Contacts of the strand formed by residues 67 - 72 (chain G) 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 ILE 67 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ARG*     3.4    21.7    -      -       -      +
     67A  LYS*     3.7     4.7    -      -       -      +
     19G  LEU*     4.9     2.7    -      -       +      -
     20G  LYS      4.0     5.2    -      -       -      +
     21G  LEU*     3.9     8.1    -      -       +      -
     38G  MET*     3.5    36.6    -      -       +      +
     40G  LEU*     3.5    37.2    -      -       +      -
     62G  ILE*     3.5    34.5    -      -       +      -
     63G  ARG      3.7     5.6    -      -       -      +
     64G  GLY*     3.2     7.9    +      -       -      +
     66G  SER*     1.3    79.1    -      -       -      +
     68G  ILE*     1.3    63.8    +      -       -      +
     69G  MET      4.3    15.3    -      -       -      +
     70G  LEU*     5.0     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 68 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  THR*     4.5    13.2    -      -       +      -
     23A  ASN*     6.1     1.8    -      -       +      -
     24A  THR*     3.6    39.3    -      -       +      +
     28A  TYR*     5.7     0.2    -      -       -      +
     63A  ILE*     3.6     5.5    -      -       -      +
     64A  ARG*     3.1    26.3    +      -       -      +
     67A  LYS*     3.9    33.8    -      -       +      +
     20G  LYS*     2.9    25.1    +      -       +      +
     21G  LEU      3.7    26.5    -      -       -      +
     22G  ASN*     4.3     9.9    -      -       -      +
     66G  SER      4.7     0.7    -      -       -      +
     67G  ILE*     1.3    75.7    -      -       -      +
     69G  MET*     1.3    68.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 69 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  TYR*     3.5    40.2    -      -       +      +
     58A  LEU*     4.8     5.4    -      -       -      -
     61A  VAL*     4.5    12.3    -      -       +      -
     62A  TYR      3.3    12.8    -      -       -      +
     63A  ILE*     4.5    14.4    -      -       +      -
     18G  SER*     4.2     8.5    -      -       -      +
     19G  LEU*     3.7     1.9    -      -       -      +
     20G  LYS*     2.8    56.5    +      -       +      +
     26G  HIS*     5.6     2.7    -      -       +      -
     67G  ILE*     4.6     4.8    -      -       -      +
     68G  ILE*     1.3    88.2    -      -       +      +
     70G  LEU*     1.3    75.8    -      -       -      +
     71G  GLU*     4.3     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  VAL*     3.3     6.1    -      -       -      +
     62A  TYR*     2.9    62.2    +      -       +      +
      9G  LEU*     4.1    17.7    -      -       +      -
     12G  PHE*     4.0    25.6    -      -       +      -
     17G  LEU*     4.1    13.9    -      -       +      -
     18G  SER      3.4     4.5    -      -       -      -
     19G  LEU*     3.2    24.5    -      -       +      -
     31G  LEU*     5.4     0.9    -      -       +      -
     38G  MET*     5.0     7.2    -      -       +      -
     40G  LEU*     4.0    27.6    -      -       +      -
     67G  ILE*     5.0     4.7    -      -       +      +
     69G  MET*     1.3    77.2    -      -       -      +
     71G  GLU*     1.3    58.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 71 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  LEU*     3.4    40.9    -      -       +      +
     59A  GLU      5.3     1.8    +      -       -      +
     60A  GLN      3.4    10.8    -      -       -      +
     61A  VAL*     4.4     6.1    -      -       +      +
     17G  LEU*     3.3     5.8    -      -       -      -
     18G  SER*     2.7    55.5    +      -       -      +
     69G  MET*     4.6     9.7    -      -       +      +
     70G  LEU*     1.3    74.5    -      -       -      +
     72G  ALA*     1.3    72.2    +      -       -      +
     73G  LEU*     3.5    21.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 72 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  GLU*     4.7     7.8    -      -       -      +
     60A  GLN*     2.9    25.4    +      -       +      +
     12G  PHE*     3.9    15.7    -      -       +      -
     15G  LYS*     5.5     0.9    -      -       +      -
     16G  LYS      4.6     0.7    -      -       -      +
     17G  LEU*     3.7    11.2    -      -       +      +
     70G  LEU      4.3     0.2    -      -       -      -
     71G  GLU*     1.3    81.4    -      -       -      +
     73G  LEU*     1.3    61.8    +      -       -      +
     74G  GLU      3.7    16.6    -      -       -      +
     76G  VAL*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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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