Contacts of the strand formed by residues 42 - 49 (chain C) in PDB entry 2E3V


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 LYS 42 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  SER*     3.0    17.2    +      -       -      -
     16B  ASP*     3.3    22.4    -      -       -      +
     30B  ASP*     2.8    30.6    +      -       -      +
     40C  ILE*     3.5     8.3    -      -       -      +
     41C  LEU*     1.3    95.7    -      -       +      +
     43C  TYR*     1.3    61.9    -      -       -      +
     59C  TRP*     3.7    17.9    -      -       +      -
     60C  TYR      3.3    13.5    -      -       -      +
     61C  ASP*     2.8    22.8    +      -       -      -
     62C  ALA      3.9     2.0    -      -       -      +
     88C  ALA*     3.6     0.2    -      -       -      -
     89C  LEU*     2.7    51.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 43 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  PRO*     4.1     9.4    -      -       +      -
     29C  PHE*     3.4    30.1    -      +       +      -
     31C  GLU*     3.4    19.5    -      -       +      +
     40C  ILE*     3.6    12.0    -      -       +      +
     42C  LYS*     1.3    73.0    -      -       -      +
     44C  LYS*     1.3    60.8    +      -       -      +
     45C  ALA      4.2     0.4    -      -       -      -
     59C  TRP*     3.4     8.6    -      -       -      -
     60C  TYR*     2.7    44.7    +      -       +      +
     62C  ALA*     3.7    35.0    -      -       +      -
     65C  ALA*     3.8    17.3    -      -       +      -
     71C  VAL*     4.4     9.0    -      -       +      -
     86C  LEU*     5.7     4.5    -      -       +      -
     87C  ALA      3.4    13.9    -      -       -      +
     88C  ALA*     3.6    22.7    -      -       +      -
     89C  LEU      4.8     0.2    -      -       -      +
   1008C  BTB      3.0    26.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 44 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  GLN*     3.1    29.7    +      -       -      +
     28B  GLN*     4.7     0.6    -      -       -      +
     43C  TYR*     1.3    76.4    -      -       -      +
     45C  ALA*     1.3    67.4    +      -       -      +
     46C  GLU*     4.2    17.9    +      -       +      +
     57C  SER*     3.6    28.5    +      -       -      -
     58C  LYS      3.4    10.3    -      -       -      +
     59C  TRP*     3.6    36.3    -      -       +      +
     60C  TYR*     4.9     0.2    -      -       -      -
     86C  LEU*     3.3     4.9    -      -       -      +
     87C  ALA*     2.8    38.3    +      -       +      +
     94C  LEU*     4.6    19.1    -      -       +      +
     97C  ILE*     4.4     3.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

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    74.5    -      -       -      +
     46C  GLU*     1.3    60.5    +      -       -      +
     47C  TRP*     4.0    12.8    -      -       +      -
     57C  SER*     3.1     7.6    -      -       -      -
     58C  LYS      2.9    30.4    +      -       -      -
     60C  TYR*     3.6    25.4    -      -       +      +
     71C  VAL*     4.4     4.5    -      -       +      -
     73C  ILE*     4.5     7.6    -      -       +      -
     85C  ARG      3.5     5.4    -      -       -      +
     86C  LEU*     3.4    21.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 46 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  LYS*     4.2    20.7    +      -       +      -
     45C  ALA*     1.3    79.0    -      -       -      +
     47C  TRP*     1.3    63.0    +      -       -      +
     55C  TRP*     3.7    21.0    -      -       +      +
     56C  HIS      3.1    11.9    -      -       -      +
     57C  SER*     3.8    10.0    -      -       -      -
     84C  VAL*     3.3     4.6    -      -       -      +
     85C  ARG*     2.8    79.7    +      -       +      +
     97C  ILE*     3.6    17.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 47 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  MSE      3.3    39.0    -      -       +      +
     68B  GLU*     4.4     0.2    -      -       +      -
     45C  ALA*     3.6     9.4    -      -       +      -
     46C  GLU*     1.3    81.5    -      -       -      +
     48C  ARG*     1.3    63.5    +      -       -      +
     55C  TRP*     3.6     3.1    -      -       -      -
     56C  HIS*     2.7    66.9    +      -       +      +
     57C  SER*     3.5    17.7    -      -       -      -
     58C  LYS*     3.5    27.8    -      -       +      -
     60C  TYR*     4.8     1.1    -      -       -      -
     73C  ILE*     3.5    44.0    -      -       +      -
     74C  VAL      4.4     1.0    +      -       -      -
     76C  LEU*     3.5    28.6    -      -       +      +
     82C  TYR*     4.0    15.7    -      +       +      -
     83C  ALA      3.1    13.7    -      -       -      +
     84C  VAL*     4.3     3.1    -      -       +      -
    103C  PHE*     5.3     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 48 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47C  TRP*     1.3    78.5    -      -       -      +
     49C  ALA*     1.3    67.9    +      -       -      +
     50C  VAL*     3.5     0.9    +      -       -      +
     52C  GLU*     3.3    30.0    +      -       +      +
     53C  GLU*     3.2    40.9    +      -       -      -
     54C  VAL      3.3    17.0    -      -       -      +
     55C  TRP*     3.2    50.6    -      -       +      +
     56C  HIS*     5.4     2.2    -      -       -      -
     82C  TYR*     3.7     4.3    -      -       -      -
     83C  ALA*     2.8    38.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 49 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  ARG*     1.3    77.0    -      -       -      +
     50C  VAL*     1.3    63.4    +      -       -      +
     51C  GLY      3.1     0.2    +      -       -      -
     52C  GLU*     2.8    44.9    +      -       +      +
     56C  HIS*     5.9     1.0    +      -       -      -
     77C  LYS*     5.4     6.7    -      -       -      -
     80C  THR*     3.9    18.4    -      -       +      -
     81C  THR      3.4     6.7    -      -       -      -
     82C  TYR*     3.4    26.0    -      -       +      +
----------------------------------------------------------
 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