Contacts of the strand formed by residues 545 - 553 (chain A) 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 GLY 545 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    469A  LYS      3.5     1.4    -      -       -      +
    470A  THR*     3.3    11.2    -      -       -      -
    471A  VAL*     2.8    40.8    +      -       -      +
    508A  PRO*     3.5     7.2    -      -       -      -
    544A  SER*     1.3    75.0    -      -       -      +
    546A  GLU*     1.3    61.8    +      -       -      -
    547A  TRP*     3.7     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 546 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468A  ARG*     2.8    53.0    +      -       -      +
    469A  LYS      3.4    14.1    -      -       -      +
    470A  THR*     3.8    16.9    +      -       -      +
    506A  VAL*     4.1     0.9    -      -       -      +
    507A  SER      3.9     2.3    -      -       -      +
    508A  PRO*     3.2    26.4    -      -       +      +
    545A  GLY*     1.3    72.3    -      -       -      -
    547A  TRP*     1.3    67.5    +      -       -      +
    548A  VAL*     4.3     4.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 547 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ILE*     6.4     0.9    -      -       +      -
    467A  VAL      3.8     0.9    -      -       -      +
    468A  ARG*     3.5     1.4    -      -       -      -
    469A  LYS*     2.9    34.6    +      -       +      +
    471A  VAL*     3.7    25.5    -      -       +      +
    484A  LEU*     4.1    18.8    -      -       +      -
    487A  ALA*     4.6     5.8    -      -       +      -
    505A  LEU*     3.7    38.6    -      -       +      -
    506A  VAL      3.3     9.0    -      -       -      -
    507A  SER*     3.6    31.0    -      -       -      -
    508A  PRO*     3.2    22.6    -      -       +      +
    535A  THR*     5.7     1.6    -      -       +      -
    538A  SER*     4.6     3.6    -      -       -      -
    541A  GLU*     5.9     0.2    -      -       -      -
    543A  PRO*     2.8    33.3    +      -       +      +
    545A  GLY      3.7     0.9    -      -       -      -
    546A  GLU*     1.3    74.0    -      -       -      +
    548A  VAL*     1.3    65.6    +      -       -      +
    566A  PHE*     5.7     6.1    -      -       +      -
    568A  LEU*     3.7    25.6    -      -       +      +
    570A  LEU*     3.9    20.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 548 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466A  GLU*     3.7    35.7    -      -       +      +
    467A  VAL      3.3     4.9    -      -       -      +
    468A  ARG*     3.4    35.9    -      -       +      +
    504A  HIS      3.7     0.7    -      -       -      +
    505A  LEU*     3.4     7.2    -      -       -      +
    506A  VAL*     2.8    53.1    +      -       +      +
    546A  GLU*     4.3     7.2    -      -       +      +
    547A  TRP*     1.3    80.3    -      -       -      +
    549A  LEU*     1.3    63.1    +      -       -      +
    550A  GLU*     4.1    14.3    +      -       +      +
    566A  PHE*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 549 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465A  LEU      3.8     0.7    -      -       -      +
    466A  GLU*     3.3     4.9    -      -       -      -
    467A  VAL*     2.8    38.6    +      -       +      +
    491A  LEU*     4.1    16.2    -      -       +      -
    503A  ILE*     3.9    17.9    -      -       +      -
    504A  HIS      3.4    12.6    -      -       -      +
    505A  LEU*     4.4     8.7    -      -       +      -
    515A  LEU*     4.3    13.9    -      -       +      -
    548A  VAL*     1.3    74.0    -      -       -      +
    550A  GLU*     1.3    61.5    +      -       -      +
    551A  ILE*     4.2    15.0    -      -       +      -
    563A  LEU*     4.1    19.5    -      -       +      -
    566A  PHE*     3.8    45.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 550 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464A  ARG*     3.7    39.1    +      -       -      +
    465A  LEU      3.4     4.0    -      -       -      -
    466A  GLU*     4.8     1.4    -      -       +      +
    502A  ALA      3.7     0.5    -      -       -      +
    503A  ILE*     3.2     6.4    -      -       -      +
    504A  HIS*     2.8    52.1    +      -       +      +
    506A  VAL*     3.8     7.2    -      -       -      +
    512A  ARG*     2.6    44.9    +      -       -      -
    548A  VAL*     4.1    16.3    -      -       +      +
    549A  LEU*     1.3    78.1    -      -       -      +
    551A  ILE*     1.3    64.3    +      -       -      +
    552A  GLU      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 551 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  ILE*     3.8    17.7    -      -       +      +
    464A  ARG*     3.3     3.8    -      -       -      +
    465A  LEU*     2.7    53.4    +      -       +      +
    491A  LEU*     5.0     1.1    -      -       +      -
    493A  LEU*     4.5    11.0    -      -       +      -
    501A  LEU*     3.8    27.1    -      -       +      -
    502A  ALA      3.5     2.9    -      -       -      +
    503A  ILE*     4.2    23.6    -      -       +      -
    549A  LEU*     4.2    12.1    -      -       +      -
    550A  GLU*     1.3    78.8    -      -       -      +
    552A  GLU*     1.3    61.7    -      -       -      +
    563A  LEU*     4.1    38.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 552 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  ILE*     5.7     0.7    -      -       -      -
    463A  LYS*     3.6     8.1    -      -       +      +
    464A  ARG*     4.3    22.2    +      -       +      +
    501A  LEU*     3.4    11.9    -      -       -      +
    502A  ALA*     3.0    44.5    +      -       +      +
    504A  HIS*     3.1    28.8    +      -       +      -
    550A  GLU*     5.6     0.4    -      -       +      -
    551A  ILE*     1.3    76.3    -      -       -      +
    553A  ASN*     1.3    63.7    +      -       -      +
    554A  THR*     3.5    13.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 553 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  ILE*     5.7     0.2    -      -       -      +
    462A  GLY      3.9     6.9    +      -       -      +
    463A  LYS*     2.9    53.0    +      -       +      +
    495A  TYR*     3.3    23.7    +      -       -      +
    500A  ASP*     3.5     7.9    -      -       -      +
    501A  LEU*     5.0     0.4    -      -       -      -
    552A  GLU*     1.3    73.6    -      -       -      +
    554A  THR*     1.3    58.4    +      -       -      +
    555A  SER*     3.1    20.4    +      -       -      -
    557A  ALA      2.9    27.5    +      -       -      -
    558A  ASN*     5.0     0.2    -      -       -      +
    559A  ASN*     2.9    26.1    +      -       -      +
----------------------------------------------------------
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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