Contacts of the strand formed by residues 512 - 516 (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 ARG 512 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422B  HIS*     3.9    14.9    -      -       -      -
    504B  HIS*     3.3    34.2    -      -       +      +
    505B  LEU      3.5     3.4    -      -       -      -
    506B  VAL*     3.9    20.4    -      -       +      +
    510B  GLY      3.4     5.9    +      -       -      +
    511B  THR*     1.3    76.0    -      -       -      +
    513B  SER*     1.3    62.9    +      -       -      +
    514B  THR*     4.9     4.5    -      -       -      +
    537B  HIS*     4.7     1.7    +      -       -      -
    550B  GLU*     2.5    46.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 513 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334B  SER*     4.1     5.4    -      -       -      -
    422B  HIS*     3.9     4.5    -      -       -      -
    504B  HIS*     3.3     1.1    -      -       -      -
    505B  LEU*     2.7    46.4    +      -       -      +
    511B  THR*     3.6     4.7    +      -       -      +
    512B  ARG*     1.3    72.8    -      -       -      +
    514B  THR*     1.3    62.1    +      -       -      +
    515B  LEU*     3.3     8.5    +      -       -      -
    535B  THR*     2.6    44.1    +      -       -      +
    537B  HIS*     3.5    13.9    -      -       -      +
    538B  SER*     4.9     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 514 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333B  CYS*     4.6     2.6    -      -       -      -
    334B  SER*     3.6    15.1    +      -       -      -
    422B  HIS*     2.9    36.6    +      -       +      -
    503B  ILE      3.6     3.1    -      -       -      -
    504B  HIS*     3.0    30.1    +      -       +      +
    512B  ARG*     3.9     5.9    +      -       -      +
    513B  SER*     1.3    70.9    -      -       -      +
    515B  LEU*     1.3    62.5    +      -       -      +
    516B  LEU      3.7    26.2    -      -       -      +
    517B  ALA*     3.9    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 515 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302B  SER*     4.4     0.7    +      -       -      -
    304B  ASN*     2.9    32.3    +      -       -      +
    333B  CYS*     5.5     0.2    -      -       -      +
    334B  SER*     3.8    14.6    -      -       -      +
    489B  ALA*     3.7    27.4    -      -       +      -
    491B  LEU*     5.1     0.4    -      -       +      -
    503B  ILE*     2.8    30.5    +      -       +      +
    505B  LEU*     3.7    27.1    -      -       +      +
    513B  SER      4.0     9.4    -      -       -      +
    514B  THR*     1.3    73.4    -      -       -      +
    516B  LEU*     1.3    61.9    +      -       -      +
    533B  PHE*     3.5    38.1    -      -       +      +
    535B  THR*     4.4    16.2    -      -       +      -
    549B  LEU*     4.2     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 516 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302B  SER*     4.4    10.1    -      -       -      +
    305B  CYS*     3.7    30.3    -      -       -      -
    498B  ARG*     4.7     4.9    -      -       +      +
    501B  LEU*     3.9    21.8    -      -       +      +
    502B  ALA*     3.0     5.7    -      -       -      -
    503B  ILE*     2.7    52.7    +      -       +      +
    514B  THR*     3.3     7.1    -      -       -      +
    515B  LEU*     1.3    80.8    -      -       -      +
    517B  ALA*     1.3    74.3    +      -       -      +
    519B  ARG*     4.6     7.4    -      -       +      +
    528B  PHE*     3.8    30.3    -      -       +      -
    533B  PHE*     4.0    10.1    -      -       +      -
----------------------------------------------------------
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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