Contacts of the strand formed by residues 278 - 283 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  PHE*     3.9    20.0    -      +       -      -
    247A  SER*     3.7    14.1    -      -       -      -
    248A  ALA      3.1    28.0    -      -       -      -
    249A  GLY*     4.7     0.2    -      -       -      -
    148B  GLN*     5.0     6.5    -      -       +      -
    149B  LEU      3.3    13.9    -      -       -      +
    150B  ILE*     4.0    12.3    -      -       +      -
    168B  TRP*     3.6     5.7    -      -       -      -
    196B  TYR*     4.2    21.1    -      +       -      -
    197B  GLY*     3.4     1.4    -      -       -      -
    198B  GLN*     2.9    72.0    +      -       +      +
    246B  TYR*     4.3     4.3    -      +       -      -
    261B  LEU*     4.4     0.7    -      -       -      +
    274B  GLY      3.8    10.8    -      -       -      -
    275B  ASP      3.8    11.4    -      -       -      -
    276B  VAL      4.0     0.7    -      -       -      -
    277B  THR*     1.3    82.7    -      -       -      +
    279B  PHE*     1.3    62.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 279 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  GLN*     3.6     0.8    -      -       -      -
    149B  LEU*     2.7    54.8    +      -       +      +
    168B  TRP*     3.7    29.8    -      +       +      -
    183B  ASN      5.5     0.2    -      -       -      -
    184B  LYS*     5.4     1.6    -      -       -      -
    185B  ILE*     3.8    22.9    -      -       +      -
    195B  ILE*     4.1    14.4    -      -       +      -
    196B  TYR*     3.3    23.1    -      -       -      -
    197B  GLY*     4.2     0.7    -      -       -      -
    212B  ILE*     4.1    21.1    -      -       +      -
    259B  LEU*     3.8    25.8    -      -       +      -
    260B  GLN*     3.8    23.1    -      -       -      -
    261B  LEU*     3.9    25.1    -      -       +      -
    278B  PHE*     1.3    76.1    -      -       -      +
    280B  GLY*     1.3    57.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 280 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  LEU      3.2    12.8    -      -       -      -
    148B  GLN*     4.1     0.4    -      -       -      -
    185B  ILE*     4.0     7.2    -      -       -      -
    195B  ILE*     3.5     5.9    -      -       -      +
    196B  TYR*     2.9    55.9    +      -       -      +
    279B  PHE*     1.3    76.1    -      -       -      +
    281B  ALA*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 281 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  ILE*     4.8     0.2    -      -       -      +
    146B  CYS*     3.3     4.5    -      -       -      +
    147B  LEU      3.0    31.2    +      -       -      +
    178B  LEU*     3.4    23.1    -      -       +      +
    185B  ILE*     4.3     6.3    -      -       +      +
    193B  PHE*     4.7     4.3    -      -       +      -
    194B  PHE      3.3    10.1    -      -       -      +
    195B  ILE*     4.2    15.9    -      -       +      -
    196B  TYR*     3.8     4.0    -      -       -      -
    259B  LEU*     4.2    14.8    -      -       +      -
    280B  GLY*     1.3    73.7    -      -       -      +
    282B  LEU*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 282 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  PHE*     5.4     7.6    -      -       +      -
    250A  ILE*     4.4    11.9    -      -       +      -
    282A  LEU*     6.5     0.2    -      -       +      -
    284A  LEU*     4.1    28.3    -      -       +      -
    144B  GLN*     3.7    39.5    -      -       +      +
    145B  ASP      3.6     3.6    -      -       -      -
    146B  CYS*     3.8    18.6    -      -       +      -
    193B  PHE*     3.3     6.6    -      -       -      -
    194B  PHE*     2.8    57.4    +      -       +      +
    196B  TYR*     5.1     0.2    -      -       +      -
    281B  ALA*     1.3    76.2    -      -       -      +
    283B  LYS*     1.3    65.3    +      -       -      +
    284B  LEU*     3.5     5.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 283 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  GLN*     3.4    27.2    +      -       -      +
    145B  ASP*     2.7    31.2    +      -       +      +
    177B  ALA*     3.9    19.5    -      -       +      -
    178B  LEU*     4.7     0.2    -      -       -      +
    189B  GLU*     3.7    21.7    +      -       +      +
    190B  THR      3.5    22.9    +      -       -      -
    191B  GLY*     4.7     4.5    -      -       -      -
    192B  TYR      3.8     4.7    -      -       -      +
    193B  PHE*     3.5    32.4    -      -       +      -
    282B  LEU*     1.3    71.5    -      -       -      +
    284B  LEU*     1.3    79.8    +      -       -      +
    285B  LEU*     5.6     1.6    -      -       -      +
----------------------------------------------------------
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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