Contacts of the strand formed by residues 49 - 55 (chain A) in PDB entry 6TT8


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 LEU 49 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ARG*     3.6     3.8    -      -       -      +
     46A  PHE*     2.7    35.4    +      -       -      +
     48A  ASP*     1.3    85.1    -      -       +      +
     50A  VAL*     1.3    60.2    +      -       -      +
     51A  PHE*     3.9    19.3    -      -       +      -
     61A  HIS*     4.7     3.4    -      -       +      +
     62A  THR      3.4    11.4    -      -       -      +
     63A  SER*     3.8    26.7    -      -       -      +
     97A  GLN*     3.6    39.3    -      -       +      +
    100A  GLN*     3.4    32.3    -      -       +      +
    101A  ILE*     3.6    21.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ASP*     3.8    33.0    -      -       +      +
     44A  GLN      3.5     7.0    -      -       -      +
     45A  ARG*     4.5    16.8    -      -       +      -
     48A  ASP      5.5     0.4    -      -       -      +
     49A  LEU*     1.3    76.8    -      -       -      +
     51A  PHE*     1.3    67.4    +      -       -      +
     52A  ARG*     5.0     1.1    -      -       +      +
     60A  GLN*     3.8     0.7    -      -       -      +
     61A  HIS*     3.5     2.8    -      -       -      -
     62A  THR*     2.7    47.2    +      -       -      +
     64A  TYR*     3.6    31.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  GLN*     2.7    48.8    +      -       -      +
     46A  PHE*     3.6    37.2    -      +       +      -
     49A  LEU*     3.9    17.5    -      -       +      -
     50A  VAL*     1.3    77.4    -      -       -      +
     52A  ARG*     1.3    59.2    +      -       -      +
     59A  TRP*     5.6     1.1    -      -       +      -
     60A  GLN      3.3     5.4    -      -       -      -
     61A  HIS*     3.5    29.6    -      -       +      -
     79A  ILE*     3.9    15.0    -      -       +      -
    100A  GLN      5.4     0.2    -      -       -      -
    101A  ILE*     3.9    24.7    -      -       +      -
    104A  TRP*     3.7    59.0    -      +       +      +
----------------------------------------------------------
 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
----------------------------------------------------------
     43A  ASP*     2.8    63.5    +      -       -      +
     50A  VAL*     5.3     1.1    -      -       +      -
     51A  PHE*     1.3    76.2    -      -       -      +
     53A  GLN*     1.3    70.5    +      -       -      +
     54A  LEU*     3.5    18.5    +      -       +      +
     59A  TRP*     4.7     3.1    -      -       -      +
     60A  GLN*     2.8    59.4    +      -       +      +
    253A  PRO*     5.7     4.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  PHE      4.4     0.2    -      -       -      -
     52A  ARG*     1.3    80.3    +      -       -      +
     54A  LEU*     1.3    62.5    +      -       -      +
     55A  ALA      3.2    28.8    +      -       -      +
     56A  PRO*     3.5    16.8    +      -       -      +
     59A  TRP*     3.0    40.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  ARG*     4.2    23.6    -      -       +      +
     53A  GLN*     1.3    81.3    -      -       -      +
     55A  ALA*     1.3    62.8    +      -       +      +
     58A  VAL*     3.1    14.6    +      -       +      +
     60A  GLN*     3.9    25.8    -      -       +      +
     78A  LEU*     3.9    19.3    -      -       +      -
    245A  MET*     3.8    34.2    -      -       +      +
    247A  VAL*     3.9     5.4    -      -       +      -
    253A  PRO*     3.7    34.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  GLN*     3.2    16.5    +      -       -      +
     54A  LEU*     1.3    76.5    -      -       -      +
     56A  PRO*     1.3    76.4    -      -       +      +
     57A  ASN*     3.1     4.3    -      -       -      +
     58A  VAL*     2.9    41.2    +      -       +      +
    201A  THR*     5.4     4.9    -      -       +      -
    203A  ILE*     4.0    15.7    -      -       +      -
    245A  MET*     5.6     1.3    -      -       +      -
----------------------------------------------------------
 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