Contacts of the strand formed by residues 336 - 342 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275C  LYS*     3.7    30.9    -      -       +      +
    276C  VAL      4.3     0.3    +      -       -      -
    277C  ARG*     2.9    41.9    +      -       +      +
    278C  GLN*     5.7     0.4    -      -       -      +
    302C  GLU*     4.1     1.0    +      -       -      +
    331C  LYS*     4.1     0.5    -      -       -      +
    332C  GLN*     3.0    36.4    +      -       +      +
    333C  GLY      3.0    19.6    +      -       -      +
    334C  GLN*     3.0    34.6    +      -       -      +
    335C  GLY*     1.3    76.4    -      -       -      +
    337C  TRP*     1.3    73.3    +      -       -      +
    353C  LYS*     5.9     1.7    -      -       -      -
    354C  TYR      3.8     4.0    -      -       -      +
    355C  ALA*     4.4     9.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 337 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329C  ILE*     4.1    14.8    -      -       +      -
    330C  GLN      3.7     3.6    -      -       -      -
    331C  LYS*     3.4    42.6    -      -       +      -
    332C  GLN*     4.5     2.5    -      -       -      +
    335C  GLY*     3.4    19.0    +      -       -      -
    336C  GLN*     1.3    82.4    -      -       -      +
    338C  THR*     1.3    66.5    +      -       -      +
    339C  TYR*     5.4     0.4    -      -       +      -
    353C  LYS*     3.2     8.0    -      -       -      +
    354C  TYR*     2.9    60.9    +      +       +      +
    364C  ASP*     3.9    32.1    -      -       +      -
    367C  GLN*     3.5    28.8    -      -       +      +
    368C  LEU*     3.6    29.4    -      -       +      -
    371C  ALA*     4.5     5.2    -      -       +      -
    392C  PRO*     5.0     1.8    -      -       +      -
    423C  VAL*     3.9    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 338 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273C  GLY*     4.0    22.0    -      -       -      +
    274C  ILE      4.2    10.8    -      -       -      +
    329C  ILE*     3.3     5.8    -      -       -      +
    330C  GLN*     2.8    53.6    +      -       -      +
    332C  GLN*     2.9    38.6    +      -       -      +
    337C  TRP*     1.3    78.4    -      -       -      +
    339C  TYR*     1.3    64.1    +      -       -      +
    340C  GLN*     4.6     4.5    -      -       -      -
    352C  GLY      3.3    10.8    -      -       -      +
    353C  LYS*     4.4     2.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 339 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272C  PRO*     5.8     0.3    -      -       -      +
    327C  ALA*     5.5     0.4    -      -       +      -
    328C  GLU      3.1    13.7    -      -       -      +
    329C  ILE*     4.0     7.2    -      -       +      -
    337C  TRP*     5.4     1.1    -      -       +      -
    338C  THR*     1.3    78.6    -      -       -      +
    340C  GLN*     1.3    70.2    +      -       -      +
    341C  ILE*     3.5    33.9    -      -       +      -
    350C  LYS*     4.3     1.6    +      -       -      -
    351C  THR*     3.5     8.4    +      -       -      -
    352C  GLY*     2.9    67.0    +      -       -      +
    353C  LYS*     3.5    14.3    +      -       -      -
    354C  TYR*     4.6     3.1    -      -       +      -
    371C  ALA*     6.3     0.2    -      -       +      -
    374C  LYS*     3.3    21.1    +      -       +      -
    375C  ILE*     3.6    43.0    -      -       +      +
    378C  GLU*     3.0    20.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 340 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272C  PRO*     4.3    17.9    -      -       +      +
    273C  GLY*     5.4     1.0    -      -       -      +
    326C  ILE      3.7     1.0    -      -       -      +
    327C  ALA*     3.3     2.8    -      -       -      +
    328C  GLU*     2.9    38.8    +      -       -      +
    330C  GLN*     2.7    45.8    +      -       -      -
    338C  THR*     4.5     4.4    +      -       -      -
    339C  TYR*     1.3    84.5    +      -       -      +
    341C  ILE*     1.3    63.3    +      -       -      +
    342C  TYR*     4.2     9.5    +      -       +      -
    348C  ASN*     3.6    33.2    -      -       -      +
    350C  LYS      3.6     5.6    -      -       -      +
    351C  THR*     4.3     7.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 341 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325C  LEU*     3.8    25.4    -      -       +      -
    326C  ILE      3.2    13.0    -      -       -      +
    327C  ALA*     3.6    17.0    -      -       +      -
    339C  TYR*     3.5    29.2    -      -       +      -
    340C  GLN*     1.3    75.8    -      -       -      +
    342C  TYR*     1.3    56.5    +      -       -      +
    348C  ASN*     3.7     2.2    -      -       -      -
    349C  LEU*     2.8    30.6    +      -       +      +
    350C  LYS*     2.9    23.3    +      -       +      +
    375C  ILE*     4.1    11.4    -      -       +      -
    378C  GLU*     4.2    10.5    -      -       -      +
    379C  SER*     4.7     4.0    -      -       -      +
    383C  TRP*     3.9    32.5    -      -       +      -
    387C  PRO*     5.1     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 342 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325C  LEU*     4.0     1.0    -      -       -      +
    326C  ILE*     2.9    64.9    +      -       +      +
    328C  GLU*     3.3    28.0    +      -       +      +
    340C  GLN*     4.6     9.2    -      -       +      -
    341C  ILE*     1.3    74.6    -      -       -      +
    343C  GLN*     1.3    73.2    +      -       -      +
    344C  GLU      3.6    11.7    -      -       -      +
    345C  PRO*     4.8     9.6    -      -       +      -
    346C  PHE*     4.8     9.0    -      -       -      -
    347C  LYS      3.4    20.6    -      -       -      +
    348C  ASN*     3.6    18.6    -      -       -      +
    349C  LEU*     4.1     6.1    -      -       -      +
    390C  LYS*     3.2    31.2    +      -       -      +
----------------------------------------------------------
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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