Contacts of the strand formed by residues 501 - 506 (chain E) in PDB entry 4RYD


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 LEU 501 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461E  ILE*     4.5     3.6    -      -       +      -
    493E  LEU*     4.0    29.2    -      -       +      -
    495E  TYR*     3.5    53.8    -      -       +      +
    498E  ARG*     3.0    19.6    +      -       -      +
    499E  GLY*     4.0     1.4    -      -       -      +
    500E  ASP*     1.3    78.9    -      -       -      +
    502E  ALA*     1.3    58.4    -      -       -      +
    503E  ILE*     4.7     7.0    -      -       +      -
    516E  LEU*     4.1    15.0    -      -       +      +
    517E  ALA      3.8     4.7    -      -       -      +
    518E  ALA*     3.5    21.0    +      -       -      -
    528E  PHE*     4.6    11.0    -      -       +      -
    551E  ILE*     3.7    23.3    -      -       +      -
    552E  GLU      3.4     7.2    -      -       -      +
    554E  THR*     4.5     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 502 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    501E  LEU*     1.3    74.5    -      -       -      +
    503E  ILE*     1.3    61.6    +      -       -      +
    504E  HIS*     4.0     9.6    -      -       +      +
    516E  LEU      3.1    11.7    -      -       -      +
    517E  ALA*     4.6     1.6    -      -       -      -
    518E  ALA      4.4     6.5    -      -       -      +
    550E  GLU      3.7     0.5    -      -       -      +
    551E  ILE*     3.5     2.9    -      -       -      -
    552E  GLU*     3.0    48.2    +      -       +      +
    554E  THR*     3.5    24.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 503 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491E  LEU*     4.0    22.4    -      -       +      -
    493E  LEU*     4.5    16.2    -      -       +      -
    501E  LEU*     4.7     5.2    -      -       +      -
    502E  ALA*     1.3    80.2    -      -       -      +
    504E  HIS*     1.3    66.4    +      -       -      +
    514E  THR*     3.5     3.1    -      -       -      -
    515E  LEU*     2.8    38.5    +      -       +      -
    516E  LEU*     2.7    46.5    +      -       +      +
    528E  PHE*     4.6     2.7    -      -       +      -
    533E  PHE*     4.3     9.4    -      -       +      -
    549E  LEU*     3.8    23.8    -      -       +      -
    550E  GLU      3.2     8.3    -      -       -      +
    551E  ILE*     4.3    16.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 504 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    502E  ALA*     4.0    12.9    -      -       +      +
    503E  ILE*     1.3    77.4    -      -       -      +
    505E  LEU*     1.3    61.9    +      -       -      +
    506E  VAL      4.3     0.4    -      -       -      -
    512E  ARG*     3.5    30.5    +      -       +      +
    513E  SER      3.3     6.3    -      -       -      +
    514E  THR*     2.9    40.3    +      -       +      -
    515E  LEU*     4.6     0.9    -      -       -      -
    517E  ALA*     6.0     0.2    -      -       -      -
    548E  VAL      3.7     0.6    -      -       -      +
    549E  LEU*     3.4     8.5    -      -       -      +
    550E  GLU*     2.8    56.4    +      -       +      +
    552E  GLU*     3.0    28.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 505 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    487E  ALA*     5.4     2.5    -      -       +      -
    488E  GLN      5.5     0.2    -      -       -      -
    489E  ALA*     4.4    13.9    -      -       +      +
    504E  HIS*     1.3    75.1    -      -       -      +
    506E  VAL*     1.3    59.3    +      -       -      +
    511E  THR      3.4     2.8    -      -       -      +
    513E  SER*     2.7    42.3    +      -       -      +
    515E  LEU*     3.8    23.6    -      -       +      -
    535E  THR*     4.7    13.0    -      -       +      -
    547E  TRP*     3.7    37.2    -      -       +      -
    548E  VAL      3.4    15.9    -      -       -      +
    549E  LEU*     4.0     8.5    -      -       +      -
    566E  PHE*     3.9    28.0    -      -       +      -
    568E  LEU*     4.3    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 506 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505E  LEU*     1.3    76.6    -      -       -      +
    507E  SER*     1.3    73.9    +      -       -      +
    510E  GLY*     3.9    18.2    -      -       -      +
    511E  THR      3.3     9.2    -      -       -      +
    512E  ARG*     4.0    26.5    -      -       +      +
    546E  GLU      4.1     0.2    -      -       -      +
    547E  TRP*     3.3    10.0    -      -       -      -
    548E  VAL*     2.8    47.6    +      -       +      +
    550E  GLU*     3.7    23.6    -      -       -      +
----------------------------------------------------------
 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