Contacts of the strand formed by residues 351 - 355 (chain B) 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 ILE 351 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  TRP*     4.4     4.5    -      -       +      -
    123B  TYR*     3.4    44.2    -      -       +      +
    201B  GLU*     3.4    34.1    -      -       +      +
    341B  TYR      4.1    14.6    -      -       -      +
    342B  SER*     4.2    13.0    -      -       -      -
    350B  GLN*     1.3    80.1    -      -       -      +
    352B  VAL*     1.3    65.6    +      -       -      +
    353B  THR*     4.6     0.2    -      -       -      -
    361B  THR      3.7     1.0    -      -       -      +
    362B  GLU*     3.4     8.1    -      -       -      -
    363B  SER      3.6     0.2    +      -       -      -
    364B  HIS*     3.1    45.3    +      -       +      +
    369B  ALA*     3.6    22.2    -      -       +      -
    373B  LEU*     4.4     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 352 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  LYS*     3.8    31.6    -      -       +      -
    120B  GLN*     4.0    30.7    -      -       +      +
    121B  GLN*     3.2    24.0    +      -       +      +
    123B  TYR*     3.0    20.8    +      -       -      +
    201B  GLU*     5.2     1.9    -      -       -      +
    211B  CYS*     4.4     2.7    -      -       -      -
    212B  GLY      4.9     0.4    -      -       -      +
    350B  GLN      4.4     5.4    -      -       -      +
    351B  ILE*     1.3    73.7    -      -       -      +
    353B  THR*     1.3    68.1    +      -       -      +
    360B  CYS*     4.3     7.6    -      -       -      -
    361B  THR      3.1     9.6    -      -       -      +
    362B  GLU*     3.9    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 353 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197B  ARG*     2.7    43.1    +      -       +      +
    200B  GLY*     3.2     6.0    -      -       -      -
    201B  GLU*     3.2    24.2    +      -       +      -
    211B  CYS*     3.5    14.2    -      -       -      -
    212B  GLY*     6.5     0.2    -      -       -      -
    352B  VAL*     1.3    76.5    -      -       -      +
    354B  THR*     1.3    65.7    +      -       -      +
    361B  THR*     2.8    49.9    +      -       +      +
    364B  HIS*     3.8    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 354 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160B  HIS*     3.5    22.9    -      -       +      +
    162B  ASP*     3.4    36.8    -      -       +      +
    163B  LEU*     4.1    14.7    -      -       +      +
    196B  THR*     2.9    27.3    +      -       -      +
    197B  ARG*     3.1    27.5    +      -       -      +
    200B  GLY*     3.2    15.1    -      -       -      -
    204B  ALA*     4.4     3.1    -      -       +      -
    211B  CYS*     4.6     4.3    -      -       -      -
    353B  THR*     1.3    79.1    +      -       -      +
    355B  ASP*     1.3    59.2    +      -       -      +
    359B  LYS      3.8     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 355 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160B  HIS*     3.1    12.0    -      -       -      -
    193B  ARG*     3.6    14.5    -      -       -      +
    196B  THR*     3.9     5.6    -      -       -      -
    197B  ARG*     2.6    46.0    +      -       -      +
    353B  THR      3.7     0.2    +      -       -      -
    354B  THR*     1.3    74.4    -      -       -      +
    356B  LEU*     1.3    81.7    +      -       -      +
    359B  LYS*     2.8    40.4    +      -       +      +
    360B  CYS      5.1     0.3    -      -       -      +
    361B  THR*     3.7    17.4    -      -       -      +
----------------------------------------------------------
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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