Contacts of the strand formed by residues 83 - 89 (chain B) 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 ARG 83 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  THR      5.9     0.2    -      -       -      +
     24B  TYR      3.8     4.7    -      -       -      +
     26B  THR*     3.4    21.6    +      -       +      +
     29B  TYR*     3.4    56.7    +      -       +      -
     58B  ALA*     4.1     0.4    -      -       -      -
     78B  ASP*     2.6    36.3    +      -       -      +
     81B  LYS*     3.0    47.8    +      -       +      +
     82B  GLY*     1.3    78.4    -      -       -      +
     84B  CYS*     1.3    62.0    +      -       -      +
     85B  TYR*     3.4     4.0    +      -       -      +
    101B  VAL*     3.2     8.0    -      -       -      +
    102B  ALA*     2.8    37.8    +      -       +      +
    104B  PRO*     4.4    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  TYR      2.9    16.7    +      -       -      +
     25B  TYR*     3.4    16.5    -      -       +      -
     26B  THR*     2.9    23.1    +      -       -      -
     54B  GLY*     3.8    35.9    -      -       -      +
     55B  ALA      4.3     0.7    -      -       -      +
     58B  ALA*     3.9     2.9    -      -       +      +
     83B  ARG*     1.3    70.8    -      -       -      +
     85B  TYR*     1.3    58.0    +      -       -      +
     86B  HIS      4.0     4.0    -      -       -      -
     87B  ILE*     3.9    28.3    -      -       -      -
     99B  CYS*     4.1     8.1    -      -       -      -
    100B  TYR      3.3    14.1    -      -       -      -
    101B  VAL*     4.4     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  TYR*     5.0     0.9    -      -       -      -
     26B  THR*     3.4    19.3    -      -       -      +
     27B  PRO*     3.4    25.7    -      -       -      +
     29B  TYR*     4.0    23.8    -      +       +      +
     31B  THR*     3.6    22.6    -      -       +      +
     37B  LEU*     3.7    23.2    -      -       +      +
     83B  ARG      3.7     9.6    -      -       -      +
     84B  CYS*     1.3    74.5    -      -       -      +
     86B  HIS*     1.3    70.8    +      -       +      +
    100B  TYR*     3.1    31.8    +      +       +      +
    101B  VAL      3.7     7.9    -      -       -      -
    102B  ALA*     3.7    30.5    -      -       +      -
    364B  PHE*     3.9    10.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  TYR*     5.0     2.4    -      -       -      -
     27B  PRO*     5.8     0.4    -      -       -      -
     84B  CYS*     3.6     2.6    -      -       -      -
     85B  TYR*     1.3    99.4    -      -       +      +
     87B  ILE*     1.3    85.9    +      -       -      +
     88B  GLU*     4.0    18.8    -      -       +      -
     99B  CYS*     3.5     0.9    -      -       -      -
    100B  TYR*     2.9    57.1    +      +       +      +
----------------------------------------------------------
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Residues in contact with ILE 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  TYR*     3.7    24.2    +      -       +      +
     50B  PRO*     3.7    17.0    -      -       +      +
     51B  GLU*     3.6    37.7    -      -       +      +
     84B  CYS*     3.9    14.8    -      -       -      -
     86B  HIS*     1.3    95.2    +      -       -      +
     88B  GLU*     1.3    64.3    +      -       -      +
     89B  PRO*     4.5     2.7    -      -       +      +
     97B  TYR*     4.0    32.3    -      -       +      -
     98B  ILE      3.5     3.1    -      -       -      -
     99B  CYS*     4.0     9.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  HIS*     4.0    15.0    -      -       +      +
     87B  ILE*     1.3    77.9    -      -       -      +
     89B  PRO*     1.3    80.5    -      -       +      +
     90B  VAL*     5.9     0.3    -      -       -      -
     97B  TYR*     3.2     5.8    -      -       -      -
     98B  ILE*     2.7    48.2    +      -       +      +
    100B  TYR*     3.2    25.4    +      -       +      -
    358B  ARG*     3.4    29.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  ILE      4.5     2.5    -      -       -      +
     88B  GLU*     1.3    99.2    -      -       +      +
     90B  VAL*     1.3    64.4    +      -       -      +
     91B  ALA*     3.7     2.3    +      -       -      +
     96B  GLN      3.8     1.1    -      -       -      +
     97B  TYR*     3.8    25.4    -      -       +      -
----------------------------------------------------------
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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