Contacts of the strand formed by residues 158 - 161 (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 VAL 158 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  GLY      4.2    16.6    -      -       -      +
    133A  ASP      2.8    11.9    +      -       -      +
    134A  VAL*     3.1    16.5    -      -       +      +
    135A  VAL*     2.9    24.2    +      -       -      -
    156A  GLY      4.5     2.5    -      -       -      +
    157A  ALA*     1.3    70.7    -      -       -      +
    159A  HIS*     1.3    63.6    +      -       -      +
    258A  PRO*     3.6    43.1    -      -       +      +
    259A  LEU      3.5     5.2    -      -       -      +
    260A  PHE*     3.7    23.3    -      -       -      +
    261A  ILE*     3.9    22.9    -      -       +      -
    275A  LEU*     5.8     0.2    -      -       +      -
    478A  PHE*     6.0     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  VAL      3.4     5.4    -      -       -      +
    137A  ILE*     3.8    23.3    -      -       +      -
    149A  MET*     3.6    30.9    -      -       +      +
    152A  CYS*     4.0    14.6    -      -       +      -
    153A  ALA*     4.8     4.5    -      -       +      -
    157A  ALA      3.4     3.0    +      -       -      -
    158A  VAL*     1.3    74.0    -      -       -      +
    160A  SER*     1.3    59.7    +      -       -      +
    161A  VAL*     3.7    10.1    -      -       -      +
    259A  LEU*     3.3    13.2    +      -       +      +
    260A  PHE*     3.2    24.9    -      +       +      +
    261A  ILE      3.0    24.1    +      -       -      +
    313A  HIS*     3.6    23.0    -      +       -      -
    318A  TYR*     2.7    29.9    +      +       -      -
----------------------------------------------------------
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Residues in contact with SER 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  VAL*     3.7    23.6    -      -       -      -
    135A  VAL      2.8     9.9    +      -       -      -
    136A  ALA*     3.3     8.3    -      -       -      +
    137A  ILE      2.9    20.6    +      -       -      -
    158A  VAL      3.8     0.2    +      -       -      -
    159A  HIS*     1.3    72.9    -      -       -      +
    161A  VAL*     1.3    63.5    +      -       -      +
    162A  ILE*     3.6    10.7    +      -       -      +
    174A  CYS*     4.9     0.7    -      -       -      +
    178A  SER*     4.4     3.9    +      -       -      -
    180A  SER*     4.5     3.1    +      -       -      -
    261A  ILE*     3.7    14.4    +      -       -      -
    263A  TYR*     3.6    28.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  ILE*     3.2    24.9    -      -       +      +
    139A  MET      5.8     2.2    -      -       -      +
    149A  MET*     3.8    23.8    -      -       +      -
    159A  HIS*     3.7    18.2    +      -       -      +
    160A  SER*     1.3    74.3    +      -       -      +
    162A  ILE*     1.3    59.6    +      -       -      +
    261A  ILE      3.9     5.3    +      -       -      +
    262A  LEU*     3.7     4.3    -      -       -      +
    307A  VAL*     3.9     8.5    -      -       +      +
    308A  GLY*     3.6    29.6    -      -       -      +
    313A  HIS*     3.5    25.4    -      -       +      +
   1801A  EDO      2.8    29.7    +      -       -      -
----------------------------------------------------------
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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