Contacts of the strand formed by residues 51 - 59 (chain r) in PDB entry 4PJO


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 LYS 51 (chain r).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39n  CYS*     3.3    10.8    +      -       -      -
     40n  GLY      3.5    15.9    -      -       -      -
     41n  ILE*     3.7    15.0    -      -       +      -
     44n  TYR*     3.3    42.6    -      -       +      -
     43r  LEU*     4.2    15.9    -      -       +      -
     44r  ILE      3.2     8.7    -      -       -      +
     45r  ASN*     3.1    24.1    +      -       -      +
     49r  ASN*     2.9    44.5    +      -       -      -
     50r  LYS*     1.3    73.1    -      -       -      +
     52r  LEU*     1.3    63.1    +      -       -      +
     53r  LEU      4.0     0.2    -      -       -      -
     71r  LYS      3.4     1.7    -      -       -      +
     72r  GLU*     3.4     2.6    -      -       -      -
     73r  MET*     2.7    43.5    +      -       +      +
     74r  TRP*     6.0     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 52 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67q  TYR*     4.8     6.7    -      -       +      -
     42r  VAL      3.5     1.9    -      -       -      +
     43r  LEU*     3.4     2.8    -      -       -      -
     44r  ILE*     2.7    49.0    +      -       +      +
     46r  CYS*     4.5    18.4    -      -       +      -
     50r  LYS*     4.5     5.2    -      -       +      -
     51r  LYS*     1.3    85.0    -      -       -      +
     53r  LEU*     1.3    60.8    +      -       -      +
     54r  GLY      4.0     0.6    +      -       -      -
     67r  LEU*     4.2     5.6    -      -       +      -
     70r  VAL*     3.8    18.2    -      -       +      -
     71r  LYS      3.5     4.0    -      -       -      -
     72r  GLU*     4.0    24.2    -      -       +      +
     99r  MET*     3.5    31.2    -      -       +      -
    101r  LEU*     3.8    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 53 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44n  TYR      4.9     1.1    -      -       -      +
     46n  ARG*     4.0    15.0    -      -       +      -
     47n  GLU*     3.8    38.1    -      -       -      +
     41r  GLN*     3.5    36.0    +      -       +      +
     42r  VAL      3.1    22.4    -      -       -      +
     43r  LEU*     3.9    11.4    -      -       +      +
     51r  LYS      4.0     0.6    -      -       -      -
     52r  LEU*     1.3    74.3    -      -       -      +
     54r  GLY*     1.3    60.2    +      -       -      +
     69r  ASN      3.6     2.1    -      -       -      +
     70r  VAL*     3.3     2.8    -      -       -      -
     71r  LYS*     2.8    42.1    +      -       +      +
     73r  MET*     3.8    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 54 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41r  GLN*     3.3     8.3    -      -       -      -
     42r  VAL*     2.9    39.5    +      -       -      +
     44r  ILE*     6.3     0.2    -      -       -      +
     52r  LEU*     4.0     1.4    +      -       -      +
     53r  LEU*     1.3    78.6    -      -       -      +
     55r  ARG*     1.3    64.2    +      -       -      -
     67r  LEU*     5.2     3.7    -      -       -      +
     68r  GLU      3.8     2.5    -      -       -      -
     69r  ASN      3.6    12.6    -      -       -      -
     70r  VAL*     4.1     8.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 55 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48n  PHE*     3.3    31.5    -      -       -      -
     53n  ASP*     3.6    12.8    +      -       -      -
     54n  ALA*     4.6     6.3    -      -       -      +
     39r  ASN*     2.8    58.1    +      -       -      +
     40r  THR      4.2     5.2    -      -       -      +
     41r  GLN*     3.5    26.2    -      -       +      +
     54r  GLY*     1.3    75.7    -      -       -      +
     56r  VAL*     1.3    64.7    +      -       -      +
     57r  LYS*     3.9     2.7    -      -       +      -
     67r  LEU*     3.2    10.1    -      -       -      +
     68r  GLU*     2.9    45.6    +      -       +      +
     69r  ASN*     4.3    20.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 56 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32r  LEU*     5.3     7.4    -      -       +      -
     35r  SER*     4.2    16.9    +      -       -      +
     36r  VAL*     3.5    38.6    -      -       +      +
     39r  ASN*     5.4     3.7    +      -       -      +
     40r  THR      4.5     3.4    +      -       -      +
     42r  VAL*     3.7    33.9    -      -       +      -
     55r  ARG*     1.3    74.2    -      -       -      +
     57r  LYS*     1.3    62.7    +      -       -      +
     58r  ALA      3.6    22.9    -      -       -      +
     59r  PHE*     4.6     3.6    -      -       +      -
     65r  MET*     4.0    22.4    -      -       +      -
     66r  VAL      3.7     3.6    -      -       -      +
     67r  LEU*     3.9     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 57 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59n  ARG*     3.7    26.6    -      -       +      +
     -2q  SER      5.6     0.3    -      -       -      +
     76q  LEU*     4.2    14.3    -      -       +      +
     77q  ASP*     2.6    40.1    +      -       -      -
     80q  LEU*     4.3    11.1    -      -       +      +
     36r  VAL*     3.9    14.1    -      -       -      +
     39r  ASN*     5.7     4.9    -      -       -      +
     55r  ARG*     3.8     3.1    +      -       +      -
     56r  VAL*     1.3    75.9    -      -       -      +
     58r  ALA*     1.3    64.1    +      -       -      +
     66r  VAL*     2.9    24.7    +      -       +      +
     68r  GLU*     3.3    45.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 58 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -2q  SER      5.0     7.9    -      -       -      +
      0q  SER*     4.3     7.6    -      -       -      +
      3q  LEU*     4.1    11.2    -      -       +      -
     80q  LEU*     4.1    28.9    -      -       +      -
     36r  VAL*     4.4     6.7    -      -       -      -
     56r  VAL*     3.5     6.4    -      -       -      +
     57r  LYS*     1.3    81.3    -      -       -      +
     59r  PHE*     1.3    67.4    +      -       -      +
     65r  MET*     3.3     2.6    -      -       -      -
     66r  VAL*     3.0    26.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 59 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -2q  SER      4.2     1.8    -      -       -      -
     -1q  GLY*     3.1    31.3    -      -       -      -
      0q  SER*     2.8    25.5    +      -       -      -
      3q  LEU*     3.6     5.6    -      -       -      +
     24r  PHE*     4.4    11.2    -      +       -      -
     29r  LEU*     3.9    22.7    -      -       +      -
     32r  LEU*     3.5    30.5    -      -       +      -
     33r  THR*     3.2    48.5    -      -       +      -
     36r  VAL*     4.0    14.1    -      -       +      -
     56r  VAL*     4.6     1.1    -      -       +      -
     58r  ALA*     1.3    77.2    -      -       -      +
     60r  ASP*     1.3    72.6    +      -       -      +
     64r  ASN      3.0    14.6    -      -       -      +
     65r  MET*     3.8    13.0    -      -       +      -
----------------------------------------------------------
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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