Contacts of the strand formed by residues 211 - 219 (chain B) in PDB entry 4LEY


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 GLU 211 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200B  TYR*     3.9    16.8    +      -       -      +
    205B  LYS*     3.7    26.4    +      -       +      +
    209B  PRO      3.6     1.2    -      -       -      -
    210B  ASN*     1.3    90.1    +      -       -      +
    212B  PHE*     1.3    68.0    +      -       -      +
    213B  ASP*     5.5     2.9    -      -       -      +
    305B  SER*     3.2    22.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ALA*     4.1    12.6    -      -       +      -
    168B  ALA*     4.3     7.6    -      -       -      -
    171B  VAL*     3.7    29.6    -      -       +      -
    200B  TYR*     3.4    51.6    -      +       -      -
    201B  TYR*     3.6    22.0    -      +       +      +
    209B  PRO*     3.3    28.7    -      -       +      -
    211B  GLU*     1.3    77.6    -      -       -      +
    213B  ASP*     1.3    66.9    +      -       -      +
    214B  VAL*     4.1     2.2    -      -       +      -
    304B  ILE*     3.5    24.5    -      -       +      -
    305B  SER      2.9     9.2    +      -       -      +
    306B  VAL*     3.4    15.9    -      -       +      +
    307B  ASP*     2.9    27.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 213 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196B  ASN*     3.7     1.4    -      -       -      -
    197B  THR*     2.9    56.2    +      -       -      +
    198B  GLY*     3.9    14.3    -      -       -      -
    199B  SER      4.9     0.7    +      -       -      -
    200B  TYR*     5.8     0.4    -      -       -      +
    201B  TYR*     3.8     5.0    -      -       -      -
    211B  GLU*     5.5     2.5    -      -       -      +
    212B  PHE*     1.3    78.5    +      -       -      +
    214B  VAL*     1.3    65.3    +      -       -      +
    307B  ASP*     3.5    23.7    -      -       -      +
    309B  ILE*     4.1    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 214 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  VAL*     5.5     0.9    -      -       +      -
    175B  VAL*     4.2    22.0    -      -       +      -
    194B  GLN*     3.6    34.3    -      -       +      +
    195B  LEU      3.9     2.0    -      -       -      +
    196B  ASN*     3.6    13.5    -      -       -      +
    201B  TYR*     4.6    10.1    -      -       -      +
    212B  PHE*     4.9     2.2    -      -       +      -
    213B  ASP*     1.3    80.2    -      -       -      +
    215B  MET*     1.3    65.5    +      -       -      +
    216B  PHE*     3.7    17.6    +      -       +      -
    306B  VAL*     4.4    12.1    -      -       +      -
    307B  ASP      3.0    11.1    +      -       -      +
    308B  ILE*     3.5     9.4    -      -       +      -
    309B  ILE*     2.9    26.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  GLU      3.2     6.1    -      -       -      +
    194B  GLN*     3.3     3.3    -      -       -      +
    195B  LEU*     2.9    57.5    +      -       +      +
    197B  THR*     3.9    30.5    -      -       -      +
    214B  VAL*     1.3    72.5    -      -       -      +
    216B  PHE*     1.3    62.7    +      -       -      +
    217B  LYS*     3.6     3.0    +      -       +      +
    309B  ILE*     3.6    23.3    -      -       +      +
    311B  ALA*     3.6    27.1    -      -       +      -
    346B  TYR*     4.2    27.1    -      -       +      -
    348B  VAL*     5.0     2.5    -      -       +      -
    366B  SER*     4.6     9.4    -      -       -      +
    368B  SER*     4.0    18.2    -      -       -      -
    369B  HIS      5.3     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  VAL*     4.2    13.9    -      -       +      -
    178B  LEU*     4.1    12.1    -      -       +      -
    179B  LEU*     3.7    50.0    -      -       +      -
    182B  MET*     4.3     8.7    -      -       +      -
    192B  VAL*     3.8    27.3    -      -       +      +
    193B  GLU      3.3     4.9    -      -       -      -
    194B  GLN*     4.4     3.4    -      -       +      -
    214B  VAL*     3.7    23.3    +      -       +      -
    215B  MET*     1.3    76.6    -      -       -      +
    217B  LYS*     1.3    61.0    +      -       -      +
    266B  PHE*     3.9    31.2    -      +       +      -
    308B  ILE*     4.0    22.2    -      -       +      -
    309B  ILE      2.9     9.9    +      -       -      +
    310B  LEU*     3.8     4.2    -      -       -      +
    311B  ALA*     2.9    23.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  GLY      4.4     0.7    -      -       -      +
    192B  VAL*     3.3     3.0    -      -       -      +
    193B  GLU*     2.8    72.8    +      -       -      +
    194B  GLN      4.3    10.1    -      -       -      -
    195B  LEU*     4.2    19.7    -      -       +      -
    215B  MET*     3.6     4.2    -      -       +      +
    216B  PHE*     1.3    73.7    -      -       -      +
    218B  LEU*     1.3    60.6    +      -       -      +
    219B  GLU      4.2     0.2    -      -       -      -
    311B  ALA*     3.3    12.3    -      -       +      +
    313B  GLU*     2.5    31.3    +      -       +      +
    346B  TYR*     3.5    42.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  GLU      4.0    17.3    -      -       -      +
    189B  PHE*     4.3    12.1    -      -       +      +
    190B  LYS      3.7    15.7    -      -       -      +
    191B  GLY*     3.8     4.9    -      -       -      +
    192B  VAL*     3.7    33.7    -      -       +      +
    216B  PHE      5.2     0.2    -      -       -      +
    217B  LYS*     1.3    75.3    -      -       -      +
    219B  GLU*     1.3    76.2    +      -       -      +
    220B  VAL*     3.3    11.2    -      -       +      +
    248B  LEU*     4.4    13.5    -      -       +      -
    262B  MET*     4.1    25.4    -      -       +      -
    310B  LEU*     5.5     1.8    -      -       +      -
    311B  ALA      2.9    13.5    +      -       -      +
    312B  LEU*     3.4     2.1    -      -       -      -
    313B  GLU*     2.9    17.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  GLY      5.2     2.2    +      -       -      -
    217B  LYS      4.2     0.4    -      -       -      -
    218B  LEU*     1.3    82.3    -      -       -      +
    220B  VAL*     1.3    63.7    +      -       -      +
    221B  PRO*     3.3    30.3    -      -       +      +
    248B  LEU*     5.9     0.3    -      -       -      +
    313B  GLU*     3.3    36.3    +      -       +      +
    314B  SER*     5.3     0.7    -      -       -      -
    315B  LYS*     3.5    39.3    +      -       +      +
----------------------------------------------------------
 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