Contacts of the strand formed by residues 65 - 69 (chain C) in PDB entry 5YL4


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 ALA 65 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  SER*     3.1    14.6    -      -       -      +
      8C  HIS*     4.2     1.6    -      -       +      -
     21C  TRP*     3.8    30.5    -      -       +      +
     63C  PRO*     3.0    10.2    +      -       +      -
     64C  ARG*     1.3    77.3    -      -       -      +
     66C  VAL*     1.3    63.8    +      -       -      +
     67C  PHE*     4.2    15.0    -      -       +      -
     91C  GLN*     2.9    31.6    +      -       -      +
    125C  LEU*     3.7     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  ILE*     5.3     0.4    -      -       +      +
      6C  SER      3.0     6.6    +      -       -      +
      7C  ILE*     3.4    10.0    -      -       +      +
      8C  HIS*     2.9    27.4    +      -       -      +
     65C  ALA*     1.3    73.6    -      -       -      +
     67C  PHE*     1.3    65.6    +      -       -      +
     68C  VAL*     3.5    25.1    -      -       +      -
     91C  GLN*     3.5    10.5    -      -       -      +
     93C  ILE*     3.7    20.9    -      -       +      -
    118C  VAL*     4.8     1.1    -      -       +      -
    121C  ARG*     4.3    12.3    -      -       +      +
    122C  ILE*     4.0    26.7    -      -       +      +
    125C  LEU*     3.5    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 67 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8C  HIS*     3.5    20.2    -      +       +      -
     14C  VAL*     3.6    46.2    -      -       +      -
     17C  GLY*     4.2     6.7    -      -       -      -
     18C  ASN*     4.2    12.1    -      -       -      -
     21C  TRP*     4.0    15.5    -      +       -      -
     65C  ALA*     4.2     8.1    -      -       +      -
     66C  VAL*     1.3    79.5    -      -       -      +
     68C  VAL*     1.3    63.7    +      -       -      +
     75C  ILE*     3.9    13.5    -      -       +      -
     78C  VAL*     4.6     7.2    -      -       +      -
     87C  PHE*     3.6    37.2    -      +       -      -
     91C  GLN      2.9     8.0    +      -       -      +
     92C  LEU*     3.8    27.1    -      -       +      -
     93C  ILE*     3.0    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  ILE*     4.4    10.3    -      -       +      -
      8C  HIS      2.8    16.7    +      -       -      +
      9C  VAL*     3.4     6.1    -      -       +      +
     10C  GLY      2.9    23.7    +      -       -      -
     14C  VAL*     4.0     1.7    -      -       -      +
     66C  VAL*     3.5    22.0    -      -       +      -
     67C  PHE*     1.3    79.9    -      -       -      +
     69C  ASP*     1.3    70.3    +      -       -      +
     70C  LEU*     5.5     1.1    -      -       +      -
     75C  ILE*     3.7     2.2    -      -       -      +
     93C  ILE*     3.5    10.8    -      -       +      +
    114C  ILE*     5.0     5.4    -      -       +      -
    118C  VAL*     3.4    38.8    -      -       +      -
    145C  THR*     6.0     0.4    -      -       +      -
    149C  PHE*     3.8    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 69 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  GLY*     3.5    23.6    -      -       -      +
     11C  GLN*     3.6    16.2    +      -       -      -
     14C  VAL*     4.6     1.3    -      -       +      +
     68C  VAL*     1.3    79.3    -      -       -      +
     70C  LEU*     1.3    73.2    +      -       -      +
     71C  GLU*     3.2    23.6    +      -       -      +
     74C  VAL*     4.3    14.2    -      -       -      +
     75C  ILE*     3.6    17.0    -      -       +      -
     93C  ILE      3.2     6.1    +      -       -      +
     94C  THR*     3.2     9.4    -      -       -      -
     95C  GLY      3.2    18.2    +      -       -      -
     98C  ASP*     5.5     0.2    -      -       -      +
    114C  ILE*     4.8     0.5    -      -       -      +
    145C  THR*     3.9    10.1    +      -       -      +
    501C  GTP      3.8     8.7    +      -       -      -
    502C   MG      4.2     5.2    -      -       -      -
----------------------------------------------------------
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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