Contacts of the strand formed by residues 278 - 283 (chain E) in PDB entry 3V56


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 PHE 278 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230D  PHE*     3.8    24.2    -      +       -      -
    247D  SER*     3.8    11.2    -      -       -      -
    248D  ALA      3.1    28.5    -      -       -      -
    249D  GLY*     4.5     0.2    -      -       -      -
    148E  GLN*     4.9     4.5    -      -       +      -
    149E  LEU      3.3    14.6    -      -       -      +
    150E  ILE*     4.0    13.0    -      -       +      -
    168E  TRP*     3.6     6.8    -      -       -      -
    196E  TYR*     4.2    22.4    -      +       -      -
    197E  GLY*     3.4     0.5    -      -       -      -
    198E  GLN*     2.9    70.5    +      -       +      +
    246E  TYR*     4.3     3.4    -      +       -      -
    261E  LEU*     4.3     0.9    -      -       -      +
    274E  GLY      3.9    10.8    -      -       -      -
    275E  ASP      3.7    12.8    -      -       -      -
    276E  VAL      4.0     0.4    -      -       -      -
    277E  THR*     1.3    80.6    -      -       -      +
    279E  PHE*     1.3    64.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 279 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148E  GLN*     3.6     0.6    -      -       -      -
    149E  LEU*     2.7    48.8    +      -       +      +
    168E  TRP*     3.7    36.3    -      +       +      -
    184E  LYS*     5.4     1.3    -      -       -      -
    185E  ILE*     3.8    23.3    -      -       +      +
    195E  ILE*     4.1     9.2    -      -       +      -
    196E  TYR*     3.3    22.7    -      -       -      -
    197E  GLY*     4.2     0.4    -      -       -      -
    212E  ILE*     4.1    25.4    -      -       +      -
    259E  LEU*     3.8    24.7    -      -       +      -
    260E  GLN*     3.8    23.3    -      -       -      -
    261E  LEU*     3.8    26.9    -      -       +      -
    278E  PHE*     1.3    77.0    -      -       -      +
    280E  GLY*     1.3    54.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 280 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147E  LEU      3.2    12.6    -      -       -      -
    148E  GLN*     4.1     0.4    -      -       -      -
    185E  ILE*     4.0     7.4    -      -       -      -
    195E  ILE*     3.6     5.7    -      -       -      +
    196E  TYR*     2.9    56.4    +      -       -      +
    279E  PHE*     1.3    76.1    -      -       -      +
    281E  ALA*     1.3    61.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 281 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250D  ILE*     4.4     1.0    -      -       -      +
    146E  CYS*     3.3     4.9    -      -       -      +
    147E  LEU      3.0    30.4    +      -       -      +
    178E  LEU*     3.4    26.9    -      -       +      +
    185E  ILE*     4.3     6.5    -      -       +      +
    193E  PHE*     4.9     4.3    -      -       +      -
    194E  PHE      3.3    10.5    -      -       -      +
    195E  ILE*     4.2    15.7    -      -       +      -
    196E  TYR*     3.7     2.8    -      -       -      -
    259E  LEU*     4.4    11.0    -      -       +      -
    280E  GLY*     1.3    75.1    -      -       -      +
    282E  LEU*     1.3    62.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 282 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194D  PHE*     5.3     5.8    -      -       +      -
    250D  ILE*     3.9    16.6    -      -       +      -
    282D  LEU*     6.5     0.4    -      -       +      -
    284D  LEU*     3.6    43.5    -      -       +      -
    144E  GLN*     3.7    34.5    -      -       +      +
    145E  ASP      3.6     8.1    -      -       -      +
    146E  CYS*     4.1     3.4    -      -       +      -
    193E  PHE*     3.3     5.9    -      -       -      -
    194E  PHE*     2.8    63.6    +      -       +      +
    196E  TYR*     5.0     0.2    -      -       +      -
    281E  ALA*     1.3    75.6    -      -       -      +
    283E  LYS*     1.3    63.0    +      -       -      +
    284E  LEU*     3.5     5.1    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 283 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144E  GLN*     3.3    27.8    +      -       -      +
    145E  ASP*     2.8    30.9    +      -       +      +
    177E  ALA*     3.8     6.3    -      -       +      +
    178E  LEU*     4.6     0.4    -      -       -      +
    189E  GLU*     2.7    38.5    +      -       -      +
    190E  THR      4.0    18.4    +      -       -      -
    191E  GLY*     4.4     4.9    -      -       -      -
    192E  TYR      4.0     3.6    -      -       -      +
    193E  PHE*     3.5    37.7    -      -       +      -
    282E  LEU*     1.3    71.8    -      -       -      +
    284E  LEU*     1.3    74.8    +      -       -      +
----------------------------------------------------------
 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