Contacts of the strand formed by residues 142 - 153 (chain B) in PDB entry 5IYB


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 THR 142 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  THR*     4.4    12.8    -      -       -      +
    130B  LYS      3.3    14.1    +      -       -      -
    131B  THR*     3.9    19.6    +      -       -      +
    140B  LEU*     3.9    27.8    -      -       +      -
    141B  GLN*     1.3    75.5    -      -       -      +
    143B  GLN*     1.3    68.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  ILE      3.8     1.4    -      -       -      +
    129B  THR*     3.7    25.2    -      -       -      +
    130B  LYS*     3.5    39.6    +      -       +      +
    141B  GLN      5.2     3.7    -      -       -      +
    142B  THR*     1.3    82.2    +      -       -      +
    144B  HIS*     1.3    63.3    +      -       -      +
    145B  GLN*     4.0    16.5    +      -       +      +
    159T  HIS*     5.8     4.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  ASP*     2.5    42.3    +      -       -      -
    128B  ILE      4.3     2.0    -      -       -      -
    129B  THR*     4.8     6.3    -      -       +      -
    143B  GLN*     1.3    74.1    -      -       -      +
    145B  GLN*     1.3    79.5    +      -       -      +
    146B  LYS*     4.3    14.0    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  ASP*     3.8     3.1    -      -       -      -
    128B  ILE*     3.6    29.1    +      -       +      +
    130B  LYS*     5.5    10.8    -      -       -      +
    143B  GLN*     4.5    17.5    +      -       +      +
    144B  HIS*     1.3    99.4    +      -       -      +
    146B  LYS*     1.3    60.4    +      -       -      +
    147B  THR*     4.0    12.9    +      -       -      +
    430B  ASN*     5.4     0.8    +      -       -      -
    431B  LEU*     3.3    32.9    -      -       -      +
    432B  GLU*     3.7    27.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  TYR*     3.0    46.2    -      -       +      -
    125B  TYR*     4.9    10.2    -      -       +      -
    126B  VAL      3.8     1.3    -      -       -      -
    127B  ASP*     3.7    23.2    +      -       -      +
    144B  HIS*     4.4    16.2    -      -       +      +
    145B  GLN*     1.3    75.1    +      -       -      +
    147B  THR*     1.3    60.9    +      -       -      +
    148B  PHE      4.2     0.5    +      -       -      -
    145T  LEU*     4.3     7.6    -      -       +      -
    148T  VAL*     4.8    18.9    -      -       +      +
    150T  THR      4.6    11.7    -      -       -      +
    151T  THR*     4.7     8.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  TYR*     3.0     7.7    -      -       -      -
    126B  VAL      2.9    33.5    +      -       -      +
    128B  ILE*     3.4    32.8    -      -       +      +
    145B  GLN*     4.0    11.6    +      -       -      +
    146B  LYS*     1.3    83.1    +      -       -      +
    148B  PHE*     1.3    75.4    -      -       -      +
    149B  ILE*     3.6     3.4    +      -       -      +
    432B  GLU*     3.9    32.6    -      -       +      +
    435B  ILE*     4.6     7.6    -      -       +      -
    151T  THR      5.4     3.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  TRP*     5.7     4.9    -      +       -      -
    123B  PRO*     3.8    16.8    -      -       +      -
    124B  LEU      3.6     7.4    -      -       -      -
    125B  TYR*     3.6    30.1    -      +       +      -
    146B  LYS      4.2     0.4    +      -       -      -
    147B  THR*     1.3    83.8    -      -       -      +
    149B  ILE*     1.3    60.5    +      -       -      +
    150B  GLY*     3.2    34.1    -      -       -      -
    151B  LYS*     4.1    20.9    -      -       +      -
    435B  ILE*     4.5     3.3    -      -       -      +
    437B  THR*     3.3    39.7    -      -       +      +
    126M  ASP*     4.3    14.6    -      -       -      -
    127M  ARG*     5.7     7.0    -      -       +      -
    129M  ASN*     5.5     2.7    -      -       -      -
