Contacts of the strand formed by residues 26 - 31 (chain C) in PDB entry 5A15


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 26 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  ALA*     6.4     0.9    -      -       +      -
     67B  LYS      3.8     8.1    -      -       -      +
     68B  ASP*     3.4    39.0    -      -       +      +
     69B  SER      4.5     1.6    -      -       -      +
     74B  PHE*     3.4    47.3    -      -       +      -
     24C  PRO*     3.5    15.8    -      -       +      +
     25C  GLU*     1.3    79.1    -      -       +      +
     27C  VAL*     1.3    64.2    +      -       -      +
     28C  GLU*     3.9     1.4    +      -       -      +
     37C  PHE*     4.2     9.1    -      -       +      -
     38C  THR      3.3    17.7    -      -       -      +
     39C  ARG*     4.2     0.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 27 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  PHE*     5.0     2.7    -      -       +      -
     24C  PRO*     4.0    16.4    -      -       +      +
     26C  VAL*     1.3    75.6    -      -       -      +
     28C  GLU*     1.3    64.8    +      -       -      +
     29C  LEU*     3.8    11.0    +      -       +      +
     36C  TYR      3.8     0.2    -      -       -      +
     37C  PHE*     3.5     5.1    -      -       -      -
     38C  THR*     2.7    34.9    +      -       +      +
     40C  HIS*     3.9    29.2    -      -       +      -
     43C  LEU*     3.8    32.8    -      -       +      -
     55C  PHE*     4.3     2.9    -      -       +      -
     73C  PHE*     3.3    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 28 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  SER*     4.9     7.8    +      -       -      -
     24C  PRO*     5.5     0.8    -      -       -      +
     26C  VAL      3.9     2.6    +      -       -      +
     27C  VAL*     1.3    72.8    -      -       -      +
     29C  LEU*     1.3    61.9    +      -       -      +
     35C  VAL*     4.0     5.8    -      -       +      +
     36C  TYR      3.7     2.5    -      -       -      -
     37C  PHE*     3.1    46.9    -      -       +      -
     72C  ARG*     3.2    44.2    +      -       +      +
     73C  PHE*     3.4    27.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 29 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  VAL*     4.2    13.9    -      -       +      +
     28C  GLU*     1.3    75.0    -      -       -      +
     30C  ASN*     1.3    61.5    +      -       -      +
     31C  VAL*     4.0    11.9    -      -       +      -
     35C  VAL*     3.3    11.1    -      -       -      +
     36C  TYR*     2.6    42.9    +      -       +      +
     38C  THR*     4.1    10.5    -      -       +      -
     43C  LEU*     3.9    22.9    -      -       +      -
     51C  LEU*     5.8     0.7    -      -       +      -
     55C  PHE*     3.7    30.3    -      -       +      -
     72C  ARG*     4.5     2.0    -      -       -      -
     73C  PHE*     3.7    17.0    -      -       +      +
     75C  ILE*     4.5    11.4    -      -       +      -
     82C  PHE*     3.8    29.6    -      -       +      -
     86C  LEU*     5.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 30 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  LEU*     1.3    73.4    -      -       -      +
     31C  VAL*     1.3    59.8    +      -       -      +
     32C  GLY      4.0     0.2    +      -       -      -
     33C  GLY*     3.0    32.2    +      -       -      -
     34C  GLN      3.8     2.9    -      -       -      -
     35C  VAL*     4.6     4.7    -      -       -      +
     68C  ASP*     3.0    39.0    +      -       -      +
     72C  ARG*     4.1    13.9    -      -       +      +
     73C  PHE      2.7    16.5    +      -       -      +
     74C  PHE*     3.3    15.0    -      -       +      -
     75C  ILE      2.9    25.1    +      -       -      -
     37D  PHE*     3.9    21.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 31 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  LEU*     4.3     8.1    -      -       +      -
     30C  ASN*     1.3    75.4    +      -       -      +
     32C  GLY*     1.3    59.1    +      -       -      +
     33C  GLY      3.0     2.5    -      -       -      -
     34C  GLN*     2.8    30.2    +      -       -      +
     36C  TYR*     4.0     9.0    -      -       +      -
     75C  ILE*     3.6    29.4    -      -       +      -
     77C  ARG*     3.6    17.9    -      -       +      +
     78C  ASP      3.8     5.8    -      -       -      +
     79C  GLY*     3.0    16.2    -      -       -      -
     82C  PHE*     3.7    54.1    -      -       +      -
----------------------------------------------------------
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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