Contacts of the strand formed by residues 444 - 450 (chain A) in PDB entry 2V3E


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 444 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LEU*     3.7    27.8    -      -       +      -
     67A  LEU*     5.3     4.0    -      -       +      -
    442A  ASN*     3.2    18.9    +      -       -      +
    443A  ASP*     1.3    83.5    -      -       -      +
    445A  ASP*     1.3    66.3    +      -       -      +
    446A  ALA*     4.2     3.6    +      -       +      -
    460A  VAL*     4.0    20.0    -      -       +      -
    461A  LEU      3.4     6.5    -      -       -      +
    462A  ASN*     3.5    28.3    -      -       +      +
    468A  VAL*     4.0    21.5    -      -       +      -
    470A  LEU*     4.4     9.2    -      -       +      -
    484A  SER*     3.4    27.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 445 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  HIS*     3.5    22.6    +      -       +      -
    368A  ILE*     3.6    31.7    -      -       +      +
    369A  THR*     5.4     0.7    +      -       -      -
    372A  LEU*     6.1     0.7    -      -       -      -
    443A  ASP      4.6     2.9    -      -       -      +
    444A  LEU*     1.3    77.6    -      -       -      +
    446A  ALA*     1.3    61.0    +      -       -      +
    460A  VAL*     3.4     2.6    -      -       -      +
    461A  LEU*     2.6    44.4    +      -       +      +
    463A  ARG*     3.1    40.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 446 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  LEU*     4.0    20.9    -      -       +      -
    368A  ILE*     3.9     6.0    -      -       -      +
    372A  LEU*     3.8    20.7    -      -       -      +
    436A  LEU*     3.8    22.8    -      -       +      +
    444A  LEU*     4.1     4.8    +      -       +      -
    445A  ASP*     1.3    75.6    -      -       -      +
    447A  VAL*     1.3    62.7    +      -       -      +
    459A  VAL      3.0    12.8    -      -       -      +
    460A  VAL*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 447 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368A  ILE*     4.0    23.8    -      -       +      -
    371A  LEU*     4.1    28.3    -      -       +      -
    372A  LEU*     4.0    18.8    -      -       +      -
    423A  PHE*     4.4     1.6    -      -       +      -
    433A  ARG*     3.9    18.6    -      -       +      -
    436A  LEU*     4.1     6.3    -      -       -      -
    446A  ALA*     1.3    76.2    -      -       -      +
    448A  ALA*     1.3    71.0    -      -       -      +
    449A  LEU*     4.0    14.6    -      -       +      +
    457A  VAL      4.0     0.2    -      -       -      +
    458A  VAL*     3.3     4.9    -      -       -      +
    459A  VAL*     3.0    40.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 448 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LEU*     3.5    31.4    -      -       +      -
    372A  LEU*     5.5     0.2    -      -       -      +
    433A  ARG*     3.5     4.2    -      -       -      +
    434A  VAL*     3.0    31.0    +      -       +      +
    435A  GLY      4.2     0.9    -      -       -      +
    436A  LEU*     3.9    23.3    -      -       +      +
    447A  VAL*     1.3    74.9    -      -       -      +
    449A  LEU*     1.3    69.6    +      -       -      +
    457A  VAL      3.4     3.8    -      -       -      -
    458A  VAL*     3.8    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 449 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LEU*     5.3     0.5    -      -       -      +
     78A  VAL*     3.4    32.5    -      -       +      -
    371A  LEU*     4.6     9.6    -      -       +      -
    427A  ILE*     3.7    34.5    -      -       +      -
    431A  SER*     4.4     5.2    -      -       -      -
    432A  GLN      3.2     9.0    -      -       -      +
    433A  ARG*     3.9    18.8    -      -       +      +
    434A  VAL*     4.1     7.5    -      -       -      +
    447A  VAL*     4.0    22.9    -      -       +      +
    448A  ALA*     1.3    82.6    -      -       -      +
    450A  MET*     1.3    61.6    +      -       -      +
    456A  ALA*     3.7     4.5    -      -       -      +
    457A  VAL*     2.8    48.4    +      -       +      +
    459A  VAL*     5.4     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 450 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LEU*     3.7    13.5    -      -       +      -
     71A  PRO*     3.3    30.7    -      -       +      -
     74A  LYS*     3.6    25.6    -      -       -      +
    430A  GLY      4.7     0.2    -      -       -      +
    431A  SER*     3.2     3.9    -      -       -      -
    432A  GLN*     2.8    44.4    +      -       +      +
    434A  VAL*     4.0    14.1    -      -       +      +
    449A  LEU*     1.3    72.7    -      -       -      +
    451A  HIS*     1.3    66.6    +      -       -      +
    454A  GLY*     3.7    15.7    -      -       -      +
    455A  SER      3.4    11.4    -      -       -      +
    456A  ALA*     4.9     3.6    -      -       +      -
    496A  ARG*     3.5    33.2    -      -       -      +
----------------------------------------------------------
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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