Contacts of the strand formed by residues 24 - 31 (chain A) in PDB entry 2PY5


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 24 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  PHE*     3.8    33.2    -      -       +      -
     14A  GLU      3.5     5.6    -      -       -      +
     15A  THR*     4.2     3.4    -      -       +      -
     23A  ARG*     1.3    83.0    +      -       -      +
     25A  TRP*     1.3    58.4    +      -       -      +
     26A  ALA*     3.2    33.0    -      -       -      +
     27A  TYR*     4.4     2.2    -      -       +      +
     42A  ASN      4.5     6.1    -      -       -      +
     43A  SER      5.3     1.1    -      -       -      +
     44A  LEU*     4.1    40.8    +      -       +      +
     69A  PHE*     3.8    24.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  GLU*     2.8    27.4    +      -       +      +
     15A  THR      3.4    40.7    +      -       -      +
     16A  THR*     3.6    16.6    -      -       +      -
     23A  ARG*     3.5     7.8    +      -       -      +
     24A  VAL*     1.3    72.9    -      -       -      +
     26A  ALA*     1.3    72.1    +      -       +      +
     42A  ASN*     3.4    29.8    -      -       -      +
    146A  ILE*     3.8    24.2    -      -       +      -
    148A  TYR*     5.0     0.6    +      -       -      +
    152A  ARG*     3.3    61.5    -      -       +      +
    153A  PRO      5.5     0.2    -      -       -      +
    156A  TYR*     4.0    16.6    -      +       +      +
    158A  ILE*     4.2     8.8    -      -       +      +
    162A  GLU*     3.7    30.1    -      -       +      -
    166A  ILE*     4.6     0.4    -      -       +      -
      7J    T      4.4     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  PHE*     3.3     1.6    -      -       -      -
     14A  GLU*     2.9    31.4    +      -       +      -
     24A  VAL*     3.2    15.0    -      -       -      +
     25A  TRP*     1.3    94.9    -      -       +      +
     27A  TYR*     1.3    59.1    +      -       -      +
     41A  GLY      3.2     6.1    -      -       -      -
     42A  ASN*     4.3     0.4    -      -       -      +
    158A  ILE*     3.7    11.7    -      -       +      -
    166A  ILE*     3.5    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ALA      3.3     7.6    -      -       -      +
     13A  PHE*     3.8    18.8    -      -       +      -
     24A  VAL*     4.7     2.2    -      -       +      -
     26A  ALA*     1.3    74.2    -      -       -      +
     28A  GLY*     1.3    65.0    +      -       -      +
     29A  TYR*     4.0    14.5    -      +       -      -
     39A  LYS*     3.5    30.0    -      -       -      +
     40A  ILE*     3.2     9.5    -      -       -      +
     41A  GLY*     2.9    58.6    +      -       -      -
     43A  SER      3.4    29.6    -      -       -      -
     46A  GLU*     2.6    31.2    +      -       -      +
     47A  PHE*     3.4    41.1    -      +       +      -
     50A  TRP*     6.5     0.2    -      -       +      -
    166A  ILE*     4.4     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  CYS*     3.2     6.1    -      -       -      +
     12A  ALA      2.9    31.4    +      -       -      +
     27A  TYR*     1.3    79.3    -      -       -      +
     29A  TYR*     1.3    60.3    +      -       -      +
     39A  LYS      3.2     9.6    -      -       -      -
     40A  ILE*     3.9    11.2    -      -       -      -
     47A  PHE*     4.5     2.5    -      -       -      -
    166A  ILE*     4.1     6.6    -      -       -      +
    170A  ILE*     3.8    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  TYR*     3.7    15.9    -      +       +      -
     10A  SER      3.3     6.1    -      -       -      -
     11A  CYS*     3.8    11.2    -      -       -      -
     27A  TYR*     4.0    20.0    -      +       -      -
     28A  GLY*     1.3    74.4    -      -       -      +
     30A  MET*     1.3    60.0    +      -       -      +
     37A  GLU*     4.6     7.4    -      -       +      -
     38A  TYR*     3.1    13.2    -      -       -      +
     39A  LYS*     2.9    71.7    +      -       +      +
     47A  PHE*     4.3     2.7    -      +       +      -
     50A  TRP*     3.6    76.3    +      +       +      -
    170A  ILE*     3.7     3.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  TYR*     3.3     4.6    -      -       -      -
     10A  SER*     2.8    38.0    +      -       -      +
     29A  TYR*     1.3    77.4    -      -       -      +
     31A  ASN*     1.3    73.0    -      -       -      +
     32A  ILE      3.2     0.2    +      -       -      -
     35A  HIS*     3.4    40.2    -      -       -      +
     37A  GLU      3.5     7.2    -      -       -      +
     38A  TYR*     3.9    17.5    -      -       +      -
    167A  LYS*     4.2    15.7    -      -       +      -
    170A  ILE*     3.8    17.0    -      -       +      +
    171A  GLN*     3.6    48.5    -      -       +      +
    174A  ALA*     4.2     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  LYS*     3.8    17.4    -      -       -      +
      8A  MET      3.5    14.5    +      -       -      +
      9A  TYR*     3.5    15.1    +      -       +      -
     30A  MET*     1.3    69.3    -      -       -      +
     32A  ILE*     1.3    64.3    +      -       -      +
     33A  GLU*     3.0    30.1    +      -       -      +
     34A  ASP*     3.1    42.6    -      -       -      +
     35A  HIS*     3.2     8.5    -      -       -      -
     37A  GLU*     2.8    39.9    +      -       -      +
----------------------------------------------------------
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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