Contacts of the strand formed by residues 343 - 349 (chain A) in PDB entry 3V4O


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 LYS 343 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  ALA*     3.6    11.9    -      -       +      -
    342A  ASP*     1.3    92.5    +      -       -      +
    344A  VAL*     1.3    57.7    +      -       -      +
    376A  LEU      2.8    26.1    +      -       -      -
    377A  ASP*     4.2     5.4    +      -       -      +
    378A  PHE*     3.3    27.3    -      -       +      -
    379A  LYS*     2.8    31.2    +      -       -      +
    407A  TYR*     3.6    21.8    -      -       +      -
    560A  LEU      2.7    30.0    +      -       -      +
    561A  THR*     3.7     6.5    +      -       -      +
    562A  ASP      2.7    27.5    +      -       -      +
    563A  PRO*     5.0     0.8    -      -       -      +
    564A  ILE*     4.0    19.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  ASP*     4.0    16.2    -      -       -      +
    343A  LYS*     1.3    80.3    -      -       -      +
    345A  ALA*     1.3    66.3    +      -       -      +
    378A  PHE*     3.6     3.8    -      -       -      -
    379A  LYS*     3.5    13.9    -      -       +      +
    398A  PHE*     3.7    23.4    -      -       +      -
    401A  LEU*     3.8    40.8    -      -       +      +
    402A  LEU*     4.0     9.0    -      -       +      -
    406A  VAL*     3.8    18.4    -      -       +      -
    407A  TYR      2.9    12.5    +      -       -      +
    408A  GLY*     3.5     1.2    -      -       -      -
    409A  LEU      2.9    22.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  VAL*     1.3    78.3    -      -       -      +
    346A  LEU*     1.3    60.8    +      -       -      +
    347A  LEU*     3.9     7.9    -      -       +      -
    373A  LEU*     3.9    23.1    -      -       +      -
    378A  PHE*     3.8    16.1    -      -       +      -
    379A  LYS      2.8    12.5    +      -       -      +
    380A  VAL*     4.4     5.6    -      -       +      -
    381A  VAL*     3.1    26.9    +      -       -      +
    398A  PHE*     4.0     5.3    -      -       -      -
    409A  LEU*     3.1    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  ALA*     1.3    73.7    -      -       -      +
    347A  LEU*     1.3    69.9    +      -       -      +
    348A  ILE*     4.1    17.0    -      -       +      -
    381A  VAL*     3.6    26.5    -      -       +      +
    383A  LEU*     4.3     2.0    -      -       +      -
    394A  ALA*     3.8    36.1    -      -       +      +
    395A  VAL*     3.9    19.5    -      -       +      -
    398A  PHE*     3.7    27.9    -      -       +      -
    409A  LEU      2.8     8.7    +      -       -      -
    410A  LEU*     3.4    26.2    -      -       +      +
    411A  TYR      2.9    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  ALA*     3.9    11.0    -      -       +      -
    346A  LEU*     1.3    83.5    -      -       -      +
    348A  ILE*     1.3    65.9    +      -       -      +
    366A  VAL*     3.8    15.0    -      -       +      +
    369A  LEU*     3.8    20.9    -      -       +      +
    370A  THR*     3.2    45.5    -      -       -      +
    373A  LEU*     3.9    20.9    -      -       +      -
    380A  VAL*     4.0     5.4    -      -       +      -
    381A  VAL      2.9    11.6    +      -       -      +
    382A  SER*     3.4     6.3    -      -       -      +
    383A  LEU*     3.0    24.1    +      -       -      +
    409A  LEU*     4.3     1.8    -      -       +      -
    411A  TYR*     3.4    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346A  LEU*     4.1    31.4    -      -       +      -
    347A  LEU*     1.3    80.5    -      -       -      +
    349A  GLY*     1.3    60.3    +      -       -      +
    350A  ASN*     3.7    23.8    -      -       -      +
    366A  VAL*     3.8     6.0    -      -       -      +
    383A  LEU*     3.4     4.0    -      -       +      +
    386A  LEU*     3.9    32.5    -      -       +      -
    391A  MET*     4.3    20.4    -      -       +      -
    394A  ALA*     4.5     5.2    -      -       +      -
    395A  VAL*     4.9     5.8    -      -       +      -
    410A  LEU*     4.9     5.6    -      -       +      -
    411A  TYR      2.9     9.4    +      -       -      +
    412A  TYR*     3.4    21.5    -      -       +      -
    413A  ALA      2.9    25.3    +      -       -      +
    425A  MET*     5.8     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  ILE*     1.3    74.3    -      -       -      +
    350A  ASN*     1.3    62.5    +      -       -      -
    351A  MET*     3.9     2.2    -      -       -      +
    362A  PRO*     3.8    13.2    -      -       -      -
    366A  VAL*     3.6    17.5    -      -       -      +
    383A  LEU      3.0    10.9    +      -       -      -
    384A  LEU*     3.1    12.3    -      -       -      +
    385A  ASP      2.8    21.8    +      -       -      -
    413A  ALA      3.3     6.7    -      -       -      -
----------------------------------------------------------
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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