Contacts of the strand formed by residues 336 - 344 (chain D) in PDB entry 3V81


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 GLN 336 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331D  LYS*     3.9     0.7    -      -       -      -
    332D  GLN*     2.9    35.7    +      -       +      -
    333D  GLY      3.2    16.2    +      -       -      +
    334D  GLN*     3.0    18.0    -      -       +      +
    335D  GLY*     1.3    77.2    -      -       -      +
    337D  TRP*     1.3    69.0    +      -       -      +
    353D  LYS*     3.3    28.2    +      -       +      +
    354D  TYR      3.5     3.6    -      -       -      -
    355D  ALA*     3.3    22.4    -      -       +      +
    427D  TYR*     2.5    37.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 337 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    408C  ALA*     3.8    25.6    -      -       +      -
    329D  ILE*     3.6    27.6    -      -       +      -
    330D  GLN      3.5     5.4    -      -       -      +
    331D  LYS*     3.5    36.8    -      -       +      -
    335D  GLY      3.5    12.7    +      -       -      -
    336D  GLN*     1.3    81.8    -      -       -      +
    338D  THR*     1.3    63.4    +      -       -      +
    339D  TYR*     4.1     2.9    +      -       +      -
    353D  LYS*     3.3     2.9    -      -       -      +
    354D  TYR*     2.8    45.6    +      -       +      +
    357D  MET*     3.6    16.8    -      -       +      -
    364D  ASP*     3.8    25.8    -      -       -      -
    367D  GLN*     3.1    33.7    +      -       +      +
    368D  LEU*     4.0    25.1    -      -       +      -
    371D  ALA*     4.9     6.7    -      -       +      -
    392D  PRO*     4.4     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 338 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242D  GLN*     3.6    19.7    -      -       -      +
    329D  ILE*     3.3     4.4    -      -       -      +
    330D  GLN*     2.6    61.4    +      -       -      +
    332D  GLN*     3.4    20.2    +      -       +      +
    337D  TRP*     1.3    74.2    -      -       -      +
    339D  TYR*     1.3    60.8    +      -       -      +
    340D  GLN*     4.2     4.0    -      -       -      -
    352D  GLY      3.4     6.5    -      -       -      -
    353D  LYS*     3.8    11.0    -      -       +      -
    426D  TRP*     3.7     6.4    -      -       -      +
    427D  TYR*     3.5    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 339 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327D  ALA*     6.1     0.4    -      -       +      -
    328D  GLU      3.0    14.6    -      -       -      +
    329D  ILE*     4.2     3.8    -      -       +      -
    337D  TRP*     4.6     2.5    -      -       +      -
    338D  THR*     1.3    75.6    -      -       -      +
    340D  GLN*     1.3    77.8    +      -       -      +
    341D  ILE*     4.3     6.5    -      -       +      -
    350D  LYS*     3.5    22.8    +      -       +      -
    351D  THR*     3.3     2.2    -      -       -      -
    352D  GLY*     2.9    57.5    +      -       -      +
    353D  LYS      4.2     0.7    -      -       -      -
    354D  TYR*     3.1    46.0    +      +       -      -
    375D  ILE*     3.5    46.9    -      -       +      -
    378D  GLU*     2.8    25.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 340 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326D  ILE      3.6     1.6    -      -       -      +
    327D  ALA*     3.4     3.5    -      -       -      +
    328D  GLU*     2.9    44.5    +      -       -      +
    330D  GLN*     2.8    42.0    +      -       -      -
    338D  THR*     3.9     1.8    -      -       -      -
    339D  TYR*     1.3    95.1    +      -       -      +
    341D  ILE*     1.3    63.5    +      -       -      +
    342D  TYR*     4.0     7.1    -      -       +      -
    348D  ASN*     3.6    16.8    -      -       -      +
    350D  LYS      3.4     7.6    -      -       -      +
    351D  THR*     3.5    17.5    -      -       +      -
    426D  TRP*     3.5    41.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 341 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325D  LEU*     4.3    24.2    -      -       +      -
    326D  ILE      3.3     9.4    -      -       -      +
    327D  ALA*     4.5     4.7    -      -       +      -
    339D  TYR*     4.3    11.2    -      -       +      -
    340D  GLN*     1.3    75.7    -      -       -      +
    342D  TYR*     1.3    65.6    +      -       -      +
    348D  ASN*     3.6     1.4    -      -       -      -
    349D  LEU*     2.9    25.4    +      -       +      -
    350D  LYS*     2.9    24.9    +      -       +      +
    375D  ILE*     3.6    33.9    -      -       +      +
    378D  GLU*     5.4     2.2    -      -       +      +
    379D  SER*     3.7    15.9    -      -       -      +
    383D  TRP*     4.0    32.3    -      -       +      -
    387D  PRO*     4.7     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 342 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325D  LEU*     4.9     3.1    -      -       -      -
    326D  ILE*     2.9    64.9    +      -       +      +
    328D  GLU*     2.8    47.8    +      -       +      -
    340D  GLN*     4.0     9.9    -      -       +      -
    341D  ILE*     1.3    76.7    -      -       -      +
    343D  GLN*     1.3    61.1    +      -       -      +
    344D  GLU*     3.7    22.2    -      -       -      +
    345D  PRO*     4.0    18.6    -      -       +      -
    346D  PHE      5.4     1.1    -      -       -      -
    347D  LYS      3.4    20.6    -      -       -      +
    348D  ASN*     3.6    18.4    -      -       -      +
    349D  LEU*     4.2     4.5    -      -       -      +
    390D  LYS*     3.9     6.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 343 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318D  TYR      4.1     3.7    -      -       -      +
    319D  TYR*     3.0    26.3    -      -       -      -
    320D  ASP*     2.8    42.5    +      -       +      -
    323D  LYS*     3.3    28.2    +      -       +      +
    324D  ASP      3.1    24.0    -      -       -      +
    325D  LEU*     3.4    12.2    -      -       +      +
    326D  ILE*     4.8     5.0    -      -       -      +
    342D  TYR*     1.3    78.5    -      -       -      +
    344D  GLU*     1.3    72.9    +      -       +      +
    345D  PRO*     4.8     0.2    -      -       -      +
    347D  LYS      4.3     3.0    +      -       -      -
    349D  LEU*     3.3    22.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 344 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323D  LYS*     2.8    46.2    +      -       -      +
    342D  TYR*     3.7     7.7    -      -       -      -
    343D  GLN*     1.3    85.3    -      -       +      +
    345D  PRO*     1.3    80.0    -      -       +      +
    346D  PHE      3.4     0.3    +      -       -      -
    347D  LYS*     3.0    30.6    +      -       +      +
----------------------------------------------------------
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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