Contacts of the strand formed by residues 216 - 220 (chain A) in PDB entry 1PG4


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 HIS 216 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  LEU*     4.0    33.4    +      -       +      +
    181A  ARG      3.7     3.0    +      -       -      +
    182A  LEU*     3.3    18.2    -      -       +      +
    183A  VAL      3.2    21.5    +      -       -      -
    214A  VAL*     3.5     8.8    -      -       -      +
    215A  GLU*     1.3   103.8    +      -       +      +
    217A  VAL*     1.3    65.4    +      -       -      +
    232A  GLY      3.2    19.6    +      -       -      -
    233A  ARG*     3.2    21.3    +      -       -      +
    235A  LEU*     4.0    16.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  VAL*     3.2    14.8    -      -       +      +
    185A  THR*     3.9    17.5    -      -       +      -
    199A  LYS*     4.5     4.5    -      -       +      -
    202A  VAL*     4.2    15.5    -      -       +      -
    206A  LEU*     3.7    29.6    -      -       +      -
    214A  VAL*     4.4     0.9    -      -       +      -
    216A  HIS*     1.3    79.6    -      -       -      +
    218A  ILE*     1.3    62.6    +      -       -      +
    219A  VAL*     3.6    20.5    +      -       +      +
    233A  ARG*     3.0    13.4    +      -       -      +
    234A  ASP*     3.3    20.8    -      -       -      +
    235A  LEU      2.9    26.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  PHE*     3.9    24.2    -      -       +      -
    123A  THR*     4.6     2.7    -      -       +      -
    124A  LEU*     4.6     3.8    -      -       +      -
    127A  LEU*     4.1    12.1    -      -       +      -
    182A  LEU*     3.9    29.6    -      -       +      -
    183A  VAL      2.8     9.6    +      -       -      +
    184A  ILE*     3.5     7.4    -      -       +      -
    185A  THR*     2.9    28.8    +      -       -      +
    217A  VAL*     1.3    74.0    -      -       -      +
    219A  VAL*     1.3    63.4    +      -       -      +
    235A  LEU*     3.3     7.0    -      -       +      +
    237A  TRP*     3.9    41.5    -      -       +      -
    240A  LEU*     3.7    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  THR*     3.5     4.3    -      -       +      -
    186A  ALA      4.0     4.3    -      -       -      -
    187A  ASP*     3.7    26.2    -      -       -      +
    199A  LYS*     3.7    29.4    -      -       +      -
    217A  VAL*     3.7    18.8    -      -       +      +
    218A  ILE*     1.3    77.6    -      -       -      +
    220A  LEU*     1.3    61.0    +      -       -      +
    227A  ILE*     4.3     7.6    -      -       +      -
    229A  TRP*     3.9    15.5    -      -       +      -
    234A  ASP*     4.7     0.9    -      -       +      -
    235A  LEU      2.6    12.2    +      -       -      +
    236A  TRP*     3.3    24.8    -      -       +      -
    237A  TRP*     2.7    29.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  MET*     4.1     8.5    -      -       +      -
    142A  VAL*     4.0    15.7    -      -       +      -
    144A  GLU*     3.7    50.5    -      -       +      +
    185A  THR      2.9    15.8    +      -       -      +
    186A  ALA*     3.2    10.5    -      -       +      -
    187A  ASP*     2.9    25.3    +      -       -      -
    219A  VAL*     1.3    75.1    -      -       -      +
    221A  LYS*     1.3    71.3    +      -       -      +
    222A  ARG*     3.2    14.8    +      -       +      -
    237A  TRP*     3.8    28.0    -      -       +      +
    902A   CL      4.1     5.6    -      -       +      -
----------------------------------------------------------
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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