Contacts of the strand formed by residues 41 - 45 (chain C) in PDB entry 2YPA


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 TYR 41 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  ASP*     3.5    19.6    -      -       -      +
     40C  ARG*     1.3   104.3    +      -       +      +
     42C  PHE*     1.3    64.1    +      -       -      +
     52C  GLU*     3.4    27.5    +      -       -      +
    324D  ARG*     3.8    23.8    -      -       +      +
    325D  LEU*     4.0    19.7    -      -       -      -
    326D  GLU*     3.7    29.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 42 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  ILE*     4.4    34.3    -      -       +      -
     39C  ASP*     5.5     0.9    -      -       +      -
     40C  ARG      4.4     5.6    -      -       -      -
     41C  TYR*     1.3    80.5    -      -       -      +
     43C  LEU*     1.3    94.7    +      -       -      +
     44C  LYS*     5.0     3.1    -      -       +      -
     49C  TYR*     4.1    27.6    -      +       +      -
     50C  TRP      3.7    12.3    -      -       -      +
     51C  HIS*     5.4     2.0    -      -       -      -
     52C  GLU*     4.5     7.4    +      -       -      +
    323D  THR      4.0     0.2    -      -       -      +
    324D  ARG*     3.9     3.1    +      -       -      +
    325D  LEU*     3.5    66.2    +      -       +      +
    327D  ASN*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 43 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  PHE*     1.3    94.1    -      -       -      +
     44C  LYS*     1.3    58.5    +      -       -      +
     49C  TYR      3.7     0.2    -      -       -      -
     50C  TRP*     2.8    39.7    +      -       +      +
     51C  HIS      3.7    19.5    -      -       -      +
     52C  GLU*     3.8    26.2    -      -       +      +
     55C  LEU*     3.8    28.3    -      -       +      -
     65C  GLY*     4.4    19.1    -      -       -      +
    322D  ILE*     4.8     6.7    -      -       +      -
    323D  THR      3.5     6.5    -      -       -      +
    324D  ARG*     3.6    37.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 44 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  PHE*     5.0     4.7    -      -       +      -
     43C  LEU*     1.3    76.3    -      -       -      +
     45C  ALA*     1.3    66.0    +      -       -      +
     47C  ASP*     4.7    15.9    -      -       -      +
     48C  GLN      3.1    18.6    -      -       -      +
     49C  TYR*     3.5    45.8    +      -       +      -
     50C  TRP*     4.1     1.6    -      -       -      -
    321D  LEU      4.2     0.7    -      -       -      +
    322D  ILE*     4.0     2.4    -      -       -      +
    323D  THR*     3.4    34.2    +      -       -      +
    325D  LEU*     5.7     7.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 45 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  LYS*     1.3    77.6    -      -       -      +
     46C  ILE*     1.3    63.5    +      -       +      +
     47C  ASP      3.2     3.1    -      -       -      -
     48C  GLN*     2.7    30.9    +      -       -      +
     50C  TRP*     3.1    23.7    +      -       +      +
     55C  LEU*     4.6    10.1    -      -       +      -
     71C  LEU*     4.0    19.7    -      -       +      -
    321D  LEU      3.8    17.5    -      -       -      +
    322D  ILE*     4.7     4.3    -      -       +      -
----------------------------------------------------------
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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