +
    183K  PRO*     5.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 21 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19J  LEU      4.8     2.9    -      -       -      -
     20J  ARG*     1.3    78.7    -      -       -      +
     22J  THR*     1.3    65.5    +      -       -      +
     23J  ASP*     4.6     0.4    -      -       -      -
     28J  GLU*     3.5     4.0    -      -       -      +
     29J  GLN*     2.6    69.2    +      -       +      +
     30J  HIS*     4.7     1.3    -      -       -      -
     31J  VAL*     5.5     0.7    -      -       +      -
     49J  PHE*     4.3     8.7    -      +       -      -
     54J  ILE*     3.7    20.2    -      -       +      -
     57J  TRP*     3.6    35.2    -      +       -      -
     67J  LEU*     3.6    27.1    -      -       +      -
     88J  ARG*     5.0     4.9    -      -       -      +
     89J  CYS      3.8    17.0    -      -       -      +
     91J  ILE*     4.1    14.6    -      -       +      -
    103J  ASP*     6.1     0.7    -      -       -      +
    180K  PHE*     3.9    20.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 22 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21J  PHE*     1.3    85.2    +      -       -      +
     23J  ASP*     1.3    75.9    +      -       -      +
     26J  GLY*     3.4    15.9    -      -       -      +
     27J  LYS      3.8     2.5    -      -       -      +
     28J  GLU*     4.4     0.3    -      -       -      -
     57J  TRP*     3.6     7.8    -      -       -      -
     88J  ARG*     4.4     5.7    +      -       -      -
     91J  ILE*     5.6     0.2    -      -       -      +
    103J  ASP*     4.5     4.4    +      -       -      +
    104J  PRO*     3.5    19.2    -      -       +      +
    105J  ARG*     5.9     4.0    -      -       -      +
    236J  GLN*     3.1    34.1    +      -       -      +
    366J  ASN*     4.4     2.0    -      -       -      +
    368J  TYR*     3.4    35.6    +      -       +      -
----------------------------------------------------------
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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