Contacts of the strand formed by residues 98 - 105 (chain T) 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 PHE 98 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12T  TYR*     3.5    38.8    -      +       -      -
     44T  PHE*     3.2     6.2    -      -       -      +
     45T  GLU      2.9    37.0    +      -       -      +
     46T  THR      5.7     5.2    -      -       -      -
     49T  GLY*     4.0    25.4    -      -       -      -
     50T  PHE*     4.5     7.0    -      +       -      -
     67T  TRP*     3.5    25.9    -      +       +      -
     96T  ASN      5.5     0.7    -      -       -      -
     97T  ALA*     1.3    74.4    -      -       -      +
     99T  ILE*     1.3    58.6    +      -       -      +
    116T  ILE*     5.1     2.5    -      -       +      -
    118T  TYR      3.5     5.2    -      -       -      +
    119T  LYS*     4.1    11.4    -      -       +      -
    120T  PRO*     3.7    24.2    -      -       +      -
    123T  TYR*     3.7    39.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 99 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42T  LEU*     4.6     9.4    -      -       +      -
     43T  GLU      3.4     9.2    -      -       -      +
     44T  PHE*     4.3     4.3    -      -       +      -
     67T  TRP*     4.4     1.3    -      -       -      -
     87T  LEU*     3.7    19.7    -      -       +      -
     90T  CYS*     3.7    32.3    -      -       +      +
     91T  LYS*     3.5    39.5    -      -       +      +
     94T  TYR      4.4     4.5    -      -       -      +
     97T  ALA*     4.0     4.9    -      -       +      +
     98T  PHE*     1.3    77.3    -      -       -      +
    100T  ARG*     1.3    67.8    +      -       -      +
    116T  ILE*     3.6     4.0    -      -       -      +
    117T  ALA*     2.8    25.9    +      -       +      -
    118T  TYR*     2.9    33.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 100 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  ASN*     4.0    23.0    +      -       -      +
    183C  LYS*     6.0     0.8    -      -       -      +
     41T  CYS      3.8     0.3    -      -       -      +
     42T  LEU*     3.4     7.3    -      -       -      +
     43T  GLU*     2.8    64.3    +      -       +      +
     64T  GLY      5.6     0.2    +      -       -      -
     65T  ARG      3.4    15.2    +      -       -      -
     66T  TYR*     5.1     0.2    -      -       -      +
     67T  TRP*     3.2    63.4    -      -       +      +
     99T  ILE*     1.3    76.0    -      -       -      +
    101T  ILE*     1.3    64.6    +      -       -      +
    102T  ILE*     3.9    13.9    -      -       +      +
    111T  GLN*     6.4     0.2    -      -       -      -
    114T  SER*     3.7    18.6    -      -       -      +
    115T  PHE      3.7    13.0    -      -       -      +
    116T  ILE*     4.3    12.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 101 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26T  LEU*     4.5     5.4    -      -       +      -
     30T  VAL*     4.6    13.2    -      -       +      -
     33T  LEU*     4.3    17.9    -      -       +      -
     40T  PRO*     5.5     0.2    -      -       +      -
     41T  CYS      3.6     7.0    -      -       -      +
     42T  LEU*     4.5    14.8    -      -       +      -
     83T  VAL*     4.6    19.5    -      -       +      -
     84T  LEU*     5.8     1.3    -      -       +      -
     87T  LEU*     4.4    15.7    -      -       +      -
    100T  ARG*     1.3    77.2    -      -       -      +
    102T  ILE*     1.3    69.7    +      -       -      +
    113T  VAL      4.3     0.2    -      -       -      -
    114T  SER*     3.3     4.2    +      -       -      -
    115T  PHE*     3.1    57.9    +      -       +      +
    117T  ALA*     3.7    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 102 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33T  LEU*     4.0     8.2    -      -       -      +
     39T  VAL      4.4     0.2    -      -       -      -
     40T  PRO*     3.4     4.0    -      -       -      +
     41T  CYS*     2.9    50.2    +      -       +      +
     43T  GLU*     3.8    33.7    -      -       +      +
    100T  ARG*     3.9    13.2    -      -       +      -
    101T  ILE*     1.3    80.5    -      -       -      +
    103T  GLY*     1.3    60.9    +      -       -      +
    104T  PHE*     3.5    31.6    -      -       +      -
    111T  GLN*     3.8    25.1    -      -       -      +
    113T  VAL      3.2     8.5    -      -       -      +
    114T  SER*     3.8    19.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 103 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33T  LEU*     4.2    17.9    -      -       -      -
     38T  TRP*     4.3     4.9    -      -       -      -
     39T  VAL      3.3     9.4    -      -       -      -
    102T  ILE*     1.3    76.8    -      -       -      +
    104T  PHE*     1.3    63.0    +      -       -      -
    111T  GLN*     3.3     4.9    -      -       -      -
    112T  CYS*     2.9    28.8    +      -       -      +
    113T  VAL*     3.0    16.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 104 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  ASN*     4.1    13.5    -      -       -      -
    187C  ARG*     3.7    33.4    -      -       -      -
     37T  LYS      4.7     0.2    -      -       -      +
     38T  TRP*     3.2    10.6    -      -       -      -
     39T  VAL*     2.8    55.6    +      -       +      +
     41T  CYS*     3.8    26.2    -      -       +      -
     69T  MET*     5.4     0.2    -      -       +      -
     73T  PRO*     4.1    22.4    -      -       +      -
     75T  PHE*     6.1     0.9    -      +       -      -
    102T  ILE*     3.5    17.3    -      -       +      -
    103T  GLY*     1.3    73.2    -      -       -      -
    105T  ASP*     1.3    62.3    +      -       -      +
    106T  SER*     3.7     5.8    +      -       -      +
    109T  GLN      6.1     1.3    -      -       -      -
    110T  VAL      4.0     3.6    -      -       -      -
    111T  GLN*     3.8    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 105 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37T  LYS      5.9     0.2    -      -       -      -
     38T  TRP*     3.3    23.8    +      -       +      -
    104T  PHE*     1.3    72.4    -      -       -      +
    106T  SER*     1.3    52.7    +      -       -      +
    107T  ASN*     3.1    23.2    +      -       -      +
    108T  ARG*     3.3    22.9    +      -       -      +
    109T  GLN*     2.7    36.2    +      -       -      -
    110T  VAL*     3.0    20.6    +      -       +      +
    112T  CYS*     3.6    20.4    -      -       -      -
----------------------------------------------------------
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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