Contacts of the strand formed by residues 338 - 344 (chain L) in PDB entry 6AHU


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 LEU 338 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112H  LEU*     3.7    48.9    -      -       +      +
    113H  ALA*     4.2     9.9    -      -       +      +
     36L  HIS*     6.1     0.2    -      -       -      -
    241L  PHE*     3.8    20.2    -      -       +      -
    313L  SER*     5.2     1.3    -      -       -      -
    314L  VAL      3.5    15.7    -      -       -      +
    315L  GLN*     3.7    28.7    -      -       +      +
    316L  GLY      4.8     0.4    -      -       -      +
    324L  TRP*     4.1     4.8    -      -       -      -
    336L  GLU*     5.1     1.1    -      -       +      +
    337L  HIS*     1.3    78.0    -      -       -      +
    339L  TYR*     1.3    88.8    +      -       -      +
    340L  ASN*     4.7     0.7    -      -       +      -
    353L  MET*     3.3     3.5    -      -       -      +
    354L  ALA*     2.5    44.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 339 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32L  LEU*     4.8     7.9    -      -       +      -
     33L  VAL*     4.0    23.3    -      -       +      +
     36L  HIS*     3.4    41.3    -      +       +      +
     39L  ASN*     3.9     6.2    +      -       -      -
    290L  ILE*     3.7    14.2    -      -       +      +
    313L  SER*     3.9     0.3    -      -       -      -
    314L  VAL*     3.3    68.4    +      -       +      +
    324L  TRP*     4.7     8.5    -      +       +      -
    338L  LEU*     1.3    85.5    -      -       -      +
    340L  ASN*     1.3    61.1    +      -       -      +
    341L  PHE*     3.5    36.1    -      +       -      -
    351L  LEU*     4.7     4.5    -      -       +      -
    352L  GLN      3.3     6.7    -      -       -      -
    353L  MET*     4.1    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 340 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112H  LEU*     4.5     0.9    -      -       -      +
    240L  LEU*     4.8     1.4    -      -       -      +
    241L  PHE*     4.0    13.1    -      -       +      -
    244L  LEU*     3.5    23.8    -      -       -      +
    311L  THR*     4.4     0.3    -      -       -      +
    312L  LEU      3.0     7.6    +      -       -      +
    313L  SER*     2.6    23.3    +      -       -      -
    338L  LEU*     4.7     1.1    -      -       +      -
    339L  TYR*     1.3    79.4    -      -       -      +
    341L  PHE*     1.3    92.2    +      -       -      +
    342L  VAL*     4.3    11.0    -      -       -      +
    350L  TRP      3.1    12.7    -      -       -      +
    351L  LEU*     3.5     8.0    -      -       -      +
    352L  GLN*     3.0    50.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 341 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22L  PHE*     5.2     0.2    -      +       -      -
     29L  HIS*     4.5     9.4    -      -       +      -
     32L  LEU*     5.4     1.8    -      -       +      -
     33L  VAL*     3.7    23.8    -      -       +      -
    290L  ILE*     6.0     0.7    -      -       +      -
    294L  LEU*     4.2    23.1    -      -       +      -
    311L  THR*     3.7     3.6    -      -       -      -
    312L  LEU*     2.6    68.0    +      -       +      +
    339L  TYR*     3.5    32.3    -      +       -      -
    340L  ASN*     1.3    80.5    +      -       -      +
    342L  VAL*     1.3    64.0    +      -       -      +
    343L  ILE*     3.6    13.7    +      -       +      +
    349L  TYR*     3.8    32.8    -      +       +      -
    350L  TRP      3.3     2.2    -      -       -      -
    351L  LEU*     3.9    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 342 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222L  LEU*     4.1    17.9    -      -       +      -
    240L  LEU*     4.0    23.3    -      -       +      -
    244L  LEU*     5.8     0.9    -      -       +      -
    309L  TRP*     3.7    30.7    -      -       +      -
    310L  VAL      3.7     3.1    -      -       -      -
    311L  THR*     5.8     1.8    -      -       +      -
    340L  ASN*     4.3    13.7    -      -       -      +
    341L  PHE*     1.3    72.6    -      -       -      +
    343L  ILE*     1.3    60.7    +      -       -      +
    344L  PHE*     3.5    17.1    -      -       +      -
    349L  TYR*     3.3     4.3    -      -       -      -
    350L  TRP*     3.2    49.4    +      -       +      +
    352L  GLN*     4.9     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 343 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22L  PHE*     3.8    30.5    -      -       +      -
    294L  LEU*     3.9    24.5    -      -       +      +
    297L  LEU*     3.9    48.5    -      -       +      +
    298L  CYS*     4.8     2.7    -      -       -      -
    301L  PHE*     4.0     6.8    -      -       +      -
    309L  TRP*     3.4     4.6    -      -       -      +
    310L  VAL*     3.1    41.3    +      -       +      +
    312L  LEU*     4.8     2.2    -      -       +      -
    341L  PHE*     3.6    17.2    -      -       +      +
    342L  VAL*     1.3    71.9    -      -       -      +
    344L  PHE*     1.3    73.3    -      -       -      +
    348L  ASP      3.6     3.6    -      -       -      -
    349L  TYR*     4.3     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 344 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222L  LEU*     3.8    37.2    -      -       +      -
    224L  SER*     3.5    28.5    -      -       -      -
    301L  PHE*     3.6    10.3    -      -       -      -
    308L  PRO      4.2     6.5    -      -       -      -
    309L  TRP*     3.8    16.6    -      +       +      -
    342L  VAL*     3.5    17.3    -      -       +      -
    343L  ILE*     1.3    86.8    -      -       -      +
    345L  ASN*     1.3    67.1    +      -       -      +
    346L  ASN*     3.3    15.9    +      -       -      +
    347L  GLN*     3.8     7.4    +      -       -      -
    348L  ASP      2.7    29.8    +      -       -      +
    350L  TRP*     3.6    44.9    -      +       -      -
----------------------------------------------------------
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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