Contacts of the strand formed by residues 547 - 556 (chain D) in PDB entry 6RIN


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 547 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516D  ASP*     2.9    31.2    +      -       +      +
    517D  CYS      3.0    28.0    +      -       -      -
    518D  VAL*     3.6    25.9    +      -       -      +
    523D  GLU*     2.7    52.2    +      -       -      +
    524D  GLY*     4.0     2.3    +      -       -      -
    546D  ALA*     1.3    70.3    -      -       -      +
    548D  VAL*     1.3    62.8    +      -       -      +
    571D  ASP*     4.5    11.0    -      -       -      +
    572D  THR      3.4    11.4    -      -       -      +
    573D  THR*     4.3    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 548 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    522D  GLY      4.5    15.7    -      -       -      +
    524D  GLY*     5.9     0.4    -      -       -      -
    525D  MET*     3.1    28.3    -      -       +      +
    527D  LEU*     3.6    20.4    -      -       +      -
    546D  ALA*     3.3    13.7    -      -       +      +
    547D  ARG*     1.3    81.6    -      -       -      +
    549D  LYS*     1.3    72.4    +      -       -      +
    550D  VAL*     3.7    10.6    +      -       +      -
    571D  ASP*     3.3     6.0    +      -       -      +
    572D  THR*     2.8    35.9    +      -       -      +
    573D  THR      5.6     0.4    -      -       -      -
    574D  VAL*     3.7    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 549 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  LEU*     4.5    19.7    -      -       +      -
     83B  LEU*     5.5     0.2    -      -       -      +
    525D  MET      3.8     3.6    +      -       -      +
    526D  VAL*     3.4    29.6    -      -       +      +
    527D  LEU      3.6     0.2    +      -       -      -
    548D  VAL*     1.3    85.2    -      -       -      +
    550D  VAL*     1.3    59.6    +      -       -      +
    569D  LEU*     5.8     9.6    -      -       +      -
    570D  LYS      3.5    11.0    -      -       -      +
    571D  ASP*     4.5    20.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 550 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  LEU*     5.6     1.8    -      -       -      -
    527D  LEU*     3.6    35.4    -      -       +      +
    529D  GLY*     5.6     3.8    -      -       -      +
    530D  PRO*     6.5     0.4    -      -       +      -
    548D  VAL*     3.7    15.0    +      -       +      +
    549D  LYS*     1.3    78.9    -      -       -      +
    551D  ARG*     1.3    68.4    +      -       -      +
    552D  ILE*     4.1    13.9    +      -       +      -
    569D  LEU*     3.2     8.9    -      -       -      -
    570D  LYS*     2.9    35.1    +      -       +      +
    572D  THR*     3.6    28.5    -      -       +      -
    574D  VAL*     6.2     2.2    -      -       +      -
    577D  ALA*     5.0    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 551 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  GLU*     3.9    24.8    +      -       -      +
     83B  LEU*     4.6    12.8    -      -       +      +
     84B  ASN*     3.0    43.4    +      -       -      +
    527D  LEU      3.5     6.8    +      -       -      +
    528D  THR*     4.1    35.0    +      -       -      +
    529D  GLY*     4.4     0.9    -      -       -      -
    530D  PRO*     4.3    11.8    -      -       -      +
    550D  VAL*     1.3    77.9    -      -       -      +
    552D  ILE*     1.3    74.0    +      -       -      +
    553D  THR*     5.1     2.2    -      -       -      +
    567D  THR*     3.8    17.4    -      -       +      +
    568D  SER      3.3    14.1    -      -       -      +
    569D  LEU*     4.3    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 552 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    530D  PRO*     4.4    20.4    -      -       +      -
    550D  VAL*     4.3    13.0    -      -       +      +
    551D  ARG*     1.3    83.3    -      -       -      +
    553D  THR*     1.3    69.7    +      -       -      +
    554D  GLU*     5.1     6.3    -      -       +      +
    566D  LYS      4.5     0.2    -      -       -      +
    567D  THR*     2.9    13.6    +      -       -      -
    568D  SER      3.0    18.4    +      -       -      +
    570D  LYS*     3.6    45.1    -      -       +      +
    577D  ALA*     5.8     3.6    -      -       +      -
    580D  TRP*     4.7    15.0    -      -       +      +
    589D  TYR*     4.1    35.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 553 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551D  ARG*     5.1     3.3    -      -       -      +
    552D  ILE*     1.3    74.8    -      -       -      +
    554D  GLU*     1.3    68.0    +      -       -      +
    555D  TYR*     4.4    17.5    -      -       +      +
    565D  ALA*     4.4     6.7    -      -       +      -
    566D  LYS      3.6    14.4    -      -       -      +
    567D  THR*     2.9    22.7    +      -       -      -
    580D  TRP*     3.9    19.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 554 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552D  ILE*     5.2     5.4    -      -       +      -
    553D  THR*     1.3    74.3    -      -       -      +
    555D  TYR*     1.3    74.7    +      -       -      +
    556D  GLU*     6.2     0.9    -      -       +      -
    564D  VAL      4.1     0.2    -      -       -      +
    565D  ALA*     4.0     0.2    -      -       -      +
    566D  LYS*     2.9    64.7    +      -       +      +
    570D  LYS*     4.6    14.7    +      -       -      -
    580D  TRP*     4.6    14.6    -      -       +      -
    587D  LEU      4.6     4.7    -      -       -      +
    588D  PRO*     3.9     4.6    -      -       -      +
    589D  TYR*     3.2    37.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 555 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553D  THR*     4.4    12.3    -      -       +      +
    554D  GLU*     1.3    87.7    -      -       -      +
    556D  GLU*     1.3    65.8    +      -       -      +
    563D  LEU*     4.6    18.4    -      -       +      -
    564D  VAL      3.5     4.5    -      -       -      +
    565D  ALA*     3.4    29.2    -      -       +      -
    566D  LYS*     6.4     0.2    -      -       -      -
    585D  LYS*     3.1    70.7    +      -       +      +
    586D  GLY*     4.2     6.5    -      -       -      +
    587D  LEU      3.5    18.8    +      -       -      +
    588D  PRO*     5.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 556 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554D  GLU*     6.2     0.9    -      -       +      -
    555D  TYR*     1.3    78.1    -      -       -      +
    557D  LYS*     1.3    62.7    +      -       +      +
    558D  ASP*     3.3    30.9    +      -       +      +
    562D  GLU      3.7     0.7    -      -       -      +
    563D  LEU*     4.3     3.1    -      -       -      +
    564D  VAL*     2.9    37.6    +      -       +      +
    566D  LYS*     5.1    13.2    -      -       +      +
    586D  GLY*     5.2     5.2    -      -       -      +
----------------------------------------------------------
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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