Contacts of the strand formed by residues 33 - 37 (chain A) in PDB entry 2YRZ


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 SER 33 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ALA*     3.3     6.4    -      -       -      -
     29A  LEU*     3.2    18.6    -      -       -      +
     30A  GLY*     2.7    44.4    +      -       -      +
     31A  PRO*     3.5     0.9    -      -       -      +
     32A  THR*     1.3    82.1    +      -       -      +
     34A  LEU*     1.3    72.1    +      -       -      +
     77A  VAL      3.3     6.3    -      -       -      -
     78A  GLU*     3.5    24.0    -      -       -      -
     80A  LEU*     4.6     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  PHE*     3.8    26.9    -      -       +      -
     28A  ALA*     3.4    32.1    -      -       +      +
     29A  LEU*     3.4     7.4    -      -       -      -
     33A  SER*     1.3    80.3    -      -       -      +
     35A  ARG*     1.3    58.3    +      -       -      +
     36A  VAL*     5.7     0.7    -      -       +      -
     76A  VAL*     3.1    12.3    -      -       -      +
     77A  VAL*     2.6    46.0    +      -       +      +
     80A  LEU*     3.4    25.1    -      -       +      -
     86A  TYR*     5.9     0.4    -      -       +      -
     88A  PHE*     4.3     8.1    -      -       +      -
    106A  ILE*     3.7    25.1    -      -       +      -
    108A  ILE*     3.5    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  VAL      2.5    23.9    -      -       -      +
     26A  PHE*     3.2     0.8    -      -       -      -
     27A  SER*     3.1    38.2    +      -       -      +
     29A  LEU*     3.8    11.3    -      -       +      +
     34A  LEU*     1.3    79.4    -      -       -      +
     36A  VAL*     1.3    56.7    +      -       -      +
     37A  SER*     3.8     4.3    +      -       -      -
     74A  SER*     4.0    25.6    +      -       -      -
     75A  VAL      3.3    13.5    -      -       -      +
     76A  VAL*     4.0    15.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  LEU*     4.0    13.7    -      -       +      -
     25A  VAL      3.2     2.5    -      -       -      -
     26A  PHE*     3.2    37.2    -      -       +      -
     34A  LEU*     4.3     1.1    -      -       +      -
     35A  ARG*     1.3    73.3    -      -       -      +
     37A  SER*     1.3    61.3    +      -       -      +
     38A  TRP*     3.2    11.7    -      -       +      -
     52A  VAL*     4.6     3.6    -      -       +      -
     74A  SER*     3.2     1.0    -      -       -      -
     75A  VAL*     2.8    46.4    +      -       +      +
     77A  VAL*     4.9     2.6    -      -       +      +
     88A  PHE*     3.7    24.5    -      -       +      -
     90A  VAL*     3.5    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  ARG      4.0     0.7    -      -       -      +
     24A  LEU*     3.4     5.3    -      -       -      -
     25A  VAL*     2.8    53.2    +      -       -      +
     35A  ARG*     5.0     5.6    -      -       -      -
     36A  VAL*     1.3    77.4    -      -       -      +
     38A  TRP*     1.3    66.5    +      -       -      +
     73A  THR*     3.2    14.5    +      -       -      -
     74A  SER*     3.8    13.1    -      -       -      -
----------------------------------------------------------
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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