Contacts of the strand formed by residues 58 - 65 (chain A) in PDB entry 1RPU


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 58 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  PRO*     3.4     6.1    -      -       -      +
     57A  LEU*     1.3    78.7    -      -       -      +
     59A  PHE*     1.3    61.5    +      -       -      -
     73A  TYR*     3.0    19.0    +      -       -      -
     74A  LEU      3.1    15.0    -      -       -      -
     75A  ARG*     4.0     0.4    -      -       -      -
     76A  TYR*     3.7    11.9    -      -       -      -
    116A  PHE*     3.6    20.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  GLY*     1.3    74.4    -      -       -      +
     60A  LYS*     1.3    66.2    +      -       -      +
     61A  GLU*     3.3    36.1    -      -       +      -
     73A  TYR*     3.3    10.2    -      -       -      -
     74A  LEU*     3.0    44.4    +      -       +      -
     76A  TYR*     3.9    13.7    -      +       +      -
     86A  VAL*     3.7    37.2    -      -       +      -
    114A  ILE*     3.6    23.8    -      -       +      -
    115A  ARG      3.4    16.6    -      -       -      +
    116A  PHE*     3.8    15.5    -      -       +      -
    141A  LYS*     3.9    16.2    -      -       -      -
    145A  LEU*     3.9    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ARG*     3.8    12.3    -      -       -      +
     59A  PHE*     1.3    78.4    -      -       -      +
     61A  GLU*     1.3    66.6    +      -       -      +
     62A  SER*     6.0     0.4    -      -       -      -
     71A  LYS*     3.6    40.6    -      -       -      +
     72A  ARG      3.3    13.7    -      -       -      +
     73A  TYR*     4.2    12.1    -      -       +      +
    113A  SER      4.0     0.2    -      -       -      +
    114A  ILE*     3.4     3.8    -      -       -      +
    115A  ARG*     3.0    40.2    +      -       +      +
      1D    C      5.8     2.9    -      -       -      -
      2D    G      3.2    31.8    +      -       -      +
      3D    U      4.7     7.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     3.8    18.6    -      -       +      -
     59A  PHE*     3.3    20.9    -      -       +      -
     60A  LYS*     1.3    78.3    -      -       -      +
     62A  SER*     1.3    64.8    +      -       -      +
     71A  LYS*     3.4     2.1    -      -       -      +
     72A  ARG*     2.8    38.2    +      -       +      +
     74A  LEU*     3.4     6.9    -      -       -      +
     89A  SER*     2.7    26.3    +      -       -      -
     90A  TRP*     3.1     7.3    +      -       -      -
    112A  TYR*     2.7    33.7    +      -       +      +
    113A  SER      3.1    12.8    -      -       -      +
    114A  ILE*     4.2     1.8    -      -       +      -
    141A  LYS*     2.9    19.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     4.2     2.7    -      -       -      -
     60A  LYS*     6.0     0.4    -      -       -      -
     61A  GLU*     1.3    77.8    -      -       -      +
     63A  TRP*     1.3    61.5    +      -       -      +
     69A  VAL*     4.3     6.9    -      -       -      +
     70A  PHE      3.0    17.3    -      -       -      -
     71A  LYS*     3.6    16.8    -      -       -      +
    111A  THR*     3.7     2.6    -      -       -      +
    112A  TYR*     3.2     8.2    -      -       -      -
    113A  SER*     2.9    41.3    +      -       -      -
     10C    C      4.7     1.0    +      -       -      -
     11C    A      3.3    21.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PRO*     4.2    13.7    -      -       +      -
     30A  PHE*     3.9    27.5    -      +       +      -
     62A  SER*     1.3    71.2    -      -       -      +
     64A  GLY*     1.3    57.8    +      -       -      +
     65A  PHE*     4.2    20.9    -      +       +      -
     69A  VAL*     3.5     2.8    -      -       -      -
     70A  PHE*     2.7    36.3    +      -       -      +
     90A  TRP*     3.4    46.0    -      +       -      -
     95A  VAL*     3.8    25.0    -      -       +      +
    110A  CYS*     5.5     0.4    -      -       +      -
    111A  THR*     3.2    26.9    -      -       -      -
    112A  TYR*     3.2    42.8    -      +       +      -
    130A  LEU*     4.2    13.9    -      -       +      -
    133A  LEU*     4.4    10.5    -      -       +      -
    134A  CYS*     3.9    20.6    -      -       -      -
    137A  ALA*     4.0     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  TRP*     1.3    75.9    -      -       -      +
     65A  PHE*     1.3    65.0    +      -       -      -
     66A  GLY      3.5     4.0    -      -       -      -
     68A  VAL      3.5     7.9    -      -       -      -
     69A  VAL*     4.0    16.2    -      -       -      -
    109A  GLY      4.6     0.2    -      -       -      -
    110A  CYS*     3.1     8.0    -      -       -      +
    111A  THR*     2.7    41.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PRO*     3.3    35.0    -      -       +      -
     63A  TRP*     4.2    18.2    -      +       +      -
     64A  GLY*     1.3    73.2    -      -       -      -
     66A  GLY*     1.3    61.4    +      -       -      +
     67A  LYS      3.3     2.6    +      -       -      -
     68A  VAL*     3.1    23.5    +      -       +      +
     70A  PHE*     3.9    19.5    -      +       -      -
     95A  VAL*     3.8    32.3    -      -       +      -
     98A  ALA*     4.6     4.3    -      -       +      -
     99A  ALA*     3.6    32.5    -      -       +      -
    102A  PHE*     4.5    20.5    -      +       +      +
    103A  LEU*     4.5    12.9    -      -       +      +
    108A  VAL*     4.6     6.3    -      -       -      +
    110A  CYS*     4.2    17.0    -      -       +      -
    130A  LEU*     4.4     8.3    -      -       +      -
----------------------------------------------------------
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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