Contacts of the strand formed by residues 90 - 101 (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 VAL 90 (chain r).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75r  THR*     3.3     4.8    +      -       -      -
     76r  GLU*     2.8    60.3    +      -       +      +
     77r  VAL*     4.9     5.4    -      -       +      -
     88r  LYS      3.4     5.7    +      -       -      +
     89r  PRO*     1.3    72.3    -      -       -      +
     91r  ASN*     1.3    76.1    -      -       -      +
     92r  LYS*     4.5    13.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 91 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44n  TYR*     5.1     8.6    +      -       +      -
     46n  ARG*     5.6     6.2    -      -       -      +
     74r  TRP      3.8     6.7    -      -       -      +
     75r  THR*     3.8    11.3    +      -       -      -
     89r  PRO      4.2     2.9    +      -       -      +
     90r  VAL*     1.3    85.3    -      -       -      +
     92r  LYS*     1.3    67.9    +      -       -      +
     93r  ASP*     5.8     1.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 92 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1384    G      5.3     2.6    +      -       -      -
    1394    G      5.1     6.5    -      -       -      +
     73r  MET*     3.3     3.6    -      -       -      +
     74r  TRP*     3.0    63.0    +      -       +      +
     76r  GLU*     3.6    45.1    +      -       +      +
     90r  VAL*     4.5    15.0    -      -       +      +
     91r  ASN*     1.3    83.5    -      -       -      +
     93r  ASP*     1.3    68.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 93 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46n  ARG*     5.3     1.7    +      -       -      -
     71r  LYS*     4.0    31.9    +      -       +      +
     72r  GLU      3.1    12.6    -      -       -      +
     73r  MET*     4.2     4.3    -      -       +      -
     74r  TRP*     3.8     6.6    -      -       -      -
     91r  ASN*     5.8     1.2    -      -       -      +
     92r  LYS*     1.3    80.3    -      -       -      +
     94r  ARG*     1.3    69.2    +      -       -      +
     95r  TYR*     4.7    12.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 94 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1364    G      5.7     0.2    -      -       -      +
     18q  GLU*     2.4    32.7    +      -       -      -
     24q  GLN*     4.8     8.7    +      -       -      +
     67q  TYR*     3.1    19.6    +      -       -      -
     69q  ILE*     3.9    10.3    -      -       -      +
     50r  LYS*     5.5     2.5    -      -       -      +
     71r  LYS*     3.4     3.1    -      -       -      -
     72r  GLU*     2.6    53.3    +      -       -      +
     74r  TRP*     4.1    11.6    -      -       +      -
     93r  ASP*     1.3    80.8    -      -       -      +
     95r  TYR*     1.3    67.1    +      -       -      +
     96r  ILE*     3.6    26.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 95 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69r  ASN      6.0     0.9    -      -       -      -
     70r  VAL      3.4    10.8    -      -       -      +
     71r  LYS*     3.9    39.2    +      -       +      -
     93r  ASP*     4.7    10.6    +      -       -      -
     94r  ARG*     1.3    78.2    -      -       -      +
     96r  ILE*     1.3    64.4    +      -       -      +
     97r  SER      4.3     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 96 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67q  TYR*     4.5     5.4    -      -       +      +
     69q  ILE*     4.0    34.1    -      -       +      -
     69r  ASN*     3.7     0.7    -      -       -      -
     70r  VAL*     2.8    39.5    +      -       +      +
     72r  GLU*     4.2    12.8    -      -       +      +
     94r  ARG*     3.6    45.3    -      -       +      +
     95r  TYR*     1.3    79.4    -      -       -      +
     97r  SER*     1.3    64.4    +      -       -      +
     98r  LYS      4.2     3.1    -      -       -      +
     99r  MET*     4.0    34.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 97 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69q  ILE*     5.8     0.4    -      -       -      +
     72q  ASP*     3.1    39.1    +      -       -      -
     68r  GLU*     3.2     6.6    -      -       -      +
     69r  ASN*     2.9    34.5    +      -       -      +
     70r  VAL*     5.5     0.4    -      -       -      -
     95r  TYR*     4.3     0.4    -      -       -      -
     96r  ILE*     1.3    76.0    -      -       -      +
     98r  LYS*     1.3    72.2    +      -       -      +
     99r  MET      4.4     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 98 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69q  ILE*     3.7     4.3    -      -       -      +
     70q  LEU*     2.7    47.9    +      -       +      +
     71q  PRO      3.7     8.7    -      -       -      +
     72q  ASP*     2.7    28.9    +      -       -      +
     73q  SER*     3.6     3.6    +      -       -      +
     74q  LEU*     2.8    31.8    +      -       +      +
     75q  PRO*     5.1     0.2    -      -       -      +
     76q  LEU*     3.8    27.2    -      -       +      +
     66r  VAL*     6.2     0.2    -      -       +      -
     67r  LEU      3.4     5.6    -      -       -      +
     68r  GLU*     4.0    17.7    -      -       +      -
     96r  ILE*     4.2     1.1    -      -       -      +
     97r  SER*     1.3    91.4    +      -       -      +
     99r  MET*     1.3    63.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 99 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67q  TYR*     3.7    29.6    -      -       +      -
     68q  PHE      3.2    14.6    -      -       -      +
     69q  ILE*     4.5     2.0    -      -       +      -
     70q  LEU*     4.0     6.1    -      -       -      +
     52r  LEU*     3.5    28.0    -      -       +      -
     66r  VAL*     3.3     9.2    -      -       -      +
     67r  LEU*     2.8    49.0    +      -       +      +
     70r  VAL*     3.9    31.0    -      -       +      -
     96r  ILE*     4.0    25.6    -      -       +      -
     98r  LYS*     1.3    76.2    -      -       -      +
    100r  PHE*     1.3    60.1    +      -       -      +
    101r  LEU*     4.0    15.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 100 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3q  LEU*     3.7    37.9    -      -       +      -
      6q  PHE*     4.2     3.1    -      +       -      -
      7q  LEU*     3.7    40.2    -      -       +      -
     36q  MET*     3.8    16.8    -      -       +      -
     65q  ILE*     6.1     0.2    -      -       +      -
     67q  TYR*     3.1     6.5    -      -       -      +
     68q  PHE*     2.8    47.6    +      +       +      -
     70q  LEU*     4.1     6.9    -      -       +      +
     64r  ASN*     3.7    26.9    -      -       +      -
     65r  MET      3.4     5.4    -      -       -      -
     66r  VAL*     3.8    17.5    -      -       +      +
     99r  MET*     1.3    76.0    -      -       -      +
    101r  LEU*     1.3    73.2    +      -       -      +
    102r  ARG      4.1     2.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 101 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66q  ARG*     3.3    13.5    -      -       -      +
     67q  TYR*     4.0    16.6    -      -       +      -
     44r  ILE*     4.3     9.6    -      -       +      -
     46r  CYS*     4.3    11.2    -      -       -      -
     52r  LEU*     3.8    20.9    -      -       +      -
     63r  CYS      5.2     0.2    -      -       -      +
     64r  ASN*     3.4     3.6    -      -       -      -
     65r  MET*     2.8    57.7    +      -       +      +
     67r  LEU*     4.5     6.1    -      -       +      -
     99r  MET*     4.0    12.0    -      -       +      +
    100r  PHE*     1.3    76.7    -      -       -      +
    102r  ARG*     1.3    82.4    +      -       -      +
    105r  SER*     4.3    11.7    -      -       -      -
    106r  VAL*     4.1    12.3    -      -       +      -
----------------------------------------------------------
 Back to top of page


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