Contacts of the strand formed by residues 545 - 553 (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 GLY 545 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    469E  LYS      3.6     1.0    -      -       -      +
    470E  THR*     3.4    10.7    -      -       -      -
    471E  VAL*     2.8    39.3    +      -       -      +
    508E  PRO*     3.5     7.6    -      -       -      -
    544E  SER*     1.3    75.8    -      -       -      +
    546E  GLU*     1.3    63.0    +      -       -      -
    547E  TRP*     3.6     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 546 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468E  ARG*     2.6    43.2    +      -       -      +
    469E  LYS      3.4    11.4    +      -       -      +
    470E  THR*     3.9    16.7    +      -       +      +
    506E  VAL      4.1     0.3    -      -       -      +
    507E  SER      3.8     2.3    -      -       -      +
    508E  PRO*     3.2    27.5    -      -       -      +
    545E  GLY*     1.3    72.3    -      -       -      -
    547E  TRP*     1.3    70.0    +      -       -      +
    548E  VAL*     4.0     7.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 547 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454E  ILE*     6.2     1.6    -      -       +      -
    467E  VAL      3.8     0.7    -      -       -      +
    468E  ARG*     3.5     2.9    -      -       -      -
    469E  LYS*     2.9    36.0    +      -       +      +
    471E  VAL*     3.7    25.3    -      -       +      +
    484E  LEU*     4.2    17.9    -      -       +      -
    487E  ALA*     4.5     6.7    -      -       +      -
    505E  LEU*     3.7    40.2    -      -       +      -
    506E  VAL      3.3    17.3    -      -       -      -
    507E  SER*     3.7    21.5    -      -       -      -
    508E  PRO*     3.3    22.8    -      -       +      +
    535E  THR*     5.7     2.2    -      -       +      -
    538E  SER*     4.7     3.8    -      -       -      -
    543E  PRO*     2.8    34.5    +      -       +      +
    545E  GLY      3.7     1.1    -      -       -      -
    546E  GLU*     1.3    73.6    -      -       -      +
    548E  VAL*     1.3    61.8    +      -       -      +
    566E  PHE*     5.7     5.6    -      -       +      -
    568E  LEU*     3.9    23.8    -      -       +      +
    570E  LEU*     4.0    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 548 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466E  GLU*     3.6    35.9    -      -       +      +
    467E  VAL      3.3     4.9    -      -       -      +
    468E  ARG*     3.6    33.0    -      -       +      +
    504E  HIS      3.7     0.7    -      -       -      +
    505E  LEU*     3.4     7.9    -      -       -      +
    506E  VAL*     2.8    50.9    +      -       +      +
    546E  GLU*     4.0     9.9    -      -       +      +
    547E  TRP*     1.3    82.0    -      -       -      +
    549E  LEU*     1.3    62.4    +      -       -      +
    550E  GLU*     4.1    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 549 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465E  LEU      3.8     0.9    -      -       -      +
    466E  GLU*     3.3     5.2    -      -       -      +
    467E  VAL*     2.8    39.4    +      -       +      +
    491E  LEU*     4.0    13.0    -      -       +      -
    503E  ILE*     3.8    18.4    -      -       +      -
    504E  HIS      3.4    13.0    -      -       -      +
    505E  LEU*     4.0    14.1    -      -       +      -
    515E  LEU*     4.1     9.6    -      -       +      -
    548E  VAL*     1.3    73.5    -      -       -      +
    550E  GLU*     1.3    62.8    +      -       -      +
    551E  ILE*     4.2    15.3    -      -       +      -
    563E  LEU*     4.0    18.6    -      -       +      -
    566E  PHE*     3.5    48.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 550 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464E  ARG*     3.7    30.6    +      -       -      +
    465E  LEU      3.4     4.9    -      -       -      +
    466E  GLU*     4.5     4.5    -      -       +      +
    502E  ALA      3.7     0.9    -      -       -      +
    503E  ILE*     3.2     6.6    -      -       -      +
    504E  HIS*     2.8    54.5    +      -       +      +
    506E  VAL*     3.7    10.7    -      -       -      +
    512E  ARG*     2.5    48.2    +      -       -      -
    548E  VAL*     4.1    16.2    -      -       +      +
    549E  LEU*     1.3    78.3    -      -       -      +
    551E  ILE*     1.3    63.9    +      -       -      +
    552E  GLU*     6.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 551 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461E  ILE*     3.8    16.2    -      -       +      +
    464E  ARG*     3.3     3.6    -      -       -      +
    465E  LEU*     2.7    55.4    +      -       +      +
    491E  LEU*     4.9     2.9    -      -       +      -
    493E  LEU*     4.4    11.9    -      -       +      -
    501E  LEU*     3.7    28.3    -      -       +      -
    502E  ALA      3.5     5.6    -      -       -      +
    503E  ILE*     4.3    18.4    -      -       +      -
    549E  LEU*     4.2    11.9    -      -       +      -
    550E  GLU*     1.3    78.5    -      -       -      +
    552E  GLU*     1.3    62.9    +      -       -      +
    563E  LEU*     4.0    38.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 552 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461E  ILE*     5.6     1.1    -      -       -      -
    463E  LYS      3.6     8.5    -      -       -      +
    464E  ARG*     4.3    16.9    +      -       +      +
    501E  LEU*     3.4    11.2    -      -       -      +
    502E  ALA*     3.0    47.1    +      -       +      +
    504E  HIS*     3.0    30.2    +      -       +      +
    550E  GLU*     5.4     1.5    -      -       +      +
    551E  ILE*     1.3    77.9    -      -       -      +
    553E  ASN*     1.3    62.9    +      -       -      +
    554E  THR*     3.5    11.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 553 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462E  GLY      3.9     9.3    +      -       -      +
    463E  LYS*     2.8    52.0    +      -       +      +
    495E  TYR*     3.2    18.8    +      -       -      +
    500E  ASP*     3.7     6.9    -      -       -      +
    501E  LEU*     5.0     0.2    -      -       -      -
    552E  GLU*     1.3    74.3    -      -       -      +
    554E  THR*     1.3    57.9    +      -       -      +
    555E  SER*     2.8    22.9    +      -       -      -
    557E  ALA      2.9    28.3    +      -       -      -
    558E  ASN*     5.0     0.2    -      -       -      +
    559E  ASN*     3.0    27.9    +      -       -      +
----------------------------------------------------------
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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