Contacts of the strand formed by residues 45 - 52 (chain A) in PDB entry 3VTW


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 45 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ILE*     4.7     2.8    -      -       -      +
     39A  ARG*     3.7    16.6    +      -       -      -
     42A  HIS*     2.8    42.1    +      -       +      +
     43A  PRO      3.4     0.2    -      -       -      -
     44A  THR*     1.3    94.2    +      -       -      +
     46A  ILE*     1.3    63.5    +      -       -      +
     47A  PRO*     3.8     4.9    -      -       -      +
     68A  LEU*     3.9    34.3    -      -       +      -
     69A  VAL      3.4     4.7    -      -       -      +
     70A  PRO*     4.1    28.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ARG*     4.4    12.8    -      -       -      +
     44A  THR      5.6     0.2    -      -       -      -
     45A  LYS*     1.3    74.7    -      -       -      +
     47A  PRO*     1.3    64.8    -      -       -      +
     48A  VAL*     3.4    21.1    -      -       +      +
     67A  PHE      3.4     2.1    -      -       -      +
     68A  LEU*     3.5     1.7    -      -       -      -
     69A  VAL      2.6    43.3    +      -       -      +
     71A  ASP*     4.1    10.1    -      -       +      -
    110A  ILE*     3.7    31.4    -      -       +      +
    111A  SER*     4.0    26.0    -      -       -      -
    114A  TYR*     3.4    46.4    -      -       +      -
    124A  LEU*     4.7     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  VAL*     4.5     9.6    -      -       +      -
     38A  ILE*     3.8    35.7    -      -       +      -
     39A  ARG*     4.3     9.4    -      -       -      +
     45A  LYS      3.8     6.3    -      -       -      +
     46A  ILE*     1.3    80.1    -      -       -      +
     48A  VAL*     1.3    64.5    +      -       -      +
     67A  PHE      3.4     6.7    -      -       -      +
     68A  LEU*     4.5     2.4    -      -       +      -
    114A  TYR*     3.9    20.5    -      -       +      +
    122A  GLY      3.8    18.2    -      -       -      +
    123A  PHE*     3.9    14.1    -      -       +      -
    124A  LEU*     3.2    21.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  ILE*     3.4    27.1    -      -       +      +
     47A  PRO*     1.3    80.2    -      -       -      +
     49A  ILE*     1.3    62.7    +      -       -      +
     50A  ILE*     3.8    14.3    +      -       +      -
     65A  THR      3.6     1.4    -      -       -      +
     66A  LYS*     4.0     0.7    -      -       -      -
     67A  PHE*     2.8    36.6    +      -       +      +
     69A  VAL*     4.1    18.4    -      -       +      -
     78A  LEU*     5.3     0.4    -      -       +      -
    110A  ILE*     4.2     9.0    -      -       +      -
    123A  PHE*     4.3     1.6    -      -       -      -
    124A  LEU*     3.2    19.5    -      -       +      +
    126A  MET*     3.6    33.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  PHE*     3.4    38.6    -      -       +      -
     48A  VAL*     1.3    71.8    -      -       -      +
     50A  ILE*     1.3    62.5    +      -       -      +
     51A  GLU*     3.7    23.6    -      -       -      +
     65A  THR*     3.5    18.4    -      -       +      +
     66A  LYS*     4.2    15.5    -      -       -      -
    123A  PHE*     3.6    29.2    -      -       +      -
    124A  LEU      2.8     9.8    +      -       -      +
    125A  TYR*     3.5    35.2    -      -       +      -
    126A  MET*     2.8    29.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  VAL*     3.8    21.1    -      -       +      -
     49A  ILE*     1.3    76.4    -      -       -      +
     51A  GLU*     1.3    69.0    +      -       -      +
     62A  LEU*     4.0    22.4    -      -       +      +
     64A  LYS      4.2     0.9    -      -       -      +
     65A  THR*     3.1    23.9    +      -       -      +
     67A  PHE*     3.8    26.9    -      -       +      -
     69A  VAL*     5.5     2.2    -      -       +      -
     78A  LEU*     5.1     4.9    -      -       +      -
     82A  ILE*     3.5    29.6    -      -       +      -
     96A  LEU*     4.5     9.0    -      -       +      -
    126A  MET*     3.4    20.6    -      -       +      +
    128A  TYR*     3.8    22.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  LYS      4.7     0.7    -      -       -      +
     21A  THR*     3.5    21.6    -      -       +      +
     22A  PHE*     2.7    34.5    +      -       -      +
     25A  ARG*     4.9     1.6    +      -       -      -
     49A  ILE*     3.7    19.0    -      -       +      +
     50A  ILE*     1.3    79.8    -      -       -      +
     52A  ARG*     1.3    64.9    +      -       -      +
     65A  THR*     4.0    14.2    -      -       +      +
    125A  TYR*     4.6     7.8    -      -       -      -
    126A  MET      2.9    11.1    +      -       -      +
    127A  VAL*     3.1    16.8    -      -       +      +
    128A  TYR*     2.9    30.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  GLU*     3.5    28.6    +      -       -      +
     51A  GLU*     1.3    79.3    -      -       -      +
     53A  TYR*     1.3    72.2    +      -       -      +
     54A  LYS*     3.4     2.9    +      -       -      -
     56A  GLU*     3.6    32.5    +      -       +      +
     59A  LEU      3.2    27.8    +      -       -      -
     60A  PRO*     3.6     9.6    -      -       -      +
     61A  VAL*     3.3    38.7    -      -       +      +
    127A  VAL*     4.5     2.2    -      -       -      +
    128A  TYR*     3.3    32.8    -      -       +      +
----------------------------------------------------------
 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