Contacts of the strand formed by residues 142 - 151 (chain A) in PDB entry 4BEI


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
----------------------------------------------------------
    135A  VAL      3.5     6.5    -      -       -      +
    136A  VAL*     4.5    13.9    -      -       +      -
    140A  GLY      3.5    14.6    +      -       -      +
    141A  LYS*     1.3    74.5    -      -       -      +
    143A  PHE*     1.3    69.7    +      -       -      +
    144A  LYS*     4.1    14.3    -      -       +      +
    210B  ASP*     3.9    40.8    -      -       +      +
    212B  LEU*     3.7    31.4    -      -       +      -
    243B  PRO*     4.5     5.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  VAL*     3.9    17.7    -      -       +      -
     40A  ILE*     3.2    64.4    -      -       +      +
     42A  ALA*     4.6     8.3    -      -       +      -
    135A  VAL*     2.8    50.2    +      -       +      +
    137A  ALA*     4.1     7.0    -      -       +      -
    141A  LYS*     3.5    40.6    -      -       +      -
    142A  VAL*     1.3    78.2    -      -       -      +
    144A  LYS*     1.3    65.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ALA*     4.4    10.0    -      -       -      +
    132A  SER*     4.4     2.2    -      -       -      +
    133A  LEU      3.2    11.0    -      -       -      +
    134A  GLN*     4.0    27.6    -      -       +      +
    142A  VAL*     4.1    11.7    -      -       +      -
    143A  PHE*     1.3    80.5    -      -       -      +
    145A  ALA*     1.3    62.1    +      -       -      +
    146A  ASN*     4.2    13.7    -      -       -      +
    246A  GLU*     2.8    37.0    +      -       -      -
   1272A  O4B      5.8     0.8    -      -       -      -
    210B  ASP*     2.9    24.0    +      -       -      +
    211B  GLY*     3.7     3.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ALA*     3.5    26.0    -      -       +      +
     43A  ASN*     3.7    23.1    -      -       -      -
     44A  LEU*     3.3    12.4    -      -       +      +
    133A  LEU*     2.8    37.4    +      -       +      +
    144A  LYS*     1.3    76.5    -      -       -      +
    146A  ASN*     1.3    62.1    +      -       -      +
    147A  GLN*     6.2     0.2    -      -       -      +
----------------------------------------------------------
 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
----------------------------------------------------------
     44A  LEU*     4.4     0.7    -      -       -      -
    130A  THR*     3.8    19.4    -      -       +      +
    131A  VAL      3.2     8.5    -      -       -      +
    132A  SER*     3.0    30.5    +      -       -      -
    144A  LYS*     4.2    12.1    -      -       -      +
    145A  ALA*     1.3    84.6    +      -       -      +
    147A  GLN*     1.3    77.8    +      -       -      +
    148A  GLU*     6.0     0.9    -      -       +      -
   1272A  O4B      4.8     8.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     3.0    38.1    -      -       +      +
     45A  SER*     4.1     4.4    -      -       -      -
     46A  LEU*     3.6    34.5    -      -       +      +
    130A  THR*     3.6     3.4    -      -       -      +
    131A  VAL*     2.7    39.7    +      -       +      +
    146A  ASN*     1.3    83.2    +      -       -      +
    148A  GLU*     1.3    65.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LEU*     3.6    10.3    -      -       -      +
     49A  ASN*     3.9    11.1    -      -       -      +
    128A  LYS*     4.6    17.5    -      -       +      +
    129A  TYR      3.3    11.9    -      -       -      +
    130A  THR*     4.6    13.9    +      -       +      +
    146A  ASN*     6.3     0.4    -      -       +      -
    147A  GLN*     1.3    84.5    +      -       -      +
    149A  PHE*     1.3    66.6    -      -       -      +
    150A  VAL*     6.4     0.4    -      -       +      -
    155A  LEU*     4.7     5.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LEU*     4.2     6.5    -      -       +      -
     49A  ASN*     3.2    25.1    -      -       -      +
     51A  LEU*     4.0    12.6    -      -       +      -
     58A  ILE*     3.7    23.8    -      -       +      -
     80A  ILE*     4.2     8.3    -      -       +      -
    118A  PHE*     4.2     5.6    -      +       -      -
    120A  VAL*     3.9    21.5    -      -       +      -
    128A  LYS*     3.8     1.7    -      -       -      +
    129A  TYR*     2.8    77.8    +      +       +      +
    131A  VAL*     3.3    34.8    -      -       +      -
    148A  GLU*     1.3    76.5    -      -       -      +
    150A  VAL*     1.3    78.0    +      -       -      +
    151A  LYS*     5.0     0.7    -      -       +      -
    155A  LEU*     4.4     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ASN      2.8    17.4    +      -       -      +
     50A  GLN*     3.8     9.9    -      -       -      +
     51A  LEU*     2.9    29.3    +      -       -      +
    127A  GLY      3.4     7.0    -      -       -      +
    128A  LYS*     4.3    15.5    -      -       +      -
    148A  GLU*     6.4     0.4    -      -       +      -
    149A  PHE*     1.3    84.7    -      -       -      +
    151A  LYS*     1.3    61.5    +      -       -      +
    153A  VAL*     3.1    35.4    -      -       +      +
    154A  ASP      4.0    12.8    -      -       -      +
    155A  LEU*     3.7    29.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  LEU*     3.3    11.4    -      -       +      -
     52A  ALA      3.7     8.7    -      -       -      +
     53A  SER      2.9    26.2    +      -       -      -
     55A  GLY*     3.7    13.7    -      -       -      -
    120A  VAL*     3.9    20.0    -      -       +      -
    121A  PRO      3.4    21.3    -      -       -      -
    122A  GLU      3.1     6.7    +      -       -      -
    124A  MET*     2.7    23.3    +      -       +      +
    125A  ALA      3.9     9.9    -      -       -      +
    126A  ASP*     3.1    21.0    +      -       -      +
    127A  GLY      2.8    34.9    +      -       -      +
    129A  TYR*     4.0    18.4    -      -       +      +
    149A  PHE*     5.0     0.2    -      -       +      -
    150A  VAL*     1.3    76.7    -      -       -      +
    152A  GLY*     1.3    62.0    +      -       -      +
    153A  VAL      3.2     4.4    +      -       -      -
----------------------------------------------------------
 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