Contacts of the strand formed by residues 447 - 451 (chain B) in PDB entry 3V4R


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 ARG 447 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445B  ASN*     3.1    57.8    +      -       -      +
    446B  GLU*     1.3    77.0    +      -       -      +
    448B  VAL*     1.4    64.8    +      -       -      +
    491B  LEU*     3.0    35.0    +      -       +      +
    492B  ARG      3.3    19.5    +      -       -      -
    493B  LEU      4.2     2.2    +      -       -      -
    494B  GLY*     3.8    18.7    -      -       -      +
    496B  TYR      4.0     0.4    -      -       -      -
    497B  ASP*     3.4    31.1    +      -       -      +
    511B  ILE*     4.6     0.7    -      -       +      -
    513B  GLU*     3.0    31.9    +      -       +      +
    514B  VAL*     3.5    19.6    -      -       +      -
    515B  SER*     3.2    22.7    +      -       -      -
    516B  LEU      3.6     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 448 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434B  LEU*     4.9     4.9    -      -       +      -
    438B  ILE*     4.1    20.0    -      -       +      +
    441B  ARG*     3.9    28.3    -      -       +      -
    447B  ARG*     1.4    77.5    -      -       -      +
    449B  LEU*     1.4    79.2    +      -       -      +
    450B  VAL*     4.2    12.1    -      -       +      -
    491B  LEU*     4.6     1.6    -      -       -      +
    497B  ASP      3.0     7.1    +      -       -      +
    498B  VAL*     3.3    17.5    -      -       +      -
    499B  LEU      3.0    24.4    +      -       -      -
    516B  LEU*     3.4    31.2    -      -       +      +
    518B  ALA*     4.9     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 449 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  VAL*     1.4    77.7    -      -       -      +
    450B  VAL*     1.3    62.1    +      -       -      +
    491B  LEU*     3.8    20.9    -      -       +      -
    499B  LEU*     3.6    31.2    -      -       +      +
    504B  LEU*     3.8    20.0    -      -       +      -
    509B  LEU*     3.5    32.1    -      -       +      +
    514B  VAL*     3.7    25.1    -      -       +      -
    516B  LEU      3.1     8.4    +      -       -      +
    517B  VAL*     3.4     9.0    -      -       +      +
    518B  ALA      2.9    24.9    +      -       -      +
    540B  ARG*     4.1    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 450 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434B  LEU*     4.6    18.2    -      -       +      -
    448B  VAL*     4.3     9.0    -      -       +      -
    449B  LEU*     1.3    76.4    -      -       -      +
    451B  THR*     1.3    59.4    +      -       -      +
    452B  THR*     4.2    11.0    -      -       +      -
    461B  LEU*     5.7     2.2    -      -       +      -
    498B  VAL*     3.7    21.8    -      -       +      -
    499B  LEU      2.7    21.8    +      -       -      +
    500B  VAL*     3.6    27.7    -      -       +      -
    501B  GLY      3.1    25.3    +      -       -      +
    504B  LEU*     3.7     7.3    -      -       -      +
    518B  ALA*     3.4    12.8    -      -       +      +
    520B  LEU*     4.4    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 451 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    450B  VAL*     1.3    73.7    -      -       -      +
    452B  THR*     1.3    59.6    +      -       -      +
    501B  GLY      3.1     5.6    -      -       -      -
    502B  ILE      3.1    16.5    +      -       -      -
    504B  LEU*     3.7    22.0    -      -       +      -
    517B  VAL*     4.9     0.9    -      -       +      -
    518B  ALA      3.0    14.2    +      -       -      +
    519B  ILE*     3.7    28.7    -      -       +      -
    520B  LEU*     3.0    30.0    +      -       -      +
    529B  ARG*     3.0    22.0    +      -       -      +
    537B  THR*     4.0    11.4    -      -       +      -
----------------------------------------------------------
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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