Contacts of the strand formed by residues 145 - 149 (chain B) in PDB entry 2Y2V


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 145 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  VAL*     4.1     4.9    -      -       +      -
    102B  TRP      3.5     3.8    -      -       -      +
    103B  THR*     3.9    28.7    -      -       +      -
    108B  PRO*     4.3    11.7    -      -       +      -
    112B  THR*     4.1    14.8    -      -       -      +
    113B  PRO      3.5    10.5    +      -       -      +
    114B  VAL*     3.3    13.4    -      -       +      +
    115B  LEU*     2.9    25.5    +      -       -      +
    143B  GLY      3.9     0.8    +      -       -      -
    144B  ALA*     1.3    72.7    -      -       -      +
    146B  LEU*     1.3    60.7    +      -       -      +
    147B  VAL*     4.6     0.7    -      -       +      -
    187B  ILE*     3.9    32.5    -      -       +      -
    190B  PHE*     5.0     0.4    -      -       +      -
    191B  GLY      4.3     0.4    -      -       -      -
    192B  GLY*     4.0    21.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  ASN      3.7     0.2    -      -       -      +
    101B  VAL*     3.3     4.9    -      -       -      +
    102B  TRP*     2.9    64.6    +      -       +      +
    115B  LEU*     3.4    16.2    -      -       +      +
    117B  TRP*     4.8     3.6    -      -       +      -
    133B  TYR      5.0     0.7    -      -       -      +
    135B  GLY*     4.3    12.3    -      -       -      +
    138B  LEU*     3.4    38.1    -      -       +      -
    139B  ALA*     5.5     0.2    -      -       +      -
    144B  ALA*     3.7     6.9    +      -       +      +
    145B  VAL*     1.3    74.5    -      -       -      +
    147B  VAL*     1.3    75.5    +      -       -      +
    148B  SER*     4.5     4.7    -      -       -      +
    200B  PHE*     4.1    11.0    -      -       +      -
    455B  PHE*     4.0    18.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  LEU*     4.6    12.8    -      -       +      -
    100B  ASN      3.2     9.6    -      -       -      +
    101B  VAL*     4.1    12.1    -      -       +      -
    114B  VAL*     3.9    13.9    -      -       +      -
    115B  LEU      2.8    12.5    +      -       -      +
    116B  ILE*     3.3    15.1    -      -       +      -
    117B  TRP      2.8    25.5    +      -       -      -
    145B  VAL*     4.6     0.4    -      -       +      -
    146B  LEU*     1.3    83.8    -      -       -      +
    148B  SER*     1.3    71.3    +      -       -      +
    149B  MET*     5.0     2.2    -      -       +      +
    179B  ALA*     5.7     0.7    -      -       +      +
    183B  VAL*     3.9    22.2    -      -       +      -
    187B  ILE*     3.8    28.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  LEU*     3.2     3.8    -      -       -      +
    100B  ASN*     2.7    59.2    +      -       -      +
    102B  TRP*     4.0     7.2    -      -       -      -
    117B  TRP*     3.7    28.5    -      -       -      -
    128B  ALA*     3.4    18.7    +      -       -      +
    133B  TYR*     5.4     2.9    +      -       -      -
    146B  LEU*     4.5     5.1    -      -       -      +
    147B  VAL*     1.3    77.7    -      -       -      +
    149B  MET*     1.3    59.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  PHE*     3.9     3.6    -      -       +      -
     98B  TYR      3.6     4.9    -      -       -      -
     99B  LEU*     3.9     9.6    -      -       +      -
    116B  ILE*     3.5    31.9    -      -       +      -
    117B  TRP      3.8    11.9    +      -       -      +
    118B  ILE*     4.2    18.8    -      -       +      -
    119B  TYR*     3.3    19.2    -      -       -      -
    128B  ALA*     3.7     4.7    -      -       -      +
    147B  VAL*     5.5     1.8    -      -       +      -
    148B  SER*     1.3    73.9    -      -       -      +
    150B  ASN*     1.3    76.5    +      -       -      +
    151B  TYR*     3.9     1.9    +      -       -      -
    176B  GLN*     4.2    23.1    -      -       +      +
    179B  ALA*     3.7    29.6    -      -       +      -
    180B  LEU*     4.0    17.5    -      -       +      -
----------------------------------------------------------
 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