Contacts of the strand formed by residues 100 - 103 (chain A) in PDB entry 1IRP


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 100 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LEU*     3.1    23.6    -      -       +      +
     70A  CYS*     3.3     9.7    -      -       -      -
     94A  LYS*     3.7    22.4    -      -       -      +
     95A  GLN      5.3     0.7    -      -       -      +
     97A  LYS      3.8     0.8    +      -       -      -
     99A  PHE*     1.4    77.5    -      -       -      +
    101A  PHE*     1.3    65.4    +      -       -      +
    115A  ALA      2.9    40.8    +      -       -      +
    116A  ALA*     4.3     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ALA*     3.3     5.7    -      -       -      +
     57A  LEU      2.8    39.6    +      -       -      +
     58A  PHE*     4.1     6.7    -      -       -      -
     59A  LEU*     3.9    27.8    -      -       +      -
     68A  LEU      3.3    27.4    -      -       -      -
     69A  SER*     3.9     7.0    -      -       -      -
     70A  CYS*     3.2    24.2    -      -       -      -
     79A  LEU*     3.5    35.0    -      -       +      -
     99A  PHE      4.5     3.1    -      -       -      -
    100A  ALA*     1.3    79.3    -      -       -      +
    102A  ILE*     1.4    66.6    +      -       -      +
    103A  ARG*     3.7    14.2    +      -       +      +
    112A  PHE*     4.9    14.6    -      +       +      -
    113A  GLU      3.0    16.6    -      -       -      +
    114A  SER*     4.6     0.7    -      -       -      -
    115A  ALA      4.8     0.4    -      -       -      -
    116A  ALA*     5.0     1.3    -      -       -      +
    134A  LEU*     4.2    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ALA*     3.7    22.9    -      -       +      -
    101A  PHE*     1.4    71.5    -      -       -      +
    103A  ARG*     1.3    64.9    +      -       -      +
    104A  SER*     3.3    12.1    +      -       -      +
    111A  SER      3.2     7.1    -      -       -      +
    112A  PHE*     3.7     0.7    -      -       -      -
    113A  GLU*     3.0    39.6    +      -       +      +
    116A  ALA*     3.2    44.0    -      -       +      +
    117A  CYS*     4.6    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  VAL*     3.6    17.4    -      -       -      +
     50A  VAL      3.0    30.5    +      -       -      -
     51A  PRO*     3.8     0.2    -      -       -      +
     55A  HIS*     2.7    60.1    +      -       +      +
     56A  ALA*     4.3     5.1    +      -       -      +
     57A  LEU      3.3    15.9    +      -       -      +
     58A  PHE*     3.4    25.3    +      -       -      +
     59A  LEU*     3.5    19.0    -      -       -      +
    101A  PHE*     3.7    12.0    +      -       +      +
    102A  ILE*     1.3    74.3    -      -       -      +
    104A  SER*     1.3    58.5    +      -       -      +
    105A  ASP*     3.1    17.5    +      -       -      +
    110A  THR*     4.2     1.6    -      -       -      +
    111A  SER      3.8     5.2    -      -       -      -
    112A  PHE*     3.9    22.0    -      -       +      -
    149A  PHE*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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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