Contacts of the strand formed by residues 98 - 105 (chain V) 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 V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12V  TYR*     3.5    39.7    -      +       -      -
     44V  PHE*     3.2     6.6    -      -       -      -
     45V  GLU      2.9    36.6    +      -       -      +
     46V  THR*     5.7     5.2    -      -       -      -
     49V  GLY*     3.9    25.8    -      -       -      -
     50V  PHE*     4.5     6.5    -      +       -      -
     67V  TRP*     3.5    25.4    -      +       +      -
     96V  ASN      5.4     1.1    -      -       -      -
     97V  ALA*     1.3    74.5    -      -       -      +
     99V  ILE*     1.3    60.0    +      -       -      +
    116V  ILE*     5.1     2.5    -      -       +      -
    118V  TYR      3.5     3.8    -      -       -      +
    119V  LYS*     4.3     9.6    -      -       +      -
    120V  PRO*     3.6    24.0    -      -       +      -
    123V  TYR*     3.8    39.9    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 99 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42V  LEU*     4.5     9.9    -      -       +      -
     43V  GLU      3.4    10.3    -      -       -      +
     44V  PHE*     4.3     4.0    -      -       +      -
     67V  TRP*     4.5     1.1    -      -       -      -
     87V  LEU*     3.8    18.4    -      -       +      -
     90V  CYS*     3.7    34.5    -      -       +      +
     91V  LYS*     3.6    37.5    -      -       +      +
     94V  TYR      4.4     4.3    -      -       -      +
     97V  ALA*     4.1     4.3    -      -       +      +
     98V  PHE*     1.3    80.6    -      -       -      +
    100V  ARG*     1.3    69.7    +      -       -      +
    116V  ILE*     3.7     2.5    -      -       -      -
    117V  ALA*     2.8    24.0    +      -       -      -
    118V  TYR*     2.9    33.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 100 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  LYS*     5.6     2.6    -      -       -      +
    187A  ARG*     5.8     0.4    -      -       -      +
    163D  ASN*     4.0    21.8    +      -       -      +
     41V  CYS      4.0     0.2    -      -       -      +
     42V  LEU*     3.5     6.2    -      -       -      +
     43V  GLU*     2.8    63.8    +      -       +      +
     65V  ARG      3.2    23.8    +      -       -      -
     66V  TYR*     4.9     0.2    -      -       -      +
     67V  TRP*     3.4    54.3    -      -       +      +
     99V  ILE*     1.3    76.0    -      -       -      +
    101V  ILE*     1.3    63.6    +      -       -      +
    102V  ILE*     4.2     7.6    -      -       +      +
    111V  GLN*     6.3     0.4    -      -       -      -
    114V  SER*     4.2    15.2    +      -       -      -
    115V  PHE      3.2    16.4    -      -       -      +
    116V  ILE*     3.9    18.6    -      -       +      +
    117V  ALA      4.1     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 101 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26V  LEU*     4.4     7.4    -      -       +      -
     30V  VAL*     4.4    14.4    -      -       +      -
     33V  LEU*     4.2    16.4    -      -       +      -
     40V  PRO*     5.2     0.4    -      -       +      -
     41V  CYS      3.7     7.6    -      -       -      +
     42V  LEU*     4.3    15.3    -      -       +      -
     83V  VAL*     4.6    20.6    -      -       +      -
     84V  LEU*     5.3     1.6    -      -       +      -
     87V  LEU*     4.5    14.4    -      -       +      -
    100V  ARG*     1.3    76.6    -      -       -      +
    102V  ILE*     1.3    69.3    +      -       -      +
    113V  VAL*     4.2     0.7    -      -       -      +
    114V  SER*     3.2     4.9    +      -       -      -
    115V  PHE*     2.9    57.5    +      -       +      -
    117V  ALA*     3.8    24.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 102 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  ARG*     4.0     5.6    -      -       -      +
     33V  LEU*     3.8     7.2    -      -       -      +
     39V  VAL      3.7     0.2    -      -       -      +
     40V  PRO*     3.4     4.3    -      -       -      +
     41V  CYS*     2.9    50.6    +      -       +      +
     43V  GLU*     3.7    37.7    -      -       +      +
    100V  ARG*     4.2     9.6    -      -       +      +
    101V  ILE*     1.3    81.1    -      -       -      +
    103V  GLY*     1.3    58.3    +      -       -      +
    104V  PHE*     3.6    30.7    -      -       +      -
    111V  GLN*     3.7    18.8    -      -       -      +
    113V  VAL      3.2     8.7    -      -       -      +
    114V  SER*     3.6    20.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 103 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33V  LEU*     3.7    21.3    -      -       -      -
     38V  TRP*     4.3     4.5    -      -       -      -
     39V  VAL      3.3     6.7    -      -       -      -
    102V  ILE*     1.3    76.0    -      -       -      +
    104V  PHE*     1.3    61.6    +      -       -      -
    111V  GLN*     3.2     6.3    -      -       -      -
    112V  CYS      3.0    27.7    +      -       -      -
    113V  VAL*     3.0    15.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 104 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  ASN*     4.1    12.6    -      -       -      -
    187A  ARG*     3.7    35.0    -      -       -      -
     37V  LYS      4.8     0.3    -      -       -      +
     38V  TRP*     3.3     8.0    -      -       -      -
     39V  VAL*     2.8    53.3    +      -       +      +
     41V  CYS*     3.7    27.1    -      -       +      -
     69V  MET*     5.4     0.7    -      -       +      -
     73V  PRO*     4.1    22.0    -      -       +      -
     75V  PHE*     6.2     0.9    -      +       -      -
    102V  ILE*     3.6    16.4    -      -       +      -
    103V  GLY*     1.3    74.1    -      -       -      -
    105V  ASP*     1.3    63.2    +      -       -      +
    106V  SER*     3.8     4.9    +      -       -      +
    109V  GLN      6.1     1.8    -      -       -      -
    110V  VAL      4.0     4.9    -      -       -      -
    111V  GLN*     3.8    24.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 105 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37V  LYS      5.9     0.2    -      -       -      -
     38V  TRP*     3.5    24.1    +      -       +      -
    103V  GLY      4.0     0.4    +      -       -      -
    104V  PHE*     1.3    73.6    -      -       -      +
    106V  SER*     1.3    52.4    +      -       -      +
    107V  ASN*     3.1    25.7    +      -       -      +
    108V  ARG*     3.4    27.3    +      -       -      +
    109V  GLN*     2.7    36.4    +      -       -      -
    110V  VAL*     3.0    19.8    +      -       +      +
    112V  CYS*     3.6    18.9    -      -       -      -
----------------------------------------------------------
 Back to top of page


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