Contacts of the strand formed by residues 237 - 241 (chain A) in PDB entry 1IR1


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 GLY 237 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  LEU*     3.9     5.4    -      -       -      +
    198A  ASP      3.1     6.7    +      -       -      -
    199A  PHE*     3.2    38.4    -      -       -      -
    200A  THR*     3.3     5.0    +      -       -      -
    225A  LEU*     4.7     5.4    -      -       -      -
    236A  LYS*     1.3    77.7    -      -       -      +
    238A  HIS*     1.3    60.0    +      -       -      +
    263A  PRO*     4.1    16.8    -      -       -      -
    264A  ILE*     4.4     2.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  ILE*     4.4     0.9    -      -       +      -
    185A  TYR*     4.1     4.9    -      +       -      -
    189A  VAL*     3.6    29.2    -      -       +      +
    200A  THR*     2.7    27.6    +      -       -      +
    201A  KCX      3.5    26.0    -      -       -      -
    202A  ASP*     2.8    24.1    +      -       -      -
    221A  CYS*     3.8    14.9    -      -       +      -
    225A  LEU*     4.2    20.9    -      -       +      +
    237A  GLY*     1.3    74.5    -      -       -      +
    239A  TYR*     1.3    63.3    +      -       -      +
    240A  LEU*     2.9    42.2    +      -       +      +
    262A  VAL*     5.8     1.8    -      -       -      +
    263A  PRO*     5.4     0.6    -      -       -      +
    264A  ILE*     3.2    13.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  PHE*     3.5    44.5    -      +       +      +
    200A  THR      3.0     7.2    +      -       -      -
    201A  KCX      3.3    23.3    -      -       +      -
    202A  ASP*     3.3    23.4    +      -       -      +
    238A  HIS*     1.3    70.4    -      -       -      +
    240A  LEU*     1.3    61.4    +      -       -      +
    241A  ASN      3.5     2.3    +      -       -      -
    264A  ILE*     3.7    37.0    -      -       +      -
    265A  VAL*     4.6     0.9    -      -       -      +
    266A  MET*     3.7    21.3    -      -       +      +
    292A  HIS*     3.3    35.9    -      +       +      -
    325A  HIS*     3.6    12.2    +      +       -      -
    399A  VAL*     3.8     4.3    -      -       -      +
    401A  GLN*     3.0    33.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  ASP*     3.6     3.8    -      -       -      +
    217A  ARG*     5.0     0.7    -      -       -      +
    218A  PHE*     3.7    65.5    -      -       +      +
    221A  CYS*     4.2    10.1    -      -       +      -
    222A  ALA      6.1     0.7    -      -       -      +
    225A  LEU*     6.0     2.2    -      -       +      -
    238A  HIS*     2.9    36.1    +      -       +      +
    239A  TYR*     1.3    71.0    -      -       -      +
    241A  ASN*     1.3    63.7    +      -       -      +
    242A  ALA*     3.4     1.6    +      -       -      -
    257A  ALA*     4.4     3.6    -      -       +      -
    260A  LEU*     4.8     3.1    -      -       +      -
    262A  VAL*     4.0    32.5    -      -       +      -
    264A  ILE      3.6     7.5    +      -       -      +
    265A  VAL*     3.3    11.6    -      -       +      +
    266A  MET      2.9    18.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  ASP*     2.8    17.7    +      -       +      +
    203A  ASP      3.4    10.1    +      -       -      -
    204A  GLU      3.2    25.7    +      -       -      -
    206A  VAL      3.3    23.6    +      -       -      +
    207A  ASN*     3.5     7.1    -      -       -      +
    217A  ARG*     4.0     4.7    +      -       -      +
    218A  PHE*     3.6    18.4    -      -       -      -
    239A  TYR      3.5     1.4    +      -       -      -
    240A  LEU*     1.3    70.0    -      -       -      +
    242A  ALA*     1.3    59.7    +      -       -      +
    243A  THR*     2.7    33.0    +      -       -      +
    253A  ARG*     4.4     7.1    +      -       -      -
    266A  MET*     3.5    31.0    -      -       +      +
    268A  ASP*     4.0     2.1    +      -       -      +
----------------------------------------------------------
 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