Contacts of the strand formed by residues 105 - 109 (chain A) in PDB entry 2PI8


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 105 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  THR      4.4     0.4    -      -       -      +
    104A  PRO*     1.3    74.0    -      -       -      +
    106A  ILE*     1.3    63.6    +      -       -      +
    107A  GLN      4.2     0.7    +      -       -      -
    155A  ASP*     5.8     0.2    -      -       -      +
    166A  TYR*     3.3    13.9    -      -       +      +
    168A  ASP*     4.0    20.2    -      -       +      -
    175A  LEU*     3.8    24.7    -      -       +      -
    313A  ILE*     3.8    26.7    -      -       +      -
    314A  GLY*     4.4     5.0    -      -       -      +
    168B  ASP*     5.3     0.9    -      -       -      +
    170B  GLY*     3.7    39.0    -      -       -      +
    172B  GLY      4.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  PRO*     4.5    13.9    -      -       +      +
    105A  VAL*     1.3    76.2    -      -       -      +
    107A  GLN*     1.3    73.7    +      -       -      +
    108A  ALA*     3.8     0.6    +      -       +      -
    120A  ILE*     5.2     0.2    -      -       +      -
    150A  SER*     3.8    21.5    -      -       -      -
    151A  ASN*     4.8     1.8    -      -       -      +
    155A  ASP*     3.2    55.2    -      -       +      +
    156A  ASN*     4.1     1.8    -      -       -      +
    159A  MSE      3.6    33.0    -      -       +      -
    166A  TYR      2.9     9.1    +      -       -      -
    167A  ILE*     3.3    20.7    -      -       +      +
    168A  ASP*     2.8    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  VAL      4.2     1.4    +      -       -      -
    106A  ILE*     1.3    76.2    -      -       -      +
    108A  ALA*     1.3    65.8    +      -       -      +
    109A  ARG*     3.1    30.6    +      -       -      +
    116A  PHE*     3.9    10.9    -      -       +      -
    150A  SER*     3.7    13.2    -      -       -      -
    151A  ASN*     3.9    23.0    +      -       -      +
    168A  ASP*     3.0    33.2    +      -       +      +
    170A  GLY*     4.6     4.8    -      -       -      +
    105B  VAL      5.5     3.3    -      -       -      +
    107B  GLN*     3.2    33.2    +      -       -      +
    168B  ASP*     5.3     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ILE*     3.8     1.1    +      -       +      +
    107A  GLN*     1.3    78.5    -      -       -      +
    109A  ARG*     1.3    80.5    +      -       -      +
    116A  PHE*     4.0     3.8    -      -       -      -
    120A  ILE*     5.0     3.4    -      -       +      -
    148A  ALA*     4.0    16.6    -      -       +      -
    149A  TYR      3.0    26.5    -      -       -      +
    150A  SER*     3.7     5.2    -      -       -      -
    167A  ILE*     4.3    10.3    -      -       +      -
    168A  ASP      2.9     6.3    +      -       -      -
    169A  PHE*     3.1    22.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  GLN*     3.1    37.0    +      -       -      +
    108A  ALA*     1.3   107.2    +      -       -      +
    110A  HIS*     1.3    61.4    +      -       -      +
    111A  THR      3.3    18.8    +      -       -      +
    113A  GLN*     4.2    17.9    +      -       +      +
    116A  PHE*     3.6    35.6    -      -       +      -
    148A  ALA*     3.4     4.9    -      -       -      +
    149A  TYR*     3.0    29.0    +      -       -      +
    169A  PHE*     3.2    29.2    +      -       -      -
    170A  GLY      4.5     2.6    +      -       -      -
    171A  ASP*     6.2     0.4    -      -       -      -
    315B  PRO*     3.1    39.8    -      -       -      +
    316B  GLU*     5.5     9.0    -      -       -      -
----------------------------------------------------------
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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