Contacts of the helix formed by residues 40 - 53 (chain B) in PDB entry 5IY8


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 40 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  GLY      3.5     0.4    -      -       -      -
     39B  LEU*     1.3    88.1    -      -       +      +
     41B  ARG*     1.3    66.2    +      -       -      +
     42B  GLN*     3.5    15.5    -      -       -      +
     43B  GLN*     3.8     7.9    +      -       +      +
     44B  LEU*     3.4    27.0    +      -       +      +
    181B  PRO*     3.6    35.0    -      -       +      +
    182B  GLY      4.2     3.4    -      -       -      +
    479B  LEU*     5.1     8.1    -      -       +      +
    482B  LEU*     3.7    41.5    -      -       +      -
    483B  ARG      5.2     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  GLU      4.8     4.2    +      -       -      -
     37B  LYS*     3.2    52.5    +      -       +      +
     38B  GLY*     4.4     4.6    +      -       -      +
     39B  LEU      4.0     0.4    -      -       -      -
     40B  VAL*     1.3    79.1    -      -       -      +
     42B  GLN*     1.3    62.5    +      -       -      +
     43B  GLN      3.2     0.2    -      -       -      -
     44B  LEU*     4.3    20.0    -      -       -      +
     45B  ASP*     2.7    65.0    +      -       -      +
     48B  ASP*     5.8     1.4    +      -       -      -
    159B  THR*     6.2     2.6    -      -       -      +
    483B  ARG*     5.8     0.2    -      -       -      +
    531B  TYR*     3.7    21.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  LEU      5.0     0.2    +      -       -      -
     40B  VAL*     4.2    13.4    -      -       -      +
     41B  ARG*     1.3    80.1    +      -       -      +
     43B  GLN*     1.3    80.0    +      -       +      +
     45B  ASP*     3.9     3.2    -      -       -      +
     46B  SER*     2.9    27.0    +      -       -      -
    395B  LEU*     3.4    24.9    -      -       +      +
    482B  LEU      3.8    22.0    +      -       -      -
    483B  ARG*     4.1    22.1    +      -       -      +
    526B  LEU*     3.9    20.3    -      -       -      +
    530B  ALA      5.3     2.3    -      -       -      +
    531B  TYR*     4.7    11.8    -      -       +      -
    532B  ILE*     4.0    29.6    -      -       +      +
    534B  VAL*     5.6     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  VAL*     3.8     8.3    +      -       +      +
     41B  ARG      3.2     1.0    -      -       -      -
     42B  GLN*     1.3    99.1    -      -       +      +
     44B  LEU*     1.3    62.1    +      -       +      +
     46B  SER*     2.8    19.1    +      -       -      -
     47B  PHE*     3.1    15.6    +      -       -      +
    155B  MET*     3.8    13.5    -      -       -      +
    183B  GLY*     3.4    28.8    +      -       -      +
    185B  PHE*     6.2     0.2    -      -       -      -
    193B  VAL*     3.8    14.6    -      -       -      +
    194B  LEU*     3.6    27.1    +      -       -      +
    395B  LEU*     4.3     8.0    -      -       -      +
    396B  ALA*     3.8    21.3    +      -       -      +
    482B  LEU*     4.0    17.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  VAL*     3.4    32.5    +      -       +      +
     41B  ARG*     3.3    26.6    +      -       -      +
     43B  GLN*     1.3    78.8    -      -       -      +
     45B  ASP*     1.3    61.6    +      -       -      +
     47B  PHE*     4.1     0.7    -      -       -      +
     48B  ASP*     3.0    31.0    +      -       -      +
    155B  MET*     4.1     4.9    -      -       -      -
    156B  LEU      3.7    22.7    -      -       -      +
    157B  ARG*     4.2     5.8    -      -       +      +
    158B  SER*     3.8    26.7    -      -       -      +
    181B  PRO      4.5     7.0    -      -       -      +
    183B  GLY*     3.8    18.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  LYS*     5.1     1.7    +      -       -      -
     41B  ARG*     2.7    51.7    +      -       -      +
     42B  GLN*     4.0     2.7    -      -       -      +
     44B  LEU*     1.3    70.6    -      -       -      +
     46B  SER*     1.3    58.8    +      -       -      +
     48B  ASP*     3.8     9.5    -      -       -      +
     49B  GLU*     2.9    32.6    +      -       -      +
    531B  TYR*     2.6    28.9    +      -       +      +
    532B  ILE      6.0     0.4    -      -       -      +
    534B  VAL*     3.9    19.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  GLN      2.9    16.6    +      -       -      -
     43B  GLN*     2.8    16.8    +      -       -      -
     45B  ASP*     1.3    77.2    -      -       -      +
     47B  PHE*     1.3    55.0    +      -       -      +
     49B  GLU*     3.9     4.9    -      -       -      +
     50B  PHE*     3.0    25.8    +      -       -      +
    395B  LEU*     3.8    17.4    -      -       -      +
    396B  ALA*     3.5    11.3    +      -       -      +
