Contacts of the strand formed by residues 31 - 39 (chain F) in PDB entry 5GAG


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 31 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  TYR*     5.6     0.2    -      -       +      -
     30F  ARG*     1.3    79.9    -      -       -      +
     32F  GLU*     1.3    64.5    +      -       -      +
     33F  LYS      4.2     1.1    -      -       -      +
     34F  ILE*     4.5     3.8    -      -       +      -
     96F  MET*     3.5    28.8    -      -       +      +
     97F  TRP*     3.9    34.9    -      -       +      -
    100F  PHE*     5.1     9.0    -      -       +      -
    156F  ILE*     3.5    31.9    -      -       +      -
    157F  THR      3.8     6.1    -      -       -      +
    158F  THR*     4.2     3.6    -      -       -      +
    169F  LEU*     4.3    15.3    -      -       +      -
    170F  LEU*     6.3     1.8    -      -       +      -
    173F  PHE*     4.3    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 32 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2315A    G      4.8     1.9    +      -       -      -
     45B    A      5.6     5.1    +      -       -      +
     30F  ARG*     3.4     4.2    +      -       -      -
     31F  VAL*     1.3    72.5    -      -       -      +
     33F  LYS*     1.3    87.1    +      -       +      +
     92F  ARG*     4.1    23.6    +      -       -      +
     93F  GLY      4.7     1.2    +      -       -      -
     96F  MET*     3.1    15.6    -      -       -      +
    157F  THR*     3.0    25.3    +      -       +      +
    158F  THR      5.5     0.5    -      -       -      +
    159F  THR*     4.4    21.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 33 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2314A    A      3.0    42.9    +      -       -      -
   2315A    G      3.1    28.5    +      -       -      -
     31F  VAL*     4.2     0.3    -      -       -      +
     32F  GLU*     1.3    97.5    -      -       +      +
     34F  ILE*     1.3    68.3    +      -       -      +
     35F  THR*     4.0     6.2    +      -       -      +
     90F  THR*     3.9    15.2    -      -       +      +
     91F  LEU      3.6    11.0    -      -       -      +
     92F  ARG*     3.8    32.0    -      -       +      +
     96F  MET*     3.8     2.2    -      -       -      -
    156F  ILE*     3.7     1.2    -      -       -      +
    157F  THR*     2.9    41.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 34 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31F  VAL*     4.9     1.8    -      -       +      -
     33F  LYS*     1.3    80.0    -      -       -      +
     35F  THR*     1.3    62.6    +      -       -      +
     36F  LEU*     3.9     9.0    -      -       +      -
     89F  VAL      3.7     1.4    -      -       -      +
     90F  THR*     4.7     0.2    -      -       -      -
     91F  LEU*     2.8    42.8    +      -       +      +
     96F  MET*     3.5    38.1    -      -       +      +
     99F  PHE*     3.7    32.8    -      -       +      -
    100F  PHE*     4.0    26.0    -      -       +      -
    154F  ILE*     5.1     1.3    -      -       +      -
    155F  THR      3.3     8.3    -      -       -      +
    156F  ILE*     3.9    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 35 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2313A    C      3.7    33.9    -      -       -      +
   2314A    A      3.6    18.4    -      -       -      +
     33F  LYS*     4.0     7.1    +      -       -      +
     34F  ILE*     1.3    71.4    -      -       -      +
     36F  LEU*     1.3    78.2    +      -       -      +
     88F  LYS*     4.6     7.2    -      -       +      -
     89F  VAL      3.4     6.1    -      -       -      +
     90F  THR*     3.4    34.2    -      -       -      +
    153F  ASP      3.7     0.5    -      -       -      +
    155F  THR*     2.9    38.4    +      -       -      +
    157F  THR*     5.5     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 36 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34F  ILE*     3.9     7.2    -      -       +      -
     35F  THR*     1.3    87.7    -      -       -      +
     37F  ASN*     1.3    61.8    +      -       -      +
     57F  LEU*     3.8    30.7    -      -       +      +
     60F  ILE*     4.1     6.7    -      -       +      -
     61F  SER*     4.0    17.9    -      -       -      -
     88F  LYS*     3.1     7.3    -      -       -      +
     89F  VAL      2.9    39.3    +      -       -      +
     91F  LEU*     4.2     8.3    -      -       +      -
     99F  PHE*     3.5    47.6    -      -       +      -
    152F  LEU*     4.4     4.3    -      -       +      -
    153F  ASP      3.2     4.3    -      -       -      +
    154F  ILE*     3.6    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 37 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2305A    U      4.2     2.9    +      -       -      +
   2312A    U      2.5    50.7    +      -       -      -
   2313A    C      3.3    36.7    +      -       -      +
     35F  THR      4.3     0.2    -      -       -      -
     36F  LEU*     1.3    76.0    -      -       -      +
     38F  MET*     1.3    64.9    +      -       -      +
     39F  GLY      3.5    10.9    -      -       -      +
     57F  LEU*     4.9     0.4    -      -       -      +
     87F  CYS      3.3    10.8    -      -       -      +
     88F  LYS*     3.8     3.5    -      -       -      +
    152F  LEU*     3.7     2.9    -      -       -      +
    153F  ASP*     2.9    53.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 38 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2305A    U      3.8     4.7    -      -       -      +
   2312A    U      4.8     0.2    +      -       -      -
     37F  ASN*     1.3    78.1    -      -       -      +
     39F  GLY*     1.3    65.1    +      -       -      +
     40F  VAL*     3.6     3.6    +      -       +      +
     53F  ALA*     3.6    26.5    -      -       +      +
     56F  ASP*     3.7    23.3    -      -       +      -
     57F  LEU*     3.7    26.0    -      -       +      +
     60F  ILE*     3.8     4.0    -      -       +      -
     86F  GLY*     3.4     2.9    -      -       -      -
     87F  CYS*     2.9    41.4    +      -       -      +
    135F  GLN*     4.9     1.1    -      -       +      -
    150F  ARG*     3.9    25.1    -      -       +      -
    151F  GLY      3.6    16.2    -      -       -      +
    152F  LEU*     3.6    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 39 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2305A    U      3.1    12.7    +      -       -      +
   2306A    C      3.0    31.4    +      -       -      +
   2307A    G      4.7     3.1    -      -       -      -
   2312A    U      4.3    18.8    +      -       -      -
     37F  ASN*     3.5     8.0    -      -       -      +
     38F  MET*     1.3    73.0    -      -       -      +
     40F  VAL*     1.3    63.0    +      -       -      +
     42F  GLU*     4.9     0.5    -      -       -      +
     85F  ILE*     4.4     4.5    -      -       -      -
     86F  GLY*     4.7     1.6    -      -       -      -
----------------------------------------------------------
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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