Contacts of the strand formed by residues 97 - 103 (chain C) 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 TYR 97 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40C  PHE      3.4     0.3    -      -       -      +
     41C  ARG*     3.4     2.8    -      -       -      -
     42C  VAL*     2.6    47.1    +      -       +      +
     44C  PRO*     4.1    10.3    -      -       +      -
     50C  PRO*     3.8    42.2    -      -       +      +
     87C  ILE*     4.1    19.7    -      -       +      -
     88C  GLU      3.4     7.0    -      -       -      +
     89C  PRO*     3.9    26.2    -      -       +      -
     90C  VAL*     3.8     3.8    -      -       -      +
     95C  ASN*     3.2    40.1    +      -       -      -
     96C  GLN*     1.3    82.1    -      -       -      +
     98C  ILE*     1.3    63.3    +      -       -      +
     99C  CYS*     3.8     9.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  ALA*     4.4     9.4    -      -       +      -
     40C  PHE      3.2     5.8    -      -       -      +
     41C  ARG*     3.9    32.5    -      -       +      +
     86C  HIS      3.9     0.7    -      -       -      +
     87C  ILE*     3.5     4.0    -      -       -      -
     88C  GLU*     2.9    45.0    +      -       +      -
     90C  VAL*     3.7    21.8    -      -       +      -
     97C  TYR*     1.3    72.3    -      -       -      +
     99C  CYS*     1.3    60.4    +      -       -      +
    100C  TYR*     3.5    32.6    -      -       +      +
    136C  GLU*     4.9     1.8    -      -       +      -
    358C  ARG*     4.5     7.4    -      -       -      +
    363C  TYR*     4.0    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  ALA      3.6     1.4    -      -       -      +
     39C  ALA*     3.7     0.3    -      -       -      -
     40C  PHE*     2.8    36.6    +      -       +      +
     42C  VAL*     3.7    31.6    -      -       +      -
     50C  PRO*     4.4     4.7    -      -       -      -
     54C  GLY*     4.0    18.8    -      -       -      -
     57C  VAL*     6.4     0.9    -      -       +      -
     84C  CYS*     4.0    13.2    -      -       -      -
     86C  HIS      3.5     4.0    -      -       -      -
     87C  ILE*     4.0    25.4    -      -       -      -
     97C  TYR*     4.4     5.4    -      -       -      -
     98C  ILE*     1.3    76.8    -      -       -      +
    100C  TYR*     1.3    63.3    +      -       -      +
    101C  VAL*     3.9     4.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 100 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  ALA      3.3     4.9    -      -       -      +
     39C  ALA*     4.2    10.1    -      -       +      -
     84C  CYS*     3.2     6.8    -      -       -      -
     85C  TYR*     3.0    51.8    +      +       +      +
     86C  HIS*     2.9    38.9    +      +       +      +
     88C  GLU*     3.0    26.8    +      -       -      -
     98C  ILE*     3.5    25.0    -      -       +      +
     99C  CYS*     1.3    74.4    -      -       -      +
    101C  VAL*     1.3    60.0    +      -       -      +
    356C  LYS*     4.5     6.2    +      -       -      -
    358C  ARG*     3.4    15.9    +      -       -      -
    363C  TYR*     3.8    16.5    -      +       +      -
    364C  PHE*     3.7    34.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  ILE      3.8     0.7    -      -       -      +
     37C  LEU*     3.4     4.0    -      -       -      -
     38C  ALA*     2.8    38.5    +      -       -      +
     40C  PHE*     4.2    20.9    -      -       +      -
     54C  GLY      4.5     4.3    -      -       -      +
     57C  VAL*     4.8     1.8    -      -       +      -
     58C  ALA*     3.9    25.8    -      -       +      +
     83C  ARG      3.2    19.3    -      -       -      +
     84C  CYS*     4.2    10.5    -      -       +      -
     85C  TYR*     3.7     3.9    -      -       -      -
     99C  CYS*     4.6     5.2    -      -       +      +
    100C  TYR*     1.3    79.2    -      -       -      +
    102C  ALA*     1.3    65.5    +      -       -      +
    103C  TYR*     3.5    34.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  TYR*     3.7    30.1    -      -       +      +
     35C  ASP*     4.1     4.9    -      -       -      +
     36C  ILE      3.6     4.0    -      -       -      -
     37C  LEU*     3.7    20.4    -      -       +      -
     82C  GLY*     3.1     6.8    -      -       -      -
     83C  ARG*     2.9    35.5    +      -       +      +
     85C  TYR*     3.8     9.6    -      -       +      -
    101C  VAL*     1.3    73.6    -      -       -      +
    103C  TYR*     1.3    62.2    +      -       -      +
    104C  PRO*     4.1     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 103 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  ASP*     3.3     5.3    -      -       -      -
     36C  ILE*     2.8    52.2    +      -       +      +
     38C  ALA*     3.8    20.2    -      -       +      -
     40C  PHE*     3.5    22.3    -      -       -      -
     57C  VAL      4.6     0.5    +      -       -      -
     58C  ALA      4.6     0.7    -      -       -      -
     61C  SER*     2.8    47.3    +      -       -      -
     62C  SER*     4.3     7.2    -      -       -      -
     82C  GLY*     4.4     0.9    -      -       -      -
    101C  VAL*     3.5    24.2    -      -       +      +
    102C  ALA*     1.3    77.9    -      -       -      +
    104C  PRO*     1.3    68.6    -      -       +      +
    107C  LEU*     4.3    13.5    -      -       +      -
    108C  PHE*     3.6    25.6    -      +       +      -
    119C  SER*     5.8     0.4    -      -       -      -
    120C  ILE*     4.1    25.2    -      -       +      +
----------------------------------------------------------
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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