Contacts of the strand formed by residues 494 - 500 (chain B) 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 494 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  VAL*     3.8     1.8    -      -       +      +
    194B  SER*     3.3     2.3    +      -       -      -
    195B  ILE*     2.9    49.7    +      -       +      +
    197B  GLY*     5.1     0.4    -      -       -      -
    431B  SER*     4.0     1.3    -      -       -      -
    433B  GLY*     3.8    15.9    -      -       -      +
    434B  LEU*     4.7     9.4    -      -       +      +
    482B  SER*     4.0    22.9    -      -       -      +
    485B  ALA*     4.2     8.3    -      -       +      -
    486B  LEU*     3.8    34.5    -      -       +      -
    490B  SER*     4.1     9.4    -      -       -      +
    492B  ASP      3.6    10.7    +      -       -      +
    493B  ASN*     1.3    78.1    -      -       -      +
    495B  SER*     1.3    64.2    +      -       -      +
    496B  ILE*     3.9    27.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 495 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  VAL      3.2     5.2    -      -       -      -
    194B  SER*     2.8    26.5    +      -       -      -
    204B  ASP*     2.8    29.8    +      -       -      +
    205B  ALA      4.6     3.1    +      -       -      -
    206B  PHE*     5.2     3.8    -      -       -      -
    241B  VAL*     4.0    22.9    -      -       -      -
    430B  ALA*     3.0     8.3    -      -       -      +
    431B  SER*     3.0    32.2    +      -       -      +
    494B  ILE*     1.3    73.0    -      -       -      +
    496B  ILE*     1.3    62.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 496 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  GLY      4.0     0.2    -      -       -      +
    192B  THR*     3.3     5.9    -      -       -      +
    193B  VAL*     2.8    47.9    +      -       +      +
    428B  ILE*     4.0    13.5    -      -       +      -
    429B  LEU      3.4     7.6    -      -       -      +
    430B  ALA*     4.2     7.2    -      -       +      -
    434B  LEU*     3.8    17.0    -      -       +      -
    478B  ALA*     4.2     2.9    -      -       +      +
    481B  LEU*     3.6    32.1    -      -       +      -
    482B  SER      3.9    12.6    -      -       -      +
    494B  ILE*     3.9    16.4    -      -       +      -
    495B  SER*     1.3    80.8    -      -       -      +
    497B  ILE*     1.3    66.8    +      -       -      +
    498B  VAL*     4.0    24.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 497 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  TRP*     4.5     4.3    -      -       +      -
    191B  GLY      3.4     9.6    -      -       -      +
    192B  THR*     4.0    16.4    -      -       +      +
    206B  PHE*     4.6     4.5    -      -       +      -
    207B  ALA      4.4     0.2    -      -       -      +
    208B  VAL*     3.9    18.4    -      -       +      -
    239B  PHE*     4.0    25.8    -      -       +      -
    240B  GLY      3.7    22.7    -      -       -      +
    241B  VAL*     3.7    26.7    -      -       +      -
    427B  LEU      3.6     1.6    -      -       -      +
    428B  ILE*     3.3     6.8    -      -       -      +
    429B  LEU*     2.8    39.6    +      -       +      +
    496B  ILE*     1.3    76.8    -      -       -      +
    498B  VAL*     1.3    64.6    +      -       -      +
    499B  ILE*     4.0    13.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 498 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  TRP*     3.1     5.5    -      -       -      +
    191B  GLY      2.9    32.5    +      -       -      +
    426B  CYS*     4.9     1.8    -      -       +      -
    427B  LEU      3.8     1.8    -      -       -      -
    428B  ILE*     4.2    14.4    -      -       +      -
    447B  ALA*     4.5     7.9    -      -       +      -
    451B  ILE*     4.1    25.8    -      -       +      -
    474B  CYS*     3.6    16.8    -      -       +      +
    477B  ALA*     4.1    10.8    -      -       +      -
    478B  ALA*     3.9    28.9    -      -       +      +
    481B  LEU*     4.2     8.5    -      -       +      -
    496B  ILE*     4.0    11.4    -      -       +      -
    497B  ILE*     1.3    76.5    -      -       -      +
    499B  ILE*     1.3    65.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 499 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  PRO*     6.3     0.2    -      -       +      -
    189B  LEU      3.3    13.2    -      -       -      +
    190B  TRP*     4.1     8.3    -      -       +      -
    239B  PHE*     3.6    45.1    -      -       +      -
    334B  VAL*     4.6     6.1    -      -       +      -
    426B  CYS*     3.0     9.3    -      -       -      +
    427B  LEU*     2.8    67.9    +      -       +      +
    429B  LEU*     4.8     5.2    -      -       +      -
    474B  CYS*     4.3     0.7    -      -       -      -
    497B  ILE*     4.0    14.8    -      -       +      +
    498B  VAL*     1.3    79.5    -      -       -      +
    500B  ASP*     1.3    67.7    +      -       -      +
    501B  LEU*     3.6    17.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 500 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187B  ILE      5.5     0.5    -      -       -      +
    189B  LEU*     2.9    41.3    +      -       +      +
    425B  GLU      4.0     2.5    -      -       -      -
    426B  CYS*     4.5     2.7    -      -       -      -
    451B  ILE*     3.8    12.2    -      -       +      +
    455B  HIS*     4.4     6.8    +      -       -      -
    466B  ARG*     5.3     0.2    +      -       -      -
    471B  ASP*     5.0     1.4    -      -       -      +
    474B  CYS*     3.4    23.2    -      -       -      -
    499B  ILE*     1.3    74.7    -      -       -      +
    501B  LEU*     1.3    65.1    +      -       -      +
    502B  LYS*     3.0    20.6    +      -       -      +
    505B  ARG*     3.0    41.0    +      -       -      +
----------------------------------------------------------
 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