    397B  GLY*     3.5    25.1    +      -       -      -
    398B  PRO*     4.8     4.7    -      -       -      +
    534B  VAL*     4.1    10.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  GLN      3.1     4.3    +      -       -      +
     44B  LEU*     4.2     2.9    -      -       -      +
     46B  SER*     1.3    77.8    +      -       -      +
     48B  ASP*     1.3    66.2    +      -       -      +
     50B  PHE*     3.1    22.8    +      +       -      +
     51B  ILE*     3.2    31.3    +      -       +      +
    152B  ILE*     4.8     3.1    -      -       +      -
    153B  PRO      3.2    22.9    -      -       -      -
    154B  ILE*     3.9    11.9    -      -       +      -
    155B  MET*     3.5    43.1    -      -       +      -
    158B  SER*     3.8    22.0    -      -       -      -
    160B  TYR*     4.9     4.9    -      +       -      -
    185B  PHE*     3.5    23.8    -      +       -      -
    396B  ALA*     4.9     0.9    -      -       +      -
    397B  GLY      4.8     1.6    -      -       -      +
    400B  LEU*     3.6    27.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  ARG*     5.8     1.2    +      -       -      -
     44B  LEU      3.0    19.1    +      -       -      +
     45B  ASP*     3.8    11.6    -      -       -      +
     47B  PHE*     1.3    78.1    -      -       -      +
     49B  GLU*     1.3    62.1    +      -       -      +
     51B  ILE      3.6     0.2    +      -       -      -
     52B  GLN*     3.1    40.0    +      -       -      +
    158B  SER*     5.5     0.9    -      -       -      -
    159B  THR*     2.5    48.3    +      -       +      +
    160B  TYR*     3.4    12.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  ASP      2.9    18.4    +      -       -      +
     46B  SER*     3.9     5.7    -      -       -      +
     48B  ASP*     1.3    78.3    -      -       -      +
     50B  PHE*     1.3    59.3    +      -       -      +
     52B  GLN*     4.6     4.7    -      -       -      +
     53B  MET*     2.9    60.5    +      -       +      +
     54B  SER*     3.6    12.3    +      -       -      -
    397B  GLY*     5.3     3.1    -      -       -      -
    398B  PRO*     5.6     3.3    -      -       -      +
    534B  VAL*     4.1    36.1    -      -       +      +
    535B  GLY      4.3     9.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  SER      3.0    16.7    +      -       -      +
     47B  PHE*     3.1    25.5    +      +       -      +
     49B  GLU*     1.3    77.1    +      -       -      +
     51B  ILE*     1.3    80.7    +      -       +      +
     54B  SER*     3.0    39.9    +      -       -      -
     55B  VAL*     3.2    27.9    +      -       +      +
     58B  ILE*     5.7     0.7    -      -       +      -
    152B  ILE*     4.7     9.9    -      -       +      -
    397B  GLY*     3.7    26.9    -      -       -      -
    400B  LEU*     3.9    21.1    -      -       +      -
    401B  ALA*     3.8    22.2    -      -       -      -
    404B  PHE*     4.2    18.4    -      +       +      -
    444B  LEU*     5.6     3.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  PHE*     3.2    19.1    +      -       +      +
     50B  PHE*     1.3    99.5    -      -       +      +
     52B  GLN*     1.3    67.2    +      -       -      +
     53B  MET      3.2     2.1    -      -       -      +
     55B  VAL*     3.1    32.1    -      -       +      +
     56B  GLN*     4.6     1.4    +      -       -      +
     91B  ILE*     5.1     5.7    -      -       +      +
     93B  LEU*     3.5    34.1    -      -       +      -
    124B  LEU*     5.5     2.2    -      -       +      -
    152B  ILE*     4.3    18.4    -      -       +      -
    154B  ILE*     5.7     0.4    -      -       +      -
    160B  TYR*     3.4    32.3    -      -       +      +
    140T  ARG      5.5     0.3    -      -       -      +
    141T  LEU*     6.0     2.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  ASP*     3.1    32.8    +      -       -      +
     49B  GLU*     4.5     2.7    -      -       -      +
     51B  ILE*     1.3    80.1    -      -       -      +
     53B  MET*     1.3    61.9    +      -       +      +
     56B  GLN*     4.8     1.4    -      -       -      +
    160B  TYR*     3.1    18.3    +      -       -      +
    140T  ARG*     3.1    42.0    -      -       +      +
    142T  SER*     5.2    12.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  GLU*     2.9    36.2    +      -       +      +
     52B  GLN*     1.3    84.0    -      -       +      +
     54B  SER*     1.3    66.0    +      -       -      +
     55B  VAL      3.4     1.6    -      -       -      -
     56B  GLN*     3.1    17.3    +      -       -      +
     57B  ARG*     3.2    34.9    +      -       +      +
    537B  GLN*     6.2     2.5    -      -       +      -
    140T  ARG*     3.8    37.9    -      -       +      +
----------------------------------------------------------
 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