Contacts of the strand formed by residues 261 - 264 (chain B) in PDB entry 3VAH


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 261 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259B  HIS      4.4     2.5    -      -       -      +
    260B  LYS*     1.3    74.5    -      -       -      +
    262B  PHE*     1.3    60.8    +      -       -      +
    263B  ILE*     4.0     6.7    -      -       +      +
    279B  LEU*     5.7     2.5    -      -       +      -
    304B  PHE*     3.3    11.1    -      -       -      +
    305B  CYS*     2.9    45.4    +      -       -      +
    306B  GLU*     6.0     0.2    -      -       -      -
    307B  TYR*     4.1    27.8    -      -       +      +
    313B  THR*     3.9    28.5    -      -       +      +
    316B  ALA*     4.6     4.0    -      -       +      -
    317B  ILE*     3.7    28.5    -      -       +      -
    332B  VAL*     4.4    15.7    -      -       +      -
    333B  GLN*     3.4    16.6    -      -       -      +
    334B  ARG*     3.8     6.5    -      -       +      +
    335B  ALA*     4.0     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261B  LEU*     1.3    73.4    -      -       -      +
    263B  ILE*     1.3    63.3    +      -       -      +
    264B  GLY*     4.0    15.0    -      -       -      -
    302B  TYR*     3.6    39.3    -      +       +      -
    303B  ALA      3.7     3.6    -      -       -      -
    304B  PHE*     3.6    21.1    -      +       -      -
    331B  LEU*     3.7    13.2    -      -       +      +
    332B  VAL*     3.5     5.9    -      -       -      +
    333B  GLN*     2.7    42.4    +      -       +      +
    335B  ALA*     3.7    10.1    -      -       +      +
      2P    U      3.8    34.5    -      -       -      -
      3P    U      3.6    48.5    -      +       +      +
----------------------------------------------------------
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Residues in contact with ILE 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261B  LEU*     4.0    10.3    -      -       +      +
    262B  PHE*     1.3    78.0    -      -       -      +
    264B  GLY*     1.3    61.0    +      -       -      +
    266B  LEU*     3.8    30.5    -      -       +      +
    275B  VAL*     5.4     3.1    -      -       +      -
    278B  LEU*     6.0     0.7    -      -       +      -
    279B  LEU*     4.0    26.2    -      -       +      -
    301B  GLY      4.2     0.2    -      -       -      +
    302B  TYR*     3.1     8.5    -      -       -      +
    303B  ALA*     2.8    55.5    +      -       +      +
    304B  PHE*     4.4     0.4    -      -       -      -
    305B  CYS*     3.9    30.5    -      -       -      +
    320B  LEU*     6.4     0.2    -      -       +      -
    330B  LEU*     4.2    17.3    -      -       +      -
    331B  LEU      3.5     3.8    -      -       -      +
    332B  VAL*     4.4    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  PHE*     4.0    18.0    -      -       -      -
    263B  ILE*     1.3    73.9    -      -       -      +
    265B  GLY*     1.3    63.6    +      -       -      -
    266B  LEU*     3.4     2.9    +      -       -      -
    301B  GLY      4.1     2.9    -      -       -      -
    302B  TYR*     4.1     1.6    -      -       -      -
    330B  LEU*     3.5     8.0    -      -       -      +
    331B  LEU*     2.8    35.3    +      -       -      +
      2P    U      4.0    12.8    -      -       -      -
----------------------------------------------------------
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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