    151T  THR*     4.4    21.7    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  VAL*     5.9     0.2    -      -       +      -
     88B  PHE*     5.6     1.8    -      -       +      -
     91B  ILE*     4.7     5.4    -      -       +      -
    124B  LEU*     3.0    45.1    +      -       +      +
    125B  TYR*     4.2     2.5    -      -       -      -
    126B  VAL*     3.7    39.0    -      -       +      +
    147B  THR*     3.9     3.1    -      -       +      +
    148B  PHE*     1.3    77.3    -      -       -      +
    150B  GLY*     1.3    58.5    +      -       -      +
    404B  PHE*     5.6     0.9    -      -       +      -
    408B  PHE*     5.1    14.4    -      -       +      -
    411B  LEU*     4.8    11.1    -      -       +      +
    435B  ILE*     4.2    28.9    -      -       +      +
    436B  LYS      4.5     0.7    -      -       -      +
    437B  THR*     3.2    27.7    -      -       -      +
    440B  ILE*     3.8    15.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 150 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  LEU*     2.8    33.8    +      -       -      +
    148B  PHE*     3.2    17.8    -      -       -      -
    149B  ILE*     1.3    84.5    -      -       -      +
    151B  LYS*     1.3    60.2    +      -       -      -
    152B  ILE      4.1     0.2    -      -       -      -
    437B  THR*     3.9     3.1    -      -       -      -
    440B  ILE*     4.2    11.9    -      -       -      -
    441B  SER*     3.1    11.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 151 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  THR      5.9     1.3    -      -       -      +
     99B  TRP*     4.8    13.4    -      -       +      -
    121B  SER*     3.9    21.4    -      -       -      +
    122B  ALA      3.5     3.6    -      -       -      +
    123B  PRO*     4.2    17.7    -      -       +      -
    148B  PHE*     4.1    14.0    -      -       +      -
    150B  GLY*     1.3    73.5    -      -       -      +
    152B  ILE*     1.3    63.9    +      -       -      +
    153B  PRO*     3.7     7.1    -      -       -      +
    440B  ILE*     4.7     0.9    -      -       -      +
    441B  SER*     2.4    53.3    +      -       -      +
    126M  ASP*     3.4    21.3    +      -       -      -
    129M  ASN*     3.0    31.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 152 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  PHE*     4.8     4.7    -      -       +      -
     50B  PHE*     4.8     9.2    -      -       +      -
     51B  ILE*     4.7    19.3    -      -       +      -
     93B  LEU*     4.6     7.0    -      -       +      -
    121B  SER*     3.5     2.0    -      -       -      -
    122B  ALA      2.8    36.8    +      -       -      +
    124B  LEU*     4.0    29.2    -      -       +      -
    151B  LYS*     1.3    72.4    -      -       -      +
    153B  PRO*     1.3    82.0    -      -       +      +
    154B  ILE*     3.5     6.0    -      -       +      +
    404B  PHE*     4.1    13.5    -      -       +      -
    440B  ILE*     3.9    20.9    -      -       +      -
    444B  LEU*     3.5    27.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 153 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  PHE*     3.3    21.7    -      -       -      -
    119B  THR*     5.5     1.1    -      -       +      -
    120B  TYR      3.9     2.0    -      -       -      +
    121B  SER*     3.6    12.1    -      -       -      -
    151B  LYS      3.7     7.0    -      -       -      +
    152B  ILE*     1.3    96.5    -      -       +      +
    154B  ILE*     1.3    60.6    +      -       -      +
    185B  PHE*     4.2     6.9    -      -       +      -
    187B  ILE*     4.0    16.4    -      -       +      -
    400B  LEU*     6.5     0.4    -      -       +      -
    444B  LEU*     4.3    23.6    -      -       +      -
    445B  LYS*     4.8     9.6    -      -       +      +
    448B  LEU*     3.6    33.7    -      -       +      -
----------------------------------------------------------
 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