Contacts of the strand formed by residues 142 - 148 (chain A) in PDB entry 2Y1Z


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 142 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  ASN*     4.3    10.8    -      -       +      +
     79A  LEU      3.3    17.9    -      -       -      +
     80A  ASP*     5.1     7.0    -      -       +      +
     81A  VAL*     4.3     1.8    -      -       -      -
    136A  SER      3.7     0.9    -      -       -      +
    137A  MET*     3.4     6.0    -      -       -      -
    138A  SER*     3.1    37.2    +      -       -      +
    140A  ASP*     4.3    15.9    -      -       +      +
    141A  GLY*     1.3    80.7    -      -       -      +
    143A  LEU*     1.3    68.2    +      -       -      +
    144A  THR*     3.9    13.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  VAL      3.5     1.9    -      -       -      +
     78A  ASN*     3.4     2.8    -      -       -      -
     79A  LEU*     2.7    66.0    +      -       +      +
     81A  VAL*     3.9    16.6    -      -       +      +
     89A  LEU*     4.6    24.5    -      -       +      -
     91A  VAL*     4.0    22.2    -      -       +      -
    100A  VAL*     4.4     9.0    -      -       +      -
    101A  HIS      6.2     0.2    -      -       -      +
    118A  PHE*     4.9     1.1    -      -       +      -
    136A  SER      3.3    17.9    -      -       -      +
    137A  MET*     4.4     7.4    -      -       +      -
    142A  VAL*     1.3    72.9    -      -       -      +
    144A  THR*     1.3    64.3    -      -       -      +
    145A  VAL*     5.0     2.5    -      -       +      -
   1152A  MRD      3.8    28.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  SER*     4.1    11.2    -      -       -      -
     77A  VAL      3.2     4.9    -      -       -      +
     78A  ASN*     2.5    29.6    +      -       -      +
    134A  THR      4.0     0.3    -      -       -      +
    135A  SER*     3.2     4.9    -      -       -      -
    136A  SER*     2.9    44.3    +      -       -      +
    142A  VAL*     3.9     8.2    +      -       -      +
    143A  LEU*     1.3    74.0    -      -       -      +
    145A  VAL*     1.3    65.0    +      -       -      +
    146A  ASN*     3.4    29.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PHE*     4.1     1.2    -      -       -      +
     76A  SER*     3.3     1.7    -      -       -      -
     77A  VAL*     2.8    47.5    +      -       +      +
     79A  LEU*     5.8     1.6    -      -       +      -
     91A  VAL*     4.2    21.1    -      -       +      -
     98A  ILE*     3.6    48.3    -      -       +      +
    100A  VAL*     4.2    11.2    -      -       +      -
    133A  ILE*     3.7    20.2    -      -       +      -
    134A  THR      3.4     6.7    -      -       -      +
    135A  SER*     4.2     4.3    -      -       -      -
    143A  LEU*     5.0     4.7    -      -       +      -
    144A  THR*     1.3    78.1    -      -       -      +
    146A  ASN*     1.3    62.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ARG*     4.1    31.1    +      -       -      +
     75A  PHE*     3.3    14.1    -      -       -      +
     76A  SER*     3.7    11.8    -      -       -      -
    132A  THR      4.0     0.9    -      -       -      +
    133A  ILE*     3.6     7.9    -      -       -      -
    134A  THR*     2.8    51.9    +      -       -      +
    135A  SER*     5.4     0.3    -      -       -      -
    136A  SER*     5.1     5.6    +      -       -      -
    144A  THR*     3.4    21.2    -      -       -      +
    145A  VAL*     1.3    76.0    -      -       -      +
    147A  GLY*     1.3    60.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ARG*     4.5     5.2    -      -       -      -
     75A  PHE*     3.1    31.7    +      -       -      +
    128A  VAL*     4.1     7.3    -      -       -      +
    132A  THR      3.9     8.1    -      -       -      -
    133A  ILE*     4.0    13.7    -      -       -      +
    146A  ASN*     1.3    76.9    -      -       -      +
    148A  PRO*     1.3    74.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ASP      3.9    12.3    -      -       -      +
     74A  ARG*     3.9    18.6    -      -       +      +
    128A  VAL*     3.5    15.9    -      -       -      +
    129A  ASP      4.8     0.7    +      -       -      -
    132A  THR*     4.1    27.8    +      -       +      +
    147A  GLY*     1.3    87.7    -      -       -      +
    149A  ARG*     1.3    65.7    +      -       -      +
    150A  LYS      3.8     1.4    +      -       -      -
----------------------------------------------------------
 Back to top of page


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