Contacts of the strand formed by residues 336 - 344 (chain A) in PDB entry 3N9V


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 TYR 336 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  ALA*     3.5    12.8    -      -       -      +
    294A  PRO*     2.7    46.8    +      -       -      +
    295A  ASP      4.4     1.6    -      -       -      -
    297A  TYR*     3.5    24.2    -      +       -      -
    330A  LEU*     3.7    31.9    -      -       +      -
    331A  HIS*     3.4    29.9    -      -       -      +
    334A  ALA*     3.5    20.2    -      -       +      -
    335A  LYS*     1.3    73.6    -      -       -      +
    337A  ALA*     1.3    59.8    +      -       -      +
    338A  LYS      4.2     0.3    +      -       -      -
    352A  TYR*     4.3     9.1    -      -       +      -
    353A  VAL*     3.4     6.7    -      -       -      +
    354A  LYS*     3.7    23.8    -      -       +      -
    355A  GLN*     4.6     4.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336A  TYR*     1.3    72.0    -      -       -      +
    338A  LYS*     1.3    68.1    +      -       -      +
    339A  VAL*     3.4     2.9    +      -       +      +
    352A  TYR*     3.2     4.5    -      -       -      -
    353A  VAL*     2.8    37.7    +      -       +      +
    355A  GLN*     3.5    34.2    -      -       -      +
    358A  ALA*     4.7     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  PHE*     3.7    40.9    -      -       +      -
    336A  TYR      4.2     0.8    +      -       -      -
    337A  ALA*     1.3    75.2    -      -       -      +
    339A  VAL*     1.3    65.5    +      -       -      +
    340A  LYS*     4.0    15.0    -      -       -      +
    341A  LEU*     4.3    26.3    -      -       +      +
    350A  LEU*     5.9     0.9    -      -       +      -
    351A  LEU      3.8     8.1    -      -       -      +
    352A  TYR*     3.8    13.4    -      -       +      -
    365B  GLU*     5.6     1.6    -      -       -      -
    425B  CYS*     3.0    40.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337A  ALA*     3.9     4.3    -      -       +      +
    338A  LYS*     1.3    80.5    -      -       -      +
    340A  LYS*     1.3    63.6    +      -       -      +
    351A  LEU*     2.7    37.4    +      -       +      +
    352A  TYR      4.4     0.2    -      -       -      -
    353A  VAL*     3.6    41.7    -      -       +      +
    358A  ALA*     5.9     1.8    -      -       +      -
    361A  ILE*     4.0    12.8    -      -       +      -
    364A  VAL*     3.8    29.5    -      -       +      +
    365B  GLU*     5.7     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  LYS*     3.7     9.9    -      -       -      +
    339A  VAL*     1.3    86.2    -      -       +      +
    341A  LEU*     1.3    79.0    +      -       -      +
    342A  ILE*     5.8     2.0    -      -       +      +
    350A  LEU*     3.6     2.3    -      -       -      -
    351A  LEU*     2.9    29.1    +      -       +      +
    364A  VAL*     3.9    27.1    -      -       +      -
    365A  GLU*     5.7     0.4    -      -       -      +
    366A  ALA*     4.0    22.5    -      -       +      +
    385A  ILE*     3.7    34.0    -      -       +      +
    340B  LYS*     4.3    19.0    -      -       -      +
    365B  GLU*     5.4     6.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  GLU*     3.9    42.4    -      -       +      +
    323A  PHE*     4.5    16.8    -      -       +      -
    338A  LYS*     4.3    19.0    -      -       +      +
    340A  LYS*     1.3    90.8    +      -       -      +
    342A  ILE*     1.3    79.2    +      -       -      +
    343A  ARG*     4.3     1.6    -      -       +      +
    348A  MET*     4.2     7.0    -      -       +      -
    349A  LEU      3.6     4.0    -      -       -      -
    350A  LEU*     3.5    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  LYS*     5.8     2.5    -      -       +      +
    341A  LEU*     1.3    80.6    -      -       -      +
    343A  ARG*     1.3    67.6    +      -       -      +
    347A  ILE      3.8     0.9    -      -       -      +
    348A  MET*     3.2     3.6    -      -       -      +
    349A  LEU*     2.9    39.9    +      -       +      +
    366A  ALA*     3.9    28.7    -      -       +      +
    367A  GLU*     4.4     2.9    -      -       -      +
    368A  THR*     3.7    28.0    -      -       +      -
    383A  VAL*     4.0    20.1    -      -       +      +
    384A  ALA      4.1     5.4    -      -       -      +
    385A  ILE*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  LEU*     4.0    24.7    -      -       -      -
    310A  ALA*     5.3     1.0    +      -       -      +
    314A  HIS*     2.7    80.3    +      -       +      -
    315A  ASP*     4.1     3.8    +      -       -      +
    316A  THR*     3.5    19.1    -      -       -      +
    319A  GLU*     2.7    35.5    +      -       -      +
    341A  LEU*     4.3     3.0    -      -       +      +
    342A  ILE*     1.3    82.1    -      -       -      +
    344A  LEU*     1.3    63.6    +      -       -      +
    345A  VAL*     2.7    43.7    +      -       -      +
    347A  ILE      3.1    15.0    -      -       -      +
    348A  MET*     4.0    10.3    -      -       +      -
    368A  THR*     4.3     7.2    -      -       -      +
    383A  VAL*     4.3     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314A  HIS*     5.1     0.7    -      -       -      -
    343A  ARG*     1.3    71.7    -      -       -      +
    345A  VAL*     1.3    63.3    +      -       +      +
    346A  GLY      2.8    17.5    +      -       -      -
    347A  ILE*     3.0    25.0    +      -       +      +
    368A  THR*     3.9    15.3    -      -       -      +
    369A  VAL      3.5    40.4    -      -       -      +
    370A  GLY*     3.7    10.3    -      -       -      +
    378A  GLY*     3.9    23.5    -      -       -      +
    380A  LYS      4.8     1.6    -      -       -      +
    382A  GLY      4.1     7.4    -      -       -      +
    383A  VAL*     3.7    15.4    -      -       +      +
----------------------------------------------------------
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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