Contacts of the strand formed by residues 161 - 170 (chain B) in PDB entry 1EKP


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 161 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  GLU*     3.7     3.8    -      -       -      +
     43B  TRP*     3.1    35.7    +      -       +      +
     48B  TRP*     5.4     0.9    -      -       +      -
    109B  LEU*     4.6     4.5    -      -       +      -
    110B  PRO*     3.8    36.1    -      -       +      -
    146B  LEU*     4.6     5.8    -      -       +      -
    147B  ILE      3.3    14.4    -      -       -      +
    149B  ASN*     4.0     6.0    +      -       -      +
    158B  PRO*     5.5     0.4    -      -       +      -
    160B  ARG*     1.3    79.2    +      -       -      +
    162B  LEU*     1.3    66.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  MET*     3.7    28.3    -      -       +      -
     41B  VAL      3.8     4.3    -      -       -      +
     42B  GLU*     3.2    41.1    -      -       +      +
     48B  TRP*     5.4     0.2    -      -       -      -
     59B  LEU*     4.9     5.4    -      -       +      -
     61B  LEU*     6.2     3.1    -      -       +      -
    145B  VAL      3.8     1.2    -      -       -      +
    146B  LEU*     3.4     4.5    -      -       -      +
    147B  ILE*     2.9    51.9    +      -       +      +
    149B  ASN*     4.6    15.3    -      -       +      +
    161B  ALA*     1.3    77.2    -      -       -      +
    163B  LEU*     1.3    65.3    +      -       -      +
    164B  PHE*     3.5    28.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 163 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  PHE*     4.3    18.6    -      -       +      -
     39B  LEU*     4.7     1.6    -      -       +      -
     40B  MET*     3.4     2.1    -      -       -      -
     41B  VAL*     2.8    54.7    +      -       +      +
     48B  TRP*     4.1    21.1    -      -       +      -
    100B  MET*     4.6    14.8    -      -       +      -
    112B  PHE*     4.5    13.9    -      -       +      -
    117B  LEU*     4.3    18.4    -      -       +      -
    145B  VAL      3.3    10.1    -      -       -      +
    146B  LEU*     3.6    15.0    -      -       +      -
    162B  LEU*     1.3    76.1    -      -       -      +
    164B  PHE*     1.3    74.2    +      -       -      +
    165B  VAL*     4.2    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 164 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  PRO*     3.5    31.4    -      -       +      -
     68A  LEU*     4.8     6.7    -      -       +      -
     69A  HIS*     4.6     2.9    -      +       -      -
     38B  MET*     4.2    16.8    -      -       +      -
     39B  LEU      3.0    15.3    -      -       -      +
     40B  MET*     4.2     7.4    -      -       -      -
     59B  LEU*     3.9    21.5    -      -       +      -
    145B  VAL*     2.8    72.6    +      -       +      +
    147B  ILE*     4.5    13.5    -      -       +      -
    162B  LEU*     3.5    20.0    -      -       +      -
    163B  LEU*     1.3    74.9    -      -       -      +
    165B  VAL*     1.3    70.5    +      -       -      +
    166B  ILE*     4.2    17.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  MET*     3.4     9.2    -      -       -      +
     39B  LEU*     3.1    53.2    +      -       +      -
    117B  LEU*     5.0     1.1    -      -       +      -
    121B  ILE*     4.3    13.9    -      -       +      -
    124B  LEU*     3.7    16.3    -      -       +      +
    142B  VAL*     3.8    29.2    -      -       +      -
    143B  ARG      3.4    10.3    -      -       -      +
    144B  PRO*     3.9    16.6    -      -       +      -
    163B  LEU*     4.2     7.9    -      -       +      -
    164B  PHE*     1.3    83.4    -      -       -      +
    166B  ILE*     1.3    65.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  PRO*     4.0    33.0    -      -       +      +
     64A  ALA*     4.4     7.9    -      -       +      -
     69A  HIS*     4.5    11.4    -      -       +      -
    153A  LEU*     4.5     4.0    -      -       +      -
     34B  PHE*     3.6    29.2    -      -       +      -
     37B  HIS      5.0     1.3    -      -       -      -
     38B  MET*     4.3    11.4    -      -       +      -
     56B  PHE*     3.6    26.7    -      -       +      -
    141B  TYR      4.0     0.3    -      -       -      +
    143B  ARG*     3.0    43.5    +      -       +      +
    164B  PHE*     4.2    12.1    -      -       +      -
    165B  VAL*     1.3    79.1    -      -       -      +
    167B  LEU*     1.3    66.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  PHE*     3.3     7.7    -      -       -      +
     35B  THR*     3.1    46.8    +      -       +      +
     37B  HIS      4.9     1.6    +      -       -      +
     56B  PHE*     5.5     0.8    -      -       -      -
    121B  ILE*     5.7     0.2    -      -       +      -
    124B  LEU*     3.6    37.5    -      -       +      +
    125B  ILE*     4.2    18.2    -      -       +      -
    128B  ASP*     4.2    12.8    -      -       +      +
    140B  LEU*     4.0    22.7    -      -       +      -
    141B  TYR      3.5     3.1    -      -       -      -
    142B  VAL*     3.7    36.1    -      -       +      -
    166B  ILE*     1.3    85.3    -      -       -      +
    168B  CYS*     1.3    65.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LEU*     4.1    15.5    -      -       -      -
     31B  GLY*     3.5    33.7    -      -       -      -
     33B  THR      2.6    24.5    -      -       -      +
     34B  PHE*     3.8     7.2    -      -       +      -
    140B  LEU*     3.8     4.9    -      -       -      +
    141B  TYR*     2.9    47.5    +      -       -      +
    143B  ARG*     6.4     0.2    -      -       -      -
    167B  LEU*     1.3    76.6    -      -       -      +
    169B  PRO*     1.3    69.2    -      -       -      +
    170B  VAL*     4.2     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  PRO*     4.7     8.1    -      -       +      -
     28B  LEU*     4.3    22.7    -      -       +      +
     29B  VAL      4.4     7.6    -      -       -      +
     33B  THR*     3.1    26.7    +      -       +      +
     35B  THR*     4.5     6.1    -      -       +      -
    131B  TRP*     3.9    38.6    -      -       +      +
    133B  PRO*     3.8    20.4    -      -       +      -
    139B  SER      3.7     7.4    -      -       -      +
    140B  LEU*     4.0     4.9    -      -       +      -
    168B  CYS*     1.3    84.7    -      -       -      +
    170B  VAL*     1.3    64.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  LEU*     4.3     6.0    -      -       -      +
     29B  VAL      5.1     0.7    -      -       -      -
     30B  PHE*     3.7    33.0    -      -       +      -
     31B  GLY      3.8    15.5    -      -       -      +
     79B  LYS*     4.3    12.8    -      -       -      +
    133B  PRO*     4.7     0.4    -      -       -      +
    138B  THR*     3.5     2.8    -      -       -      -
    139B  SER*     3.0    53.2    +      -       -      +
    141B  TYR*     4.0    18.4    -      -       +      -
    168B  CYS*     3.7     9.9    -      -       -      +
    169B  PRO*     1.3    80.4    -      -       -      +
    171B  GLY*     1.3    68.3    +      -       -      +
----------------------------------------------------------
 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