Contacts of the strand formed by residues 347 - 354 (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 ILE 347 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  PHE      3.5     5.6    -      -       -      +
    302A  GLN*     4.5     2.2    -      -       +      +
    343A  ARG*     3.1     3.9    -      -       -      -
    344A  LEU*     3.0    42.4    +      -       +      +
    345A  VAL      3.4     0.6    -      -       -      -
    346A  GLY*     1.3    79.8    -      -       -      +
    348A  MET*     1.3    59.0    +      -       -      +
    378A  GLY      4.5     6.7    -      -       -      +
    379A  ASN      5.5     1.1    -      -       -      +
    380A  LYS*     4.1     6.1    -      -       -      -
    381A  GLY      3.5    36.3    -      -       -      +
    382A  GLY      4.3     0.9    -      -       -      +
    383A  VAL*     3.7    15.2    -      -       +      +
    398A  ASN*     3.6    39.7    -      -       -      +
    399A  SER*     4.8     1.8    -      -       -      -
    400A  HIS*     3.7    26.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  VAL      3.9     0.7    -      -       -      +
    300A  GLY*     3.4     0.7    -      -       -      -
    301A  PHE*     2.8    67.0    +      -       +      +
    304A  LEU*     3.9    29.4    -      -       +      -
    319A  GLU*     4.1    26.7    -      -       -      +
    322A  TRP*     4.3     8.7    -      -       +      -
    323A  PHE      4.8     0.9    -      -       -      +
    341A  LEU*     4.2     5.4    -      -       +      -
    342A  ILE      3.2    12.6    -      -       -      +
    343A  ARG*     4.0    16.6    -      -       +      -
    346A  GLY      3.9     1.2    +      -       -      -
    347A  ILE*     1.3    76.1    -      -       -      +
    349A  LEU*     1.3    62.7    -      -       -      +
    350A  LEU*     4.0    28.5    -      -       +      -
    383A  VAL*     4.5     0.4    -      -       -      -
    398A  ASN*     2.9     5.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  CYS      4.5     0.9    -      -       -      -
    299A  VAL      3.3    32.3    -      -       -      +
    300A  GLY*     3.8     7.9    -      -       -      +
    341A  LEU*     3.6     3.1    -      -       -      -
    342A  ILE*     2.9    35.6    +      -       +      -
    348A  MET*     1.3    74.8    -      -       -      +
    350A  LEU*     1.3    66.6    +      -       -      +
    383A  VAL*     3.9    16.8    -      -       +      +
    384A  ALA*     4.5     0.4    -      -       -      -
    385A  ILE*     3.8    23.5    -      -       +      +
    396A  VAL*     3.4    48.7    -      -       +      +
    398A  ASN*     4.0    17.0    -      -       +      +
    445A  LEU*     4.4     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  TYR      3.4     3.7    -      -       -      +
    298A  CYS*     3.5     2.8    -      -       -      -
    299A  VAL*     2.9    38.9    +      -       +      +
    301A  PHE*     4.3     3.4    -      -       +      -
    323A  PHE*     4.0    15.5    -      -       +      -
    326A  VAL*     4.0    24.9    -      -       +      -
    338A  LYS*     5.8     0.9    -      -       +      -
    340A  LYS      3.6     2.7    -      -       -      +
    341A  LEU*     3.5    41.3    -      -       +      -
    348A  MET*     4.0    24.5    -      -       +      -
    349A  LEU*     1.3    78.1    -      -       -      +
    351A  LEU*     1.3    60.1    +      -       -      +
    352A  TYR*     3.8    33.4    -      -       +      +
    385A  ILE*     4.3     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  VAL*     3.6    30.7    -      -       +      -
    297A  TYR      3.3     6.3    -      -       -      +
    298A  CYS*     4.1    11.7    -      -       +      -
    338A  LYS*     3.7     3.5    -      -       -      +
    339A  VAL*     2.7    61.5    +      -       +      -
    340A  LYS      2.9    13.1    +      -       -      +
    349A  LEU*     6.0     0.2    -      -       +      -
    350A  LEU*     1.3    74.4    -      -       -      +
    352A  TYR*     1.3    55.6    +      -       -      +
    353A  VAL*     5.0     2.0    -      -       +      -
    385A  ILE*     3.8    28.0    -      -       +      +
    387A  PHE*     3.6    42.2    -      -       +      -
    396A  VAL*     5.4     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  VAL*     3.4     4.7    -      -       -      +
    297A  TYR*     2.7    54.7    +      -       +      +
    299A  VAL*     5.0     1.8    -      -       +      -
    323A  PHE*     3.0    33.4    +      +       -      -
    326A  VAL*     3.5    32.4    -      -       +      +
    327A  SER*     2.8    30.1    +      -       -      -
    330A  LEU*     3.6    23.1    -      -       +      -
    336A  TYR*     4.3    14.8    -      -       +      -
    337A  ALA      3.2     9.0    -      -       -      +
    338A  LYS*     3.8    22.4    -      -       +      -
    339A  VAL      4.3     0.4    -      -       -      +
    350A  LEU*     3.8    19.0    -      -       +      +
    351A  LEU*     1.3    76.5    -      -       -      +
    353A  VAL*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  ASP      3.3     8.7    -      -       -      +
    296A  VAL*     4.1    21.1    -      -       +      -
    336A  TYR*     3.4     6.1    -      -       -      -
    337A  ALA*     2.8    29.9    +      -       +      +
    339A  VAL*     3.6    21.5    -      -       +      -
    351A  LEU*     5.0     2.9    -      -       +      -
    352A  TYR*     1.3    79.5    -      -       -      +
    354A  LYS*     1.3    73.0    +      -       -      +
    357A  HIS*     4.2     7.9    -      -       +      -
    358A  ALA*     4.0    24.9    -      -       +      +
    361A  ILE*     3.8    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  ALA*     3.8    19.5    +      -       -      +
    294A  PRO      3.5    26.0    -      -       -      +
    295A  ASP*     2.9    37.7    +      -       -      +
    334A  ALA*     3.9    23.8    -      -       +      -
    335A  LYS      3.4     8.5    -      -       -      +
    336A  TYR*     3.7    10.2    -      -       +      -
    353A  VAL*     1.3    75.8    -      -       -      +
    355A  GLN*     1.3    67.3    +      -       -      +
    356A  GLU*     4.2    23.2    +      -       +      +
    357A  HIS*     2.8    27.3    +      -       +      +
    358A  ALA      3.5     5.7    +      -       -      -
----------------------------------------------------------
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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