Contacts of the strand formed by residues 26 - 34 (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 HIS 26 (chain g).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34e  TRP*     5.3     0.2    -      -       -      -
     18g  SER*     2.3    37.0    +      -       -      -
     19g  LEU      3.3    21.5    +      -       -      -
     20g  LYS*     4.3    11.7    -      -       +      -
     21g  LEU*     5.0     0.4    -      -       -      -
     24g  GLY      4.0     2.4    +      -       -      +
     25g  ARG*     1.3    76.7    -      -       -      +
     27g  VAL*     1.3    74.5    +      -       -      +
     28g  GLN*     3.9    14.1    -      -       +      -
     47g  GLU      2.7    28.6    -      -       -      +
     48g  MET*     3.6    26.6    +      -       +      +
     69g  MET*     5.6     2.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 27 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34e  TRP*     3.5    36.8    -      -       +      -
     86e  LEU*     4.5     2.7    -      -       +      -
     18g  SER*     3.6     0.3    -      -       -      -
     19g  LEU*     2.6    52.3    +      -       +      +
     21g  LEU*     4.3    10.8    -      -       +      -
     26g  HIS*     1.3    86.9    +      -       -      +
     28g  GLN*     1.3    65.3    +      -       -      +
     42g  ILE*     5.4     0.7    -      -       +      -
     45g  CYS*     3.4    26.0    -      -       -      -
     46g  VAL      3.5     9.6    -      -       -      +
     47g  GLU*     3.9     6.7    -      -       -      +
     48g  MET*     4.3     0.4    -      -       -      -
     62g  ILE*     4.4    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 28 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16g  LYS*     3.5    29.5    -      -       -      +
     17g  LEU      3.1    14.1    -      -       -      +
     18g  SER*     4.0     5.5    -      -       -      -
     19g  LEU*     4.4     1.3    -      -       -      -
     26g  HIS*     3.9     9.8    -      -       +      -
     27g  VAL*     1.3    82.8    -      -       -      +
     29g  GLY*     1.3    59.1    +      -       -      +
     42g  ILE*     4.7     1.3    -      -       -      -
     45g  CYS*     3.2     3.8    -      -       -      +
     46g  VAL*     2.7    40.9    +      -       +      +
     48g  MET*     2.2    41.4    -      -       +      +
     73g  LEU*     3.7    17.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 29 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15g  LYS      3.5     0.7    -      -       -      +
     16g  LYS*     4.0     7.8    -      -       -      +
     17g  LEU*     2.6    46.8    +      -       -      +
     19g  LEU*     4.8     0.6    -      -       -      +
     28g  GLN*     1.3    77.5    -      -       -      +
     30g  ILE*     1.3    62.8    +      -       -      -
     31g  LEU      3.8     0.2    +      -       -      -
     42g  ILE*     3.5    16.7    -      -       -      +
     43g  ASP      3.7     6.1    -      -       -      -
     44g  GLU      3.8     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14g  ASP*     3.7    24.2    -      -       +      +
     15g  LYS      3.2     2.5    -      -       -      -
     16g  LYS*     4.0    26.2    -      -       +      +
     29g  GLY*     1.3    74.6    -      -       -      -
     31g  LEU*     1.3    61.2    +      -       -      +
     32g  ARG*     3.2    43.4    +      -       -      +
     42g  ILE*     3.5     1.9    -      -       -      +
     43g  ASP*     2.8    40.9    +      -       +      +
     44g  GLU*     3.5    41.3    -      -       +      +
     74g  GLU*     5.7     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9g  LEU*     4.1    23.6    -      -       +      +
     12g  PHE*     3.6    34.1    -      -       +      +
     13g  MET*     3.5     7.7    -      -       -      +
     14g  ASP*     2.8    29.0    +      -       -      -
     15g  LYS      3.0     8.3    +      -       -      +
     17g  LEU*     3.5    27.1    -      -       +      -
     29g  GLY      3.8     1.0    +      -       -      -
     30g  ILE*     1.3    69.0    -      -       -      +
     32g  ARG*     1.3    61.1    +      -       -      +
     33g  GLY      3.3    29.2    -      -       -      +
     34g  PHE*     4.7     2.2    -      -       +      -
     40g  LEU*     4.1    17.3    -      -       +      -
     41g  VAL      3.4    10.3    -      -       -      +
     42g  ILE*     3.7    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 32 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14e  MET*     3.7     5.2    -      -       -      -
     15e  VAL*     3.3    34.7    +      -       +      -
     13g  MET*     3.6    10.9    -      -       -      +
     14g  ASP*     3.0    30.2    +      -       -      +
     30g  ILE*     3.2    33.7    +      -       -      +
     31g  LEU*     1.3    73.3    -      -       -      +
     33g  GLY*     1.3    57.3    +      -       -      +
     41g  VAL*     2.9    24.3    +      -       +      -
     43g  ASP*     2.4    44.6    +      -       +      +
     44g  GLU*     4.1    13.5    +      -       -      -
     59g  MET*     4.7     2.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 33 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14e  MET*     3.8     7.2    -      -       -      -
     15e  VAL      3.0    16.3    +      -       -      -
     17e  PRO*     4.5     0.2    -      -       -      -
     13g  MET*     3.9     6.7    -      -       -      -
     31g  LEU*     3.3    10.7    -      -       -      +
     32g  ARG*     1.3    80.8    -      -       -      +
     34g  PHE*     1.3    65.2    +      -       -      +
     40g  LEU*     3.4     0.3    -      -       -      -
     41g  VAL*     2.8    35.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 34 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14e  MET*     3.7    26.9    -      -       +      +
     16e  GLN*     4.0     6.9    +      -       -      +
     17e  PRO*     3.8    10.9    -      -       -      +
      6g  PRO*     4.9     6.7    -      -       +      -
      7g  PRO*     3.5    27.6    -      -       +      -
      9g  LEU*     3.3    47.3    -      -       +      -
     10g  LYS*     4.0     9.4    -      -       +      -
     13g  MET*     3.6    23.8    -      -       +      -
     31g  LEU*     4.7     3.4    -      -       +      -
     33g  GLY*     1.3    76.3    -      -       -      +
     35g  ASP*     1.3    75.9    +      -       -      +
     38g  MET*     5.3     0.2    -      -       -      -
     39g  ASN      3.1    14.4    -      -       -      +
     40g  LEU*     3.6    14.4    -      -       +      -
----------------------------------------------------------
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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