Contacts of the strand formed by residues 3 - 9 (chain C) in PDB entry 2Y05


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 MET 3 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  SER*     1.3    85.3    +      -       -      +
      4C  THR*     1.3    60.4    +      -       -      +
     26C  THR*     3.4    31.2    -      -       +      -
     27C  SER*     3.4    16.4    -      -       -      +
     28C  GLU*     4.2    12.3    -      -       +      +
     29C  LEU*     5.0     2.7    -      -       -      +
     94C  HIS*     3.4    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 4 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  MET*     1.3    75.4    -      -       -      +
      5C  LYS*     1.3    64.3    +      -       -      +
      6C  THR*     4.0    11.7    -      -       -      +
     25C  LYS      3.8     0.5    -      -       -      +
     26C  THR*     3.3     6.0    -      -       -      +
     27C  SER*     3.0    55.6    +      -       -      +
     29C  LEU*     4.1    18.8    -      -       +      +
     92C  THR*     3.1     8.1    +      -       -      +
     93C  THR*     3.3     4.2    +      -       -      -
     94C  HIS*     2.9    42.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 5 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  THR*     1.3    72.9    -      -       -      +
      6C  THR*     1.3    61.9    +      -       -      +
     24C  LEU*     4.2    19.0    -      -       +      +
     25C  LYS      3.3     5.6    -      -       -      +
     26C  THR*     4.1    20.9    -      -       +      +
     92C  THR*     3.3     4.2    +      -       -      -
     93C  THR*     2.9    41.6    +      -       +      +
    306C  PHE*     3.4    29.0    -      -       +      +
    307C  GLU*     4.2    18.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 6 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  THR*     4.0    11.3    -      -       -      +
      5C  LYS*     1.3    73.4    -      -       -      +
      7C  TRP*     1.3    65.7    +      -       -      +
      8C  THR*     3.7     8.5    +      -       +      +
     23C  GLU      3.6     1.6    -      -       -      +
     24C  LEU*     3.5     3.9    -      -       -      +
     25C  LYS*     2.8    42.0    +      -       -      +
     27C  SER*     4.7     3.3    +      -       -      -
     62C  THR*     3.3    42.2    -      -       +      +
     91C  TRP      3.3     6.1    -      -       -      +
     92C  THR*     3.0    18.4    +      -       -      +
    306C  PHE*     4.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 7 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  THR*     1.3    69.7    -      -       -      +
      8C  THR*     1.3    60.3    +      -       -      +
     19C  ASN      5.5     0.9    -      -       -      -
     22C  PHE*     3.7    28.5    -      -       +      -
     23C  GLU*     3.6     8.7    -      -       -      -
     24C  LEU*     3.4    48.7    -      -       +      +
     62C  THR*     3.6     7.4    -      -       -      +
     63C  MET*     3.0    24.8    +      -       +      +
     91C  TRP*     2.9    33.4    +      +       +      +
    306C  PHE*     2.9    50.5    +      +       -      -
    307C  GLU*     3.1    27.4    -      -       +      -
    309C  MET*     4.0     8.1    -      -       +      -
    310C  PRO*     3.4    23.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 8 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  THR*     4.3    15.3    -      -       +      +
      7C  TRP*     1.3    78.4    -      -       -      +
      9C  LEU*     1.3    61.7    +      -       -      +
     10C  LYS*     5.2     0.2    -      -       -      -
     22C  PHE*     3.5    10.4    -      -       -      +
     23C  GLU*     2.7    54.1    +      -       -      +
     25C  LYS*     4.3    24.1    +      -       +      -
     60C  GLY*     3.5    24.1    -      -       -      +
     61C  ASP      3.2    11.0    -      -       -      +
     62C  THR*     4.1     8.3    -      -       -      +
     63C  MET*     4.4     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 9 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8C  THR*     1.3    70.1    -      -       -      +
     10C  LYS*     1.3    60.8    +      -       -      +
     11C  LYS      3.4    24.0    -      -       -      +
     12C  HIS*     3.6    35.4    -      -       +      +
     13C  PHE*     3.4    36.3    -      -       +      -
     21C  ASP      3.8     3.8    -      -       -      +
     22C  PHE*     5.2     1.1    -      -       +      -
     54C  ALA*     3.7    15.9    -      -       +      +
     57C  LEU*     3.9    16.2    -      -       +      +
     58C  LYS      4.8     4.9    -      -       -      +
     59C  GLU*     3.4     4.3    -      -       -      -
     60C  GLY*     2.7    31.9    +      -       -      -
     61C  ASP      2.8    14.7    +      -       -      +
     63C  MET*     4.1    15.9    -      -       -      +
----------------------------------------------------------
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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