Contacts of the strand formed by residues 50 - 54 (chain E) in PDB entry 1PPF


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 ASN 50 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48E  ALA*     4.4     1.7    -      -       -      +
     49E  PRO*     1.3    82.5    -      -       -      +
     51E  PHE*     1.4    89.8    +      -       -      +
    107E  GLN*     3.6    17.5    -      -       -      +
    108E  LEU*     2.9    33.2    +      -       +      +
    110E  GLY      3.3    23.8    -      -       -      +
    111E  SER*     4.2     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 51 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46E  LEU*     4.5     0.4    -      -       -      +
     47E  ILE*     3.1    33.1    +      -       +      +
     48E  ALA*     3.3    19.1    +      -       +      +
     49E  PRO      3.5     0.2    -      -       -      -
     50E  ASN*     1.4   111.9    -      -       -      +
     52E  VAL*     1.3    67.0    -      -       -      +
     87E  ARG*     5.9     0.7    -      -       -      -
     89E  PHE*     4.0     5.8    -      +       -      -
    105E  ILE*     3.8    24.7    -      -       +      -
    106E  LEU      3.6     2.0    -      -       -      -
    107E  GLN*     3.5    41.1    -      -       +      -
    108E  LEU*     4.3     0.6    -      -       -      +
    241E  ILE*     3.4    35.4    -      -       +      -
    242E  ILE*     3.8    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 52 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  VAL*     4.2    11.9    -      -       +      -
     33E  LEU*     4.6     0.7    -      -       +      -
     44E  ALA*     4.0    16.2    -      -       +      -
     45E  THR      3.4     7.6    -      -       -      +
     46E  LEU*     3.4    33.0    -      -       +      -
     47E  ILE*     4.3     3.6    -      -       -      -
     51E  PHE*     1.3    74.5    -      -       -      +
     53E  MET*     1.3    59.4    +      -       -      +
     66E  VAL*     4.2    13.7    -      -       +      -
     68E  LEU*     4.4     0.7    -      -       +      -
    104E  VAL      4.0     0.2    -      -       -      +
    105E  ILE*     3.3     4.7    -      -       -      +
    106E  LEU*     2.7    68.8    +      -       +      +
    108E  LEU*     4.0    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 53 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  ALA*     3.2     4.6    -      -       -      -
     45E  THR*     2.9    41.4    +      -       -      +
     47E  ILE*     4.0    26.0    -      -       +      +
     52E  VAL*     1.3    75.7    -      -       -      +
     54E  SER*     1.3    64.1    +      -       -      +
    103E  ILE*     4.1    13.5    -      -       +      -
    104E  VAL      3.3     9.6    -      -       -      +
    105E  ILE*     3.9    13.0    -      -       +      -
    123E  LEU*     4.2     5.4    -      -       +      -
    196E  GLY      4.2     2.1    -      -       -      +
    209E  ILE*     4.0    27.8    -      -       +      -
    212E  ILE*     3.6    32.5    -      -       +      +
    231E  VAL*     4.1     9.4    -      -       +      -
    238E  ILE*     4.2    17.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 54 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  LEU*     3.7    15.7    -      -       -      +
     43E  GLY      2.7    25.2    +      -       -      -
     44E  ALA*     4.0     7.2    -      -       -      -
     53E  MET*     1.3    76.7    -      -       -      +
     55E  ALA*     1.3    61.9    +      -       -      +
     58E  CYS*     4.1     7.0    -      -       -      -
     59E  VAL*     6.1     0.2    -      -       -      -
    103E  ILE*     3.4     5.4    -      -       -      -
    104E  VAL*     2.7    43.1    +      -       -      +
    106E  LEU*     4.7     5.6    -      -       -      +
    196E  GLY*     3.6     9.6    -      -       -      -
    212E  ILE*     3.7    14.8    -      -       -      +
----------------------------------------------------------
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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