Contacts of the strand formed by residues 110 - 118 (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 VAL 110 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  ILE*     5.7     1.3    -      -       +      -
    156B  GLN*     3.4    42.8    -      -       +      +
    159B  ARG*     5.5     9.6    -      -       +      -
    160B  ASP*     5.5     3.4    -      -       -      +
    165B  TYR*     5.7     1.8    -      -       +      -
    104T  PHE*     4.8     3.3    -      -       -      -
    105T  ASP*     3.0    23.7    +      -       +      +
    108T  ARG*     3.5    58.1    -      -       +      +
    109T  GLN*     1.3    76.0    -      -       -      +
    111T  GLN*     1.3    66.5    +      -       -      +
    112T  CYS*     3.3     9.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 111 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159B  ARG*     5.1     3.3    -      -       -      -
    160B  ASP*     5.4     2.2    +      -       -      +
    165B  TYR*     3.2    64.5    -      -       +      +
    166B  GLY      4.6     0.5    +      -       -      -
    183C  LYS*     4.0     9.5    -      -       -      +
    187C  ARG*     2.9    34.0    +      -       -      +
     43T  GLU*     5.3     1.4    +      -       -      -
    100T  ARG*     6.0     0.4    -      -       -      +
    102T  ILE*     3.8    31.6    -      -       +      +
    103T  GLY      3.3    11.7    -      -       -      +
    104T  PHE*     3.8    19.5    -      -       +      +
    110T  VAL*     1.3    73.9    -      -       -      +
    112T  CYS*     1.3    59.3    +      -       -      +
    113T  VAL      3.4     6.1    -      -       -      +
    114T  SER*     4.4     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 112 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  GLY*     3.4    22.4    -      -       -      +
    396B  ASP*     4.5     7.9    -      -       -      +
     32T  TYR*     5.4     1.0    +      -       -      -
     38T  TRP*     3.7    40.6    -      -       +      -
    103T  GLY      2.9     7.2    +      -       -      +
    105T  ASP*     3.6    31.6    -      -       -      -
    108T  ARG*     3.7    25.4    -      -       -      -
    110T  VAL*     3.3     4.7    +      -       -      -
    111T  GLN*     1.3    72.6    -      -       -      +
    113T  VAL*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 113 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  TYR*     4.7     2.0    -      -       -      -
    166B  GLY*     4.5     4.9    -      -       -      -
    432B  ASN*     5.7     1.1    -      -       -      +
     29T  GLN*     5.5     2.7    -      -       -      +
     32T  TYR*     4.0    19.1    -      -       +      -
     33T  LEU*     4.2    20.0    -      -       +      -
     38T  TRP*     3.7    26.2    -      -       +      -
    101T  ILE      4.4     2.7    -      -       -      +
    102T  ILE*     3.2     4.3    -      -       -      +
    103T  GLY*     3.0    32.1    +      -       -      +
    111T  GLN*     3.4     4.6    -      -       -      +
    112T  CYS*     1.3    86.5    -      -       -      +
    114T  SER*     1.3    69.0    +      -       -      +
    115T  PHE*     3.7    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 114 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  TYR*     4.0    35.8    +      -       -      +
    166B  GLY*     5.0     0.8    -      -       -      -
     13T  GLU*     5.5     2.6    -      -       -      +
     14T  THR*     3.8    22.9    +      -       -      +
    100T  ARG*     3.7    22.2    -      -       -      -
    101T  ILE      3.3     7.6    -      -       -      -
    102T  ILE*     3.8     8.5    -      -       -      +
    111T  GLN*     4.4     1.0    +      -       -      -
    113T  VAL*     1.3    80.3    -      -       -      +
    115T  PHE*     1.3    66.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 115 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12T  TYR      5.2     2.2    -      -       -      -
     14T  THR*     3.7    19.3    -      -       +      +
     15T  LEU*     4.2    17.0    -      -       +      -
     21T  LEU*     4.5    13.0    -      -       +      -
     26T  LEU*     3.6    27.6    -      -       +      -
     29T  GLN*     3.9    30.5    -      -       +      -
     30T  VAL*     4.8     5.2    -      -       +      -
     33T  LEU*     5.5     1.1    -      -       +      -
    100T  ARG*     4.4     2.4    -      -       -      +
    101T  ILE*     3.1    56.0    +      -       +      -
    113T  VAL*     3.7    28.9    -      -       +      -
    114T  SER*     1.3    76.1    +      -       -      +
    116T  ILE*     1.3    79.4    +      -       -      +
    117T  ALA*     3.4     1.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 116 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12T  TYR*     3.7    46.6    +      -       +      +
     14T  THR      5.1     0.6    +      -       -      -
     21T  LEU*     5.2     4.9    -      -       -      +
     67T  TRP*     4.4    18.4    -      -       +      -
     98T  PHE*     5.1     2.2    -      -       +      -
     99T  ILE      3.6     8.1    -      -       -      +
    100T  ARG*     4.3    20.6    -      -       -      +
    115T  PHE*     1.3    83.0    -      -       -      +
    117T  ALA*     1.3    61.7    +      -       -      +
    118T  TYR*     3.5    24.0    -      -       -      +
    119T  LYS*     3.5    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 117 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26T  LEU*     4.3    14.8    -      -       +      +
     87T  LEU*     4.0    24.6    -      -       +      +
     91T  LYS*     5.8     0.5    -      -       -      +
     99T  ILE      2.8     9.1    +      -       -      +
    101T  ILE*     3.7    35.9    -      -       +      -
    115T  PHE*     3.4     4.8    +      -       +      -
    116T  ILE*     1.3    75.5    -      -       -      +
    118T  TYR*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 118 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87T  LEU*     4.7     1.8    -      -       +      -
     91T  LYS*     3.6    39.3    -      -       +      -
     94T  TYR      4.1     4.0    -      -       -      -
     95T  PRO*     2.7    38.8    +      -       +      +
     97T  ALA      3.2    28.7    -      -       -      -
     98T  PHE*     3.5     3.3    -      -       -      -
     99T  ILE*     2.9    52.5    +      -       +      -
    116T  ILE*     3.5     8.3    -      -       -      +
    117T  ALA*     1.3    82.1    -      -       -      +
    119T  LYS*     1.3    82.0    +      -       -      +
    120T  PRO*     4.3     2.3    -      -       -      +
    121T  ALA      5.3     0.3    +      -       -      -
----------------------------------------------------------
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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