Contacts of the strand formed by residues 278 - 283 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230E  PHE*     3.9    20.6    -      +       -      -
    247E  SER*     3.7    12.8    -      -       -      -
    248E  ALA      3.1    28.5    -      -       -      -
    249E  GLY*     4.7     0.2    -      -       -      -
    148F  GLN*     5.0     6.1    -      -       +      -
    149F  LEU      3.3    14.4    -      -       -      +
    150F  ILE*     3.9    13.5    -      -       +      -
    168F  TRP*     3.6     6.6    -      -       -      -
    196F  TYR*     4.2    19.1    -      +       -      -
    197F  GLY*     3.4     1.4    -      -       -      -
    198F  GLN*     2.9    70.8    +      -       +      +
    246F  TYR*     4.2     8.3    -      +       -      -
    261F  LEU*     4.4     0.7    -      -       -      +
    274F  GLY      3.9    11.2    -      -       -      -
    275F  ASP      3.7    11.7    -      -       -      -
    276F  VAL      4.0     0.2    -      -       -      -
    277F  THR*     1.3    81.9    -      -       -      +
    279F  PHE*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 279 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148F  GLN*     4.6     0.2    -      -       -      -
    149F  LEU*     2.7    49.6    +      -       +      +
    168F  TRP*     3.6    37.7    -      +       +      -
    183F  ASN      5.5     0.4    -      -       -      -
    184F  LYS*     5.4     1.1    -      -       -      -
    185F  ILE*     3.8    23.1    -      -       +      -
    195F  ILE*     4.1     8.3    -      -       +      -
    196F  TYR*     3.3    23.8    -      -       -      -
    197F  GLY*     4.2     0.4    -      -       -      -
    212F  ILE*     4.1    24.7    -      -       +      -
    259F  LEU*     3.8    26.7    -      -       +      -
    260F  GLN*     3.8    23.1    -      -       -      -
    261F  LEU*     3.8    25.1    -      -       +      -
    278F  PHE*     1.3    76.8    -      -       -      +
    280F  GLY*     1.3    55.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 280 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147F  LEU      3.2    12.6    -      -       -      -
    148F  GLN*     4.1     0.2    -      -       -      -
    185F  ILE*     4.0     7.2    -      -       -      -
    195F  ILE*     3.6     6.4    -      -       -      +
    196F  TYR*     2.9    56.4    +      -       -      +
    279F  PHE*     1.3    77.7    -      -       -      +
    281F  ALA*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 281 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250E  ILE*     5.0     0.2    -      -       -      +
    146F  CYS*     3.3     4.7    -      -       -      +
    147F  LEU      3.0    30.4    +      -       -      +
    178F  LEU*     3.4    23.8    -      -       +      +
    185F  ILE*     4.3     6.3    -      -       +      +
    193F  PHE*     4.7     3.8    -      -       +      -
    194F  PHE      3.3     9.0    -      -       -      +
    195F  ILE*     4.2    15.9    -      -       +      -
    196F  TYR*     3.8     4.0    -      -       -      -
    259F  LEU*     4.2    15.0    -      -       +      -
    280F  GLY*     1.3    74.3    -      -       -      +
    282F  LEU*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 282 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194E  PHE*     5.6     4.9    -      -       +      -
    250E  ILE*     4.1    15.7    -      -       +      -
    284E  LEU*     3.9    25.4    -      -       +      -
    144F  GLN*     3.7    39.5    -      -       +      +
    145F  ASP      3.7     2.9    -      -       -      +
    146F  CYS*     3.7    24.0    -      -       +      -
    193F  PHE*     3.3     3.3    -      -       -      -
    194F  PHE*     2.7    61.3    +      -       +      +
    196F  TYR*     5.0     0.2    -      -       +      -
    281F  ALA*     1.3    76.8    -      -       -      +
    283F  LYS*     1.3    63.3    +      -       -      +
    284F  LEU*     3.5     4.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 283 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144F  GLN*     3.4    27.9    +      -       -      +
    145F  ASP*     2.8    28.4    +      -       +      +
    177F  ALA*     3.6    20.2    -      -       +      -
    178F  LEU*     4.7     0.2    -      -       -      +
    189F  GLU*     3.1    33.7    +      -       -      +
    190F  THR      3.8    19.5    +      -       -      -
    191F  GLY*     4.4     4.7    -      -       -      -
    192F  TYR      4.0     4.5    -      -       -      +
    193F  PHE*     3.5    30.9    -      -       +      -
    282F  LEU*     1.3    73.1    -      -       -      +
    284F  LEU*     1.3    72.2    +      -       -      +
----------------------------------------------------------
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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