Contacts of the strand formed by residues 43 - 51 (chain A) in PDB entry 2NSQ


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 PRO 43 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     3.9    20.9    -      -       +      -
     41A  SER*     3.5    13.9    -      -       -      +
     42A  ASP*     1.3    87.8    -      -       -      +
     44A  TYR*     1.3    60.0    +      -       -      +
     65A  THR*     3.4     0.8    -      -       -      -
     66A  ILE*     2.9    42.3    +      -       -      +
     69A  THR*     3.4    24.9    -      -       +      +
     72A  PRO*     4.0     9.4    -      -       +      -
     74A  TRP*     3.2    22.6    +      -       +      -
     93A  VAL*     4.4     4.3    -      -       +      -
     94A  PHE      3.1    10.3    -      -       -      +
     95A  ASP*     4.4     0.2    -      -       -      -
    105A  LEU*     4.8     2.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  PRO*     1.3    72.5    -      -       -      +
     45A  VAL*     1.3    71.6    +      -       -      +
     46A  LYS*     4.2     8.0    -      -       +      +
     62A  GLN*     3.5    38.5    +      -       +      -
     63A  THR*     3.4    14.1    -      -       -      +
     64A  LYS      3.4    15.9    -      -       -      +
     65A  THR*     3.6    17.7    -      -       -      +
     74A  TRP*     3.7     4.3    -      -       -      +
     93A  VAL*     3.4     5.5    -      -       -      +
     94A  PHE*     2.9    69.5    +      +       +      +
     96A  GLU*     3.7    19.7    -      -       +      -
    102A  ASP*     2.6    36.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  VAL*     3.8    11.9    -      -       +      -
     44A  TYR*     1.3    77.0    -      -       -      +
     46A  LYS*     1.3    68.6    +      -       -      +
     47A  LEU*     3.6    14.8    -      -       +      +
     62A  GLN*     3.1     3.8    -      -       -      +
     63A  THR*     2.8    46.6    +      -       +      -
     74A  TRP*     3.4    38.1    -      -       +      -
     91A  PHE*     4.1    24.0    -      -       +      -
     92A  GLU      3.3    10.8    -      -       -      +
     93A  VAL*     4.3     4.5    -      -       +      -
    146A  LEU*     4.0    11.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  TYR*     4.0    10.6    -      -       +      +
     45A  VAL*     1.3    72.2    -      -       -      +
     47A  LEU*     1.3    63.3    +      -       -      +
     48A  SER*     3.9    19.4    +      -       -      +
     57A  GLU*     4.6     7.5    +      -       -      -
     60A  LEU*     4.4    26.4    -      -       -      +
     61A  VAL      3.6     9.0    -      -       -      +
     62A  GLN*     4.0    10.5    -      -       +      +
     90A  LEU      3.5     1.6    -      -       -      +
     91A  PHE*     3.5     2.4    -      -       -      -
     92A  GLU*     2.8    56.2    +      -       -      +
     94A  PHE*     4.1    21.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  VAL*     4.2     2.5    -      -       +      -
     26A  VAL*     3.9    11.0    -      -       +      -
     45A  VAL*     3.6    27.8    -      -       +      +
     46A  LYS*     1.3    74.2    -      -       -      +
     48A  SER*     1.3    60.6    +      -       -      +
     49A  LEU      4.2     0.7    -      -       -      -
     59A  ALA      3.7     1.2    -      -       -      +
     60A  LEU*     3.4     4.9    -      -       -      +
     61A  VAL*     2.7    41.0    +      -       +      +
     63A  THR*     4.3     7.0    -      -       +      -
     78A  PHE*     3.9    25.8    -      -       +      -
     80A  PHE*     3.8    36.2    -      -       +      -
     89A  LEU*     4.6     4.0    -      -       +      -
     90A  LEU      3.4     5.6    -      -       -      +
     91A  PHE*     3.7    32.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LYS*     3.9    17.0    +      -       -      +
     47A  LEU*     1.3    72.3    -      -       -      +
     49A  LEU*     1.3    64.6    +      -       -      +
     50A  TYR*     3.7     7.9    -      -       -      -
     57A  GLU*     4.8     6.8    +      -       -      -
     59A  ALA      3.4     4.3    -      -       -      -
     60A  LEU*     3.4    22.5    -      -       -      +
     89A  LEU*     3.5     4.4    -      -       -      +
     90A  LEU*     2.8    52.0    +      -       -      +
     92A  GLU*     4.4     6.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  TYR      4.6     2.5    -      -       -      +
     11A  GLY*     4.7     2.5    -      -       -      -
     47A  LEU      4.2     0.4    -      -       -      -
     48A  SER*     1.3    73.0    -      -       -      +
     50A  TYR*     1.3    56.8    +      -       -      +
     57A  GLU*     3.6     2.9    -      -       -      +
     58A  LEU*     2.7    53.9    +      -       +      -
     59A  ALA*     2.9    26.5    +      -       +      +
     80A  PHE*     4.1    15.6    -      -       +      -
     81A  ARG      3.4    25.1    -      -       -      +
     82A  VAL*     3.6    23.8    -      -       +      -
     87A  HIS*     4.1    14.1    -      -       +      +
     88A  ARG      3.6    13.7    -      -       -      +
     89A  LEU*     3.6    18.6    -      -       +      +
    112A  LEU*     4.1     6.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  SER*     3.7    15.0    -      -       -      +
     49A  LEU*     1.3    77.9    -      -       -      +
     51A  VAL*     1.3    81.7    +      -       -      +
     52A  ALA*     4.3     1.3    -      -       -      -
     55A  ASN*     3.1    32.7    +      -       +      -
     56A  ARG      3.3    18.6    -      -       -      +
     57A  GLU*     4.0     6.1    -      -       +      +
     58A  LEU*     4.0     6.7    -      -       -      +
     87A  HIS*     3.3     4.0    -      -       -      +
     88A  ARG*     2.9    75.7    +      -       +      +
     90A  LEU*     4.0    16.8    -      -       +      -
    109A  ASP*     2.6    39.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  GLU*     4.8     0.4    -      -       -      +
     50A  TYR*     1.3    78.6    -      -       -      +
     52A  ALA*     1.3    70.0    +      -       -      +
     54A  GLU*     3.6    28.5    -      -       +      +
     55A  ASN      2.9    26.5    +      -       -      -
     56A  ARG*     2.9    41.4    +      -       +      +
     58A  LEU*     3.7    27.4    -      -       +      -
     86A  ASN*     3.7    14.1    -      -       +      +
     87A  HIS*     4.0    10.5    -      -       +      +
----------------------------------------------------------
 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