Contacts of the strand formed by residues 148 - 154 (chain B) in PDB entry 4KAL


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 ALA 148 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  PHE*     3.3    16.6    -      -       +      +
      5B  LEU*     3.9    26.9    -      -       +      +
    144B  VAL      3.1    14.8    +      -       -      +
    145B  VAL      3.3     7.0    +      -       -      +
    146B  ALA      3.5     1.0    +      -       -      -
    147B  ASP*     1.3    78.9    -      -       -      +
    149B  LYS*     1.3    65.1    +      -       -      +
    150B  VAL*     3.3     9.7    +      -       -      +
    151B  THR*     4.3     3.9    +      -       -      +
    179B  ARG*     3.2    24.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      0B  THR*     3.5    28.2    +      -       +      +
      2B  PHE      3.0    10.4    +      -       -      +
      3B  ASP*     2.9    35.6    +      -       -      +
    147B  ASP      4.2     0.2    +      -       -      -
    148B  ALA*     1.3    70.9    -      -       -      +
    150B  VAL*     1.3    63.3    +      -       +      +
    179B  ARG*     3.6    15.4    -      -       -      +
    180B  GLU*     3.1    23.4    +      -       -      +
    287B  THR*     3.0    39.1    +      -       +      +
    288B  GLN*     5.1     2.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 150 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  ASP      3.0     8.5    +      -       -      +
      4B  VAL*     3.3     6.8    -      -       +      -
      5B  LEU*     2.9    25.6    +      -       -      +
    148B  ALA*     3.9     4.5    -      -       -      +
    149B  LYS*     1.3    83.4    -      -       +      +
    151B  THR*     1.3    66.8    +      -       -      +
    152B  TYR*     4.4     3.6    -      -       +      +
    180B  GLU*     3.3    16.8    -      -       +      +
    182B  SER*     3.9    26.9    -      -       -      -
    209B  ILE*     4.8     3.4    -      -       +      -
    283B  LEU*     4.1    16.4    -      -       +      -
    286B  TYR*     4.1    22.4    -      -       +      -
    287B  THR*     3.7    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 151 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LEU*     3.2    38.2    -      -       +      +
      7B  VAL*     4.3    11.4    -      -       +      -
    145B  VAL*     3.8    14.7    +      -       -      +
    148B  ALA*     4.3     6.4    +      -       -      +
    150B  VAL*     1.3    72.5    -      -       -      +
    152B  TYR*     1.3    57.8    +      -       -      +
    153B  PHE*     5.5     0.7    -      -       +      -
    167B  ILE*     6.0     0.7    -      -       +      -
    170B  CYS*     4.2    13.9    -      -       +      -
    174B  ALA*     4.7     2.2    -      -       -      +
    179B  ARG*     5.8     0.4    -      -       -      +
    180B  GLU      3.0     7.5    +      -       -      -
    181B  MSE      3.3    33.4    -      -       +      +
    182B  SER      2.7    31.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 152 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  VAL*     4.5     2.2    -      -       +      -
      5B  LEU      2.8    12.8    +      -       -      +
      6B  THR*     3.1    25.2    -      -       +      -
      7B  VAL*     2.9    25.5    +      -       -      +
     58B  SER*     4.8     3.7    +      -       -      -
     59B  ALA*     4.4    12.6    -      -       +      -
     62B  THR*     3.9    22.9    +      -       +      -
    150B  VAL*     4.6     1.3    -      -       +      -
    151B  THR*     1.3    74.1    -      -       -      +
    153B  PHE*     1.3    65.8    +      -       -      +
    182B  SER*     3.1    29.4    -      -       -      -
    184B  THR*     3.2    40.2    -      -       +      +
    211B  PHE*     3.6    24.4    -      +       -      +
    275B  GLY      5.0     2.1    +      -       -      -
    276B  ASP*     5.0     1.4    +      -       -      -
    279B  ALA*     3.5    20.7    -      -       +      +
    283B  LEU*     3.7    22.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 153 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  VAL*     3.4    12.6    -      -       +      +
    151B  THR*     5.5     0.7    -      -       +      -
    152B  TYR*     1.3    81.2    -      -       -      +
    154B  GLU*     1.3    69.9    +      -       -      +
    157B  LEU*     4.1     1.1    -      -       +      -
    158B  TRP*     3.7    21.5    -      +       -      -
    167B  ILE*     3.6    44.2    -      -       +      -
    181B  MSE      3.6    30.1    -      -       +      -
    182B  SER      2.9    30.9    +      -       -      -
    183B  MSE      3.2    36.0    -      -       +      -
    184B  THR*     3.1    27.3    +      -       -      +
    201B  LEU*     4.2     7.9    -      -       +      -
    206B  LYS      5.4     0.2    -      -       -      -
    207B  VAL*     3.6    21.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  VAL      3.3     3.4    +      -       -      +
      8B  GLY*     3.2    14.2    -      -       -      -
      9B  ASN*     2.9    22.9    +      -       -      +
     57B  GLY      4.0     0.7    -      -       -      -
     58B  SER*     3.3    21.2    +      -       -      +
     59B  ALA*     2.7    40.5    +      -       +      +
     60B  GLY      4.7     0.2    +      -       -      -
    153B  PHE*     1.3    84.4    -      -       -      +
    155B  GLY*     1.3    58.5    +      -       -      +
    156B  TYR*     3.6    15.3    -      -       +      +
    157B  LEU*     2.9    29.2    +      -       +      +
    158B  TRP*     4.4     1.4    -      -       -      -
    184B  THR*     3.8     9.6    -      -       +      -
    186B  SER*     3.7     5.8    -      -       -      +
    401B  ADN      3.3    20.7    -      -       -      -
----------------------------------------------------------
 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