Contacts of the strand formed by residues 334 - 345 (chain C) in PDB entry 1NVP


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 VAL 334 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332C  GLU*     3.1    42.3    +      -       +      +
    333C  ASN*     1.3    78.6    -      -       -      +
    335C  VAL*     1.3    72.0    +      -       -      +
    336C  VAL*     3.8    24.2    -      -       +      -
    357C  ILE      3.9     1.3    -      -       -      +
    358C  MET*     3.4     3.3    -      -       -      -
    359C  ASN*     3.1    32.5    +      -       +      +
    360C  LEU*     4.7     0.7    -      -       -      +
      8D  ASN*     5.1    15.9    -      -       -      +
     93D  VAL*     4.4     0.4    -      -       -      +
     94D  LYS*     3.3    20.2    -      -       +      +
     96D  VAL*     5.3     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 335 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334C  VAL*     1.3    81.1    -      -       -      +
    336C  VAL*     1.3    67.3    +      -       -      +
    337C  CYS*     4.1    17.5    -      -       -      -
    353C  LEU*     5.2     2.0    -      -       +      -
    357C  ILE      3.7     3.8    -      -       -      +
    358C  MET*     3.6    27.1    -      -       +      -
    360C  LEU*     4.7     1.1    -      -       +      -
    367C  PHE*     4.0    25.6    -      -       +      -
     81D  PHE*     4.4     7.2    -      -       +      -
     93D  VAL*     4.0    18.8    -      -       +      -
     94D  LYS      2.9     5.9    +      -       -      +
     95D  ILE*     3.4    21.4    -      -       +      -
     96D  VAL      2.9    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 336 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334C  VAL*     3.8    17.0    -      -       +      -
    335C  VAL*     1.3    77.7    -      -       -      +
    337C  CYS*     1.3    60.5    +      -       -      +
    356C  GLY*     3.3     1.6    -      -       -      -
    357C  ILE      3.1    32.4    +      -       -      +
      5D  LEU*     2.9    56.3    -      -       +      +
      6D  TYR*     3.8     9.3    -      -       +      +
      8D  ASN*     4.2    18.8    -      -       +      +
      9D  THR*     4.6    10.3    -      -       +      -
     96D  VAL*     3.5    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 337 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335C  VAL*     4.1    10.5    -      -       +      -
    336C  VAL*     1.3    78.1    -      -       -      +
    338C  GLN*     1.3    67.0    -      -       -      +
    353C  LEU*     3.9    26.7    -      -       -      -
    354C  LYS      3.2    14.6    -      -       -      +
    355C  ASP      3.6     7.6    -      -       -      -
    356C  GLY*     3.6    10.1    -      -       -      -
    367C  PHE*     3.9     4.3    -      -       +      -
      5D  LEU*     3.1    17.6    -      -       -      +
     95D  ILE*     4.2     2.5    -      -       -      -
     96D  VAL      3.0    10.5    +      -       -      +
     97D  ALA*     3.1    21.7    -      -       -      -
     98D  CYS      3.0    18.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 338 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337C  CYS*     1.3    78.9    -      -       -      +
    339C  TYR*     1.3    58.7    +      -       -      +
    353C  LEU*     3.6     3.1    -      -       -      -
    354C  LYS*     3.0    54.2    +      -       +      +
    355C  ASP*     4.0    18.2    +      -       -      +
      3D  TYR*     4.4    16.7    -      -       +      -
      5D  LEU*     3.6    11.6    -      -       +      +
      6D  TYR*     2.6    27.3    +      -       -      +
     45D  ASN*     3.9    12.9    +      -       -      +
     97D  ALA*     4.2     3.1    -      -       -      -
     98D  CYS*     2.8    21.3    -      -       +      +
     99D  ASP      4.2    11.4    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    338C  GLN*     1.3    74.7    -      -       -      +
    340C  ASP*     1.3    71.3    +      -       -      +
    341C  LYS*     4.6     1.6    -      -       -      +
    342C  ILE*     3.9    20.4    -      -       +      -
    352C  HIS      3.8     3.1    -      -       -      -
    353C  LEU*     3.8    18.8    -      -       +      -
    354C  LYS*     5.0     2.9    -      -       -      -
     67D  PHE*     3.6    12.6    -      -       -      -
     70D  ASN*     2.8    26.5    +      -       -      +
     72D  TRP*     3.6    26.7    -      +       -      -
     97D  ALA*     3.3    24.7    -      -       +      -
     98D  CYS      2.7    24.2    +      -       -      -
     99D  ASP*     3.2    60.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 340 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338C  GLN      4.2     0.2    +      -       -      -
    339C  TYR*     1.3    81.6    -      -       -      +
    341C  LYS*     1.3    73.6    +      -       +      +
    352C  HIS*     2.8    24.8    +      -       +      +
    353C  LEU      4.5     2.9    -      -       -      +
    354C  LYS*     3.3    47.8    +      -       -      +
    369C  LYS*     5.2     7.8    -      -       -      +
     99D  ASP*     5.0     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 341 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339C  TYR*     5.0     1.3    -      -       -      -
    340C  ASP*     1.3    89.9    -      -       +      +
    342C  ILE*     1.3    69.7    +      -       -      +
    343C  HIS*     4.1     2.7    -      -       +      -
    350C  LYS      4.1     1.4    -      -       -      +
    351C  PHE      3.9     0.2    -      -       -      -
    352C  HIS*     2.9    45.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 342 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339C  TYR*     3.9    25.9    -      -       +      -
    341C  LYS*     1.3    83.5    -      -       -      +
    343C  HIS*     1.3    62.6    +      -       -      +
    349C  TRP*     3.9    30.7    -      -       +      -
    350C  LYS      3.7     4.9    -      -       -      +
    351C  PHE*     4.2     9.9    -      -       +      -
    353C  LEU*     4.1    11.9    -      -       +      -
     72D  TRP*     3.6    38.5    -      -       +      +
     74D  PHE*     3.9    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 343 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341C  LYS*     5.5     2.7    -      -       +      -
    342C  ILE*     1.3    76.6    -      -       -      +
    344C  ARG*     1.3    77.6    +      -       -      +
    345C  SER*     3.2    21.4    +      -       -      -
    348C  LYS      5.0     1.6    -      -       -      -
    349C  TRP*     3.2     9.3    -      -       -      +
    350C  LYS*     2.8    56.4    +      -       +      +
    352C  HIS*     6.2     1.6    -      -       +      +
      6E    G      3.4    36.0    +      -       -      -
      7E    G      3.7    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 344 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  GLU*     5.4     1.4    +      -       -      -
    203A  ARG*     2.9    35.6    -      -       -      +
    343C  HIS*     1.3    88.5    +      -       -      +
    345C  SER*     1.3    68.3    +      -       -      +
    346C  LYS*     2.8    51.7    +      -       -      +
    348C  LYS      3.2     9.9    -      -       -      +
    349C  TRP*     3.6    46.5    -      -       +      +
      4F    T      4.3     9.5    +      -       -      -
      5F    T      2.9    32.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 345 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343C  HIS*     3.2    23.3    +      -       -      -
    344C  ARG*     1.3    71.7    +      -       -      +
    346C  LYS*     1.3    76.4    +      -       -      +
    348C  LYS*     2.7    35.0    +      -       -      +
      6E    G      4.5     9.9    +      -       -      -
      7E    G      5.2     1.4    +      -       -      -
----------------------------------------------------------
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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