Contacts of the strand formed by residues 501 - 506 (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 LEU 501 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  ILE*     4.4     2.0    -      -       +      -
    493B  LEU*     4.0    22.7    -      -       +      -
    495B  TYR*     3.5    61.5    -      -       +      +
    498B  ARG*     3.0    24.9    +      -       +      +
    499B  GLY      4.0     0.9    -      -       -      +
    500B  ASP*     1.3    78.9    -      -       -      +
    502B  ALA*     1.3    59.2    +      -       -      +
    503B  ILE*     4.7     6.7    -      -       +      -
    516B  LEU*     3.9    15.8    -      -       +      +
    517B  ALA      3.8     4.3    -      -       -      +
    518B  ALA*     3.5    20.5    +      -       -      -
    528B  PHE*     4.7     5.6    -      -       +      -
    551B  ILE*     3.8    23.3    -      -       +      -
    552B  GLU      3.4     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 502 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    501B  LEU*     1.3    73.8    -      -       -      +
    503B  ILE*     1.3    63.4    +      -       -      +
    504B  HIS*     3.8    10.6    +      -       +      +
    516B  LEU      3.0    11.2    -      -       -      +
    517B  ALA*     4.7     1.1    -      -       -      -
    518B  ALA      4.4     7.6    -      -       -      +
    550B  GLU      3.8     1.0    -      -       -      +
    551B  ILE*     3.6     0.7    -      -       -      -
    552B  GLU*     3.0    46.2    +      -       +      +
    554B  THR*     3.5    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 503 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491B  LEU*     4.0    26.0    -      -       +      -
    493B  LEU*     4.3    18.2    -      -       +      -
    501B  LEU*     4.7     4.5    -      -       +      -
    502B  ALA*     1.3    80.6    -      -       -      +
    504B  HIS*     1.3    67.3    +      -       -      +
    514B  THR*     3.5     1.9    -      -       -      -
    515B  LEU*     2.8    34.4    +      -       +      -
    516B  LEU*     2.7    43.1    +      -       +      +
    528B  PHE*     4.9     2.2    -      -       +      -
    533B  PHE*     4.5     8.1    -      -       +      -
    549B  LEU*     3.7    23.1    -      -       +      -
    550B  GLU      3.2     9.6    -      -       -      +
    551B  ILE*     4.1    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 504 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    502B  ALA*     3.8    13.9    -      -       +      +
    503B  ILE*     1.3    80.5    +      -       -      +
    505B  LEU*     1.3    60.5    +      -       -      +
    512B  ARG*     3.3    30.7    +      -       +      +
    513B  SER      3.3     7.2    -      -       -      +
    514B  THR*     3.0    36.4    +      -       +      -
    515B  LEU*     4.6     1.3    -      -       -      -
    517B  ALA*     5.9     0.2    -      -       -      -
    548B  VAL      3.7     0.8    -      -       -      +
    549B  LEU*     3.4     7.9    -      -       -      +
    550B  GLU*     2.8    57.0    +      -       +      +
    552B  GLU*     3.0    29.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 505 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    487B  ALA*     5.4     2.0    -      -       +      -
    488B  GLN      5.5     0.2    -      -       -      -
    489B  ALA*     4.3    14.4    -      -       +      +
    504B  HIS*     1.3    75.4    -      -       -      +
    506B  VAL*     1.3    60.8    +      -       -      +
    511B  THR      3.3     2.6    -      -       -      +
    513B  SER*     2.7    44.9    +      -       -      +
    515B  LEU*     3.7    17.9    -      -       +      -
    535B  THR*     4.6    16.6    -      -       +      -
    547B  TRP*     3.7    38.4    -      -       +      -
    548B  VAL      3.4    17.9    -      -       -      +
    549B  LEU*     4.2     7.0    -      -       +      -
    566B  PHE*     4.1    25.8    -      -       +      -
    568B  LEU*     4.2    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 506 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505B  LEU*     1.3    77.4    -      -       -      +
    507B  SER*     1.3    74.0    +      -       -      +
    510B  GLY*     3.9    17.7    -      -       -      +
    511B  THR      3.3     9.0    -      -       -      +
    512B  ARG*     3.9    39.3    -      -       +      +
    546B  GLU      4.1     0.5    -      -       -      +
    547B  TRP*     3.3     9.6    -      -       -      -
    548B  VAL*     2.8    48.8    +      -       +      +
    550B  GLU*     4.0     8.7    -      -       -      +
----------------------------------------------------------
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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