Contacts of the strand formed by residues 101 - 109 (chain C) in PDB entry 3RT0


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 ILE 101 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  TRP*     3.4     7.1    -      -       -      -
     94C  ILE*     3.8    16.9    -      -       +      +
     95C  LEU*     3.8     0.9    -      -       -      -
     96C  ASP*     2.9    39.5    +      -       +      +
     99C  GLU*     3.7    28.3    -      -       +      +
    100C  HIS*     1.3    82.6    -      -       -      +
    102C  LEU*     1.3    66.7    +      -       -      +
    119C  THR*     3.9    22.9    -      -       +      -
    120C  ILE      3.3     8.5    -      -       -      +
    121C  SER*     3.9    14.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  TRP*     4.4     2.2    -      -       +      -
     46C  VAL*     3.6    31.6    -      -       +      +
     47C  ARG*     4.4    10.8    -      -       -      +
     49C  PHE*     4.7     8.3    -      -       +      -
     55C  TYR*     5.8     2.5    -      -       -      +
     75C  ARG*     5.6     1.6    -      -       -      +
     92C  LEU*     3.5    24.7    -      -       +      -
     94C  ILE      3.3     5.8    -      -       -      +
     95C  LEU*     3.8    22.2    -      -       +      -
    101C  ILE*     1.3    77.6    -      -       -      +
    103C  GLY*     1.3    60.4    +      -       -      +
    104C  ILE*     3.6    25.5    +      -       +      +
    118C  SER      4.0     0.5    -      -       -      +
    119C  THR*     3.5     1.2    -      -       -      -
    120C  ILE*     2.9    53.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 103 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  LEU*     3.4     7.8    -      -       -      +
     93C  GLU*     2.8    30.6    +      -       -      -
     94C  ILE*     2.8    31.5    +      -       -      +
    102C  LEU*     1.3    74.3    -      -       -      +
    104C  ILE*     1.3    56.4    +      -       -      -
    118C  SER      3.3    10.5    -      -       -      -
    119C  THR*     4.4     6.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 104 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  PHE*     3.3    43.1    -      -       +      -
     56C  LYS*     6.1     0.2    -      -       -      +
     75C  ARG*     3.9    16.8    -      -       -      +
     90C  GLU*     4.2    15.5    -      -       +      -
     91C  VAL      3.4     7.6    -      -       -      +
     92C  LEU*     4.2     1.3    -      -       +      -
     93C  GLU*     4.2     5.9    -      -       -      +
    102C  LEU*     3.6    29.1    +      -       +      -
    103C  GLY*     1.3    76.4    -      -       -      +
    105C  ARG*     1.3    73.2    -      -       -      +
    106C  ILE*     4.5     5.2    -      -       +      +
    116C  TYR*     5.3     3.6    -      -       +      -
    117C  SER*     3.3     5.0    -      -       -      -
    118C  SER*     3.0    40.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 105 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  GLU*     3.3     2.4    -      -       -      -
     91C  VAL*     2.9    37.4    +      -       +      +
     93C  GLU*     3.3    34.6    +      -       +      +
    104C  ILE*     1.3    80.8    -      -       -      +
    106C  ILE*     1.3    66.3    +      -       -      +
    107C  VAL*     3.7    23.3    +      -       +      -
    115C  ASN*     3.7    39.6    +      -       -      +
    116C  TYR      3.3     7.6    -      -       -      +
    117C  SER*     3.7    24.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 106 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  SER*     3.6     9.0    -      -       -      +
     89C  THR      3.4    11.0    -      -       -      +
     90C  GLU*     3.7    19.3    -      -       +      +
    104C  ILE*     4.9     2.2    -      -       +      -
    105C  ARG*     1.3    81.5    +      -       -      +
    107C  VAL*     1.3    61.8    -      -       -      +
    108C  GLY      3.5     1.8    -      -       -      +
    111C  HIS*     2.9    45.5    -      -       +      +
    113C  LEU*     4.4    14.9    -      -       +      +
    115C  ASN*     4.7     6.2    +      -       -      -
    116C  TYR*     2.7    62.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 107 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74C  VAL*     5.5     2.0    -      -       +      -
     89C  THR*     2.8    38.6    +      -       +      +
     90C  GLU*     4.3     6.7    -      -       -      +
     91C  VAL*     4.0    16.8    -      -       +      +
    105C  ARG*     3.7    24.2    -      -       +      -
    106C  ILE*     1.3    76.9    -      -       -      +
    108C  GLY*     1.3    59.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 108 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89C  THR*     2.9    29.5    +      -       -      -
    106C  ILE*     3.5     2.6    -      -       -      +
    107C  VAL*     1.3    79.3    -      -       -      +
    109C  GLY*     1.3    54.1    +      -       -      -
    111C  HIS*     2.7    29.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 109 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  GLU*     6.1     0.2    -      -       -      -
     87C  LYS*     3.3    27.8    -      -       -      -
     88C  SER*     3.9     4.5    -      -       -      -
     89C  THR*     4.1     3.3    +      -       -      -
    108C  GLY*     1.3    73.9    -      -       -      -
    110C  ASP*     1.3    58.5    +      -       -      -
    111C  HIS*     3.4    12.0    +      -       -      +
----------------------------------------------------------
 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