Contacts of the strand formed by residues 63 - 68 (chain B) in PDB entry 3H44


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 GLU 63 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  LYS*     4.4    10.0    +      -       -      +
     61B  LYS      5.1     4.0    -      -       -      +
     62B  ARG*     1.3    74.0    -      -       -      +
     64B  TYR*     1.3    63.2    +      -       -      +
     77B  LEU      3.7     0.3    -      -       -      +
     78B  ILE*     3.4     5.4    -      -       -      +
     79B  SER*     2.8    48.4    +      -       -      +
     81B  PRO*     6.0     0.9    -      -       +      -
    264B  LEU*     3.5    26.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  HIS*     5.7     3.5    -      -       -      -
     54B  ILE*     3.8    30.4    +      -       +      +
     56B  LYS*     4.1    17.1    -      -       +      +
     60B  ASP*     2.8    29.0    +      -       -      -
     62B  ARG*     3.2    37.6    +      -       +      -
     63B  GLU*     1.3    80.0    -      -       -      +
     65B  ARG*     1.3    61.3    +      -       -      +
     76B  LEU*     3.9    11.2    -      -       +      -
     77B  LEU      3.4     3.4    -      -       -      -
     78B  ILE*     3.5    34.8    -      -       +      -
    264B  LEU*     3.7     7.7    -      -       -      +
    433B  TYR*     3.0    21.4    +      -       -      -
    450B  LEU*     3.5    33.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ILE*     3.7    30.9    -      -       +      +
     51B  GLY      4.1     7.4    -      -       -      +
     54B  ILE*     4.2     3.4    -      -       -      -
     64B  TYR*     1.3    74.3    -      -       -      +
     66B  GLY*     1.3    71.3    +      -       -      +
     67B  LEU*     4.8     5.4    -      -       -      -
     76B  LEU*     3.8     4.0    -      -       -      -
     77B  LEU*     2.9    44.1    +      -       +      +
    264B  LEU*     2.8    57.9    +      -       +      +
    265B  ASP*     3.0    23.4    +      -       -      -
    268B  THR*     2.8    34.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  GLY*     2.8    26.3    +      -       -      -
     54B  ILE*     3.7    19.4    -      -       -      +
     65B  ARG*     1.3    80.3    -      -       -      +
     67B  LEU*     1.3    63.5    +      -       -      +
     75B  VAL      3.1    13.0    -      -       -      -
     76B  LEU*     3.8     8.9    -      -       -      +
    446B  LEU*     4.6    10.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  ILE*     4.4    12.3    -      -       +      -
     49B  ARG      3.1    17.9    -      -       -      +
     50B  ILE*     4.0    11.4    -      -       +      +
     51B  GLY      4.5     0.7    -      -       -      +
     65B  ARG*     4.1     5.8    -      -       -      +
     66B  GLY*     1.3    77.5    -      -       -      +
     68B  GLU*     1.3    59.5    +      -       -      +
     69B  LEU*     3.7    31.0    -      -       +      +
     74B  LYS*     3.9     0.6    -      -       -      -
     75B  VAL*     2.8    52.1    +      -       +      +
     77B  LEU*     3.6    32.5    -      -       +      -
    268B  THR*     4.8    11.9    -      -       +      -
    271B  VAL*     5.5     3.1    -      -       +      -
    272B  VAL*     5.6     0.4    -      -       +      -
    446B  LEU*     4.6     9.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  ILE*     3.5     1.6    -      -       -      +
     48B  LYS*     2.7    66.6    +      -       +      +
     49B  ARG*     2.8    55.8    +      -       +      +
     67B  LEU*     1.3    74.1    -      -       -      +
     69B  LEU*     1.3    60.4    +      -       -      +
     72B  GLY*     3.8    23.9    -      -       -      +
     73B  ILE      3.5    10.8    -      -       -      +
     74B  LYS*     4.6    13.8    -      -       +      +
    446B  LEU*     5.3     3.0    -      -       +      +
----------------------------------------------------------
 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