Contacts of the strand formed by residues 22 - 26 (chain X) in PDB entry 1IRA


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 22 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15X  ILE      4.3     8.3    -      -       -      +
     16X  TRP*     4.0    15.5    -      -       +      -
     20X  GLN      4.1     7.0    -      -       -      +
     21X  LYS*     1.3    76.4    -      -       -      +
     23X  PHE*     1.3    67.6    +      -       -      +
     24X  TYR*     4.2     1.6    +      -       -      -
     32X  ALA*     3.1     6.2    -      -       -      -
     33X  GLY      2.9    34.7    +      -       -      +
     34X  TYR*     5.1     0.2    -      -       -      -
     35X  LEU*     3.6    27.0    +      -       -      +
     43X  GLU*     4.2    24.2    -      -       -      +
    109Y  LYS      5.8     3.4    -      -       -      +
    111Y  LYS*     4.6     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 23 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15X  ILE*     3.8    36.4    +      -       +      -
     16X  TRP*     5.7     0.4    -      -       -      -
     17X  ASP      5.5     0.7    -      -       -      -
     21X  LYS      5.1     5.2    -      -       -      -
     22X  THR*     1.3    85.5    +      -       -      +
     24X  TYR*     1.3    65.7    +      -       -      +
     30X  LEU*     4.2    26.7    -      -       +      -
     31X  VAL      3.3     3.1    -      -       -      +
     32X  ALA*     4.0     3.6    -      -       +      -
     43X  GLU*     3.5     7.4    -      -       -      +
     44X  GLU*     2.9    37.0    +      -       +      +
     46X  ILE*     4.6    10.1    -      -       +      -
     67X  LEU*     5.9     2.2    -      -       +      -
    121X  LEU*     4.8     7.6    -      -       +      -
    123X  THR*     3.7    22.7    -      -       +      -
    131X  VAL*     3.8    33.0    -      -       +      -
    146X  PHE*     3.6    28.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 24 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22X  THR      4.2     4.0    -      -       -      -
     23X  PHE*     1.3    75.3    -      -       -      +
     25X  LEU*     1.3    71.1    +      -       -      +
     26X  ARG*     2.9    31.8    +      -       +      -
     30X  LEU*     3.7     6.8    -      -       -      +
     31X  VAL*     2.9    56.9    +      -       +      +
     33X  GLY*     3.7    24.5    -      -       -      -
     34X  TYR      5.4     0.7    -      -       -      -
     35X  LEU*     3.7    28.9    -      -       +      -
     42X  LEU*     3.2    32.3    -      -       +      +
     44X  GLU*     3.9     5.8    -      -       -      -
    128X  ASP*     3.1    19.1    +      -       -      +
      8Y  GLU*     5.5     0.2    -      -       -      -
      9Y  LYS*     6.0     0.2    -      -       -      -
     10Y  ILE*     3.9    30.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 25 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24X  TYR*     1.3    82.0    -      -       -      +
     26X  ARG*     1.3    60.8    +      -       -      +
     27X  ASN      4.1     0.6    +      -       -      -
     28X  ASN*     3.9    19.3    -      -       -      +
     29X  GLN      3.6    11.7    -      -       -      +
     30X  LEU*     3.7    32.5    -      -       +      +
     42X  LEU      4.7     0.4    +      -       -      -
     44X  GLU*     4.2    11.7    +      -       +      +
     60X  ILE*     4.5     6.3    -      -       +      -
     61X  HIS*     3.5    33.9    -      -       +      +
     65X  MET*     4.7     2.0    -      -       +      -
     80X  LEU*     3.8    19.5    -      -       +      -
      9Y  LYS*     3.3    34.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 26 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24X  TYR*     2.9    35.1    +      -       +      -
     25X  LEU*     1.3    73.2    -      -       -      +
     27X  ASN*     1.3    72.6    +      -       +      +
     29X  GLN*     2.9    26.9    +      -       -      +
     31X  VAL*     3.5    27.1    -      -       +      +
    128X  ASP*     3.1    43.1    +      -       -      +
      6Y  ARG*     5.1     4.3    -      -       -      +
      8Y  GLU*     3.1    37.5    +      -       -      +
      9Y  LYS*     5.5     1.1    -      -       -      +
     10Y  ILE*     4.7     4.0    -      -       -      +
     25Y  PRO*     4.4    23.9    +      -       -      +
     26Y  LEU      5.4     0.7    -      -       -      -
     27Y  ASN*     3.7    27.7    -      -       -      +
----------------------------------------------------------
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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