Contacts of the strand formed by residues 19 - 24 (chain X) in PDB entry 1T6B


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 19 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18X  GLY*     1.3    71.5    -      -       -      -
     20X  LEU*     1.3    65.9    +      -       -      +
     21X  GLY*     3.4     1.7    +      -       -      -
     37X  SER*     3.2    21.9    -      -       -      -
     38X  SER*     3.5    11.3    +      -       -      -
     40X  THR      6.0     0.2    -      -       -      +
     43X  LEU*     4.8    13.4    -      -       +      +
     65X  TRP*     4.3    23.9    -      -       +      -
     66X  SER      3.7     5.4    -      -       -      +
     67X  GLY*     3.5    31.2    -      -       -      +
     68X  PHE      3.9    14.1    -      -       -      +
    116X  ILE*     4.1    20.9    -      -       +      -
    118X  ILE*     4.4    10.3    -      -       +      -
    134X  LEU*     4.6     5.2    -      -       +      -
    151X  LEU*     3.9    29.5    -      -       +      +
    152X  GLN      4.0     3.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 20 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18X  GLY      3.7     3.4    +      -       -      -
     19X  LEU*     1.3    69.7    -      -       -      +
     21X  GLY*     1.3    59.0    +      -       -      +
     22X  TYR*     3.0    39.3    -      -       +      +
     35X  VAL*     4.2     8.1    -      -       +      -
     36X  THR      3.8    16.4    -      -       -      +
     37X  SER*     4.3     5.6    -      -       -      -
     64X  ILE      3.9     0.9    -      -       -      +
     65X  TRP*     3.2     5.3    -      -       -      -
     66X  SER*     2.9    42.2    +      -       -      +
    153X  LEU*     3.9     6.3    -      -       +      +
    154X  PRO*     4.0    15.9    -      -       +      -
    156X  LEU*     4.6    14.4    -      -       +      -
    182X  GLY*     4.0    16.4    -      -       -      +
    236X  PHE*     3.6    30.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 21 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19X  LEU      3.4     1.6    +      -       -      -
     20X  LEU*     1.3    74.1    -      -       -      +
     22X  TYR*     1.3    62.7    +      -       -      -
     23X  TYR*     3.8     8.6    -      -       -      -
     34X  VAL      3.7     0.9    -      -       -      +
     35X  VAL*     3.3     7.8    -      -       -      +
     36X  THR      2.7    40.3    +      -       -      -
     64X  ILE      3.4     0.7    -      -       -      -
     65X  TRP*     3.4    24.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 22 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20X  LEU*     3.0    29.5    -      -       +      +
     21X  GLY*     1.3    72.7    -      -       -      -
     23X  TYR*     1.3    63.5    +      -       -      +
     24X  PHE*     3.5    24.1    -      +       +      -
     32X  PRO*     5.4     2.5    -      -       +      -
     34X  VAL      3.4     2.7    -      -       -      -
     35X  VAL*     3.5    35.9    -      -       +      -
     63X  ALA*     3.0     6.9    -      -       -      +
     64X  ILE*     2.8    58.2    +      -       +      +
     65X  TRP*     5.6     0.2    -      -       -      -
     66X  SER*     5.4     6.3    -      -       -      -
    156X  LEU*     5.3     0.9    -      -       -      +
    175X  VAL*     4.7    20.4    -      -       +      +
    177X  ASP*     4.7     5.7    +      -       -      +
    182X  GLY*     2.9    23.3    +      -       -      -
    184X  PRO*     3.7    24.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 23 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21X  GLY*     3.8    20.6    -      -       -      -
     22X  TYR*     1.3    76.7    -      -       -      +
     24X  PHE*     1.3    55.1    +      -       -      +
     32X  PRO*     3.5     2.5    -      -       -      +
     33X  MET*     2.6    34.9    +      -       -      -
     34X  VAL*     2.9    24.7    +      -       +      +
     36X  THR*     4.0    11.7    -      -       +      +
     43X  LEU*     2.7    26.1    +      -       -      -
     44X  SER      4.7     0.2    +      -       -      -
     45X  ILE*     3.6    36.4    -      -       +      +
     60X  PHE*     4.0    34.1    -      +       +      -
     62X  SER      3.9     3.6    -      -       -      -
     63X  ALA*     4.2     9.9    -      -       +      -
     65X  TRP*     3.2    32.8    +      +       -      -
    130X  LEU*     4.0    10.8    -      -       +      -
    200X  ARG*     5.9     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 24 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22X  TYR*     3.5    37.2    -      +       +      -
     23X  TYR*     1.3    74.5    -      -       -      +
     25X  SER*     1.3    60.3    +      -       -      +
     26X  ASP*     3.4    16.6    -      -       -      +
     29X  PHE*     3.3    51.1    -      +       +      -
     31X  ALA      3.2    24.7    -      -       -      +
     32X  PRO*     3.5    22.0    -      -       +      -
     60X  PHE*     3.1    11.3    -      -       -      -
     61X  GLN      3.0    22.7    +      -       -      -
     62X  SER*     2.8    33.7    +      -       -      +
     64X  ILE*     4.1    11.4    -      -       +      -
    175X  VAL*     6.3     2.5    -      -       -      -
    176X  PRO*     6.3     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