Contacts of the strand formed by residues 382 - 386 (chain A) in PDB entry 1PG3


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 ILE 382 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ILE*     3.8    20.2    -      -       +      -
    292A  VAL      4.6     2.0    -      -       -      +
    293A  PHE*     3.9    26.9    -      -       -      +
    294A  ASP*     4.7     4.7    -      -       +      +
    352A  ASN      3.0     4.2    +      -       -      +
    353A  ILE*     3.4    26.1    -      -       +      -
    354A  LEU      3.0    24.5    +      -       -      -
    380A  LEU*     3.9     0.9    -      -       -      +
    381A  ARG*     1.3    93.9    +      -       +      +
    383A  LEU*     1.3    79.4    +      -       -      +
    407A  CYS*     3.9     2.7    -      -       -      +
    408A  PRO*     4.0    10.1    -      -       +      +
    410A  VAL*     4.5    11.0    -      -       +      -
    427A  PRO*     3.8    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  PHE*     5.7     0.7    -      -       -      -
    354A  LEU*     3.3    22.7    -      -       +      -
    380A  LEU*     4.0    10.8    -      -       +      -
    382A  ILE*     1.3    79.3    -      -       -      +
    384A  GLY*     1.3    52.7    +      -       -      +
    398A  TYR*     3.7    42.2    -      -       +      +
    399A  TRP*     4.4     1.6    -      -       -      -
    402A  ILE*     4.0    13.7    -      -       +      -
    403A  GLY*     3.5    30.7    -      -       -      +
    407A  CYS*     4.0    11.7    -      -       +      +
    408A  PRO      3.0    15.7    +      -       -      +
    409A  VAL*     3.1    16.3    -      -       +      -
    410A  VAL*     2.7    36.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 384 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  PHE*     4.8     0.8    -      -       -      -
    354A  LEU      2.7    14.1    +      -       -      -
    355A  TYR*     3.6    14.8    -      -       -      -
    356A  THR      3.0    14.6    +      -       -      +
    383A  LEU*     1.3    75.8    -      -       -      +
    385A  SER*     1.3    60.0    +      -       -      -
    398A  TYR*     3.0    21.1    +      -       -      -
    409A  VAL*     4.8     0.2    -      -       -      -
    410A  VAL*     3.3    20.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 385 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  TYR*     3.8     2.3    -      -       -      -
    356A  THR      3.2     6.3    -      -       -      -
    358A  PRO*     3.4    26.2    -      -       -      +
    361A  ILE*     4.5     2.8    -      -       -      +
    384A  GLY*     1.3    75.2    -      -       -      -
    386A  VAL*     1.3    64.2    +      -       -      +
    390A  ILE*     4.1    15.1    -      -       -      +
    398A  TYR*     4.6    10.3    -      -       -      -
    409A  VAL*     4.7     6.5    -      -       -      -
    410A  VAL      2.9     8.7    +      -       -      +
    411A  ASP*     3.4    18.6    +      -       -      +
    412A  THR*     3.0    27.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 386 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  ALA*     5.6     0.2    -      -       +      -
    311A  THR*     4.1     3.1    -      -       +      +
    355A  TYR*     3.0    45.5    -      -       +      +
    356A  THR      3.1    12.1    +      -       -      +
    357A  ALA*     3.4     9.4    -      -       -      +
    358A  PRO*     3.2    19.4    -      -       -      +
    385A  SER*     1.3    76.6    +      -       -      +
    387A  GLY*     1.3    73.7    -      -       -      +
    388A  GLU      3.5     3.4    -      -       -      -
    412A  THR*     3.4    10.8    -      -       -      +
    414A  TRP*     3.3    21.1    -      -       +      +
    990A  COA      3.8    21.2    -      -       -      -
    999A  PRX      3.9    15.7    -      -       +      -
----------------------------------------------------------
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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