Contacts of the strand formed by residues 47 - 51 (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 ILE 47 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  GLN      3.0     2.4    -      -       -      +
     13A  ALA*     3.6     2.0    -      -       -      -
     14A  PHE*     2.8    40.5    +      -       +      +
     31A  LEU*     6.2     0.2    -      -       +      -
     45A  GLU      4.0     4.0    -      -       -      +
     46A  LYS*     1.3    73.3    -      -       -      +
     48A  ASP*     1.4    57.9    +      -       -      +
     49A  VAL      3.5     0.7    +      -       -      -
     59A  LEU*     3.8    36.6    -      -       +      -
     60A  GLY*     3.3    33.9    -      -       -      +
     61A  ILE*     3.5    10.8    -      -       -      +
     62A  HIS*     3.6    31.0    -      -       +      +
     66A  MET      3.9     3.1    -      -       -      +
     68A  LEU*     3.8    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     2.6    43.3    +      -       -      +
      2A  ARG*     3.2    21.3    +      -       -      +
     11A  MET*     4.3     3.5    -      -       -      +
     12A  GLN*     3.1    54.2    +      -       -      -
     13A  ALA*     4.9     0.4    -      -       -      +
     47A  ILE*     1.4    68.8    -      -       -      +
     49A  VAL*     1.3    56.2    +      -       -      +
     50A  VAL*     3.4     1.2    -      -       -      +
     59A  LEU*     3.4     4.5    -      -       -      -
     60A  GLY      2.9    41.0    +      -       -      +
     61A  ILE*     3.5     9.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  GLN*     3.1    48.1    +      -       +      +
     14A  PHE*     3.7    28.5    -      -       +      -
     47A  ILE      3.5     0.8    +      -       -      -
     48A  ASP*     1.3    71.8    -      -       -      +
     50A  VAL*     1.4    59.0    +      -       -      +
     51A  PRO*     4.0     3.9    -      -       +      +
     55A  HIS*     5.0    11.0    -      -       +      +
     59A  LEU*     3.8    18.6    -      -       +      -
    103A  ARG*     3.6    37.2    -      -       -      +
    149A  PHE*     5.0     6.3    -      -       +      -
    151A  GLU*     6.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET      3.3    34.3    -      -       -      +
      2A  ARG*     4.5     4.7    -      -       +      -
     12A  GLN*     3.6    13.9    -      -       -      +
     48A  ASP*     3.4    11.6    +      -       -      +
     49A  VAL*     1.4    70.5    -      -       -      +
     51A  PRO*     1.4    64.5    -      -       +      +
     57A  LEU*     3.1    23.2    -      -       +      +
     58A  PHE*     3.1    25.8    +      -       +      -
     91A  GLU      3.7    23.6    -      -       -      +
     92A  ASN*     4.6     5.2    -      -       -      +
    103A  ARG*     3.0    15.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  GLN*     4.3     9.2    -      -       -      +
     49A  VAL*     4.0     7.0    -      -       +      +
     50A  VAL*     1.4    85.5    -      -       +      +
     52A  ILE*     1.4    62.5    +      -       -      +
     53A  GLU*     4.4     6.5    -      -       -      +
     55A  HIS*     3.3    41.5    -      -       -      +
     57A  LEU*     3.5     8.8    -      -       +      +
     92A  ASN      3.5    13.7    -      -       -      +
    103A  ARG*     4.4     0.4    -      -       -      +
----------------------------------------------------------
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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